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%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
%% Created for Sergei Pond at 2024-01-30 15:31:19 -0500
%% Saved with string encoding Unicode (UTF-8)
@article{Ge:2021aa,
abstract = {ABSTRACTBy analyzing an unprecedentedly large, longitudinal HIV-1 CRF07\_BC sequence dataset collected from China in the past two decades, we sought to build CRF07_BC lengthwise transmission networks, and understand its transmission dynamics. We divided CRF07_BC into two clusters based on phylogenetic analysis and an estimation of the pairwise genetic distance at 0.7%. Of 6213 sequences, 3607 (58.1%) linked to ≥1 other sequence. CRF07_BC was divided into two clusters: 07BC_O and 07BC_N. The 07BC_O is the original CRF07_BC, circulating in people who inject drugs (PWID) and heterosexuals, predominantly in southwestern and northwestern provinces of China. The 07BC_N is a new cluster, identified mostly in men having sex with men (MSM) in the northern provinces of China. Bayesian analysis indicates that CRF07_BC has experienced two phases of exponential growth, which was first driven by 07BC_O then 07BC_N. Compared to 07BC_O, the proportion of the parameter of population transmission risk (TR) of 07BC_N has risen constantly. The power-law function analyses reveal that 07BC_N has increased over years with higher degree. In 07BC_N, only 13.16% of MSM were linked to other risk groups, but these links represent 41.45%, 54.25%, and 55.07% of links among heterosexual females, heterosexual males, and male PWID respectively. This study indicates that CRF07_BC has evolved into two clusters in China, and their distributions are distinct across risk groups and geographical regions. 07BC_N shows a greater risk of transmission, and has gradually replaced 07BC_O. Furthermore, the results show that strengthening the MSM interventions could lower the rapidity of 07BC_N transmission in all risk groups.},
author = {Ge, Zhangwen and Feng, Yi and Zhang, Hua and Rashid, Abdur and Zaongo, Silvere D and Li, Kang and Yu, Yueyang and Lv, Bowen and Sun, Jia and Liang, Yanling and Xing, Hui and S{\"o}nnerborg, Anders and Ma, Ping and Shao, Yiming},
date-added = {2024-01-30 15:31:01 -0500},
date-modified = {2024-01-30 15:31:16 -0500},
doi = {10.1080/22221751.2021.1978822},
journal = {Emerg Microbes Infect},
journal-full = {Emerging microbes \& infections},
keywords = {CRF07_BC; China; HIV-1; molecular epidemiology; risk factors; surveillance; transmission cluster},
mesh = {Adult; China; Cross-Sectional Studies; Female; Geography; HIV Infections; HIV-1; Homosexuality, Female; Homosexuality, Male; Humans; Male; Molecular Epidemiology; Primary Prevention; Sexual and Gender Minorities; Substance-Related Disorders; Young Adult},
month = {Dec},
number = {1},
pages = {1919-1930},
pmc = {PMC8477959},
pmid = {34498547},
pst = {ppublish},
title = {{HIV-1 CRF07\_BC} transmission dynamics in {China}: two decades of national molecular surveillance},
volume = {10},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1080/22221751.2021.1978822}}
@article{Ragonnet-Cronin:2018aa,
abstract = {BACKGROUND: Patients who do not disclose their sexuality, including men who do not disclose same-sex behaviour, are difficult to characterise through traditional epidemiological approaches such as interviews. Using a recently developed method to detect large networks of viral sequences from time-resolved trees, we localised non-disclosed men who have sex with men (MSM) in UK transmission networks, gaining crucial insight into the behaviour of this group.
METHODS: For this phylogenetic analysis, we obtained HIV pol sequences from the UK HIV Drug Resistance Database (UKRDB), a central repository for resistance tests done as part of routine clinical care throughout the UK. Sequence data are linked to demographic and clinical data held by the UK Collaborative HIV Cohort study and the national HIV/AIDS reporting system database. Initially, we reconstructed maximum likelihood phylogenies from these sequences, then sequences were selected for time-resolved analysis in BEAST if they were clustered with at least one other sequence at a genetic distance of 4·5% or less with support of at least 90%. We used time-resolved phylogenies to create networks by linking together nodes if sequences shared a common ancestor within the previous 5 years. We identified potential non-disclosed MSM (pnMSM), defined as self-reported heterosexual men who clustered only with men. We measured the network position of pnMSM, including betweenness (a measure of connectedness and importance) and assortativity (the propensity for nodes sharing attributes to link).
FINDINGS: 14 405 individuals were in the network, including 8452 MSM, 1743 heterosexual women and 1341 heterosexual men. 249 pnMSM were identified (18·6% of all clustered heterosexual men) in the network. pnMSM were more likely to be black African (p<0·0001), less likely to be infected with subtype B (p=0·006), and were slightly older (p=0·002) than the MSM they clustered with. Mean betweenness centrality was lower for pnMSM than for MSM (1·31, 95% CI 0·48-2·15 in pnMSM vs 2·24, 0·98-3·51 in MSM; p=0·002), indicating that pnMSM were in peripheral positions in MSM clusters. Assortativity by risk group was higher than expected (0·037 vs -0·037, p=0·01) signifying that pnMSM were linked to each other. We found that self-reported heterosexual men were more likely to link MSM and heterosexual women than heterosexual women were to link MSM and heterosexual men (Fisher's exact test p=0·0004; OR 2·24) but the number of such transmission chains was small (only 54 in total vs 32 in women).
INTERPRETATION: pnMSM are a subgroup distinct from both MSM and from heterosexual men. They are more likely to choose sexual partners who are also pnMSM and might exhibit lower-risk sexual behaviour than MSM (eg, choosing low-risk partners or consistently using condoms). Heterosexual men are the group most likely to be diagnosed with late-stage disease (ie, low CD4 counts) and non-disclosed MSM might put female partners at higher risk than heterosexual men because non-disclosed MSM have male partners. Hence, pnMSM require specific consideration to ensure they are included in public health interventions.
FUNDING: National Institutes of Health.},
author = {Ragonnet-Cronin, Manon and Hu{\'e}, St{\'e}phane and Hodcroft, Emma B and Tostevin, Anna and Dunn, David and Fawcett, Tracy and Pozniak, Anton and Brown, Alison E and Delpech, Valerie and Brown, Andrew J Leigh and {UK HIV Drug Resistance Database}},
date-added = {2024-01-30 14:49:57 -0500},
date-modified = {2024-01-30 14:50:05 -0500},
doi = {10.1016/S2352-3018(18)30062-6},
journal = {Lancet HIV},
journal-full = {The lancet. HIV},
mesh = {Adult; Cluster Analysis; Contact Tracing; Female; HIV Infections; Heterosexuality; Homosexuality; Humans; Male; Population Surveillance; Sexual Behavior; Sexual Partners; Truth Disclosure; United Kingdom},
month = {Jun},
number = {6},
pages = {e309-e316},
pmid = {29893244},
pst = {ppublish},
title = {Non-disclosed men who have sex with men in {UK HIV} transmission networks: phylogenetic analysis of surveillance data},
volume = {5},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1016/S2352-3018(18)30062-6}}
@article{Foster:2014aa,
abstract = {BACKGROUND: An increase in non-B HIV-1 infections among men who have sex with men (MSM) in the United Kingdom (UK) has created opportunities for novel recombinants to arise and become established. We used molecular mapping to characterize the importance of such recombinants to the UK HIV epidemic, in order to gain insights into transmission dynamics that can inform control strategies.
METHODS AND RESULTS: A total of 55,556 pol (reverse transcriptase and protease) sequences in the UK HIV Drug Resistance Database were analyzed using Subtype Classification Using Evolutionary Algorithms (SCUEAL). Overall 72 patients shared the same A1/D recombination breakpoint in pol, comprising predominantly MSM but also heterosexuals and injecting drug users (IDUs). In six MSM, full-length single genome amplification of plasma HIV-1 RNA was performed in order to characterize the A1/D recombinant. Subtypes and recombination breakpoints were identified using sliding window and jumping profile hidden markov model approaches. Global maximum likelihood trees of gag, pol and env genes were drawn using FastTree version 2.1. Five of the six strains showed the same novel A1/D recombinant (8 breakpoints), which has been classified as CRF50_A1D. The sixth strain showed a complex CRF50_A1D/B/U structure. Divergence dates and phylogeographic inferences were determined using Bayesian Evolutionary Analysis using Sampling Trees (BEAST). This estimated that CRF50_A1D emerged in the UK around 1992 in MSM, with subsequent transmissions to heterosexuals and IDUs. Analysis of CRF50_A1D/B/U demonstrated that around the year 2000 CRF50_A1D underwent recombination with a subtype B strain.
CONCLUSIONS: We report the identification of CRF50_A1D, a novel circulating recombinant that emerged in UK MSM around 1992, with subsequent onward transmission to heterosexuals and IDUs, and more recent recombination with subtype B. These findings highlight the changing dynamics of HIV transmission in the UK and the converging of the two previously distinct MSM and heterosexual epidemics.},
author = {Foster, Geraldine M and Ambrose, John C and Hu{\'e}, St{\'e}phane and Delpech, Valerie C and Fearnhill, Esther and Abecasis, Ana B and Leigh Brown, Andrew J and Geretti, Anna Maria and {UK HIV Drug Resistance Database}},
date-added = {2024-01-30 11:34:59 -0500},
date-modified = {2024-01-30 11:35:19 -0500},
doi = {10.1371/journal.pone.0083337},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Algorithms; Base Sequence; DNA Primers; Evolution, Molecular; HIV-1; Homosexuality, Male; Humans; Likelihood Functions; Male; Phylogeny; Polymerase Chain Reaction; Recombination, Genetic; Risk Factors; United Kingdom},
number = {1},
pages = {e83337},
pmc = {PMC3893077},
pmid = {24454702},
pst = {epublish},
title = {Novel {HIV-1} recombinants spreading across multiple risk groups in the {United Kingdom}: the identification and phylogeography of Circulating Recombinant Form (CRF) 50\_A1D},
volume = {9},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0083337}}
@article{Yebra:2015aa,
abstract = {HIV prevalence has decreased in Uganda since the 1990s, but remains substantial within high-risk groups. Here, we reconstruct the history and spread of HIV subtypes A1 and D in Uganda and explore the transmission dynamics in high-risk populations. We analysed HIV pol sequences from female sex workers in Kampala (n = 42), Lake Victoria fisher-folk (n = 46) and a rural clinical cohort (n = 74), together with publicly available sequences from adjacent regions in Uganda (n = 412) and newly generated sequences from samples taken in Kampala in 1986 (n = 12). Of the sequences from the three Ugandan populations, 60 (37.1 %) were classified as subtype D, 54 (33.3 %) as subtype A1, 31 (19.1 %) as A1/D recombinants, six (3.7 %) as subtype C, one (0.6 %) as subtype G and 10 (6.2 %) as other recombinants. Among the A1/D recombinants we identified a new candidate circulating recombinant form. Phylodynamic and phylogeographic analyses using BEAST indicated that the Ugandan epidemics originated in 1960 (1950-1968) for subtype A1 and 1973 (1970-1977) for D, in rural south-western Uganda with subsequent spread to Kampala. They also showed extensive interconnection with adjacent countries. The sequence analysis shows both epidemics grew exponentially during the 1970s-1980s and decreased from 1992, which agrees with HIV prevalence reports in Uganda. Inclusion of sequences from the 1980s indicated the origin of both epidemics was more recent than expected and substantially narrowed the confidence intervals in comparison to previous estimates. We identified three transmission clusters and ten pairs, none of them including patients from different populations, suggesting active transmission within a structured transmission network.},
author = {Yebra, Gonzalo and Ragonnet-Cronin, Manon and Ssemwanga, Deogratius and Parry, Chris M and Logue, Christopher H and Cane, Patricia A and Kaleebu, Pontiano and Brown, Andrew J Leigh},
date-added = {2024-01-30 11:33:35 -0500},
date-modified = {2024-01-30 11:33:46 -0500},
doi = {10.1099/vir.0.000107},
journal = {J Gen Virol},
journal-full = {The Journal of general virology},
mesh = {Cohort Studies; Female; Genotype; HIV Infections; HIV-1; Humans; Molecular Epidemiology; Molecular Sequence Data; Phylogeny; Sequence Analysis, DNA; Sequence Homology; Uganda; pol Gene Products, Human Immunodeficiency Virus},
month = {Jul},
number = {Pt 7},
pages = {1890-8},
pmc = {PMC4635457},
pmid = {25724670},
pst = {ppublish},
title = {Analysis of the history and spread of {HIV-1} in Uganda using phylodynamics},
volume = {96},
year = {2015},
bdsk-url-1 = {https://doi.org/10.1099/vir.0.000107}}
@article{Abidi:2021aa,
abstract = {BACKGROUND: HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes.
METHODS: For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used.
RESULTS: Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1.
CONCLUSION: The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region.},
author = {Abidi, Syed Hani and Aibekova, Lazzat and Davlidova, Salima and Amangeldiyeva, Aidana and Foley, Brian and Ali, Syed},
date-added = {2024-01-30 11:13:31 -0500},
date-modified = {2024-01-30 11:13:44 -0500},
doi = {10.1371/journal.pone.0260604},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Amino Acid Sequence; Evolution, Molecular; Genotype; HIV Infections; HIV Reverse Transcriptase; HIV-1; Humans; Mutation; Phylogeny; USSR},
number = {12},
pages = {e0260604},
pmc = {PMC8668117},
pmid = {34898626},
pst = {epublish},
title = {Origin and evolution of {HIV-1} subtype {A6}},
volume = {16},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0260604}}
@article{Wertheim:2014aa,
abstract = {Human immunodeficiency virus type 1 (HIV-1) is pandemic, but its contemporary global transmission network has not been characterized. A better understanding of the properties and dynamics of this network is essential for surveillance, prevention, and eventual eradication of HIV. Here, we apply a simple and computationally efficient network-based approach to all publicly available HIV polymerase sequences in the global database, revealing a contemporary picture of the spread of HIV-1 within and between countries. This approach automatically recovered well-characterized transmission clusters and extended other clusters thought to be contained within a single country across international borders. In addition, previously undescribed transmission clusters were discovered. Together, these clusters represent all known modes of HIV transmission. The extent of international linkage revealed by our comprehensive approach demonstrates the need to consider the global diversity of HIV, even when describing local epidemics. Finally, the speed of this method allows for near-real-time surveillance of the pandemic's progression.},
author = {Wertheim, Joel O and Leigh Brown, Andrew J and Hepler, N Lance and Mehta, Sanjay R and Richman, Douglas D and Smith, Davey M and Kosakovsky Pond, Sergei L},
date-added = {2024-01-26 14:29:13 -0500},
date-modified = {2024-01-26 14:29:23 -0500},
doi = {10.1093/infdis/jit524},
journal = {J Infect Dis},
journal-full = {The Journal of infectious diseases},
keywords = {human immunodeficiency virus; molecular epidemiology; transmission network},
mesh = {Cluster Analysis; Computational Biology; Databases, Genetic; Disease Transmission, Infectious; Genetic Variation; Global Health; HIV Infections; HIV-1; Humans; Molecular Epidemiology; Pandemics},
month = {Jan},
number = {2},
pages = {304-13},
pmc = {PMC3873788},
pmid = {24151309},
pst = {ppublish},
title = {The global transmission network of {HIV-1}},
volume = {209},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1093/infdis/jit524}}
@article{doi:10.1080/19312450709336664,
author = {Andrew F. Hayes and Klaus Krippendorff},
date-added = {2024-01-26 14:17:58 -0500},
date-modified = {2024-01-26 14:17:58 -0500},
doi = {10.1080/19312450709336664},
eprint = {https://doi.org/10.1080/19312450709336664},
journal = {Communication Methods and Measures},
number = {1},
pages = {77-89},
publisher = {Routledge},
title = {Answering the Call for a Standard Reliability Measure for Coding Data},
url = {https://doi.org/10.1080/19312450709336664},
volume = {1},
year = {2007},
bdsk-url-1 = {https://doi.org/10.1080/19312450709336664}}
@article{Penn:2008aa,
abstract = {A hallmark of the human immunodeficiency virus 1 (HIV-1) is its rapid rate of evolution within and among its various subtypes. Two complementary hypotheses are suggested to explain the sequence variability among HIV-1 subtypes. The first suggests that the functional constraints at each site remain the same across all subtypes, and the differences among subtypes are a direct reflection of random substitutions, which have occurred during the time elapsed since their divergence. The alternative hypothesis suggests that the functional constraints themselves have evolved, and thus sequence differences among subtypes in some sites reflect shifts in function. To determine the contribution of each of these two alternatives to HIV-1 subtype evolution, we have developed a novel Bayesian method for testing and detecting site-specific rate shifts. The RAte Shift EstimatoR (RASER) method determines whether or not site-specific functional shifts characterize the evolution of a protein and, if so, points to the specific sites and lineages in which these shifts have most likely occurred. Applying RASER to a dataset composed of large samples of HIV-1 sequences from different group M subtypes, we reveal rampant evolutionary shifts throughout the HIV-1 proteome. Most of these rate shifts have occurred during the divergence of the major subtypes, establishing that subtype divergence occurred together with functional diversification. We report further evidence for the emergence of a new sub-subtype, characterized by abundant rate-shifting sites. When focusing on the rate-shifting sites detected, we find that many are associated with known function relating to viral life cycle and drug resistance. Finally, we discuss mechanisms of covariation of rate-shifting sites.},
author = {Penn, Osnat and Stern, Adi and Rubinstein, Nimrod D and Dutheil, Julien and Bacharach, Eran and Galtier, Nicolas and Pupko, Tal},
date-added = {2024-01-25 10:31:37 -0500},
date-modified = {2024-01-25 10:31:37 -0500},
doi = {10.1371/journal.pcbi.1000214},
journal = {PLoS Comput Biol},
journal-full = {PLoS computational biology},
mesh = {Adaptation, Biological; Amino Acid Sequence; Bayes Theorem; Drug Resistance, Multiple, Viral; Evolution, Molecular; Genetic Speciation; Geography; HIV Infections; HIV-1; Humans; Models, Biological; Phylogeny; Proteomics; Time Factors; Virus Internalization},
month = {Nov},
number = {11},
pages = {e1000214},
pmc = {PMC2566816},
pmid = {18989394},
pst = {ppublish},
title = {Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes},
volume = {4},
year = {2008},
bdsk-url-1 = {https://doi.org/10.1371/journal.pcbi.1000214}}
@article{Ng:2022aa,
abstract = {BACKGROUND: Despite the clinical burden attributable to rhinovirus (RV) infections, the RV transmission dynamics and the impact of interventions on viral transmission remain elusive.
METHODS: A total of 3,935 nasopharyngeal specimens were examined, from which the VP4/VP2 gene was sequenced and genotyped. RV transmission clusters were reconstructed using the genetic threshold of 0.005 substitutions/site, estimated from the global VP4/VP2 sequences. A transmission cluster is characterized by the presence of at least two individuals (represent by nodes), whose viral sequences are genetically linked (represent by undirected edges) at the estimated genetic distance threshold supported by bootstrap value of ≥ 90%. To assess the impact of facemask, pleconaril and social distancing on RV transmission clusters, trials were simulated for interventions with varying efficacy and were evaluated based on the reduction in the number of infected patients (nodes) and the reduction in the number of nodes-connecting edges. The putative impact of intervention strategies on RV transmission clusters was evaluated through 10,000 simulations.
RESULTS: A substantial clustering of 168 RV transmission clusters of varying sizes were observed. This suggests that RV disease burden observed in the population was largely due to multiple sub-epidemics, predominantly driven by RV-A, followed by RV-C and -B. No misclassification of RV species and types were observed, suggesting the specificity and sensitivity of the analysis. Through 10,000 simulations, it was shown that social distancing may be effective in decelerating RV transmission, by removing more than 95% of nodes and edges within the RV transmission clusters. However, facemask removed less than 8% and 66% of nodes and edges, respectively, conferring moderate advantage in limiting RV transmission.
CONCLUSION: Here, we presented a network-based approach of which the degree of RV spread that fuel disease transmission in the region was mapped for the first time. The utilization of RV transmission clusters in assessing the putative impact of interventions on disease transmission at the population level was demonstrated.},
author = {Ng, Kim Tien and Ng, Liang Jie and Oong, Xiang Yong and Chook, Jack Bee and Chan, Kok Gan and Takebe, Yutaka and Kamarulzaman, Adeeba and Tee, Kok Keng},
date-added = {2024-01-23 14:41:30 -0500},
date-modified = {2024-01-23 14:41:30 -0500},
doi = {10.1186/s12985-022-01762-w},
journal = {Virol J},
journal-full = {Virology journal},
keywords = {Acute respiratory tract infection; Interventions; Rhinovirus; Transmission clusters; VP4/VP2 gene},
mesh = {Enterovirus Infections; Genotype; Humans; Nasopharynx; Phylogeny; Picornaviridae Infections; Respiratory Tract Infections; Rhinovirus},
month = {Mar},
number = {1},
pages = {36},
pmc = {PMC8894564},
pmid = {35246187},
pst = {epublish},
title = {Application of a VP4/VP2-inferred transmission clusters in estimating the impact of interventions on rhinovirus transmission},
volume = {19},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1186/s12985-022-01762-w}}
@article{Ye:2023aa,
abstract = {In China, few molecular epidemiological data on hepatitis C virus (HCV) are available and all previous studies were limited by small sample sizes or specific population characteristics. Here, we report characterization of the epidemic history and transmission dynamics of HCV strains in China. We included HCV sequences of individuals belonging to three HCV surveillance programs: 1) patients diagnosed with HIV infection at the Beijing HIV laboratory network, most of whom were people who inject drugs and former paid blood donors, 2) men who have sex with men, and 3) the general population. We also used publicly available HCV sequences sampled in China in our study. In total, we obtained 1,603 Ns5b and 865 C/E2 sequences from 1,811 individuals. The most common HCV strains were subtypes 1b (29.1%), 3b (25.5%) and 3a (15.1%). In transmission network analysis, factors independently associated with clustering included the region (OR: 0.37, 95% CI: 0.19-0.71), infection subtype (OR: 0.23, 95% CI: 0.1-0.52), and sampling period (OR: 0.43, 95% CI: 0.27-0.68). The history of the major HCV subtypes was complex, which coincided with some important sociomedical events in China. Of note, five of eight HCV subtype (1a, 1b, 2a, 3a, and 3b), which constituted 81.8% HCV strains genotyped in our study, showed a tendency towards decline in the effective population size during the past decade until present, which is a good omen for the goal of eliminating HCV by 2030 in China.},
author = {Ye, Jingrong and Sun, Yanming and Li, Jia and Lu, Xinli and Zheng, Minna and Liu, Lifeng and Yu, Fengting and He, Shufang and Xu, Conghui and Ren, Xianlong and Wang, Juan and Chen, Jing and Ruan, Yuhua and Feng, Yi and Shao, Yiming and Xing, Hui and Lu, Hongyan},
date-added = {2024-01-23 14:01:42 -0500},
date-modified = {2024-01-23 14:01:42 -0500},
doi = {10.1371/journal.pone.0296053},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Male; Humans; Hepacivirus; HIV Infections; Homosexuality, Male; Phylogeny; Sexual and Gender Minorities; Hepatitis C; China; Genotype},
number = {12},
pages = {e0296053},
pmc = {PMC10734925},
pmid = {38128044},
pst = {epublish},
title = {Distribution pattern, molecular transmission networks, and phylodynamic of hepatitis C virus in China},
volume = {18},
year = {2023},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0296053}}
@article{Chan:2020aa,
abstract = {INTRODUCTION: Sexual acquisition has emerged as a transmission route for hepatitis C virus (HCV) of growing importance among human immunodeficiency virus (HIV)-positive populations. In Western countries, HCV epidemics have been increasingly detected among men who have sex with men (MSM). This review describes the molecular epidemiology of sexually acquired HCV infection in the Asia-Pacific region.
METHODS: A systematic search was performed on PubMed in March 2019. Either abstract or full-text of each publication in the search results was screened for eligibility. Studies from different countries/cities involving eligible cases, who acquired HCV sexually with identified subtype, were synthesized for the evaluation of molecular epidemiology in the Asia-Pacific region. Two large-scale systematic reviews on the genotype distribution of HCV at a population level and among PWID were used as references for comparison.
RESULTS AND DISCUSSION: Overall, 13 full-text articles with 549 subjects originating from nine countries/cities were reviewed. A total of five genotypes and 14 subtypes were identified, dominated by subtypes 1b (23.0%), 2a (19.1%) and 3a (29.5%). A majority of the infected cases occurred in HIV-positive MSM. In some places, notably Hong Kong, India and Indonesia, the predominant subtype in sexually acquired HCV infection in MSM was different from that circulating in the general population. Shared transmission networks between people who inject drugs (PWID) and MSM were shown in Australia and New Zealand, whereas overlapping risk elicited from a small number of subjects existed in Tokyo, Taipei and Guangxi. MSM-specific clusters were identified in Hong Kong, Taipei and Hubei.
CONCLUSIONS: The distribution of sexually acquired HCV was sparsely scattered across countries/cities in the Asia-Pacific region. The threat of overlapping risk differed by locations, whereas transnational outbreaks remained uncommon. The paucity of information has hindered progress with comprehensive assessment in the Asia-Pacific region, where seroprevalence of HCV among HIV-positive MSM was relatively high.},
author = {Chan, Chin Pok and Uemura, Haruka and Kwan, Tsz Ho and Wong, Ngai Sze and Oka, Shinichi and Chan, Denise Pui Chung and Lee, Shui Shan},
date-added = {2024-01-23 13:48:11 -0500},
date-modified = {2024-01-23 13:48:11 -0500},
doi = {10.1002/jia2.25618},
journal = {J Int AIDS Soc},
journal-full = {Journal of the International AIDS Society},
keywords = {Asia-Pacific; HIV; genotype; hepatitis C; molecular epidemiology; sexually transmitted diseases},
mesh = {Asia; Hepacivirus; Hepatitis C; Humans; Molecular Epidemiology; Sexual Behavior; Sexually Transmitted Diseases, Viral},
month = {Sep},
number = {9},
pages = {e25618},
pmc = {PMC7511596},
pmid = {32969173},
pst = {ppublish},
title = {Review on the molecular epidemiology of sexually acquired hepatitis C virus infection in the Asia-Pacific region},
volume = {23},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1002/jia2.25618}}
@article{Paraschiv:2017aa,
abstract = {Co-infections with HIV and HCV are very frequent among people who inject drugs (PWID). However, very few studies comparatively reconstructed the transmission patterns of both viruses in the same population. We have recruited 117 co-infected PWID during a recent HIV outbreak in Romania. Phylogenetic analyses were performed on HIV and HCV sequences in order to characterize and compare transmission dynamics of the two viruses. Three large HIV clusters (2 subtype F1 and one CRF14_BG) and thirteen smaller HCV transmission networks (genotypes 1a, 1b, 3a, 4a and 4d) were identified. Eighty (65%) patients were both in HIV and HCV transmission chains and 70 of those shared the same HIV and HCV cluster with at least one other patient. Molecular clock analysis indicated that all identified HIV clusters originated around 2006, while the origin of the different HCV clusters ranged between 1980 (genotype 1b) and 2011 (genotypes 3a and 4d). HCV infection preceded HIV infection in 80.3% of cases. Coincidental transmission of HIV and HCV was estimated to be rather low (19.65%) and associated with an outbreak among PWID during detention in the same penitentiary. This study has reconstructed and compared the dispersion of these two viruses in a PWID population.},
author = {Paraschiv, Simona and Banica, Leontina and Nicolae, Ionelia and Niculescu, Iulia and Abagiu, Adrian and Jipa, Raluca and Pineda-Pe{\~n}a, Andrea-Clemencia and Pingarilho, Marta and Neaga, Emil and Theys, Kristof and Libin, Pieter and Otelea, Dan and Abecasis, Ana},
date-added = {2024-01-23 13:45:36 -0500},
date-modified = {2024-01-23 13:45:57 -0500},
doi = {10.1371/journal.pone.0185866},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Adult; Coinfection; Disease Outbreaks; Drug Users; Female; Genotype; HIV; HIV Infections; Hepacivirus; Hepatitis C; Humans; Male; Phylogeny; Romania},
number = {10},
pages = {e0185866},
pmc = {PMC5633171},
pmid = {29016621},
pst = {epublish},
title = {Epidemic dispersion of {HIV} and {HCV} in a population of co-infected {Romania} injecting drug users},
volume = {12},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0185866}}
@article{Murphy:2019aa,
abstract = {BACKGROUND: Molecular phylogenetics are generally used to confirm hepatitis C virus (HCV) transmission events. In addition, the Laboratoire de sant{\'e} publique du Qu{\'e}bec (LSPQ) has been using molecular phylogenetics for surveillance of HCV genotyping since November 2001.
OBJECTIVES: To describe the emergence of a specific lineage of HCV genotype 4d (G4d) and its characteristics using molecular phylogenetics as a surveillance tool for identifying HCV strain clustering.
METHODS: The LSPQ prospectively applied Sanger sequencing and phylogenetic analysis to determine the HCV genotype on samples collected from November 2001 to December 2017. When a major G4d cluster was identified, demographic information, HIV-infection status and syphilis test results were analyzed.
RESULTS: Phylogenetic analyses performed on approximately 22,000 cases identified 122 G4d cases. One major G4d cluster composed of 37 cases was singled out. Two cases were identified in 2010, 10 from 2011-2014 and 25 from 2015-2017. Cases in the cluster were concentrated in two urban health regions. Compared to the other G4d cases, cluster cases were all male (p<0.001) and more likely to be HIV-positive (adjusted risk ratio: 4.4; 95% confidence interval: 2.5-7.9). A positive syphilis test result was observed for 27 (73%) of the cluster cases. The sequences in this cluster and of four outlier cases were located on the same monophyletic lineage as G4d sequences reported in HIV-positive men who have sex with men (MSM) in Europe.
CONCLUSION: Molecular phylogenetics enabled the identification and surveillance of ongoing transmission of a specific HCV G4d lineage in HIV-positive and HIV-negative men in Quebec and its cross-continental spread. This information can orient intervention strategies to avoid transmission of HCV in MSM.},
author = {Murphy, D G and Dion, R and Simard, M and Vachon, M L and Martel-Laferri{\`e}re, V and Serhir, B and Longtin, J},
date-added = {2024-01-23 13:29:23 -0500},
date-modified = {2024-01-23 13:29:23 -0500},
doi = {10.14745/ccdr.v45i09a02},
journal = {Can Commun Dis Rep},
journal-full = {Canada communicable disease report = Releve des maladies transmissibles au Canada},
keywords = {G4d; HCV; MSM; cluster; genotype; men who have sex with men; molecular epidemiology; phylogenetic analyses; surveillance},
month = {Sep},
number = {9},
pages = {230-237},
pmc = {PMC6781953},
pmid = {31650986},
pst = {epublish},
title = {Molecular surveillance of hepatitis C virus genotypes identifies the emergence of a genotype 4d lineage among men in Quebec, 2001-2017},
volume = {45},
year = {2019},
bdsk-url-1 = {https://doi.org/10.14745/ccdr.v45i09a02}}
@article{Jia:2023aa,
abstract = {OBJECT: The hepatitis C virus (HCV) is prevalent across China, with a distinctive genotypic distribution that varies by geographical region and mode of transmission. Yunnan is one such geographical region wherein the local population continues to experience a high level of HCV infection, severely straining public health resources. This high prevalence is likely due to the increased incidence of intravenous drug use in that region, as Yunnan is a major point of entry for illegal heroin into China.
METHODS: We investigated 510 individuals with chronic HCV infections in Yunnan Province from 2008 through 2018. Using reverse transcription PCR and Sanger sequencing to amplify and sequence samples. Bayesian analyses was performed to estimate the common ancestors and Bayesian skyline plot to estimate the effective viral population size. Molecular network was conducted to explore the characteristics of HCV transmission.
RESULTS: We successfully amplified and sequenced a total of 503 viral samples and genotyped each as either 3b (37.6%), 3a (21.9%), 1b (19.3%), 2a (10.5%), HCV-6 (10.1%), or 1a (0.6%). Over this 11-year period, we observed that the proportion of 3a and 3b subtypes markedly increased and, concomitantly, that the proportion of 1b and 2a subtypes decreased. We also performed Bayesian analyses to estimate the common ancestors of the four major subtypes, 1b, 2a, 3a, and 3b. Finally, we determined that our Bayesian skyline plot and transmission network data correlated well with the changes we observed in the proportions of HCV subtypes over time.
CONCLUSIONS: Taken together, our results indicate that the prevalence of HCV 3a and 3b subtypes is rapidly increasing in Yunnan, thus demonstrating a steadily growing public health requirement to implement more stringent preventative and therapeutic measures to curb the spread of the virus.},
author = {Jia, Yuanyuan and Zou, Xiu and Yue, Wei and Liu, Jin and Yue, Ming and Liu, Yang and Liu, Li and Huang, Peng and Feng, Yue and Xia, Xueshan},
date-added = {2024-01-23 12:20:09 -0500},
date-modified = {2024-01-23 13:29:30 -0500},
doi = {10.3389/fcimb.2023.1092936},
journal = {Front Cell Infect Microbiol},
journal-full = {Frontiers in cellular and infection microbiology},
keywords = {Bayesian analysis; RT-PCR; genotype; hepatitis C virus; network; transmission},
mesh = {Humans; Hepatitis C, Chronic; Bayes Theorem; China; Hepatitis C; Hepacivirus; Genotype; Phylogeny},
pages = {1092936},
pmc = {PMC10366605},
pmid = {37496804},
pst = {epublish},
title = {The distribution of hepatitis {C} viral genotypes shifted among chronic hepatitis C patients in Yunnan, China, between 2008-2018},
volume = {13},
year = {2023},
bdsk-url-1 = {https://doi.org/10.3389/fcimb.2023.1092936}}
@article{Perez-Losada:2017aa,
abstract = {BACKGROUND: Washington DC has a high burden of HIV with a 2.0% HIV prevalence. The city is a national and international hub potentially containing a broad diversity of HIV variants; yet few sequences from DC are available on GenBank to assess the evolutionary history of HIV in the US capital. Towards this general goal, here we analyze extensive sequence data and investigate HIV diversity, phylodynamics, and drug resistant mutations (DRM) in DC.
METHODS: Molecular HIV-1 sequences were collected from participants infected through 2015 as part of the DC Cohort, a longitudinal observational study of HIV+ patients receiving care at 13 DC clinics. Sequences were paired with Cohort demographic, risk, and clinical data and analyzed using maximum likelihood, Bayesian and coalescent approaches of phylogenetic, network and population genetic inference. We analyzed 601 sequences from 223 participants for int (~864 bp) and 2,810 sequences from 1,659 participants for PR/RT (~1497 bp).
RESULTS: Ninety-nine and 94% of the int and PR/RT sequences, respectively, were identified as subtype B, with 14 non-B subtypes also detected. Phylodynamic analyses of US born infected individuals showed that HIV population size varied little over time with no significant decline in diversity. Phylogenetic analyses grouped 13.5% of the int sequences into 14 clusters of 2 or 3 sequences, and 39.0% of the PR/RT sequences into 203 clusters of 2-32 sequences. Network analyses grouped 3.6% of the int sequences into 4 clusters of 2 sequences, and 10.6% of the PR/RT sequences into 76 clusters of 2-7 sequences. All network clusters were detected in our phylogenetic analyses. Higher proportions of clustered sequences were found in zip codes where HIV prevalence is highest (r = 0.607; P<0.00001). We detected a high prevalence of DRM for both int (17.1%) and PR/RT (39.1%), but only 8 int and 12 PR/RT amino acids were identified as under adaptive selection. We observed a significant (P<0.0001) association between main risk factors (men who have sex with men and heterosexuals) and genotypes in the five well-supported clusters with sufficient sample size for testing.
DISCUSSION: Pairing molecular data with clinical and demographic data provided novel insights into HIV population dynamics in Washington, DC. Identification of populations and geographic locations where clustering occurs can inform and complement active surveillance efforts to interrupt HIV transmission.},
author = {P{\'e}rez-Losada, Marcos and Castel, Amanda D and Lewis, Brittany and Kharfen, Michael and Cartwright, Charles P and Huang, Bruce and Maxwell, Taylor and Greenberg, Alan E and Crandall, Keith A and {DC Cohort Executive Committee}},
date-added = {2024-01-22 08:09:49 -0500},
date-modified = {2024-01-22 08:10:01 -0500},
doi = {10.1371/journal.pone.0185644},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Adult; Cohort Studies; District of Columbia; Drug Resistance, Viral; Female; HIV Infections; HIV-1; Humans; Male; Middle Aged; Phylogeny},
number = {9},
pages = {e0185644},
pmc = {PMC5621693},
pmid = {28961263},
pst = {epublish},
title = {Characterization of {HIV} diversity, phylodynamics and drug resistance in {Washington, DC}},
volume = {12},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0185644}}
@article{Yan:2021aa,
abstract = {BACKGROUND: Post-migration infection and domestic transmission of HIV-1 between immigrants and local population are critical for the HIV epidemic, but have not been addressed thus far in China.
METHODS: Transmission clusters were analyzed with two cluster reconstruction methods, HIV-TRACE and Cluster Picker, using 1695 HIV-1 pol sequences obtained from 139 HIV-infected foreigners and 1556 Chinese natives in Guangzhou, China from 2008 to 2012. The geographic origin of the HIV-1 sequences was further determined by PastML while the factors associated with recent HIV-1 transmission were documented by logistic regression analysis.
RESULTS: HIV-1 genotypes that are prevalent in African and East Asian countries were identified in HIV-infected Chinese subjects and vice versa. In addition, more NRTI drug resistance mutations were found in HIV-infected foreigners than in native Chinese (p < 0.001). HIV-1 transmission between HIV-infected foreigners and native Chinese individuals was documented in 12.95% (18/139) of the HIV-infected foreigners. Furthermore, Asian (odds ratio [OR] = 3.45), male (OR = 16.88) and those with known HIV-1 infection routes (OR = 3.23) were more likely associated with recent HIV-1 transmission in China. The Chinese natives linked to recent HIV-1 transmission were more likely to be infected through men who have sex with men (OR = 3.05) or people who inject drugs (OR = 3.05), rather than by heterosexual transmission.
CONCLUSION: Our study demonstrates the impact of recent HIV-1 transmission between HIV-infected foreigners and Chinese natives on the HIV-1 epidemic in Guangzhou, China. Moreover, the results highlight the importance of phylogenetic analysis of HIV-1 surveillance data and the need for specific prevention strategies that target the immigrant population.},
author = {Yan, Huanchang and Wu, Hao and Xia, Yonghe and Huang, Liping and Liang, Yuanhao and Li, Qingmei and Chen, Ling and Han, Zhigang and Tang, Shixing},
date-added = {2024-01-21 10:29:07 -0500},
date-modified = {2024-01-21 10:29:07 -0500},
doi = {10.1016/j.meegid.2021.104870},
journal = {Infect Genet Evol},
journal-full = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
keywords = {Ancestral construction; Cluster analysis; HIV-1; Immigrant; Transmission network},
mesh = {Adult; China; Cities; Female; HIV Infections; HIV-1; Humans; Male; Middle Aged; Phylogeny; Transients and Migrants; Young Adult},
month = {Aug},
pages = {104870},
pmid = {33901684},
pst = {ppublish},
title = {Acquisition and transmission of HIV-1 among migrants and Chinese in Guangzhou, China from 2008 to 2012: Phylogenetic analysis of surveillance data},
volume = {92},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1016/j.meegid.2021.104870}}
@article{Leal:2020aa,
abstract = {The HIV-1 epidemic in Brazil has been growing in northeast and north regions, particularly an increase in AIDS cases among the younger male population has been observed. This study aims to characterize the HIV-1 genetic diversity and to evaluate its antiretroviral resistance profile among individuals presenting virological failure in the state of Maranh{\~a}o-Brazil. HIV-1 pol gene sequences from 633 patients on antiretroviral therapy were obtained from the Department of Surveillance, Prevention and Control of Sexually Transmitted Infections, HIV/AIDS and Viral Hepatitis of the Brazilian Ministry of Health. Phylogenetic and recombination analyses were performed to characterize viral genetic diversity. The presence of antiretroviral resistance mutations was assessed using the HIV Drug Resistance Database online platform of Stanford University. A predominance of subtype B (84.5%) was observed, followed by recombinant BF (9.5%), where more than half of the sequences were dispersed in 3 clusters. Antiretroviral resistance was detected in 74.1% of the sequences, and it was significantly higher for nucleoside analogue reverse-transcriptase inhibitors (NRTIs) than for non-nucleoside analogue reverse-transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs). Inference of putative transmissions clusters identified 11 clusters with 22 query sequences (22/633, 3.5%). Thus, we conclude that continuous monitoring of the molecular epidemiology of HIV-1 is essential for prevention strategies, epidemic control, and treatment adequacy.},
author = {Leal, {\'E}lcio and Arrais, Claudia Regina and Barreiros, Marta and Farias Rodrigues, Jessyca Kalynne and Silva Sousa, Nilviane Pires and Duarte Costa, Daniel and Rodrigo Pereira Santos, Francisco Dimitre and Dantas Silva, Antonio and Silva Viana, Antonia Iracilda E and Barros, Allan Kardec and Lima, Kledoaldo},
date-added = {2023-10-20 17:03:41 -0400},
date-modified = {2023-10-20 17:03:41 -0400},
doi = {10.1371/journal.pone.0230878},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Anti-HIV Agents; Brazil; Drug Resistance, Viral; Genetic Variation; HIV-1; Humans; pol Gene Products, Human Immunodeficiency Virus},
number = {3},
pages = {e0230878},
pmc = {PMC7100926},
pmid = {32218587},
pst = {epublish},
title = {Characterization of HIV-1 genetic diversity and antiretroviral resistance in the state of Maranh{\~a}o, Northeast Brazil},
volume = {15},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0230878}}
@article{Yu:2022aa,
abstract = {Prevalence of drug resistance (DR) challenges the epidemic control of human immunodeficiency virus (HIV)-1. However, little is known about DR among patients with antiretroviral therapy (ART) failure in Guangxi province, China. This cross-sectional study was aimed to investigate the prevalence of DR and the characteristics of DR sequences in the genetic transmission network among HIV-1 patients with ART failure in Guangxi. We enrolled 358 eligible patients between 2012 and 2018. Blood samples were subjected to reverse transcription polymerase chain reaction, followed by sequencing of the HIV-1 polymerase (pol) gene. An online subtyping tool and neighbor-joining phylogenetic tree were used to determine the genotype. HIV-TRACE tool was used to constructed transmission network with a pairwise genetic distance of 0.013. DR was analyzed using the Stanford University HIV Drug Resistance Database. We obtained 293 pol-sequences from participants; CRF01_AE (75.4%), CRF 08_BC (15.7%), and CRF07_BC (8.5%) were the main subtypes, and an A1 subtype was detected in Guangxi for the first time. The overall prevalence of DR was 32.4% (95/293). Among those with identified DR, 25.6% were against non-nucleoside analog reverse-transcriptase inhibitors (NNRTIs), 17.7% were against nucleoside analog reverse-transcriptase inhibitors (NRTIs), and 14.3% were against both NRTIs and NNRTIs. The common drug-resistant mutations were M184V (10.2%), K103N (10.6%) and V179D (6.1%). The patients located in the southern Guangxi [adjust odds ratio (AOR) = 10.87], or whose blood plasma were taken in 2017-2018 (AOR = 3.98) had an increased risk of DR. Of the CRF01_AE, CRF07_BC, and CRF08_BC sequences, 18.6%, 8.0%, and 13.0% fell into clusters, respectively. Nine (9.7%) sequences from patients with DR fell into three clusters. The largest cluster containing 11 individuals was the CRF01_AE subtype, 27.3% of whom were DR patients. Although the prevalence of DR among ART failure patients in Guangxi was at a low level, the continuous surveillance of DR in ART patients is necessary.},
author = {Yu, Dee and Liang, Bingyu and Yang, Yuan and Liu, Jie and Liang, Huayue and Zhang, Fei and Jiang, Jiaxiao and Huang, Jiegang and Zhong, Shanmei and Qin, Cai and Jiang, Junjun and Liang, Hao and Ye, Li},
date-added = {2023-10-20 16:39:26 -0400},
date-modified = {2023-10-20 16:39:26 -0400},
doi = {10.1089/AID.2021.0181},
journal = {AIDS Res Hum Retroviruses},
journal-full = {AIDS research and human retroviruses},
keywords = {Guangxi; HIV-1 drug resistance; antiretroviral therapy; genetic transmission networks; virological failure},
mesh = {Humans; HIV Infections; Acquired Immunodeficiency Syndrome; Prevalence; Phylogeny; Cross-Sectional Studies; China; HIV-1; Reverse Transcriptase Inhibitors; Genotype; Mutation; Drug Resistance; DNA-Directed RNA Polymerases; Drug Resistance, Viral},
month = {Oct},
number = {10},
pages = {822-830},
pmid = {35972723},
pst = {ppublish},
title = {Prevalence of Drug Resistance and Genetic Transmission Networks Among Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome Patients with Antiretroviral Therapy Failure in Guangxi, China},
volume = {38},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1089/AID.2021.0181}}
@article{Li:2022aa,
abstract = {BACKGROUND: HIV drug resistance increased with the widespread use of antiretroviral drugs, and posed great threat to antiretroviral therapy (ART). Pu'er Prefecture, lying in the southwest of Yunnan Province, China, borders Myanmar, Laos and Vietnam, is also the area where AIDS was discovered earlier, however, in which there has been no information on HIV drug resistance.
METHODS: A cross-sectional survey of pretreatment drug resistance (PDR) was conducted in Pu'er Prefecture in 2021. Partial pol gene sequences were obtained to analyze drug resistance and construct genetic transmission network. HIV drug resistance was analyzed using the Stanford University HIVdb algorithm.
RESULTS: A total of 295 sequences were obtained, among which 11 HIV-1 strain types were detected and CRF08_BC (62.0%, 183/295) was the predominant one. Drug resistance mutations (DRMs) were detected in 42.4% (125/295) of the sequences. The prevalence of PDR to any antiretroviral drugs, nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) were 10.8% (32/295), 9.5% (28/295), 1.0% (3/295) and 0.3% (1/295), respectively. The risk of PDR occurrence was higher among individuals with CRF01_AE strain types. HIV-1 molecular network was constructed, in which 56.0% (42/75) of links were transregional, and 54.7% (41/75) of links were associated with Lancang County. Among the sequences in the network, 36.8% (35/95) harbored DRMs, and 9.5% (9/95) were drug resistance strains. Furthermore, 8 clusters had shared DRM.
CONCLUSION: The overall prevalence of PDR in this study was in a moderate level, but NNRTIs resistance was very approaching to the threshold of public response initiation. PDR was identified in the transmission network, and DRMs transmission was observed. These findings suggested that the consecutive PDR surveillance should be conducted in this region.},
author = {Li, Difei and Chen, Huichao and Li, Huilan and Ma, Yanling and Dong, Lijuan and Dai, Jie and Jin, Xiaomei and Yang, Min and Zeng, Zhijun and Sun, Pengyan and Song, Zhizhong and Chen, Min},
date-added = {2023-10-20 13:05:59 -0400},
date-modified = {2023-10-20 13:05:59 -0400},
doi = {10.1186/s12879-022-07734-3},
journal = {BMC Infect Dis},
journal-full = {BMC infectious diseases},
keywords = {Genetic transmission network; HIV; Pretreatment drug resistance},
mesh = {Anti-HIV Agents; Anti-Retroviral Agents; China; Cross-Sectional Studies; Drug Resistance, Viral; Genotype; HIV Infections; HIV Seropositivity; HIV-1; Humans; Protease Inhibitors; Reverse Transcriptase Inhibitors},
month = {Sep},
number = {1},
pages = {741},
pmc = {PMC9483295},
pmid = {36117159},
pst = {epublish},
title = {HIV-1 pretreatment drug resistance and genetic transmission network in the southwest border region of China},
volume = {22},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1186/s12879-022-07734-3}}
@article{Billings:2019aa,
abstract = {BACKGROUND: HIV-1 circulating recombinant forms (CRF) containing subtype B are uncommon in sub-Saharan Africa. Prevalent infections observed during enrollment of a prospective study of men who have sex with men (MSM) from Lagos, Nigeria, revealed the presence of a family of subtype B and CRF02_AG recombinants. This report describes the HIV-1 genetic diversity within a high-risk, high-prevalence, and previously undersampled cohort of Nigerian MSM.
METHODS: Between 2013 and 2016, 672 MSM were enrolled at the Lagos site of the TRUST/RV368 study. Prevalent HIV-1 infections were initially characterized by pol sequencing and phylogenetic subtyping analysis. Samples demonstrating the presence of subtype B were further characterized by near full-length sequencing, phylogenetic, and Bayesian analyses.
RESULTS: Within this cohort, HIV-1 prevalence was 59%. The major subtype was CRF02_AG (57%), followed by CRF02/B recombinants (15%), subtype G (13%), and smaller amounts of A1, B, and other recombinants. Nine clusters of closely related pol sequences indicate ongoing transmission events within this cohort. Among the CRF02_AG/B, a new CRF was identified and termed CRF95_02B. Shared risk factors and Bayesian phylogenetic inference of the new CRF95_02B and the similarly structured CRF56_cpx indicate a Nigerian or West African origin of CRF56_cpx before its observation in France.
CONCLUSION: With high HIV-1 prevalence, new strains, and multiple transmission networks, this cohort of Nigerian MSM represents a previously hidden reservoir of HIV-1 strains, including the newly identified CRF95_02B and closely related CRF56_cpx. These strains will need to be considered during vaccine selection and development to optimize the design of a globally effective HIV-1 vaccine.},
author = {Billings, Erik and Kijak, Gustavo H and Sanders-Buell, Eric and Ndembi, Nicaise and O'Sullivan, Anne Marie and Adebajo, Sylvia and Kokogho, Afoke and Milazzo, Mark and Lombardi, Kara and Baral, Stefan and Nowak, Rebecca and Ramadhani, Habib and Gramzinski, Robert and Robb, Merlin L and Michael, Nelson L and Charurat, Manhattan E and Ake, Julie and Crowell, Trevor A and Tovanabutra, Sodsai and {MHRP Viral Sequencing Core and the TRUST/RV368 Study Group}},
date-added = {2023-10-20 12:17:14 -0400},
date-modified = {2023-10-20 17:10:52 -0400},
doi = {10.1097/QAI.0000000000002076},
journal = {J Acquir Immune Defic Syndr},
journal-full = {Journal of acquired immune deficiency syndromes (1999)},
mesh = {Adult; Bayes Theorem; France; Genome, Viral; HIV Infections; HIV-1; Homosexuality, Male; Humans; Male; Molecular Epidemiology; Nigeria; Phylogeny; Prevalence; Prospective Studies; Recombination, Genetic; Sexual and Gender Minorities; Young Adult},
month = {Aug},
number = {5},
pages = {578-584},
pmc = {PMC6625905},
pmid = {31107298},
pst = {ppublish},
title = {New Subtype B Containing HIV-1 Circulating Recombinant of sub-Saharan Africa Origin in Nigerian Men Who Have Sex With Men},
volume = {81},
year = {2019},
bdsk-url-1 = {https://doi.org/10.1097/QAI.0000000000002076}}
@article{Chen:2023aa,
abstract = {BACKGROUND: In Guangxi province of China, there is a high prevalence of HIV in the general population and in men who have sex with men (MSM). However, there is still a low proportion of MSM among people living with HIV. This apparent contradiction could be due to the high proportion of potential non-disclosed MSM (pnMSM) among reported heterosexual men. We analyzed the genetic linkage of HIV specimens to address this problem aiming to (1) identify the optimal genetic distance threshold, which gave the highest number of genetic clusters, (2) document the proportion of potential non-disclosed MSM (pnMSM) among self-reported heterosexual men, and (3) determine predictors for pnMSM.
METHODS: Pairwise genetic distances were computed among all samples. The genetic distance threshold giving the highest number of genetic clusters was identified. Self-reported heterosexual men were identified as belonging to the pnMSM group if they could be linked to any MSM in their cluster. Multinomial logistic regression was used to determine associated factors of being pnMSM.
RESULTS: The optimal genetic distance threshold was 0.75% substitutions/site. Among 896 self-reported heterosexual men, the frequency (percentage and 95% confidence interval) was 62 (6.9%, 5.2-8.6%) for pnMSM, 779 (86.9%, 84.7-89.1%) for indeterminate men and 55 (6.1%, 4.5-7.7%) for potential heterosexual men, respectively. Self-reported heterosexual men who were younger, single and more educated were more likely to be pnMSM.
CONCLUSION: Based on these findings, there is a need to pay more attention to sexually active, young and educated self-reported heterosexual men and provide them with voluntary counselling and testing and specific HIV prevention services.},
author = {Chen, Yi and Lan, Guanghua and Feng, Yi and Ruan, Yuhua and Shen, Zhiyong and McNeil, Edward B and Tang, Kailing and Huang, Jinghua and Shao, Yiming and Lin, Mei and Chongsuvivatwong, Virasakdi},
date-added = {2023-10-20 12:00:36 -0400},
date-modified = {2023-10-20 12:00:36 -0400},
doi = {10.1371/journal.pone.0283031},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Male; Humans; Heterosexuality; Homosexuality, Male; HIV Infections; Self Report; Gene Regulatory Networks; Sexual and Gender Minorities; China},
number = {3},
pages = {e0283031},
pmc = {PMC10065240},
pmid = {37000807},
pst = {epublish},
title = {Inferring potential non-disclosed men who have sex with men among self-reported heterosexual men with HIV in Southwest China: A genetic network study},
volume = {18},
year = {2023},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0283031}}
@article{Fabeni:2020aa,
abstract = {We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2-3 sequences), medium (MMTCs, 4-9 sequences) and large (LMTCs, ≥10 sequences). Among 3499 drug-na{\"\i}ve individuals enrolled in the Italian Cohort Naive Antiretroviral (ICONA) cohort (2804 natives; 695 migrants), 726 (20.8%; 644 natives, 82 migrants) were involved in 228 MTCs (6 LMTCs, 36 MMTCs, 186 SMTCs). Migrants contributed 14.4% to SMTCs, 7.6% to MMTCs and 7.1% to LMTCs, respectively. HIV-1 non-B subtypes were found in 51 MTCs; noteworthy was that non-B infections involved in MTCs were more commonly found in natives (n = 47) than in migrants (n = 4). Factors such as Italian origin, being men who have sex with men (MSM), younger age, more recent diagnosis and a higher CD4 count were significantly associated with MTCs. Our findings show that HIV-1 clustering transmission among newly diagnosed individuals living in Italy is prevalently driven by natives, mainly MSM, with a more recent diagnosis and frequently infected with HIV-1 non-B subtypes. These results can contribute to monitoring of the HIV epidemic and guiding the public health response to prevent new HIV infections.},
author = {Fabeni, Lavinia and Santoro, Maria Mercedes and Lorenzini, Patrizia and Rusconi, Stefano and Gianotti, Nicola and Costantini, Andrea and Sarmati, Loredana and Antinori, Andrea and Ceccherini-Silberstein, Francesca and d'Arminio Monforte, Antonella and Saracino, Annalisa and Girardi, Enrico and On Behalf Of The Icona Foundation Study Cohort},
date-added = {2023-10-20 11:46:56 -0400},
date-modified = {2023-10-20 11:46:56 -0400},
doi = {10.3390/v12080791},
journal = {Viruses},
journal-full = {Viruses},
keywords = {bioinformatics; cluster detection; drug resistance testing; human immunodeficiency virus (HIV); migrants; molecular epidemiology; phylogenetic analysis; risk factors; subtypes; transmission networks and clusters},
mesh = {Adult; Cohort Studies; Emigrants and Immigrants; Female; Genotype; HIV Infections; HIV-1; Humans; Italy; Male; Middle Aged; Phylogeny; Sexual and Gender Minorities; pol Gene Products, Human Immunodeficiency Virus},
month = {Jul},
number = {8},
pmc = {PMC7472346},
pmid = {32718024},
pst = {epublish},
title = {Evaluation of HIV Transmission Clusters among Natives and Foreigners Living in Italy},
volume = {12},
year = {2020},
bdsk-url-1 = {https://doi.org/10.3390/v12080791}}
@article{Temereanca:2017aa,
abstract = {UNLABELLED: Injection drug use is increasingly an important route of HIV transmission in Romania (from 1.5% of the newly diagnosed cases prior to 2010 to 31% in 2013). In this study we investigated the viral characteristics and relationships in newly HIV infected persons who inject drugs in Bucharest, Romania.
RESULTS: HIV-1 pol sequencing, followed by phylogenetic and clustering analysis was performed on blood from 37 injecting drug users (IDUs) newly diagnosed with HIV infection. While HIV subtype F1, the dominant strain in Romania since 1990, remains prevalent, new subtypes were found including G, B, B/G and B/F recombinants. Overall, 27 of the available sequences (72.9%) clustered with at least one other. Network and phylogenetic analysis revealed tight monophyletic clusters for both subtypes F and G, with short genetic distances between sequences, suggesting recent numerous acute to acute transmissions or single burst-type episodes. No transmitted drug-resistance mutations were identified. Greater immunosuppression was present in subjects forming the subtype G cluster, possibly indicating a faster rate of progression associated with this subtype.
CONCLUSIONS: The recent increasing numbers of IDU related HIV transmissions in Bucharest, has resulted in closely-knit transmission networks that maychange the genetic profile of the local HIV epidemic.},
author = {Temereanca, Aura and Oprea, Cristiana and Wertheim, Joel O and Ianache, Irina and Ceausu, Emanoil and Cernescu, Costin and Mehta, Sanjay R and Ruta, Simona},
date-added = {2023-10-20 10:49:46 -0400},
date-modified = {2023-10-20 10:49:46 -0400},
journal = {Rom Biotechnol Lett},
journal-full = {Romanian biotechnological letters},
keywords = {HIV; drug use; subtype F; subtype G; transmission networks},
number = {1},
pages = {12307-12315},
pmc = {PMC5713907},
pmid = {29213206},
pst = {ppublish},
title = {HIV transmission clusters among injecting drug users in Romania},
volume = {22},
year = {2017}}
@article{Stecher:2018aa,
abstract = {Using HIV sequence data to characterize clusters of HIV transmission may provide insight into the epidemic. Phylogenetic and network analyses were performed to infer putative relationships between HIV-1 partial pol sequences from 2,774 individuals receiving care in three German regions between 1999-2016. The regions have in common that they host some of the largest annual festivals in Europe (Carnival and Oktoberfest). Putative links with sequences (n = 150,396) from the Los Alamos HIV Sequence database were evaluated. A total of 595/2,774 (21.4%) sequences linked with at least one other sequence, forming 184 transmission clusters. Clustering individuals were significantly more likely to be younger, male, and report sex with men as their main risk factor (p < 0.001 each). Most clusters (77.2%) consisted exclusively of men; 41 (28.9%) of these included men reporting sex with women. Thirty-two clusters (17.4%) contained sequences from more than one region; clustering men were significantly more likely to be in a position bridging regional HIV epidemics than clustering women (p = 0.027). We found 236 clusters linking 547 sequences from our sample with sequences from the Los Alamos database (n = 1407; 31% from other German centres). These results highlight the pitfalls of focusing HIV prevention efforts on specific risk groups or specific locales.},
author = {Stecher, Melanie and Chaillon, Antoine and Eberle, Josef and Behrens, Georg M N and Eis-H{\"u}binger, Anna-Maria and Lehmann, Clara and Jablonka, Alexandra and Bogner, Johannes and F{\"a}tkenheuer, Gerd and Spinner, Christoph D and Wasmuth, Jan-Christian and Kaiser, Rolf and Mehta, Sanjay R and Vehreschild, Joerg Janne and Hoenigl, Martin},
date-added = {2023-10-19 08:10:10 -0400},
date-modified = {2023-10-19 08:10:10 -0400},
doi = {10.1038/s41598-018-25004-8},
journal = {Sci Rep},
journal-full = {Scientific reports},
mesh = {Adult; Cluster Analysis; Epidemics; Female; Germany; HIV Infections; HIV-1; Heterosexuality; Holidays; Homosexuality, Male; Humans; Incidence; Male; Middle Aged; Molecular Epidemiology; Risk Factors; Sex Factors},
month = {May},
number = {1},
pages = {6799},
pmc = {PMC5931588},
pmid = {29717148},
pst = {epublish},
title = {Molecular Epidemiology of the HIV Epidemic in Three German Metropolitan Regions - Cologne/Bonn, Munich and Hannover, 1999-2016},
volume = {8},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1038/s41598-018-25004-8}}
@article{Grabowski:2014aa,
abstract = {BACKGROUND: It is often assumed that local sexual networks play a dominant role in HIV spread in sub-Saharan Africa. The aim of this study was to determine the extent to which continued HIV transmission in rural communities--home to two-thirds of the African population--is driven by intra-community sexual networks versus viral introductions from outside of communities.
METHODS AND FINDINGS: We analyzed the spatial dynamics of HIV transmission in rural Rakai District, Uganda, using data from a cohort of 14,594 individuals within 46 communities. We applied spatial clustering statistics, viral phylogenetics, and probabilistic transmission models to quantify the relative contribution of viral introductions into communities versus community- and household-based transmission to HIV incidence. Individuals living in households with HIV-incident (n = 189) or HIV-prevalent (n = 1,597) persons were 3.2 (95% CI: 2.7-3.7) times more likely to be HIV infected themselves compared to the population in general, but spatial clustering outside of households was relatively weak and was confined to distances <500 m. Phylogenetic analyses of gag and env genes suggest that chains of transmission frequently cross community boundaries. A total of 95 phylogenetic clusters were identified, of which 44% (42/95) were two individuals sharing a household. Among the remaining clusters, 72% (38/53) crossed community boundaries. Using the locations of self-reported sexual partners, we estimate that 39% (95% CI: 34%-42%) of new viral transmissions occur within stable household partnerships, and that among those infected by extra-household sexual partners, 62% (95% CI: 55%-70%) are infected by sexual partners from outside their community. These results rely on the representativeness of the sample and the quality of self-reported partnership data and may not reflect HIV transmission patterns outside of Rakai.
CONCLUSIONS: Our findings suggest that HIV introductions into communities are common and account for a significant proportion of new HIV infections acquired outside of households in rural Uganda, though the extent to which this is true elsewhere in Africa remains unknown. Our results also suggest that HIV prevention efforts should be implemented at spatial scales broader than the community and should target key populations likely responsible for introductions into communities.},
author = {Grabowski, Mary K and Lessler, Justin and Redd, Andrew D and Kagaayi, Joseph and Laeyendecker, Oliver and Ndyanabo, Anthony and Nelson, Martha I and Cummings, Derek A T and Bwanika, John Baptiste and Mueller, Amy C and Reynolds, Steven J and Munshaw, Supriya and Ray, Stuart C and Lutalo, Tom and Manucci, Jordyn and Tobian, Aaron A R and Chang, Larry W and Beyrer, Chris and Jennings, Jacky M and Nalugoda, Fred and Serwadda, David and Wawer, Maria J and Quinn, Thomas C and Gray, Ronald H and {Rakai Health Sciences Program}},
date-added = {2023-10-18 17:46:41 -0400},
date-modified = {2023-10-18 17:46:41 -0400},
doi = {10.1371/journal.pmed.1001610},
journal = {PLoS Med},
journal-full = {PLoS medicine},
mesh = {Adolescent; Adult; Epidemics; Female; HIV Infections; HIV Seropositivity; HIV-1; Humans; Incidence; Male; Middle Aged; Models, Theoretical; Phylogeny; Prevalence; Rural Population; Sexual Behavior; Uganda; Young Adult},
month = {Mar},
number = {3},
pages = {e1001610},
pmc = {PMC3942316},
pmid = {24595023},
pst = {epublish},
title = {The role of viral introductions in sustaining community-based HIV epidemics in rural Uganda: evidence from spatial clustering, phylogenetics, and egocentric transmission models},
volume = {11},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1371/journal.pmed.1001610}}
@article{Gibson:2019aa,
abstract = {Washington, DC consistently has one of the highest annual rates of new HIV-1 diagnoses in the United States over the last 10 years. To guide intervention and prevention strategies to combat DC HIV infection, it is helpful to understand HIV transmission dynamics in a historical context. Toward this aim, we conducted a retrospective study (years 1987-2015) of 3,349 HIV pol sequences (1,026 bp) from 1,996 individuals living in the DC area belonging to three different cohorts. We coupled HIV sequence data with clinical information (sex, risk factor, race/ethnicity, viral load, subtype, anti-retroviral regimen) to identify circulating drug resistant mutations (DRM) and transmission clusters and assess their persistence over time. Of the transmission clusters identified in the DC area, 78.0 and 31.7% involved MSM and heterosexuals, respectively. The longest spread of time for a single cluster was 5 years (2007-2012) using a distance-based network inference approach and 27 years (1987-2014) using a maximum likelihood phylogenetic approach. We found eight subtypes and nine recombinants. Genetic diversity increased steadily over time with a slight peak in 2009 and remained constant thereafter until 2015. Nucleotide diversity also increased over time while relative genetic diversity (BEAST) remained relatively steady over the last 28 years with slight increases since 2000 in subtypes B and C. Sequences from individuals on drug therapy contained the highest total number of DRMs (1,104-1,600) and unique DRMs (63-97) and the highest proportion (>20%) of resistant individuals. Heterosexuals (43.94%), MSM (40.13%), and unknown (44.26%) risk factors showed similar prevalence of DRMs, while injection drug users had a lower prevalence (33.33%). Finally, there was a 60% spike in the number of codons with DRMs between 2007 and 2010. Past patterns of HIV transmission and DRM accumulation over time described here will help to predict future efficacy of ART drugs based on DRMs persisting over time and identify risk groups of interest for prevention and intervention efforts within the DC population. Our results show how longitudinal data can help to understand the temporal dynamics of HIV-1 at the local level.},
author = {Gibson, Keylie M and Steiner, Margaret C and Kassaye, Seble and Maldarelli, Frank and Grossman, Zehava and P{\'e}rez-Losada, Marcos and Crandall, Keith A},
date-added = {2023-10-18 17:28:09 -0400},
date-modified = {2023-10-18 17:28:09 -0400},
doi = {10.3389/fmicb.2019.00369},
journal = {Front Microbiol},
journal-full = {Frontiers in microbiology},
keywords = {DC; HIV-1; Washington; drug resistance mutations; phylodynamics; transmission networks},
pages = {369},
pmc = {PMC6418020},
pmid = {30906285},
pst = {epublish},
title = {A 28-Year History of HIV-1 Drug Resistance and Transmission in Washington, DC},
volume = {10},
year = {2019},
bdsk-url-1 = {https://doi.org/10.3389/fmicb.2019.00369}}
@article{Zai:2020aa,
abstract = {To investigate the genetic diversity, spatiotemporal dynamics, and transmission networks of HIV-1 CRF55_01B epidemic in China. A total of 209 partial pol gene sequences of HIV-1 CRF55_01B were sampled during 2007-2015 from 7 provinces of China. Phylogenetic analyses and trait diffusion process of these sequences were performed using Bayesian methods. Distance-based molecular network analyses were performed to infer putative relationships. Characteristics of genetically linked individuals were analyzed. Our study identified that HIV-1 CRF55_01B likely originated among men who have sex with men (MSM) in Guangdong province in January 2003 (April 2000-April 2005), and that Guangdong province and MSM are major hubs for the spread of the HIV-1 CRF55_01B epidemic in China. A Bayesian Skygrid plot revealed that the effective population size of HIV-1 CRF55_01B experienced increased phase followed by a plateau. All sequences from persons of unknown risk clustered within groups who reported MSM risk. This could be because Chinese MSM may not report such risk due to HIV/AIDS-related stigmatization and discrimination. This study inferred the transmission dynamics of the HIV-1 CRF55_01B epidemic in China at high resolution. The methods developed in this study may be critical for designing effective HIV prevention strategies in China and beyond.},
author = {Zai, Junjie and Liu, Haizhou and Lu, Zhenzhen and Chaillon, Antoine and Smith, Davey and Li, Yi and Li, Xingguang},
date-added = {2023-10-18 08:49:32 -0400},
date-modified = {2023-10-18 17:39:42 -0400},
doi = {10.1038/s41598-020-61870-x},
journal = {Sci Rep},
journal-full = {Scientific reports},
mesh = {China; Female; Genetic Linkage; Genome, Viral; HIV Infections; HIV-1; Homosexuality, Male; Humans; Male; Phylogeny; pol Gene Products, Human Immunodeficiency Virus},
month = {Mar},
number = {1},
pages = {5098},
pmc = {PMC7083841},
pmid = {32198405},
pst = {epublish},
title = {Tracing the transmission dynamics of HIV-1 CRF55\_01B},
volume = {10},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1038/s41598-020-61870-x}}
@article{Little:2014aa,
abstract = {OBJECTIVE: To reconstruct the local HIV-1 transmission network from 1996 to 2011 and use network data to evaluate and guide efforts to interrupt transmission.
DESIGN: HIV-1 pol sequence data were analyzed to infer the local transmission network.
METHODS: We analyzed HIV-1 pol sequence data to infer a partial local transmission network among 478 recently HIV-1 infected persons and 170 of their sexual and social contacts in San Diego, California. A transmission network score (TNS) was developed to estimate the risk of HIV transmission from a newly diagnosed individual to a new partner and target prevention interventions.
RESULTS: HIV-1 pol sequences from 339 individuals (52.3%) were highly similar to sequences from at least one other participant (i.e., clustered). A high TNS (top 25%) was significantly correlated with baseline risk behaviors (number of unique sexual partners and insertive unprotected anal intercourse (p = 0.014 and p = 0.0455, respectively) and predicted risk of transmission (p<0.0001). Retrospective analysis of antiretroviral therapy (ART) use, and simulations of ART targeted to individuals with the highest TNS, showed significantly reduced network level HIV transmission (p<0.05).
CONCLUSIONS: Sequence data from an HIV-1 screening program focused on recently infected persons and their social and sexual contacts enabled the characterization of a highly connected transmission network. The network-based risk score (TNS) was highly correlated with transmission risk behaviors and outcomes, and can be used identify and target effective prevention interventions, like ART, to those at a greater risk for HIV-1 transmission.},
author = {Little, Susan J and Kosakovsky Pond, Sergei L and Anderson, Christy M and Young, Jason A and Wertheim, Joel O and Mehta, Sanjay R and May, Susanne and Smith, Davey M},
date-added = {2023-10-18 08:33:13 -0400},
date-modified = {2023-10-18 08:33:13 -0400},
doi = {10.1371/journal.pone.0098443},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Adult; California; Cluster Analysis; Female; HIV Infections; HIV-1; Humans; Male; Mass Screening; Middle Aged; Population Surveillance; Sequence Analysis, DNA; Sexual Behavior; Sexual Partners; Young Adult; pol Gene Products, Human Immunodeficiency Virus},
number = {6},
pages = {e98443},
pmc = {PMC4047027},
pmid = {24901437},
pst = {epublish},
title = {Using HIV networks to inform real time prevention interventions},
volume = {9},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0098443}}
@article{Inzaule:2023aa,
abstract = { * Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens. * HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens. * Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines. * Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing. * In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions. * Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.},
author = {Inzaule, Seth C and Siedner, Mark J and Little, Susan J and Avila-Rios, Santiago and Ayitewala, Alisen and Bosch, Ronald J and Calvez, Vincent and Ceccherini-Silberstein, Francesca and Charpentier, Charlotte and Descamps, Diane and Eshleman, Susan H and Fokam, Joseph and Frenkel, Lisa M and Gupta, Ravindra K and Ioannidis, John P A and Kaleebu, Pontiano and Kantor, Rami and Kassaye, Seble G and Kosakovsky Pond, Sergei L and Kouamou, Vinie and Kouyos, Roger D and Kuritzkes, Daniel R and Lessells, Richard and Marcelin, Anne-Genevieve and Mbuagbaw, Lawrence and Minalga, Brian and Ndembi, Nicaise and Neher, Richard A and Paredes, Roger and Pillay, Deenan and Raizes, Elliot G and Rhee, Soo-Yon and Richman, Douglas D and Ruxrungtham, Kiat and Sabeti, Pardis C and Schapiro, Jonathan M and Sirivichayakul, Sunee and Steegen, Kim and Sugiura, Wataru and van Zyl, Gert U and Vandamme, Anne-Mieke and Wensing, Annemarie M J and Wertheim, Joel O and Gunthard, Huldrych F and Jordan, Michael R and Shafer, Robert W},
date-added = {2023-10-17 12:11:34 -0400},
date-modified = {2023-10-17 12:11:34 -0400},
doi = {10.1371/journal.pmed.1004293},
journal = {PLoS Med},
journal-full = {PLoS medicine},
month = {Sep},
number = {9},
pages = {e1004293},
pmc = {PMC10558071},
pmid = {37738247},
pst = {epublish},
title = {Recommendations on data sharing in HIV drug resistance research},
volume = {20},
year = {2023},
bdsk-url-1 = {https://doi.org/10.1371/journal.pmed.1004293}}
@article{RePEc:adr:anecst:y:2012:i:107-108:p:33-48,
abstract = {Homophily is the tendency of people to associate relatively more with those who are similar to them than with those who are not. In Golub and Jackson (2010a), we introduced degree-weighted homophily (DWH), a new measure of this phenomenon, and showed that it gives a lower bound on the time it takes for a certain natural best-reply or learning process operating in a social network to converge. Here we show that, in important settings, the DWH convergence bound does substantially better than previous bounds based on the Cheeger inequality. We also develop a new complementary upper bound on convergence time, tightening the relationship between DWH and updating processes on networks. In doing so, we suggest that DWH is a natural homophily measure because it tightly tracks a key consequence of homophily - namely, slowdowns in updating processes.},
author = {Golub, Benjamin and Jackson, Matthew},
date-added = {2023-10-17 10:22:14 -0400},
date-modified = {2023-10-17 10:22:14 -0400},
journal = {Annals of Economics and Statistics},
number = {107-108},
pages = {33-48},
title = {Network Structure and the Speed of Learning Measuring Homophily Based on its Consequences},
url = {https://EconPapers.repec.org/RePEc:adr:anecst:y:2012:i:107-108:p:33-48},
year = {2012},
bdsk-url-1 = {https://EconPapers.repec.org/RePEc:adr:anecst:y:2012:i:107-108:p:33-48}}
@article{robinson_how_2013,
abstract = {The characteristics of the host contact network over which a pathogen is transmitted affect both epidemic spread and the projected effectiveness of control strategies. Given the importance of understanding these contact networks, it is unfortunate that they are very difficult to measure directly. This challenge has led to an interest in methods to infer information about host contact networks from pathogen phylogenies, because in shaping a pathogen's opportunities for reproduction, contact networks also shape pathogen evolution. Host networks influence pathogen phylogenies both directly, through governing opportunities for evolution, and indirectly by changing the prevalence and incidence. Here, we aim to separate these two effects by comparing pathogen evolution on different host networks that share similar epidemic trajectories. This approach allows use to examine the direct effects of network structure on pathogen phylogenies, largely controlling for confounding differences arising from population dynamics. We find that networks with more heterogeneous degree distributions yield pathogen phylogenies with more variable cluster numbers, smaller mean cluster sizes, shorter mean branch lengths, and somewhat higher tree imbalance than networks with relatively homogeneous degree distributions. However, in particular for dynamic networks, we find that these direct effects are relatively modest. These findings suggest that the role of the epidemic trajectory, the dynamics of the network and the inherent variability of metrics such as cluster size must each be taken into account when trying to use pathogen phylogenies to understand characteristics about the underlying host contact network.},
author = {Robinson, Katy and Fyson, Nick and Cohen, Ted and Fraser, Christophe and Colijn, Caroline},
doi = {10.1371/journal.pcbi.1003105},
issn = {1553-7358},
journal = {PLOS Computational Biology},
keywords = {Chlamydia infection, Epidemiology, Pathogens, Phylogenetic analysis, Phylogenetics, Population dynamics, Sexually transmitted diseases, Trees},
month = jun,
note = {Publisher: Public Library of Science},
number = {6},
pages = {e1003105},
title = {How the {Dynamics} and {Structure} of {Sexual} {Contact} {Networks} {Shape} {Pathogen} {Phylogenies}},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003105},
urldate = {2023-08-09},
volume = {9},
year = {2013},
bdsk-url-1 = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003105},
bdsk-url-2 = {https://doi.org/10.1371/journal.pcbi.1003105}}
@article{goodreau_assessing_2006,
abstract = {Geneticists seeking to understand HIV-1 evolution among human hosts generally assume that hosts represent a panmictic population. Social science research demonstrates that the network patterns over which HIV-1 spreads are highly nonrandom, but the effect of these patterns on the genetic diversity of HIV-1 and other sexually transmitted pathogens has yet to be thoroughly examined. In addition, interhost phylogenetic models rarely account explicitly for genetic diversity arising from intrahost dynamics. This study outlines a graph-theoretic framework (exponential random graph modeling, ERGM) for the estimation, inference, and simulation of dynamic partnership networks. This approach is used to simulate HIV-1 transmission and evolution under eight mixing patterns resembling those observed in empirical human populations, while simultaneously incorporating intrahost viral diversity. Models of parametric growth fit panmictic populations well, yielding estimates of total viral effective population on the order of the product of infected host size and intrahost effective viral population size. Populations exhibiting patterns of nonrandom mixing differ more widely in estimates of effective population size they yield, however, and reconstructions of population dynamics can exhibit severe errors if panmixis is assumed. I discuss implications for HIV-1 phylogenetics and the potential for ERGM to provide a general framework for addressing these issues.},
author = {Goodreau, Steven M},
doi = {10.1534/genetics.103.024612},
issn = {1943-2631},
journal = {Genetics},
month = apr,
number = {4},
pages = {2033--2045},
title = {Assessing the {Effects} of {Human} {Mixing} {Patterns} on {Human} {Immunodeficiency} {Virus}-1 {Interhost} {Phylogenetics} {Through} {Social} {Network} {Simulation}},
url = {https://doi.org/10.1534/genetics.103.024612},
urldate = {2023-08-09},
volume = {172},
year = {2006},
bdsk-url-1 = {https://doi.org/10.1534/genetics.103.024612}}
@article{weaver_datamonkey_2018,
abstract = {Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey.org, and the underlying codebase is available from https://github.com/veg/datamonkey-js.},
author = {Weaver, Steven and Shank, Stephen D. and Spielman, Stephanie J. and Li, Michael and Muse, Spencer V. and Kosakovsky Pond, Sergei L.},
doi = {10.1093/molbev/msx335},
issn = {1537-1719},
journal = {Molecular Biology and Evolution},
keywords = {evolutionary inference, natural selection, recombination, statistical methods, web application},
month = mar,
number = {3},
pages = {773--777},
pmcid = {PMC5850112},
pmid = {29301006},
shorttitle = {Datamonkey 2.0},
title = {Datamonkey 2.0: {A} {Modern} {Web} {Application} for {Characterizing} {Selective} and {Other} {Evolutionary} {Processes}},
volume = {35},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1093/molbev/msx335}}
@article{jombart_reconstructing_2011,
abstract = {Epidemiology and public health planning will increasingly rely on the analysis of genetic sequence data. In particular, genetic data coupled with dates and locations of sampled isolates can be used to reconstruct the spatiotemporal dynamics of pathogens during outbreaks. Thus far, phylogenetic methods have been used to tackle this issue. Although these approaches have proved useful for informing on the spread of pathogens, they do not aim at directly reconstructing the underlying transmission tree. Instead, phylogenetic models infer most recent common ancestors between pairs of isolates, which can be inadequate for densely sampled recent outbreaks, where the sample includes ancestral and descendent isolates. In this paper, we introduce a novel method based on a graph approach to reconstruct transmission trees directly from genetic data. Using simulated data, we show that our approach can efficiently reconstruct genealogies of isolates in situations where classical phylogenetic approaches fail to do so. We then illustrate our method by analyzing data from the early stages of the swine-origin A/H1N1 influenza pandemic. Using 433 isolates sequenced at both the hemagglutinin and neuraminidase genes, we reconstruct the likely history of the worldwide spread of this new influenza strain. The presented methodology opens new perspectives for the analysis of genetic data in the context of disease outbreaks.},
author = {Jombart, T. and Eggo, R. M. and Dodd, P. J. and Balloux, F.},
copyright = {2011 The Genetics Society},
doi = {10.1038/hdy.2010.78},
issn = {1365-2540},
journal = {Heredity},
keywords = {Infectious-disease epidemiology, Phylogenetics},
month = feb,
note = {Number: 2 Publisher: Nature Publishing Group},
number = {2},
pages = {383--390},
shorttitle = {Reconstructing disease outbreaks from genetic data},
title = {Reconstructing disease outbreaks from genetic data: a graph approach},
url = {https://www.nature.com/articles/hdy201078},
urldate = {2023-07-28},
volume = {106},
year = {2011},
bdsk-url-1 = {https://www.nature.com/articles/hdy201078},
bdsk-url-2 = {https://doi.org/10.1038/hdy.2010.78}}
@article{murphy_molecular_2019,
abstract = {BACKGROUND: Molecular phylogenetics are generally used to confirm hepatitis C virus (HCV) transmission events. In addition, the Laboratoire de sant{\'e} publique du Qu{\'e}bec (LSPQ) has been using molecular phylogenetics for surveillance of HCV genotyping since November 2001.
OBJECTIVES: To describe the emergence of a specific lineage of HCV genotype 4d (G4d) and its characteristics using molecular phylogenetics as a surveillance tool for identifying HCV strain clustering.
METHODS: The LSPQ prospectively applied Sanger sequencing and phylogenetic analysis to determine the HCV genotype on samples collected from November 2001 to December 2017. When a major G4d cluster was identified, demographic information, HIV-infection status and syphilis test results were analyzed.
RESULTS: Phylogenetic analyses performed on approximately 22,000 cases identified 122 G4d cases. One major G4d cluster composed of 37 cases was singled out. Two cases were identified in 2010, 10 from 2011-2014 and 25 from 2015-2017. Cases in the cluster were concentrated in two urban health regions. Compared to the other G4d cases, cluster cases were all male (p{\textless}0.001) and more likely to be HIV-positive (adjusted risk ratio: 4.4; 95\% confidence interval: 2.5-7.9). A positive syphilis test result was observed for 27 (73\%) of the cluster cases. The sequences in this cluster and of four outlier cases were located on the same monophyletic lineage as G4d sequences reported in HIV-positive men who have sex with men (MSM) in Europe.
CONCLUSION: Molecular phylogenetics enabled the identification and surveillance of ongoing transmission of a specific HCV G4d lineage in HIV-positive and HIV-negative men in Quebec and its cross-continental spread. This information can orient intervention strategies to avoid transmission of HCV in MSM.},
author = {Murphy, D. G. and Dion, R. and Simard, M. and Vachon, M. L. and Martel-Laferri{\`e}re, V. and Serhir, B. and Longtin, J.},
doi = {10.14745/ccdr.v45i09a02},
issn = {1188-4169},
journal = {Canada Communicable Disease Report = Releve Des Maladies Transmissibles Au Canada},
keywords = {G4d, HCV, MSM, cluster, genotype, men who have sex with men, molecular epidemiology, phylogenetic analyses, surveillance},
month = sep,
number = {9},
pages = {230--237},
pmcid = {PMC6781953},
pmid = {31650986},
title = {Molecular surveillance of hepatitis {C} virus genotypes identifies the emergence of a genotype 4d lineage among men in {Quebec}, 2001-2017},
volume = {45},
year = {2019},
bdsk-url-1 = {https://doi.org/10.14745/ccdr.v45i09a02}}
@article{paraskevis_application_2016,
abstract = {HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.},
author = {Paraskevis, D. and Nikolopoulos, G. K. and Magiorkinis, G. and Hodges-Mameletzis, I. and Hatzakis, A.},
doi = {10.1016/j.meegid.2016.06.021},
issn = {1567-7257},
journal = {Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases},
keywords = {HIV Infections, HIV-1, Humans, Molecular Epidemiology, Molecular epidemiology, Public Health, Public health},
month = dec,
pages = {159--168},
pmid = {27312102},
title = {The application of {HIV} molecular epidemiology to public health},
volume = {46},
year = {2016},
bdsk-url-1 = {https://doi.org/10.1016/j.meegid.2016.06.021}}
@article{von_rotz_systematic_2023,
abstract = {BACKGROUND: We sought to decipher transmission pathways in healthcare-associated infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within our hospital by epidemiological work-up and complementary whole genome sequencing (WGS). We report the findings of the four largest epidemiologic clusters of SARS-CoV-2 transmission occurring during the second wave of the pandemic from 11/2020 to 12/2020.
METHODS: At the University Hospital Basel, Switzerland, systematic outbreak investigation is initiated at detection of any nosocomial case of SARS-CoV-2 infection, as confirmed by polymerase chain reaction, occurring more than five days after admission. Clusters of nosocomial infections, defined as the detection of at least two positive patients and/or healthcare workers (HCWs) within one week with an epidemiological link, were further investigated by WGS on respective strains.
RESULTS: The four epidemiologic clusters included 40 patients and 60 HCWs. Sequencing data was available for 70\% of all involved cases (28 patients and 42 HCWs), confirmed epidemiologically suspected in house transmission in 33 cases (47.1\% of sequenced cases) and excluded transmission in the remaining 37 cases (52.9\%). Among cases with identical strains, epidemiologic work-up suggested transmission mainly through a ward-based exposure (24/33, 72.7\%), more commonly affecting HCWs (16/24, 66.7\%) than patients (8/24, 33.3\%), followed by transmission between patients (6/33, 18.2\%), and among HCWs and patients (3/33, 9.1\%, respectively two HCWs and one patient).
CONCLUSIONS: Phylogenetic analyses revealed important insights into transmission pathways supporting less than 50\% of epidemiologically suspected SARS-CoV-2 transmissions. The remainder of cases most likely reflect community-acquired infection randomly detected by outbreak investigation. Notably, most transmissions occurred between HCWs, possibly indicating lower perception of the risk of infection during contacts among HCWs.},
author = {von Rotz, Matthias and Kuehl, Richard and Durovic, Ana and Zingg, Sandra and Apitz, Anett and Wegner, Fanny and Seth-Smith, Helena M. B. and Roloff, Tim and Leuzinger, Karoline and Hirsch, Hans H. and Kuster, Sabine and Battegay, Manuel and Mariani, Luigi and Schaeren, Stefan and Bassetti, Stefano and Banderet-Uglioni, Florian and Egli, Adrian and Tschudin-Sutter, Sarah},
doi = {10.1186/s13756-023-01242-y},
issn = {2047-2994},
journal = {Antimicrobial Resistance and Infection Control},
keywords = {COVID-19, Cross Infection, Disease Outbreaks, Epidemiologic cluster, Humans, Nosocomial outbreaks, Outbreak investigation, Phylogeny, SARS-CoV-2, SARS-CoV-2 cluster, Tertiary Care Centers, Whole genome sequencing},
month = apr,
number = {1},
pages = {38},
pmcid = {PMC10119817},
pmid = {37085891},
title = {A systematic outbreak investigation of {SARS}-{CoV}-2 transmission clusters in a tertiary academic care center},
volume = {12},
year = {2023},
bdsk-url-1 = {https://doi.org/10.1186/s13756-023-01242-y}}
@article{campigotto_utility_2023,
abstract = {An understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission in schools is important. It is often difficult, using epidemiological information alone, to determine whether cases associated with schools represent multiple introductions from the community or transmission within the school. We describe the use of whole genome sequencing (WGS) in multiple schools to investigate outbreaks of SARS-CoV-2 in the pre-Omicron period.},
author = {Campigotto, Aaron and Chris, Allison and Orkin, Julia and Lau, Lynette and Marshall, Christian and Bitnun, Ari and Buchan, Sarah A and MacDonald, Liane and Thampi, Nisha and McCready, Janine and Juni, Peter and Parekh, Rulan S and Science, Michelle},
doi = {10.1097/INF.0000000000003834},
issn = {0891-3668},
journal = {The Pediatric Infectious Disease Journal},
month = apr,
number = {4},
pages = {324--331},
pmcid = {PMC9990487},
pmid = {36795555},
title = {Utility of {SARS}-{CoV}-2 {Genomic} {Sequencing} for {Understanding} {Transmission} and {School} {Outbreaks}},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9990487/},
urldate = {2023-08-03},
volume = {42},
year = {2023},
bdsk-url-1 = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9990487/},
bdsk-url-2 = {https://doi.org/10.1097/INF.0000000000003834}}
@article{thoma_challenge_2022,
abstract = {Background
Despite the adoption of strict infection prevention and control measures, many hospitals have reported outbreaks of multidrug-resistant organisms (MDRO) during the Coronavirus 2019 (COVID-19) pandemic. Following an outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB) in our institution, we sought to systematically analyse characteristics of MDRO outbreaks in times of COVID-19, focussing on contributing factors and specific challenges in controlling these outbreaks.
Methods
We describe results of our own CRAB outbreak investigation and performed a systematic literature review for MDRO (including Candida auris) outbreaks which occurred during the COVID-19 pandemic (between December 2019 and March 2021). Search terms were related to pathogens/resistance mechanisms AND COVID-19. We summarized outbreak characteristics in a narrative synthesis and contrasted contributing factors with implemented control measures.
Results
The CRAB outbreak occurred in our intensive care units between September and December 2020 and comprised 10 patients (thereof seven with COVID-19) within two distinct genetic clusters (both ST2 carrying OXA-23). Both clusters presumably originated from COVID-19 patients transferred from the Balkans. Including our outbreak, we identified 17 reports, mostly caused by Candida auris (n = 6) or CRAB (n = 5), with an overall patient mortality of 35\% (68/193). All outbreaks involved intensive care settings. Non-adherence to personal protective equipment (PPE) or hand hygiene (n = 11), PPE shortage (n = 8) and high antibiotic use (n = 8) were most commonly reported as contributing factors, followed by environmental contamination (n = 7), prolonged critical illness (n = 7) and lack of trained HCW (n = 7). Implemented measures mainly focussed on PPE/hand hygiene audits (n = 9), environmental cleaning/disinfection (n = 9) and enhanced patient screening (n = 8). Comparing potentially modifiable risk factors and control measures, we found the largest discrepancies in the areas of PPE shortage (risk factor in 8 studies, addressed in 2 studies) and patient overcrowding (risk factor in 5 studies, addressed in 0 studies).
Conclusions
Reported MDRO outbreaks during the COVID-19 pandemic were most often caused by CRAB (including our outbreak) and C. auris. Inadequate PPE/hand hygiene adherence, PPE shortage, and high antibiotic use were the most commonly reported potentially modifiable factors contributing to the outbreaks. These findings should be considered for the prevention of MDRO outbreaks during future COVID-19 waves.
Supplementary Information
The online version contains supplementary material available at 10.1186/s13756-022-01052-8.},
author = {Thoma, Reto and Seneghini, Marco and Seiffert, Salom{\'e} N. and Vuichard Gysin, Danielle and Scanferla, Giulia and Haller, Sabine and Flury, Domenica and Boggian, Katia and Kleger, Gian-Reto and Filipovic, Miodrag and Nolte, Oliver and Schlegel, Matthias and Kohler, Philipp},
doi = {10.1186/s13756-022-01052-8},
issn = {2047-2994},
journal = {Antimicrobial Resistance and Infection Control},
month = jan,
pages = {12},
pmcid = {PMC8777447},
pmid = {35063032},
shorttitle = {The challenge of preventing and containing outbreaks of multidrug-resistant organisms and {Candida} auris during the coronavirus disease 2019 pandemic},
title = {The challenge of preventing and containing outbreaks of multidrug-resistant organisms and {Candida} auris during the coronavirus disease 2019 pandemic: report of a carbapenem-resistant {Acinetobacter} baumannii outbreak and a systematic review of the literature},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8777447/},
urldate = {2023-07-28},
volume = {11},
year = {2022},
bdsk-url-1 = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8777447/},
bdsk-url-2 = {https://doi.org/10.1186/s13756-022-01052-8}}
@article{mai_mycobacterium_2018,
abstract = {Vietnam has a high burden of tuberculosis (TB) and multidrug-resistant (MDR) TB, but drug resistance patterns and TB transmission dynamics among TB/human immunodeficiency virus (HIV) coinfected patients are not well described. We characterized 200 Mycobacterium tuberculosis isolates from TB/HIV coinfected patients diagnosed at the main TB referral hospital in Ho Chi Minh City, Vietnam. Phenotypic drug susceptibility testing (DST) for first-line drugs, spoligotyping, and 24-locus mycobacterial interspersed repetitive unit (MIRU-24) analysis was performed on all isolates. The 24-locus mycobacterial interspersed repetitive unit clusters and MDR isolates were subjected to whole genome sequencing (WGS). Most of the TB/HIV coinfected patients were young (162/174; 93.1\% aged {\textless} 45 years) males (173; 86.5\% male). Beijing (98; 49.0\%) and Indo-Oceanic (70; 35.0\%) lineage strains were most common. Phenotypic drug resistance was detected in 84 (42.0\%) isolates, of which 17 (8.5\%) were MDR; three additional MDR strains were identified on WGS. Strain clustering was reduced from 84.0\% with spoligotyping to 20.0\% with MIRU-24 typing and to 13.5\% with WGS. Whole genome sequencing identified five additional clusters, or members of clusters, not recognized by MIRU-24. In total, 13 small (two to three member) WGS clusters were identified, with less clustering among drug susceptible (2/27; 7.4\%) than among drug-resistant strains (25/27; 92.6\%). On phylogenetic analysis, strains from TB/HIV coinfected patients were interspersed among strains from the general community; no major clusters indicating transmission among people living with HIV were detected. Tuberculosis/HIV coinfection in Vietnam was associated with high rates of drug resistance and limited genomic evidence of ongoing M. tuberculosis transmission among HIV-infected patients.},
author = {Mai, Trinh Quynh and Martinez, Elena and Menon, Ranjeeta and Van Anh, Nguyen Thi and Hien, Nguyen Tran and Marais, Ben J. and Sintchenko, Vitali},
doi = {10.4269/ajtmh.18-0185},
issn = {0002-9637},
journal = {The American Journal of Tropical Medicine and Hygiene},
month = dec,
number = {6},
pages = {1397--1406},
pmcid = {PMC6283501},
pmid = {30382014},
title = {Mycobacterium tuberculosis {Drug} {Resistance} and {Transmission} among {Human} {Immunodeficiency} {Virus}--{Infected} {Patients} in {Ho} {Chi} {Minh} {City}, {Vietnam}},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283501/},
urldate = {2023-07-28},
volume = {99},
year = {2018},
bdsk-url-1 = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283501/},
bdsk-url-2 = {https://doi.org/10.4269/ajtmh.18-0185}}
@article{golub_how_2012,
abstract = {We examine how the speed of learning and best-response processes depends on homophily: the tendency of agents to associate disproportionately with those having similar traits. When agents' beliefs or behaviors are developed by averaging what they see among their neighbors, then convergence to a consensus is slowed by the presence of homophily but is not influenced by network density (in contrast to other network processes that depend on shortest paths). In deriving these results, we propose a new, general measure of homophily based on the relative frequencies of interactions among different groups. An application to communication in a society before a vote shows how the time it takes for the vote to correctly aggregate information depends on the homophily and the initial information distribution.},
author = {Golub, Benjamin and Jackson, Matthew O.},
doi = {10.1093/qje/qjs021},
issn = {0033-5533},
journal = {The Quarterly Journal of Economics},
month = aug,
number = {3},
pages = {1287--1338},
title = {How {Homophily} {Affects} the {Speed} of {Learning} and {Best}-{Response} {Dynamics}},
url = {https://doi.org/10.1093/qje/qjs021},
urldate = {2023-07-27},
volume = {127},
year = {2012},
bdsk-url-1 = {https://doi.org/10.1093/qje/qjs021}}
@article{tamura_estimation_1993,
abstract = {Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition/transversion ratio for the entire control region was approximately 15 and nearly the same for the two species. The 95\% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.},
author = {Tamura, K and Nei, M},
doi = {10.1093/oxfordjournals.molbev.a040023},
issn = {0737-4038},
journal = {Molecular Biology and Evolution},
month = may,
number = {3},
pages = {512--526},
title = {Estimation of the number of nucleotide substitutions in the control region of mitochondrial {DNA} in humans and chimpanzees.},
url = {https://doi.org/10.1093/oxfordjournals.molbev.a040023},
urldate = {2023-07-26},
volume = {10},
year = {1993},
bdsk-url-1 = {https://doi.org/10.1093/oxfordjournals.molbev.a040023}}
@article{bbosa_short_2020,
abstract = {HIV-TRAnsmission Cluster Engine (HIV-TRACE) and Cluster Picker are some of the most widely used programs for identifying HIV-1 transmission networks from nucleotide sequences. However, choosing between these tools is subjective and often a matter of personal preference. Because these software use different algorithms to detect HIV-1 transmission networks, their optimal use is better suited with different sequence data sets and under different scenarios. The performance of these tools has previously been evaluated across a range of genetic distance thresholds without an assessment of the differences in the structure of networks identified. In this study, we tested both programs on the same HIV-1 pol sequence data set (n = 2,017) from three Ugandan populations to examine their performance across different risk groups and evaluate the structure of networks identified. HIV-TRACE that uses a single-linkage algorithm identified more nodes in the same networks that were connected by sparse links than Cluster Picker. This suggests that the choice of the program used for identifying networks should depend on the study aims, the characteristics of the population being investigated, dynamics of the epidemic, sampling design, and the nature of research questions being addressed for optimum results. HIV-TRACE could be more applicable with larger data sets where the aim is to identify larger clusters that represent distinct transmission chains and in more diverse populations where infection has occurred over a period of time. In contrast, Cluster Picker is applicable in situations where more closely connected clusters are expected in the studied populations.},
author = {Bbosa, Nicholas and Ssemwanga, Deogratius and Kaleebu, Pontiano},
doi = {10.1089/AID.2020.0033},
issn = {1931-8405},
journal = {AIDS research and human retroviruses},
keywords = {Base Sequence, Cluster Analysis, Cluster Picker, HIV Infections, HIV-1, HIV-TRACE, Humans, Molecular Epidemiology, Phylogeny, cluster, pair, transmission network},
month = nov,
number = {11},
pages = {948--951},
pmcid = {PMC7698971},
pmid = {32693608},
shorttitle = {Short {Communication}},
title = {Short {Communication}: {Choosing} the {Right} {Program} for the {Identification} of {HIV}-1 {Transmission} {Networks} from {Nucleotide} {Sequences} {Sampled} from {Different} {Populations}},
volume = {36},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1089/AID.2020.0033}}
@article{brenner_role_2021,
abstract = {Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70\% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.},
author = {Brenner, Bluma G. and Ibanescu, Ruxandra-Ilinca and Osman, Nathan and Cuadra-Foy, Ernesto and Oliveira, Maureen and Chaillon, Antoine and Stephens, David and Hardy, Isabelle and Routy, Jean-Pierre and Thomas, R{\'e}jean and Baril, Jean-Guy and Leblanc, Roger and Tremblay, Cecile and Roger, Michel and The Montreal Primary Hiv Infection Phi Cohort Study Group, null},
doi = {10.3390/v13081643},
issn = {1999-4915},
journal = {Viruses},
keywords = {Adult, Aged, Aged, 80 and over, Epidemics, Female, HIV Infections, HIV-1, HIV-1 transmission, HIV-TRACE, Homosexuality, Male, Humans, Male, Middle Aged, Phylogeny, Quebec, Young Adult, men having sex with men, migration, non-B subtypes, phylogenetics, treatment-as-prevention},
month = aug,
number = {8},
pages = {1643},
pmcid = {PMC8402830},
pmid = {34452506},
shorttitle = {The {Role} of {Phylogenetics} in {Unravelling} {Patterns} of {HIV} {Transmission} towards {Epidemic} {Control}},
title = {The {Role} of {Phylogenetics} in {Unravelling} {Patterns} of {HIV} {Transmission} towards {Epidemic} {Control}: {The} {Quebec} {Experience} (2002-2020)},
volume = {13},
year = {2021},
bdsk-url-1 = {https://doi.org/10.3390/v13081643}}
@article{chato_public_2020,
abstract = {Genetic clustering is a popular method for characterizing variation in transmission rates for rapidly evolving viruses, and could potentially be used to detect outbreaks in 'near real time'. However, the statistical properties of clustering are poorly understood in this context, and there are no objective guidelines for setting clustering criteria. Here, we develop a new statistical framework to optimize a genetic clustering method based on the ability to forecast new cases. We analysed the pairwise Tamura-Nei (TN93) genetic distances for anonymized HIV-1 subtype B pol sequences from Seattle (n = 1,653) and Middle Tennessee, USA (n = 2,779), and northern Alberta, Canada (n = 809). Under varying TN93 thresholds, we fit two models to the distributions of new cases relative to clusters of known cases: 1, a null model that assumes cluster growth is strictly proportional to cluster size, i.e. no variation in transmission rates among individuals; and 2, a weighted model that incorporates individual-level covariates, such as recency of diagnosis. The optimal threshold maximizes the difference in information loss between models, where covariates are used most effectively. Optimal TN93 thresholds varied substantially between data sets, e.g. 0.0104 in Alberta and 0.016 in Seattle and Tennessee, such that the optimum for one population would potentially misdirect prevention efforts in another. For a given population, the range of thresholds where the weighted model conferred greater predictive accuracy tended to be narrow ($\pm$0.005 units), and the optimal threshold tended to be stable over time. Our framework also indicated that variation in the recency of HIV diagnosis among clusters was significantly more predictive of new cases than sample collection dates (ΔAIC {\textgreater} 50). These results suggest that one cannot rely on historical precedence or convention to configure genetic clustering methods for public health applications, especially when translating methods between settings of low-level and generalized epidemics. Our framework not only enables investigators to calibrate a clustering method to a specific public health setting, but also provides a variable selection procedure to evaluate different predictive models of cluster growth.},
author = {Chato, Connor and Kalish, Marcia L. and Poon, Art F. Y.},
doi = {10.1093/ve/veaa011},
issn = {2057-1577},
journal = {Virus Evolution},
keywords = {HIV prevention, genetic clustering, modifiable areal unit problem, molecular epidemiology, virus evolution},
month = jan,
number = {1},
pages = {veaa011},
pmcid = {PMC7069216},
pmid = {32190349},
shorttitle = {Public health in genetic spaces},
title = {Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection},
volume = {6},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1093/ve/veaa011}}
@article{dalai_combining_2018,
abstract = {The HIV epidemic in San Mateo County is sustained by multiple overlapping risk groups and is an important hub for HIV transmission in northern California. Limited access to care has led historically to delayed clinical presentation, higher rates of opportunistic infections, and an increased prevalence of antiretroviral drug resistance. The virologic and clinical consequences of treatment within these multiple ethnic and behavioral groups are poorly understood, highlighting the need for efficient surveillance strategies that are able to elucidate transmission networks and drug resistance patterns. We obtained sequence data from a group of 316 HIV-positive individuals in the San Mateo AIDS Program over a 14-year period and integrated epidemiologic, phylogenetic, and network approaches to characterize transmission clusters, risk factors and drug resistance. Drug resistance mutations were identified using the Stanford HIV Drug Resistance Database. A maximum likelihood tree was inferred in RAxML and subjected to clustering analysis in Cluster Picker. Network analysis using pairwise genetic distances was performed in HIV-TRACE. Participants were primarily male (60\%), white Hispanics and non-Hispanics (32\%) and African American (20.6\%). The most frequent behavior risk factor was male-male sex (33.5\%), followed by heterosexual (23.4\%) and injection drug use (9.5\%). Nearly all sequences were subtype B (96\%) with subtypes A, C, and CRF01\_AE also observed. Sequences from 65\% of participants had at least one drug resistance mutation. Clustered transmissions included a higher number of women when compared to non-clustered individuals and were more likely to include heterosexual or people who inject drugs (PWID). Detailed analysis of the largest network (N = 47) suggested that PWID played a central role in overall transmission of HIV-1 as well as bridging men who have sex with men (MSM) transmission with heterosexual/PWID among primarily African American men. Combined phylogenetic and network analysis of HIV sequence data identified several overlapping risk factors in the epidemic, including MSM, heterosexual and PWID transmission with a disproportionate impact on African Americans and a high prevalence of drug resistance.},
author = {Dalai, Sudeb C. and Junqueira, Dennis Maletich and Wilkinson, Eduan and Mehra, Renee and Kosakovsky Pond, Sergei L. and Levy, Vivian and Israelski, Dennis and de Oliveira, Tulio and Katzenstein, David},
doi = {10.3389/fmicb.2018.02799},
issn = {1664-302X},
journal = {Frontiers in Microbiology},
keywords = {California, HIV, network, phylogenetics, transmission links},
pages = {2799},
pmcid = {PMC6292275},
pmid = {30574123},
title = {Combining {Phylogenetic} and {Network} {Approaches} to {Identify} {HIV}-1 {Transmission} {Links} in {San} {Mateo} {County}, {California}},
volume = {9},
year = {2018},
bdsk-url-1 = {https://doi.org/10.3389/fmicb.2018.02799}}
@article{di_giallonardo_subtype-specific_2021,
abstract = {INTRODUCTION: The human immunodeficiency virus 1 (HIV-1) pandemic is characterized by numerous distinct sub-epidemics (clusters) that continually fuel local transmission. The aims of this study were to identify active growing clusters, to understand which factors most influence the transmission dynamics, how these vary between different subtypes and how this information might contribute to effective public health responses.
METHODS: We used HIV-1 genomic sequence data linked to demographic factors that accounted for approximately 70\% of all new HIV-1 notifications in New South Wales (NSW). We assessed differences in transmission cluster dynamics between subtype B and circulating recombinant form 01\_AE (CRF01\_AE). Separate phylogenetic trees were estimated using 2919 subtype B and 473 CRF01\_AE sequences sampled between 2004 and 2018 in combination with global sequence data and NSW-specific clades were classified as clusters, pairs or singletons. Significant differences in demographics between subtypes were assessed with Chi-Square statistics.
RESULTS: We identified 104 subtype B and 11 CRF01\_AE growing clusters containing a maximum of 29 and 11 sequences for subtype B and CRF01\_AE respectively. We observed a {\textgreater} 2-fold increase in the number of NSW-specific CRF01\_AE clades over time. Subtype B clusters were associated with individuals reporting men who have sex with men (MSM) as their transmission risk factor, being born in Australia, and being diagnosed during the early stage of infection (p {\textless} 0.01). CRF01\_AE infections clusters were associated with infections among individuals diagnosed during the early stage of infection (p {\textless} 0.05) and CRF01\_AE singletons were more likely to be from infections among individuals reporting heterosexual transmission (p {\textless} 0.05). We found six subtype B clusters with an above-average growth rate ({\textgreater}1.5 sequences / 6-months) and which consisted of a majority of infections among MSM. We also found four active growing CRF01\_AE clusters containing only infections among MSM. Finally, we found 47 subtype B and seven CRF01\_AE clusters that contained a large gap in time ({\textgreater}1 year) between infections and may be indicative of intermediate transmissions via undiagnosed individuals.
CONCLUSIONS: The large number of active and growing clusters among MSM are the driving force of the ongoing epidemic in NSW for subtype B and CRF01\_AE.},
author = {Di Giallonardo, Francesca and Pinto, Angie N. and Keen, Phillip and Shaik, Ansari and Carrera, Alex and Salem, Hanan and Selvey, Christine and Nigro, Steven J. and Fraser, Neil and Price, Karen and Holden, Joanne and Lee, Frederick J. and Dwyer, Dominic E. and Bavinton, Benjamin R. and Geoghegan, Jemma L. and Grulich, Andrew E. and Kelleher, Anthony D. and {NSW HIV Prevention Partnership Project}},
doi = {10.1002/jia2.25655},
issn = {1758-2652},
journal = {Journal of the International AIDS Society},
keywords = {Australia, Cluster Analysis, Female, HIV Infections, HIV-1, HIV1, Heterosexuality, Homosexuality, Male, Humans, Longitudinal Studies, Male, New South Wales, Phylogeny, Recombination, Genetic, Risk Factors, Sexual and Gender Minorities, demographic differences, early infections, public health, subtype B and CRF01\_AE, transmission cluster},
month = jan,
number = {1},
pages = {e25655},
pmcid = {PMC7817915},
pmid = {33474833},
title = {Subtype-specific differences in transmission cluster dynamics of {HIV}-1 {B} and {CRF01}\_AE in {New} {South} {Wales}, {Australia}},
volume = {24},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1002/jia2.25655}}
@article{ding_characterizing_2022,
abstract = {We aimed to elucidate the characteristics of HIV molecular epidemiology and identify transmission hubs in eastern China using genetic transmission network and lineage analyses. HIV-TRACE was used to infer putative relationships. Across the range of epidemiologically-plausible genetic distance (GD) thresholds (0.1--2.0\%), a sensitivity analysis was performed to determine the optimal threshold, generating the maximum number of transmission clusters and providing reliable resolution without merging different small clusters into a single large cluster. Characteristics of genetically linked individuals were analyzed using logistic regression. Assortativity (shared characteristics) analysis was performed to infer shared attributes between putative partners. 1,993 persons living with HIV-1 were enrolled. The determined GD thresholds within subtypes CRF07\_BC, CRF01\_AE, and B were 0.5\%, 1.2\%, and 1.7\%, respectively, and 826 of 1,993 (41.4\%) sequences were linked with at least one other sequence, forming 188 transmission clusters of 2--80 sequences. Clustering rates for the main subtypes CRF01\_AE, CRF07\_BC, and B were 50.9\% (523/1027), 34.2\% (256/749), and 32.1\% (25/78), respectively. Median cluster sizes of these subtypes were 2 (2--52, n = 523), 2 (2--80, n = 256), and 3 (2--6, n = 25), respectively. Subtypes in individuals diagnosed and residing in Hangzhou city (OR = 1.423, 95\% CI: 1.168--1.734) and men who have sex with men (MSM) were more likely to cluster. Assortativity analysis revealed individuals were more likely to be genetically linked to individuals from the same age group (AIage = 0.090, P{\textless}0.001) and the same area of residency in Zhejiang (AIcity = 0.078, P{\textless}0.001). Additionally, students living with HIV were more likely to be linked with students than show a random distribution (AI student = 0.740, P{\textless}0.01). These results highlight the importance of Hangzhou City in the regional epidemic and show that MSM comprise the population rapidly transmitting HIV in Zhejiang Province. We also provide a molecular epidemiology framework for improving our understanding of HIV transmission dynamics in eastern China.},
author = {Ding, Xiaobei and Chaillon, Antoine and Pan, Xiaohong and Zhang, Jiafeng and Zhong, Ping and He, Lin and Chen, Wanjun and Fan, Qin and Jiang, Jun and Luo, Mingyu and Xia, Yan and Guo, Zhihong and Smith, Davey M.},
doi = {10.1371/journal.pone.0269973},
issn = {1932-6203},
journal = {PLOS ONE},
keywords = {China, Genetic linkage, HIV, HIV diagnosis and management, HIV epidemiology, HIV-1, Medical risk factors, Men who have sex with men},
month = jun,
note = {Publisher: Public Library of Science},
number = {6},
pages = {e0269973},
shorttitle = {Characterizing genetic transmission networks among newly diagnosed {HIV}-1 infected individuals in eastern {China}},
title = {Characterizing genetic transmission networks among newly diagnosed {HIV}-1 infected individuals in eastern {China}: 2012--2016},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0269973},
urldate = {2022-10-05},
volume = {17},
year = {2022},
bdsk-url-1 = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0269973},
bdsk-url-2 = {https://doi.org/10.1371/journal.pone.0269973}}
@article{erly_predictive_2021,
abstract = {BACKGROUND: Pillar 4 of the United States' End the HIV Epidemic plan is to respond quickly to HIV outbreaks, but the utility of CDC's tool for identifying HIV outbreaks through time-space cluster detection has not been evaluated. The objective of this evaluation is to quantify the ability of the CDC time-space cluster criterion to predict future HIV diagnoses and to compare it to a space-time permutation statistic implemented in SaTScan software.
SETTING: Washington State from 2017 to 2019.
METHODS: We applied both cluster criteria to incident HIV cases in Washington State to identify clusters. Using a repeated-measures Poisson model, we calculated a rate ratio comparing the 6 months after cluster detection with a baseline rate from 24 to 12 months before the cluster was detected. We also compared the demographics of cases within clusters with all other incident cases.
RESULTS: The CDC criteria identified 17 clusters containing 192 cases in the 6 months after cluster detection, corresponding to a rate ratio of 1.25 (95\% confidence interval: 0.95 to 1.65) relative to baseline. The time-space permutation statistic identified 5 clusters containing 25 cases with a rate ratio of 2.27 (95\% confidence interval: 1.28 to 4.03). Individuals in clusters identified by the new criteria were more likely to be of Hispanic origin (61\% vs 20\%) and in rural areas (51\% vs 12\%).
CONCLUSIONS: The space-time permutation cluster analysis is a promising tool for identification of clusters with the largest growth potential for whom interruption may prove most beneficial.},
author = {Erly, Steven J. and Naismith, Kelly and Kerani, Roxanne and Buskin, Susan E. and Reuer, Jennifer R.},
doi = {10.1097/QAI.0000000000002675},
issn = {1944-7884},
journal = {Journal of Acquired Immune Deficiency Syndromes (1999)},
keywords = {Cluster Analysis, Disease Outbreaks, HIV Infections, HIV-1, Humans, Population Surveillance, Time Factors, Washington},
month = jul,
number = {3},
pages = {912--917},
pmid = {33675622},
title = {Predictive {Value} of {Time}-{Space} {Clusters} for {HIV} {Transmission} in {Washington} {State}, 2017-2019},
volume = {87},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1097/QAI.0000000000002675}}
@article{fujimoto_methodological_2021,
abstract = {This study introduces an innovative methodological approach to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations in the culturally and racially/ethnically diverse context of Houston, TX, the largest city in the Southern United States. Using 6332 HIV-1 pol sequences from persons newly diagnosed with HIV during the period 2010--2018, we reconstructed HIV-1 transmission clusters, using the HIV-TRAnsmission Cluster Engine (HIV-TRACE); inferred demographic and risk parameters on HIV-1 transmission dynamics by jointly estimating viral transmission rates across racial/ethnic, age, and transmission risk groups; and modeled the degree of network connectivity by using generalized estimating equations (GEE). Our results indicate that Hispanics/Latinos are most vulnerable to the structure of transmission clusters and serve as a bridge population, acting as recipients of transmissions from Whites (3.0 state changes/year) and from Blacks (2.6 state changes/year) as well as sources of transmissions to Whites (1.8 state changes/year) and to Blacks (1.2 state changes/year). There were high rates of transmission and high network connectivity between younger and older Hispanics/Latinos as well as between younger and older Blacks. Prevention and intervention efforts are needed for transmission clusters that involve younger racial/ethnic minorities, in particular Hispanic/Latino youth, to reduce onward transmission of HIV in Houston.},
author = {Fujimoto, Kayo and Bahl, Justin and Wertheim, Joel O. and Del Vecchio, Natascha and Hicks, Joseph T. and Damodaran, Lambodhar and Hallmark, Camden J. and Lavingia, Richa and Mora, Ricardo and Carr, Michelle and Yang, Biru and Schneider, John A. and Hwang, Lu-Yu and McNeese, Marlene},
copyright = {2021 The Author(s)},
doi = {10.1038/s41598-021-82673-8},
issn = {2045-2322},
journal = {Scientific Reports},