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For: Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A, Leigh Brown AJ. Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog 2009;5:e1000590. [PMID: 19779560 PMCID: PMC2742734 DOI: 10.1371/journal.ppat.1000590] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 08/25/2009] [Indexed: 11/25/2022]  Open
Number Cited by Other Article(s)
1
Pimentel V, Pineda-Peña A, Sebastião CS, de Paula JL, Ahagon CM, Pingarilho M, Martins MRO, Coelho LPO, Matsuda EM, Alves D, Abecasis AB, Brígido LFM. Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil. Front Public Health 2024;12:1384512. [PMID: 38903572 PMCID: PMC11187794 DOI: 10.3389/fpubh.2024.1384512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024]  Open
2
Novitsky V, Steingrimsson J, Howison M, Dunn CW, Gillani FS, Fulton J, Bertrand T, Howe K, Bhattarai L, Ronquillo G, MacAskill M, Bandy U, Hogan J, Kantor R. Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic. AIDS 2023;37:389-399. [PMID: 36695355 PMCID: PMC9881752 DOI: 10.1097/qad.0000000000003426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
3
Skums P, Mohebbi F, Tsyvina V, Baykal PI, Nemira A, Ramachandran S, Khudyakov Y. SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework. Cell Syst 2022;13:844-856.e4. [PMID: 36265470 PMCID: PMC9590096 DOI: 10.1016/j.cels.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 01/26/2023]
4
Kusejko K, Tschumi N, Chaudron SE, Nguyen H, Battegay M, Bernasconi E, Böni J, Huber M, Calmy A, Cavassini M, Egle A, Grabmeier-Pfistershammer K, Haas B, Hirsch H, Klimkait T, Öllinger A, Perreau M, Ramette A, Flury BB, Sarcletti M, Scherrer A, Schmid P, Yerly S, Zangerle R, Günthard HF, Kouyos RD. Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics. J Acquir Immune Defic Syndr 2022;90:e4-e12. [PMID: 35298446 PMCID: PMC9394492 DOI: 10.1097/qai.0000000000002949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/23/2022] [Indexed: 11/25/2022]
5
Gil H, Delgado E, Benito S, Georgalis L, Montero V, Sánchez M, Cañada-García JE, García-Bodas E, Díaz A, Thomson MM. Transmission Clusters, Predominantly Associated With Men Who Have Sex With Men, Play a Main Role in the Propagation of HIV-1 in Northern Spain (2013–2018). Front Microbiol 2022;13:782609. [PMID: 35432279 PMCID: PMC9009226 DOI: 10.3389/fmicb.2022.782609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022]  Open
6
Piterskiy MV, Gusev AG, Khodakov OA, Zakharova YA, Semenov AV. HIV-1 subtype diversity, phylogenetic analysis and study of drug resistance in strains circulating in the Ural Federal District. JOURNAL OF MICROBIOLOGY, EPIDEMIOLOGY AND IMMUNOBIOLOGY 2022. [DOI: 10.36233/0372-9311-178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
7
Orlovich Y, Kukharenko K, Kaibel V, Skums P. Scale-Free Spanning Trees and Their Application in Genomic Epidemiology. J Comput Biol 2021;28:945-960. [PMID: 34491104 PMCID: PMC8670573 DOI: 10.1089/cmb.2020.0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]  Open
8
O'Keefe KJ, Pipkin S, Fatch R, Scheer S, Liegler T, McFarland W, Grant RM, Truong HHM. Non-B variants of HIV-1 in San Francisco, California. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021;90:104677. [PMID: 33321227 PMCID: PMC10686190 DOI: 10.1016/j.meegid.2020.104677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 11/26/2022]
9
Using phylogenetic surveillance and epidemiological data to understand the HIV-1 transmission dynamics in French Guiana. AIDS 2021;35:979-984. [PMID: 33470610 DOI: 10.1097/qad.0000000000002817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
10
Monroe-Wise A, Mbogo L, Guthrie B, Bukusi D, Sambai B, Chohan B, Scott J, Cherutich P, Musyoki H, Bosire R, Dunbar M, Macharia P, Masyuko S, Wilkinson E, De Oliveira T, Ludwig-Barron N, Sinkele B, Herbeck J, Farquhar C. Peer-mediated HIV assisted partner services to identify and link to care HIV-positive and HCV-positive people who inject drugs: a cohort study protocol. BMJ Open 2021;11:e041083. [PMID: 33895711 PMCID: PMC8074565 DOI: 10.1136/bmjopen-2020-041083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
11
Fritsch HM, Tanuri A, Pinto AR, Gräf T. Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil. INFECTION GENETICS AND EVOLUTION 2021;92:104854. [PMID: 33839313 DOI: 10.1016/j.meegid.2021.104854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/28/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
12
Lai A, Giacomet V, Bergna A, Zuccotti GV, Zehender G, Clerici M, Trabattoni D, Fenizia C. Early-Transmitted Variants and Their Evolution in a HIV-1 Positive Couple: NGS and Phylogenetic Analyses. Viruses 2021;13:v13030513. [PMID: 33808903 PMCID: PMC8003824 DOI: 10.3390/v13030513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/05/2022]  Open
13
Dennis AM, Hué S, Billock R, Levintow S, Sebastian J, Miller WC, Eron JJ. Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina. J Infect Dis 2021;221:1321-1330. [PMID: 31028702 DOI: 10.1093/infdis/jiz176] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022]  Open
14
Liu M, Han X, Zhao B, An M, He W, Wang Z, Qiu Y, Ding H, Shang H. Dynamics of HIV-1 Molecular Networks Reveal Effective Control of Large Transmission Clusters in an Area Affected by an Epidemic of Multiple HIV Subtypes. Front Microbiol 2020;11:604993. [PMID: 33281803 PMCID: PMC7691493 DOI: 10.3389/fmicb.2020.604993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/27/2020] [Indexed: 01/20/2023]  Open
15
Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. Nat Commun 2020;11:5542. [PMID: 33139735 PMCID: PMC7608612 DOI: 10.1038/s41467-020-19198-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/23/2020] [Indexed: 12/02/2022]  Open
16
Sacks-Davis R, Chibo D, Peach E, Aleksic E, Crowe SM, El Hayek C, Marukutira T, Higgins N, Stoove M, Hellard M. Phylogenetic clustering networks among heterosexual migrants with new HIV diagnoses post-migration in Australia. PLoS One 2020;15:e0237469. [PMID: 32870911 PMCID: PMC7462279 DOI: 10.1371/journal.pone.0237469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/27/2020] [Indexed: 01/28/2023]  Open
17
Differences of cytotoxic T-lymphocyte pressure and divergent evolution of several CRF07_BC clusters circulating in men who have sex with men in China. INFECTION GENETICS AND EVOLUTION 2020;85:104486. [PMID: 32771701 DOI: 10.1016/j.meegid.2020.104486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/01/2020] [Accepted: 07/28/2020] [Indexed: 01/23/2023]
18
Understanding disclosed and cryptic HIV transmission risk via genetic analysis: what are we missing and when does it matter? Curr Opin HIV AIDS 2020;14:205-212. [PMID: 30946142 DOI: 10.1097/coh.0000000000000537] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
19
Factors influencing HIV-1 phylogenetic clustering. Curr Opin HIV AIDS 2020;14:161-172. [PMID: 30882487 DOI: 10.1097/coh.0000000000000540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
20
Gräf T, Delatorre E, Bello G. Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences. Mem Inst Oswaldo Cruz 2020;115:e190461. [PMID: 32187328 PMCID: PMC7098263 DOI: 10.1590/0074-02760190461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 12/14/2022]  Open
21
What Proportion of HIV-Infected Foreign-Born Individuals in the United States Have Been Infected After Immigrating to the United States? J Acquir Immune Defic Syndr 2020;77:e35-e36. [PMID: 29189418 DOI: 10.1097/qai.0000000000001594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
22
Mittler JE, Murphy JT, Stansfield SE, Peebles K, Gottlieb GS, Abernethy NF, Reid MC, Goodreau SM, Herbeck JT. Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model. PLoS Comput Biol 2019;15:e1007561. [PMID: 31846456 PMCID: PMC6938382 DOI: 10.1371/journal.pcbi.1007561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 12/31/2019] [Accepted: 11/23/2019] [Indexed: 01/05/2023]  Open
23
Lodi S, Günthard HF, Gill J, Phillips AN, Dunn D, Vu Q, Siemieniuk R, Garcia F, Logan R, Jose S, Bucher HC, Scherrer AU, Reiss P, van Sighem A, Boender TS, Porter K, Gilson R, Paraskevis D, Simeon M, Vourli G, Moreno S, Jarrin I, Sabin C, Hernán MA. Effectiveness of Transmitted Drug Resistance Testing Before Initiation of Antiretroviral Therapy in HIV-Positive Individuals. J Acquir Immune Defic Syndr 2019;82:314-320. [PMID: 31609929 PMCID: PMC7830777 DOI: 10.1097/qai.0000000000002135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
24
Rose R, Hall M, Redd AD, Lamers S, Barbier AE, Porcella SF, Hudelson SE, Piwowar-Manning E, McCauley M, Gamble T, Wilson EA, Kumwenda J, Hosseinipour MC, Hakim JG, Kumarasamy N, Chariyalertsak S, Pilotto JH, Grinsztejn B, Mills LA, Makhema J, Santos BR, Chen YQ, Quinn TC, Fraser C, Cohen MS, Eshleman SH, Laeyendecker O. Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort. J Infect Dis 2019;220:1406-1413. [PMID: 30590741 PMCID: PMC6761953 DOI: 10.1093/infdis/jiy734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]  Open
25
Ragonnet-Cronin M, Jackson C, Bradley-Stewart A, Aitken C, McAuley A, Palmateer N, Gunson R, Goldberg D, Milosevic C, Leigh Brown AJ. Recent and Rapid Transmission of HIV Among People Who Inject Drugs in Scotland Revealed Through Phylogenetic Analysis. J Infect Dis 2019;217:1875-1882. [PMID: 29546333 DOI: 10.1093/infdis/jiy130] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/08/2018] [Indexed: 11/13/2022]  Open
26
Balaban M, Moshiri N, Mai U, Jia X, Mirarab S. TreeCluster: Clustering biological sequences using phylogenetic trees. PLoS One 2019;14:e0221068. [PMID: 31437182 PMCID: PMC6705769 DOI: 10.1371/journal.pone.0221068] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/26/2019] [Indexed: 02/01/2023]  Open
27
Chung YS, Choi JY, Yoo MS, Seong JH, Choi BS, Kang C. Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012. PLoS One 2019;14:e0217817. [PMID: 31166970 PMCID: PMC6550428 DOI: 10.1371/journal.pone.0217817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/21/2019] [Indexed: 11/29/2022]  Open
28
Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany. J Virol 2019;93:JVI.02238-18. [PMID: 30944175 DOI: 10.1128/jvi.02238-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/13/2019] [Indexed: 12/15/2022]  Open
29
Mehta SR, Schairer C, Little S. Ethical issues in HIV phylogenetics and molecular epidemiology. Curr Opin HIV AIDS 2019;14:221-226. [PMID: 30946143 PMCID: PMC6450547 DOI: 10.1097/coh.0000000000000538] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
30
Ragonnet-Cronin M, Hué S, Hodcroft EB, Tostevin A, Dunn D, Fawcett T, Pozniak A, Brown AE, Delpech V, Brown AJL. Non-disclosed men who have sex with men in UK HIV transmission networks: phylogenetic analysis of surveillance data. Lancet HIV 2019;5:e309-e316. [PMID: 29893244 DOI: 10.1016/s2352-3018(18)30062-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 11/18/2022]
31
Delgado E, Benito S, Montero V, Cuevas MT, Fernández-García A, Sánchez-Martínez M, García-Bodas E, Díez-Fuertes F, Gil H, Cañada J, Carrera C, Martínez-López J, Sintes M, Pérez-Álvarez L, Thomson MM. Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain. Front Microbiol 2019;10:655. [PMID: 31001231 PMCID: PMC6457325 DOI: 10.3389/fmicb.2019.00655] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022]  Open
32
Caution is needed in interpreting HIV transmission chains by ultradeep sequencing. AIDS 2019;33:691-699. [PMID: 30585843 DOI: 10.1097/qad.0000000000002105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
33
Wertheim JO, Murrell B, Mehta SR, Forgione LA, Kosakovsky Pond SL, Smith DM, Torian LV. Growth of HIV-1 Molecular Transmission Clusters in New York City. J Infect Dis 2018;218:1943-1953. [PMID: 30010850 PMCID: PMC6217720 DOI: 10.1093/infdis/jiy431] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/10/2018] [Indexed: 11/12/2022]  Open
34
Coltart CEM, Hoppe A, Parker M, Dawson L, Amon JJ, Simwinga M, Geller G, Henderson G, Laeyendecker O, Tucker JD, Eba P, Novitsky V, Vandamme AM, Seeley J, Dallabetta G, Harling G, Grabowski MK, Godfrey-Faussett P, Fraser C, Cohen MS, Pillay D. Ethical considerations in global HIV phylogenetic research. Lancet HIV 2018;5:e656-e666. [PMID: 30174214 PMCID: PMC7327184 DOI: 10.1016/s2352-3018(18)30134-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/28/2018] [Accepted: 06/06/2018] [Indexed: 01/01/2023]
35
HIV-genetic diversity and drug resistance transmission clusters in Gondar, Northern Ethiopia, 2003-2013. PLoS One 2018;13:e0205446. [PMID: 30304061 PMCID: PMC6179264 DOI: 10.1371/journal.pone.0205446] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022]  Open
36
Parveen N, Moodie EEM, Cox J, Lambert G, Otis J, Roger M, Brenner B. New Challenges in HIV Research: Combining Phylogenetic Cluster Size and Epidemiological Data. ACTA ACUST UNITED AC 2018. [DOI: 10.1515/em-2017-0017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
37
Patiño-Galindo JÁ, González-Candelas F. Molecular evolution methods to study HIV-1 epidemics. Future Virol 2018;13:399-404. [PMID: 29967650 DOI: 10.2217/fvl-2017-0159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 04/04/2018] [Indexed: 01/17/2023]
38
Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics. PLoS Pathog 2018;14:e1006895. [PMID: 29462208 PMCID: PMC5877888 DOI: 10.1371/journal.ppat.1006895] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/30/2018] [Accepted: 01/23/2018] [Indexed: 11/23/2022]  Open
39
Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population. INFECTION GENETICS AND EVOLUTION 2017;58:77-82. [PMID: 29253674 DOI: 10.1016/j.meegid.2017.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/10/2017] [Accepted: 12/14/2017] [Indexed: 12/12/2022]
40
HIV Transmission Dynamics Among Foreign-Born Persons in the United States. J Acquir Immune Defic Syndr 2017;76:445-452. [PMID: 28902072 DOI: 10.1097/qai.0000000000001541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kiwuwa-Muyingo S, Nazziwa J, Ssemwanga D, Ilmonen P, Njai H, Ndembi N, Parry C, Kitandwe PK, Gershim A, Mpendo J, Neilsen L, Seeley J, Seppälä H, Lyagoba F, Kamali A, Kaleebu P. HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PLoS One 2017;12:e0185818. [PMID: 29023474 PMCID: PMC5638258 DOI: 10.1371/journal.pone.0185818] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/20/2017] [Indexed: 02/04/2023]  Open
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Lam CR, Holtz TH, Leelawiwat W, Mock PA, Chonwattana W, Wimonsate W, Varangrat A, Thienkrua W, Rose C, Chitwarakorn A, Curlin ME. Subtypes and Risk Behaviors Among Incident HIV Cases in the Bangkok Men Who Have Sex with Men Cohort Study, Thailand, 2006-2014. AIDS Res Hum Retroviruses 2017;33:1004-1012. [PMID: 28019101 DOI: 10.1089/aid.2016.0119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
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Turk T, Bachmann N, Kadelka C, Böni J, Yerly S, Aubert V, Klimkait T, Battegay M, Bernasconi E, Calmy A, Cavassini M, Furrer H, Hoffmann M, Günthard HF, Kouyos RD. Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis. eLife 2017;6:28721. [PMID: 28895527 PMCID: PMC5650480 DOI: 10.7554/elife.28721] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/28/2017] [Indexed: 11/14/2022]  Open
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Dearlove BL, Xiang F, Frost SDW. Biased phylodynamic inferences from analysing clusters of viral sequences. Virus Evol 2017;3:vex020. [PMID: 28852573 PMCID: PMC5570026 DOI: 10.1093/ve/vex020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
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Inferring HIV-1 Transmission Dynamics in Germany From Recently Transmitted Viruses. J Acquir Immune Defic Syndr 2017;73:356-363. [PMID: 27400403 DOI: 10.1097/qai.0000000000001122] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Defining HIV-1 transmission clusters based on sequence data. AIDS 2017;31:1211-1222. [PMID: 28353537 PMCID: PMC5482559 DOI: 10.1097/qad.0000000000001470] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012. PLoS One 2017;12:e0170601. [PMID: 28489920 PMCID: PMC5425008 DOI: 10.1371/journal.pone.0170601] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/06/2017] [Indexed: 12/12/2022]  Open
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The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data. INFECTION GENETICS AND EVOLUTION 2017;52:100-105. [PMID: 28427935 DOI: 10.1016/j.meegid.2017.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/30/2017] [Accepted: 04/05/2017] [Indexed: 01/05/2023]
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van de Laar TJ, Bezemer D, van Laethem K, Vandewalle G, de Smet A, van Wijngaerden E, Claas EC, van Sighem AI, Vandamme AM, Compernolle V, Zaaijer HL. Phylogenetic evidence for underreporting of male-to-male sex among human immunodeficiency virus-infected donors in the Netherlands and Flanders. Transfusion 2017;57:1235-1247. [PMID: 28375576 DOI: 10.1111/trf.14097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/14/2016] [Accepted: 01/08/2017] [Indexed: 12/13/2022]
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Sallam M, Esbjörnsson J, Baldvinsdóttir G, Indriðason H, Björnsdóttir TB, Widell A, Gottfreðsson M, Löve A, Medstrand P. Molecular epidemiology of HIV-1 in Iceland: Early introductions, transmission dynamics and recent outbreaks among injection drug users. INFECTION GENETICS AND EVOLUTION 2017;49:157-163. [PMID: 28082188 DOI: 10.1016/j.meegid.2017.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/19/2016] [Accepted: 01/02/2017] [Indexed: 10/20/2022]
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