Molecular network-based intervention brings us closer to ending the HIV pandemic
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Xiaoxu Han | Bin Zhao | Minghui An | Ping Zhong | Hong Shang | Ming-hui An | Xiaoxu Han | Bin Zhao | H. Shang | P. Zhong
[1] R. Redfield,et al. Ending the HIV Epidemic: A Plan for the United States. , 2019, JAMA.
[2] Xiang He,et al. Tracing the origin and history of HIV-1 subtype B′ epidemic by near full-length genome analyses , 2012, AIDS.
[3] Tong Zhang,et al. Targeting HIV Prevention Based on Molecular Epidemiology Among Deeply Sampled Subnetworks of Men Who Have Sex With Men. , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[4] C. Delaugerre,et al. Spatiotemporal dynamics of HIV-1 transmission in France (1999–2014) and impact of targeted prevention strategies , 2017, Retrovirology.
[5] G. Vanham,et al. Evolutionary Dynamics and Complicated Genetic Transmission Network Patterns of HIV-1 CRF01_AE among MSM in Shanghai, China , 2016, Scientific Reports.
[6] Ben Murrell,et al. Growth of HIV-1 Molecular Transmission Clusters in New York City , 2018, The Journal of infectious diseases.
[7] G. Magiorkinis,et al. Molecular Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)–Infected Individuals in a Network-Based Intervention (Transmission Reduction Intervention Project): Phylogenetics Identify HIV-1–Infected Individuals With Social Links , 2018, The Journal of infectious diseases.
[8] R. Nsubuga,et al. Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations , 2019, Scientific Reports.
[9] Steven Weaver,et al. HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. , 2018, Molecular biology and evolution.
[10] Y. Takebe,et al. Reconstituting the Epidemic History of HIV Strain CRF01_AE among Men Who Have Sex with Men (MSM) in Liaoning, Northeastern China: Implications for the Expanding Epidemic among MSM in China , 2012, Journal of Virology.
[11] S. Ho,et al. Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences , 2017, Scientific Reports.
[12] X. Chen,et al. A Large-scale Survey of CRF55_01B from Men-Who-Have-Sex-with-Men in China: implying the Evolutionary History and Public Health Impact , 2015, Scientific Reports.
[13] Hao Wu,et al. Transmission network characteristics based on env and gag sequences from MSM during acute HIV-1 infection in Beijing, China , 2017, Archives of Virology.
[14] W. Liu,et al. A New Migration Map of HIV-1 CRF07_BC in China: Analysis of Sequences from 12 Provinces over a Decade , 2012, PloS one.
[15] Z. Butt,et al. Spatial epidemiology of HIV-hepatitis co-infection in the State of Michigan: a cohort study , 2015, Infectious diseases.
[16] Michael W. Spiller,et al. HIV Infection Linked to Injection Use of Oxymorphone in Indiana, 2014-2015. , 2016, The New England journal of medicine.
[17] Debra Hanson,et al. Detailed Transmission Network Analysis of a Large Opiate-Driven Outbreak of HIV Infection in the United States , 2017, The Journal of infectious diseases.
[18] A. France,et al. Molecular Epidemiology and the Transformation of HIV Prevention , 2018, JAMA.
[19] Maurizio Zazzi,et al. A novel methodology for large-scale phylogeny partition , 2011, Nature communications.
[20] Irene A. Doherty,et al. Leveraging Phylogenetics to Understand HIV Transmission and Partner Notification Networks , 2018, Journal of acquired immune deficiency syndromes.
[21] O. Ng,et al. HIV-1 transmission networks among men who have sex with men in Asia. , 2014, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[22] Anne M Johnson,et al. Determinants of HIV-1 transmission in men who have sex with men: a combined clinical, epidemiological and phylogenetic approach , 2010, AIDS.
[23] F. Ceccherini‐Silberstein,et al. Characterisation of HIV-1 molecular transmission clusters among newly diagnosed individuals infected with non-B subtypes in Italy , 2019, Sexually Transmitted Infections.
[24] M. Ragonnet-Cronin,et al. HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data. , 2019, The lancet. HIV.
[25] J. O. Wertheim,et al. Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States , 2015, Journal of acquired immune deficiency syndromes.
[26] Ann M. Dennis,et al. Characterizing HIV transmission networks across the United States. , 2012, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[27] J. Albert,et al. HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries , 2016, Virus evolution.
[28] Sergei L. Kosakovsky Pond,et al. The global transmission network of HIV-1. , 2014, The Journal of infectious diseases.
[29] Wai Lok Sibon Li,et al. Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. , 2012, Molecular biology and evolution.
[30] David Stephens,et al. The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data , 2015, BMC Bioinformatics.
[31] Anna Urbanska,et al. HIV-1 Subtype D Infections among Caucasians from Northwestern Poland—Phylogenetic and Clinical Analysis , 2012, PloS one.
[32] A. Leigh Brown,et al. Recent and Rapid Transmission of HIV Among People Who Inject Drugs in Scotland Revealed Through Phylogenetic Analysis , 2018, The Journal of infectious diseases.
[33] C. Fraser,et al. Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control , 2018, The Journal of infectious diseases.
[34] Sergei L. Kosakovsky Pond,et al. Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California. , 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[35] M. Suchard,et al. The early spread and epidemic ignition of HIV-1 in human populations , 2014, Science.
[36] O. Laeyendecker,et al. Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. , 2016, AIDS research and human retroviruses.
[37] Jan Albert,et al. Defining HIV-1 transmission clusters based on sequence data , 2017, AIDS.
[38] D. Richman,et al. HIV-1 Clade B pol Evolution following Primary Infection , 2013, PloS one.
[39] Joel O. Wertheim,et al. Using HIV Networks to Inform Real Time Prevention Interventions , 2014, PloS one.
[40] A. Oster,et al. HIV Transmission Dynamics Among Foreign-Born Persons in the United States , 2017, Journal of acquired immune deficiency syndromes.
[41] N. Pantazis,et al. HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors , 2019, BMC Medicine.
[42] Bei Wu,et al. Identifying Symptom Clusters Among People Living With HIV on Antiretroviral Therapy in China: A Network Analysis. , 2019, Journal of pain and symptom management.
[43] Ann M. Dennis,et al. Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic , 2016, Scientific Reports.
[44] Davey M. Smith,et al. First Appearance of HIV-1 CRF07_BC and CRF08_BC Outside China. , 2016, AIDS research and human retroviruses.
[45] Christopher H Woelk,et al. A public health model for the molecular surveillance of HIV transmission in San Diego, California , 2009, AIDS.
[46] Sebastián Duchêne,et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis , 2018, bioRxiv.
[47] J P Bru,et al. Acute HIV infection: impact on the spread of HIV and transmission of drug resistance , 2001, AIDS.
[48] T. Musa,et al. Multiple introductions and onward transmission of HIV-1 subtype B strains in Shanghai, China. , 2017, The Journal of infection.
[49] P. Kaleebu,et al. HIV subtype diversity worldwide , 2019, Current opinion in HIV and AIDS.
[50] C. Nielsen,et al. Molecular Investigation of Transmission of Human Immunodeficiency Virus Type 1 in a Criminal Case , 2001, Clinical Diagnostic Laboratory Immunology.
[51] M. Stanojevic,et al. Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach , 2019, Front. Microbiol..
[52] A. Poon. Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks , 2016, Virus evolution.
[53] Xiaoxu Han,et al. HIV prevention: Bring safe sex to China , 2012, Nature.
[54] Samantha Lycett,et al. Automated analysis of phylogenetic clusters , 2013, BMC Bioinformatics.
[55] Esther Fearnhill,et al. Transmission Network Parameters Estimated From HIV Sequences for a Nationwide Epidemic , 2011, The Journal of infectious diseases.
[56] M. Salemi,et al. The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis , 2019, Scientific Reports.
[57] S. Little,et al. Ethical issues in HIV phylogenetics and molecular epidemiology , 2019, Current opinion in HIV and AIDS.
[58] Daniel L. Ayres,et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.
[59] C. Delaugerre,et al. In-depth Sampling of High-risk Populations to Characterize HIV Transmission Epidemics Among Young MSM Using PrEP in France and Quebec , 2019, Open forum infectious diseases.
[60] Tulio de Oliveira,et al. Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study. , 2017, The lancet. HIV.
[61] P. Lemey,et al. Phylogenetic Reconstruction of a Known HIV-1 CRF04_cpx Transmission Network Using Maximum Likelihood and Bayesian Methods , 2004, Journal of Molecular Evolution.
[62] A. Trkola,et al. Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis , 2017, eLife.
[63] Min Zhang,et al. Identification of 3 Distinct HIV-1 Founding Strains Responsible for Expanding Epidemic Among Men Who Have Sex With Men in 9 Chinese Cities , 2013, Journal of acquired immune deficiency syndromes.
[64] Ellsworth M. Campbell,et al. Natural selection favoring more transmissible HIV detected in United States molecular transmission network , 2019, Nature Communications.
[65] P. Kazanjian. UNAIDS 90‐90‐90 Campaign to End the AIDS Epidemic in Historic Perspective , 2017, The Milbank quarterly.
[66] Kimberly C. Brouwer,et al. HIV Transmission Networks in the San Diego–Tijuana Border Region , 2015, EBioMedicine.
[67] Beda Joos,et al. Estimating the basic reproductive number from viral sequence data. , 2012, Molecular biology and evolution.
[68] M. Egger,et al. Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland. , 2014, American journal of epidemiology.
[69] Sikhulile Moyo,et al. Impact of sampling density on the extent of HIV clustering. , 2014, AIDS research and human retroviruses.
[70] J. Whitworth,et al. Molecular epidemiological analysis of HIV in sexual networks in Uganda , 1998, AIDS.
[71] M. Melbye,et al. The origin and emergence of an HIV-1 epidemic: from introduction to endemicity , 2014, AIDS.
[72] Xiong He,et al. Phylogenetic and temporal dynamics of human immunodeficiency virus type 1B in China: four types of B strains circulate in China. , 2014, AIDS research and human retroviruses.
[73] James H McMahon,et al. 90-90-90: how do we get there? , 2014, The lancet. HIV.
[74] P. Ghys,et al. Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis. , 2019, The Lancet. Infectious diseases.
[75] M. Hoenigl,et al. Hotspots of Transmission Driving the Local Human Immunodeficiency Virus Epidemic in the Cologne-Bonn Region, Germany. , 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[76] Xiaomei Jin,et al. HIV-1 genetic transmission networks among men who have sex with men in Kunming, China , 2018, PloS one.
[77] Xiang He,et al. Phylodynamics of major CRF01_AE epidemic clusters circulating in mainland of China , 2017, Scientific Reports.
[78] M. Suchard,et al. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. , 2012, Molecular biology and evolution.
[79] Cynthia A. Derdeyn,et al. Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Transmission in a Heterosexual Cohort of Discordant Couples in Zambia , 2002, Journal of Virology.
[80] Ben Murrell,et al. Social and Genetic Networks of HIV-1 Transmission in New York City , 2017, PLoS pathogens.
[81] M. Ciccozzi,et al. HIV-1 subtype C transmission network: the phylogenetic reconstruction strongly supports the epidemiological data. , 2010, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.
[82] Art F. Y. Poon,et al. Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study , 2016, The lancet. HIV.
[83] Anthony K. Waruru,et al. Finding Hidden HIV Clusters to Support Geographic-Oriented HIV Interventions in Kenya , 2018, Journal of acquired immune deficiency syndromes.
[84] A. France,et al. Novel Method for Rapid Detection of Spatiotemporal HIV Clusters Potentially Warranting Intervention , 2019, Emerging infectious diseases.
[85] M. Salemi,et al. The Threshold Bootstrap Clustering: A New Approach to Find Families or Transmission Clusters within Molecular Quasispecies , 2010, PloS one.
[86] Davey M. Smith,et al. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals , 2016, Journal of medical virology.
[87] V. Isham,et al. Modeling infectious disease dynamics in the complex landscape of global health , 2015, Science.
[88] Ann M. Dennis,et al. Integration of Contact Tracing and Phylogenetics in an Investigation of Acute HIV Infection , 2017, Sexually transmitted diseases.
[89] Stéphane Hué,et al. HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy , 2004, AIDS.
[90] M. Uhlén,et al. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[91] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.