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Li X, Tamim S, Trovão NS. The emergence and circulation of human immunodeficiency virus (HIV)-1 subtype C. J Med Microbiol 2024; 73. [PMID: 38757423 DOI: 10.1099/jmm.0.001827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Introduction. Human immunodeficiency virus (HIV)-1 subtype C is the most prevalent globally and is thought to have originated in non-human primates in the Democratic Republic of Congo.Hypothesis/Gap Statement. Although the global dominance of HIV-1 subtype C is well established, a thorough understanding of its evolutionary history and transmission dynamics across various risk populations remains elusive. The current knowledge is insufficient to fully capture the global diversification and dissemination of this subtype.Aim. We for the first time sought to investigate the global evolutionary history and spatiotemporal dynamics of HIV-1 subtype C using a selection of maximum-likelihood-based phylodynamic approaches on a total of 1210 near full-length genomic sequences sampled from 32 countries, collected in 4 continents, with sampling dates between 1986-2019 among various risk groups were analysed.Methodology. We subsampled the HIV-1 subtype C genomic datasets based on continent and risk group traits, and performed nucleotide substitution model selection analysis, maximum likelihood (ML) phylogenetic reconstruction, phylogenetic tree topology similarity analysis, temporal signal analysis and traced the timings of viral spread both geographically and by risk group.Results. Based on the phylodynamic analyses of four datasets (full1210, locrisk626, loc562 and risk393), we inferred the time to the most recent common ancestor (TMRCA) in the 1930s and an evolutionary rate of 0.0023 substitutions per site per year. The total number of introduction events of HIV-1 subtype C between continents and between risk groups is estimated to be 71 and 115, respectively. The largest number of introductions occurred from Africa to Europe (n=32), from not-recorded to heterosexual (n=40) and from heterosexual to not-recorded (n=51) risk groups.Conclusion. Our results emphasize that HIV subtype C has mainly spread from Africa to Europe, likely through heterosexual transmission.
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Affiliation(s)
- Xingguang Li
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, 315000, PR China
| | - Sana Tamim
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
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2
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Yang Q, Wang B, Lemey P, Dong L, Mu T, Wiebe RA, Guo F, Trovão NS, Park SW, Lewis N, Tsui JLH, Bajaj S, Cheng Y, Yang L, Haba Y, Li B, Zhang G, Pybus OG, Tian H, Grenfell B. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nat Commun 2024; 15:1126. [PMID: 38321046 PMCID: PMC10847442 DOI: 10.1038/s41467-024-45462-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.
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Affiliation(s)
- Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Ben Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tong Mu
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - R Alex Wiebe
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Fengyi Guo
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Nicola Lewis
- Animal and Plant Health Agency-Weybridge, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Department of Virology, Addlestone, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | | | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, UK
| | - Yachang Cheng
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Luojun Yang
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China.
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
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3
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Serwin K, Scheibe K, Urbańska A, Aksak-Wąs B, Karasińska-Cieślak M, Ząbek P, Siwak E, Cielniak I, Jabłonowska E, Wójcik-Cichy K, Jakubowski P, Bociąga-Jasik M, Witor A, Szymczak A, Szetela B, Parczewski M. Phylodynamic evolution of HIV-1 A6 sub-subtype epidemics in Poland. J Med Virol 2024; 96:e29482. [PMID: 38381668 DOI: 10.1002/jmv.29482] [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] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The human immunodeficiency virus type 1 (HIV-1) A6 sub-subtype is highly prevalent in Eastern Europe. Over the past decade, the dissemination of the A6 lineage has been expanding in Poland. The recent Russian invasion of Ukraine may further escalate the spread of this sub-subtype. While evolutionary studies using viral sequences have been instrumental in identifying the HIV epidemic patterns, the origins, and dynamics of the A6 sub-subtype in Poland remain to be explored. We analyzed 1185 HIV-1 A6 pol sequences from Poland, along with 8318 publicly available sequences from other countries. For analyses, phylogenetic tree construction, population dynamics inference, Bayesian analysis, and discrete phylogeographic modeling were employed. Of the introduction events to Poland, 69.94% originated from Ukraine, followed by 29.17% from Russia. Most A6 sequences in Poland (53.16%) formed four large clades, with their introductions spanning 1993-2008. Central and Southern Polish regions significantly influenced migration events. Transmissions among men who have sex with men (MSM) emerged as the dominant risk group for virus circulation, representing 72.92% of migration events. Sequences from migrants were found primarily outside the large clades. Past migration from Ukraine has fueled the spread of the A6 sub-subtype and the current influx of war-displaced people maintains the growing national epidemic.
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Affiliation(s)
- Karol Serwin
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Kaja Scheibe
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bogusz Aksak-Wąs
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Malwina Karasińska-Cieślak
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Piotr Ząbek
- Department of Adults' Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Siwak
- Department of Adults' Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Cielniak
- Faculty of Medical Science, Collegium Medicum Cardinal Stefan Wyszynski University in Warsaw, Warsaw, Poland
| | - Elżbieta Jabłonowska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | - Kamila Wójcik-Cichy
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | | | - Monika Bociąga-Jasik
- Department of Infectious and Tropical Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Adam Witor
- Regional Hospital, Out-Patient's Clinic for Immune Deficiency, Chorzów, Poland
| | - Aleksandra Szymczak
- Department of Infectious Diseases, Liver Disease and Acquired Immune Deficiencies, Wroclaw Medical University, Wrocław, Poland
| | - Bartosz Szetela
- Department of Infectious Diseases, Liver Disease and Acquired Immune Deficiencies, Wroclaw Medical University, Wrocław, Poland
| | - Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
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4
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Nduva GM, Otieno F, Kimani J, Sein Y, Arimide DA, Mckinnon LR, Cholette F, Lawrence MK, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Medstrand P, Sanders EJ, Esbjörnsson J, Hassan AS. Temporal trends and transmission dynamics of pre-treatment HIV-1 drug resistance within and between risk groups in Kenya, 1986-2020. J Antimicrob Chemother 2024; 79:287-296. [PMID: 38091580 PMCID: PMC10832587 DOI: 10.1093/jac/dkad375] [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: 08/07/2023] [Accepted: 11/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Evidence on the distribution of pre-treatment HIV-1 drug resistance (HIVDR) among risk groups is limited in Africa. We assessed the prevalence, trends and transmission dynamics of pre-treatment HIVDR within and between MSM, people who inject drugs (PWID), female sex workers (FSWs), heterosexuals (HETs) and perinatally infected children in Kenya. METHODS HIV-1 partial pol sequences from antiretroviral-naive individuals collected from multiple sources between 1986 and 2020 were used. Pre-treatment reverse transcriptase inhibitor (RTI), PI and integrase inhibitor (INSTI) mutations were assessed using the Stanford HIVDR database. Phylogenetic methods were used to determine and date transmission clusters. RESULTS Of 3567 sequences analysed, 550 (15.4%, 95% CI: 14.2-16.6) had at least one pre-treatment HIVDR mutation, which was most prevalent amongst children (41.3%), followed by PWID (31.0%), MSM (19.9%), FSWs (15.1%) and HETs (13.9%). Overall, pre-treatment HIVDR increased consistently, from 6.9% (before 2005) to 24.2% (2016-20). Among HETs, pre-treatment HIVDR increased from 6.6% (before 2005) to 20.2% (2011-15), but dropped to 6.5% (2016-20). Additionally, 32 clusters with shared pre-treatment HIVDR mutations were identified. The majority of clusters had R0 ≥ 1.0, indicating ongoing transmissions. The largest was a K103N cluster involving 16 MSM sequences sampled between 2010 and 2017, with an estimated time to the most recent common ancestor (tMRCA) of 2005 [95% higher posterior density (HPD), 2000-08], indicating propagation over 12 years. CONCLUSIONS Compared to HETs, children and key populations had higher levels of pre-treatment HIVDR. Introduction of INSTIs after 2017 may have abrogated the increase in pre-treatment RTI mutations, albeit in the HET population only. Taken together, our findings underscore the need for targeted efforts towards equitable access to ART for children and key populations in Kenya.
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Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Yiakon Sein
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | - Dawit A Arimide
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Lyle R Mckinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Morris K Lawrence
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - Moses Masika
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Gaudensia Mutua
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Susan M Graham
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Department of Medicine, Global Health and Epidemiology, University of Washington, Seattle, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Matt A Price
- IAVI, NewYork, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology & Biostatistics, University of Illinois at Chicago, Chicago, IL, USA
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Eduard J Sanders
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
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Tetzlaff SJ, Vizentin‐Bugoni J, Sperry JH, Davis MA, Clark RW, Repp RA, Schuett GW. Fission-fusion dynamics in the social networks of a North American pitviper. Ecol Evol 2023; 13:e10339. [PMID: 37554395 PMCID: PMC10405236 DOI: 10.1002/ece3.10339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
Many animal species exist in fission-fusion societies, where the size and composition of conspecific groups change spatially and temporally. To help investigate such phenomena, social network analysis (SNA) has emerged as a powerful conceptual and analytical framework for assessing patterns of interconnectedness and quantifying group-level interactions. We leveraged behavioral observations via radiotelemetry and genotypic data from a long-term (>10 years) study on the pitviper Crotalus atrox (western diamondback rattlesnake) and used SNA to quantify the first robust demonstration of social network structures for any free-living snake. Group-level interactions among adults in this population resulted in structurally modular networks (i.e., distinct clusters of interacting individuals) for fidelis use of communal winter dens (denning network), mating behaviors (pairing network), and offspring production (parentage network). Although the structure of each network was similar, the size and composition of groups varied among them. Specifically, adults associated with moderately sized social groups at winter dens but often engaged in reproductive behaviors-both at and away from dens-with different and fewer partners. Additionally, modules formed by individuals in the pairing network were frequently different from those in the parentage network, likely due to multiple mating, long-term sperm storage by females, and resultant multiple paternity. Further evidence for fission-fusion dynamics exhibited by this population-interactions were rare when snakes were dispersing to and traversing their spring-summer home ranges (to which individuals show high fidelity), despite ample opportunities to associate with numerous conspecifics that had highly overlapping ranges. Taken together, we show that long-term datasets incorporating SNA with spatial and genetic information provide robust and unique insights to understanding the social structure of cryptic taxa that are understudied.
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Affiliation(s)
- Sasha J. Tetzlaff
- U.S. Army ERDC‐CERLChampaignIllinoisUSA
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois Urbana‐ChampaignChampaignIllinoisUSA
| | - Jeferson Vizentin‐Bugoni
- Programa de Pós‐Graduação em Biologia Animal, Instituto de BiologiaUniversidade Federal de PelotasPelotasBrazil
| | - Jinelle H. Sperry
- U.S. Army ERDC‐CERLChampaignIllinoisUSA
- Department of Natural Resources and Environmental SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Mark A. Davis
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois Urbana‐ChampaignChampaignIllinoisUSA
- Department of Natural Resources and Environmental SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Rulon W. Clark
- Chiricahua Desert MuseumRodeoNew MexicoUSA
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
| | | | - Gordon W. Schuett
- Chiricahua Desert MuseumRodeoNew MexicoUSA
- Department of Biology, Neuroscience InstituteGeorgia State UniversityAtlantaGeorgiaUSA
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6
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Gulinaizhaer A, Zou M, Ma S, Yao Y, Fan X, Wu G. Isothermal nucleic acid amplification technology in HIV detection. Analyst 2023; 148:1189-1208. [PMID: 36825492 DOI: 10.1039/d2an01813f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.
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Affiliation(s)
- Abudushalamu Gulinaizhaer
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Xiaobo Fan
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China. .,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, Jiangsu, China
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7
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Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus Evol 2023; 9:vead010. [PMID: 36860641 PMCID: PMC9969415 DOI: 10.1093/ve/vead010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, which enables reconstruction of the origin and subsequent geographic spread of pathogens. Such inference is, however, potentially affected by geographic sampling bias. Here, we investigated the impact of sampling bias on the spatiotemporal reconstruction of viral epidemics using Bayesian discrete phylogeographic models and explored different operational strategies to mitigate this impact. We considered the continuous-time Markov chain (CTMC) model and two structured coalescent approximations (Bayesian structured coalescent approximation [BASTA] and marginal approximation of the structured coalescent [MASCOT]). For each approach, we compared the estimated and simulated spatiotemporal histories in biased and unbiased conditions based on the simulated epidemics of rabies virus (RABV) in dogs in Morocco. While the reconstructed spatiotemporal histories were impacted by sampling bias for the three approaches, BASTA and MASCOT reconstructions were also biased when employing unbiased samples. Increasing the number of analyzed genomes led to more robust estimates at low sampling bias for the CTMC model. Alternative sampling strategies that maximize the spatiotemporal coverage greatly improved the inference at intermediate sampling bias for the CTMC model, and to a lesser extent, for BASTA and MASCOT. In contrast, allowing for time-varying population sizes in MASCOT resulted in robust inference. We further applied these approaches to two empirical datasets: a RABV dataset from the Philippines and a SARS-CoV-2 dataset describing its early spread across the world. In conclusion, sampling biases are ubiquitous in phylogeographic analyses but may be accommodated by increasing the sample size, balancing spatial and temporal composition in the samples, and informing structured coalescent models with reliable case count data.
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Affiliation(s)
| | | | | | | | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, 25-28 rue du Docteur Roux, Paris 75014, France,WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, 28 rue du Docteur Roux, Paris 75724, France
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8
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Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [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: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
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Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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9
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HIV / AIDS as a model for emerging infectious disease: origin, dating and circumstances of an emblematic epidemiological success. Presse Med 2022; 51:104128. [PMID: 35623545 DOI: 10.1016/j.lpm.2022.104128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/12/2022] [Indexed: 11/22/2022] Open
Abstract
In June 1981, the Centers for Disease Control (CDC) "Morbidity and Mortality Weekly Report" described the first cases of what was to be known as the Acquired Immunodeficiency Syndrome (AIDS). Two years later, the agent responsible for the disease, the human immunodeficiency virus (HIV), was identified. Since then, according to the World Health Organization an estimated 40 million people have died from the disease. Where does this virus come from, and why such an emergence in the late 20th century? These are the questions that it is now possible to answer in large part thanks to the numerous studies published over a little more than three decades. As with other emerging infectious diseases, initial cross-species transmission from an animal reservoir and subsequent favorable sociological factors associated with the evolution of human societies have led to the spread of a dramatic disease, for which no vaccine is presently available.
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Revisiting the recombinant history of HIV-1 group M with dynamic network community detection. Proc Natl Acad Sci U S A 2022; 119:e2108815119. [PMID: 35500121 PMCID: PMC9171507 DOI: 10.1073/pnas.2108815119] [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: 11/29/2022] Open
Abstract
Recombination is a major mechanism through which HIV type 1 (HIV-1) maintains genetic diversity and interferes with viral eradication efforts. There is growing evidence demonstrating a recombinant origin of primate lentiviruses including HIV-1 group M (HIV-1/M). Inferring the extent of recombination across the entire HIV-1/M genome is of great importance as it provides deeper insights into the origin, dynamics, and evolution of the global pandemic. Here we propose an alternative method that can reconstruct the extent of genome-wide recombination in HIV-1, uncover reticulate patterns, and serve as a framework for HIV-1 classification. Our method provides an alternative approach for understanding the roles of virus recombination in the early evolutionary history of zoonosis for other emerging viruses. The prevailing abundance of full-length HIV type 1 (HIV-1) genome sequences provides an opportunity to revisit the standard model of HIV-1 group M (HIV-1/M) diversity that clusters genomes into largely nonrecombinant subtypes, which is not consistent with recent evidence of deep recombinant histories for simian immunodeficiency virus (SIV) and other HIV-1 groups. Here we develop an unsupervised nonparametric clustering approach, which does not rely on predefined nonrecombinant genomes, by adapting a community detection method developed for dynamic social network analysis. We show that this method (dynamic stochastic block model [DSBM]) attains a significantly lower mean error rate in detecting recombinant breakpoints in simulated data (quasibinomial generalized linear model (GLM), P<8×10−8), compared to other reference-free recombination detection programs (genetic algorithm for recombination detection [GARD], recombination detection program 4 [RDP4], and RDP5). When this method was applied to a representative sample of n = 525 actual HIV-1 genomes, we determined k = 29 as the optimal number of DSBM clusters and used change-point detection to estimate that at least 95% of these genomes are recombinant. Further, we identified both known and undocumented recombination hotspots in the HIV-1 genome and evidence of intersubtype recombination in HIV-1 subtype reference genomes. We propose that clusters generated by DSBM can provide an informative framework for HIV-1 classification.
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Nduva GM, Otieno F, Kimani J, Wahome E, McKinnon LR, Cholette F, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Baele G, Lemey P, Hassan AS, Sanders EJ, Esbjörnsson J. Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study. Virus Evol 2022; 8:veac016. [PMID: 35356640 PMCID: PMC8962731 DOI: 10.1093/ve/veac016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 'hotspots' and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986-2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.
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Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Frederick Otieno
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Elizabeth Wahome
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Lyle R McKinnon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Private Bag X7, Congella 4013, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Canada
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Center for Global Health Research, KEMRI-CGHR, P.O. Box 20778-00202, Kisumu, Kenya
| | - Moses Masika
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Gaudensia Mutua
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Omu Anzala
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Susan M Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Office of the Chair, UW Box # 351619, Seattle, DC, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Matt A Price
- IAVI Global Headquarters, 125 Broad Street, 9th Floor, New York, NY 10004, USA
- Department of Epidemiology and Biostatistics, University of California, Mission Hall: Global Health & Clinical Sciences Building, 550 16th Street, 2nd Floor, San Francisco, CA 94158-2549, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, 1603 W Taylor St, Chicago, IL 60612, USA
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
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Arimide DA, Esquivel-Gómez LR, Kebede Y, Sasinovich S, Balcha T, Björkman P, Kühnert D, Medstrand P. Molecular Epidemiology and Transmission Dynamics of the HIV-1 Epidemic in Ethiopia: Epidemic Decline Coincided With Behavioral Interventions Before ART Scale-Up. Front Microbiol 2022; 13:821006. [PMID: 35283836 PMCID: PMC8914292 DOI: 10.3389/fmicb.2022.821006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundEthiopia is one of the sub-Saharan countries hit hard by the HIV epidemic. Previous studies have shown that subtype C dominates the Ethiopian HIV-1 epidemic, but the evolutionary and temporal dynamics of HIV-1 in Ethiopia have not been closely scrutinized. Understanding the evolutionary and epidemiological pattern of HIV is vital to monitor the spread, evaluate and implement HIV prevention strategies.MethodsWe analyzed 1,276 Ethiopian HIV-1 subtype C polymerase (pol sequences), including 144 newly generated sequences, collected from different parts of the country from 1986 to 2017. We employed state-of-art maximum likelihood and Bayesian phylodynamic analyses to comprehensively describe the evolutionary dynamics of the HIV-1 epidemic in Ethiopia. We used Bayesian phylodynamic models to estimate the dynamics of the effective population size (Ne) and reproductive numbers (Re) through time for the HIV epidemic in Ethiopia.ResultsOur analysis revealed that the Ethiopian HIV-1 epidemic originated from two independent introductions at the beginning of the 1970s and 1980s from eastern and southern African countries, respectively, followed by epidemic growth reaching its maximum in the early 1990s. We identified three large clusters with a majority of Ethiopian sequences. Phylodynamic analyses revealed that all three clusters were characterized by high transmission rates during the early epidemic, followed by a decline in HIV-1 transmissions after 1990. Re was high (4–6) during the earlier time of the epidemic but dropped significantly and remained low (Re < 1) after the mid-1990. Similarly, with an expected shift in time, the effective population size (Ne) steadily increased until the beginning of 2000, followed by a decline and stabilization until recent years. The phylodynamic analyses corroborated the modeled UNAIDS incidence and prevalence estimates.ConclusionThe rapid decline in the HIV epidemic took place a decade before introducing antiretroviral therapy in Ethiopia and coincided with early behavioral, preventive, and awareness interventions implemented in the country. Our findings highlight the importance of behavioral interventions and antiretroviral therapy scale-up to halt and maintain HIV transmissions at low levels (Re < 1). The phylodynamic analyses provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.
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Affiliation(s)
- Dawit Assefa Arimide
- Department of Translational Medicine, Lund University, Malmo, Sweden
- TB/HIV Department, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Luis Roger Esquivel-Gómez
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany
| | - Yenew Kebede
- Africa Centre for Disease Prevention and Control, Africa Union Commission, Addis Ababa, Ethiopia
| | | | - Taye Balcha
- Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Per Björkman
- Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmo, Sweden
- *Correspondence: Patrik Medstrand,
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An M, Zheng C, Li H, Chen L, Yang Z, Gan Y, Han X, Zhao J, Shang H. Independent epidemic patterns of HIV-1 CRF01_AE lineages driven by mobile population in Shenzhen, an immigrant city of China. Virus Evol 2021; 7:veab094. [PMID: 35299786 PMCID: PMC8923236 DOI: 10.1093/ve/veab094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022] Open
Abstract
Abstract
Shenzhen, a city with >12 million migrant population, may play a key role in the spread of human immunodeficiency virus (HIV)-1 in China. The transmission dynamics of CRF01_AE, a predominant subtype in Shenzhen, is a good model to characterize the impact of human mobility on HIV-1 epidemic locally and nationally. We used phylodynamic and phylogeographic methods to estimate the viral transmission dynamics and migration trajectory of variable lineages based on 1,423 CRF01_AE sequences in Shenzhen sampled between 2006 and 2015. Eleven lineages of CRF01_AE were detected in Shenzhen. Of those, four main lineages originated during the 1990s. Their basic viral reproduction number (R0) ranged 1.96–3.92. The effective viral reproduction number (Re) of two lineages prevalent among heterosexuals/people who inject drugs had reduced <1 at the end of sampling, and the main sources were the intra-provincial immigrants (72 per cent) for one and local residents of Shenzhen (91 per cent) for another. Within two lineages among men who have sex with men (MSM), Re had been above or close to 1 at the end of sampling, and the immigrants from Jiangxi/Shaanxi and Hubei as sources accounted for 93 per cent and 68 per cent of all viral migration events, respectively. Moreover, no obvious recipients were found throughout the viral migration history for any lineage. Our findings demonstrate that HIV epidemic is declining in Shenzhen, which coincided with the initiation of the interventions during the 2000s. However, the obvious differences of the epidemic patterns between lineages emphasize the importance of further targeting interventions and continued molecular tracing, focusing on high-risk transmission sources among MSM.
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Affiliation(s)
- Minghui An
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
- Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Hao Li
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Zhengrong Yang
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Yongxia Gan
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
- Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, No 8, Longyuan Road, Shenzhen, Guangdong 518055, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
- Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, No 155, Nanjing North Street, Shenyang, Liaoning 110001, China
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Dellicour S, Gill MS, Faria NR, Rambaut A, Pybus OG, Suchard MA, Lemey P. Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST. Mol Biol Evol 2021; 38:3486-3493. [PMID: 33528560 PMCID: PMC8321535 DOI: 10.1093/molbev/msab031] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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Li Y, Chen X, Zhao Y, Wan Z, Zeng Y, Ma Y, Zhou L, Xu G, Reboud J, Cooper JM, Zhang C. A rapid variant-tolerant reverse transcription loop-mediated isothermal amplification assay for the point of care detection of HIV-1. Analyst 2021; 146:5347-5356. [PMID: 34323889 DOI: 10.1039/d1an00598g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human immunodeficiency virus (HIV) continues to be a major burden on public health globally with on-going increases in the number of new infections each year. Rapid and sensitive point-of-care tests allow timely interventions and are essential to control the spread of the disease. However the highly variable nature of the virus, resulting in the evolution of many subtypes and inter-subtype recombinants, poses important challenges for its diagnosis. Here we describe a variant-tolerant reverse-transcription RT-LAMP amplification of the virus's INT gene, providing a simple to use, rapid (<30 min) in vitro point-of-care diagnostic test with a limit of detection <18 copies/reaction. The assay was first validated in clinical studies of patient samples, using both established RT-LAMP and RT-qPCR assays for reference, with results showing that this new variant-tolerant HIV-1 RT-LAMP diagnostic test is highly sensitive without compromising its high specificity for HIV-1 subtypes. The diagnostic test was subsequently configured within an easy-to-read paper microfluidic lateral flow test and was validated clinically using patient samples, demonstrating its future potential for use in timely, effective, low cost HIV diagnostics in global regions where healthcare resources may be limited.
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Affiliation(s)
- Yingxue Li
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
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Nduva GM, Nazziwa J, Hassan AS, Sanders EJ, Esbjörnsson J. The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review. Viruses 2021; 13:1174. [PMID: 34205246 PMCID: PMC8235305 DOI: 10.3390/v13061174] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.
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Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Eduard J. Sanders
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
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Farinre O, Gounder K, Reddy T, Tongo M, Hare J, Chaplin B, Gilmour J, Kanki P, Mann JK, Ndung'u T. Subtype-specific differences in Gag-protease replication capacity of HIV-1 isolates from East and West Africa. Retrovirology 2021; 18:11. [PMID: 33952315 PMCID: PMC8097975 DOI: 10.1186/s12977-021-00554-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/12/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The HIV-1 epidemic in sub-Saharan Africa is heterogeneous with diverse unevenly distributed subtypes and regional differences in prevalence. Subtype-specific differences in disease progression rate and transmission efficiency have been reported, but the underlying biological mechanisms have not been fully characterized. Here, we tested the hypothesis that the subtypes prevalent in the East Africa, where adult prevalence rate is higher, have lower viral replication capacity (VRC) than their West African counterparts where adult prevalence rates are lower. RESULTS Gag-protease sequencing was performed on 213 and 160 antiretroviral-naïve chronically infected participants from West and East Africa respectively and bioinformatic tools were used to infer subtypes and recombination patterns. VRC of patient-derived gag-protease chimeric viruses from West (n = 178) and East (n = 114) Africa were determined using a green fluorescent protein reporter-based cell assay. Subtype and regional differences in VRC and amino acid variants impacting VRC were identified by statistical methods. CRF02_AG (65%, n = 139), other recombinants (14%, n = 30) and pure subtypes (21%, n = 44) were identified in West Africa. Subtypes A1 (64%, n = 103), D (22%, n = 35), or recombinants (14%, n = 22) were identified in East Africa. Viruses from West Africa had significantly higher VRC compared to those from East Africa (p < 0.0001), with subtype-specific differences found among strains within West and East Africa (p < 0.0001). Recombination patterns showed a preference for subtypes D, G or J rather than subtype A in the p6 region of gag, with evidence that subtype-specific differences in this region impact VRC. Furthermore, the Gag A83V polymorphism was associated with reduced VRC in CRF02_AG. HLA-A*23:01 (p = 0.0014) and HLA-C*07:01 (p = 0.002) were associated with lower VRC in subtype A infected individuals from East Africa. CONCLUSIONS Although prevalent viruses from West Africa displayed higher VRC than those from East Africa consistent with the hypothesis that lower VRC is associated with higher population prevalence, the predominant CRF02_AG strain in West Africa displayed higher VRC than other prevalent strains suggesting that VRC alone does not explain population prevalence. The study identified viral and host genetic determinants of virus replication capacity for HIV-1 CRF02_AG and subtype A respectively, which may have relevance for vaccine strategies.
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Affiliation(s)
- Omotayo Farinre
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Kamini Gounder
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
| | - Tarylee Reddy
- Biostatistics Research Unit, South African Medical Research Council, Durban, South Africa
| | - Marcel Tongo
- Centre of Research for Emerging and Re-Emerging Diseases (CREMER), Yaoundé, Cameroon
| | - Jonathan Hare
- International AIDS Vaccine Initiative (IAVI) Human Immunology Laboratory (HIL), Imperial College, London, UK
- IAVI Global Headquarters, 125 Broad Street, 9th Floor,, New York, NY, USA
| | - Beth Chaplin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI) Human Immunology Laboratory (HIL), Imperial College, London, UK
- IAVI Global Headquarters, 125 Broad Street, 9th Floor,, New York, NY, USA
| | - Phyllis Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Africa Health Research Institute, Durban, 4001, South Africa.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Max Planck Institute for Infection Biology, Berlin, Germany.
- Division of Infection and Immunity, University College London, London, UK.
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18
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Tongo M, Martin DP, Dorfman JR. Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods. Genes (Basel) 2021; 12:genes12040517. [PMID: 33918115 PMCID: PMC8065694 DOI: 10.3390/genes12040517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022] Open
Abstract
The Congo Basin region is believed to be the site of the cross-species transmission event that yielded HIV-1 group M (HIV-1M). It is thus likely that the virus has been present and evolving in the region since that cross-species transmission. As HIV-1M was only discovered in the early 1980s, our directly observed record of the epidemic is largely limited to the past four decades. Nevertheless, by exploiting the genetic relatedness of contemporary HIV-1M sequences, phylogenetic methods provide a powerful framework for investigating simultaneously the evolutionary and epidemiologic history of the virus. Such an approach has been taken to find that the currently classified HIV-1 M subtypes and Circulating Recombinant Forms (CRFs) do not give a complete view of HIV-1 diversity. In addition, the currently identified major HIV-1M subtypes were likely genetically predisposed to becoming a major component of the present epidemic, even before the events that resulted in the global epidemic. Further efforts have identified statistically significant hot- and cold-spots of HIV-1M subtypes sequence inheritance in genomic regions of recombinant forms. In this review we provide ours and others recent findings on the emergence and spread of HIV-1M variants in the region, which have provided insights into the early evolution of this virus.
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Affiliation(s)
- Marcel Tongo
- Center for Research on Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Correspondence:
| | - Darren P. Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Jeffrey R. Dorfman
- Division of Medical Virology, School of Pathology, Faculty of Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
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19
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Whitmer SLM, Lo MK, Sazzad HMS, Zufan S, Gurley ES, Sultana S, Amman B, Ladner JT, Rahman MZ, Doan S, Satter SM, Flora MS, Montgomery JM, Nichol ST, Spiropoulou CF, Klena JD. Inference of Nipah virus evolution, 1999-2015. Virus Evol 2021; 7:veaa062. [PMID: 34422315 PMCID: PMC7947586 DOI: 10.1093/ve/veaa062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite near-annual human outbreaks of Nipah virus (NiV) disease in Bangladesh, typically due to individual spillover events from the local bat population, only twenty whole-genome NiV sequences exist from humans and ten from bats. NiV whole-genome sequences from annual outbreaks have been challenging to generate, primarily due to the low viral load in human throat swab and serum specimens. Here, we used targeted enrichment with custom NiV-specific probes and generated thirty-five additional unique full-length genomic sequences directly from human specimens and viral isolates. We inferred the temporal and geographic evolutionary history of NiV in Bangladesh and expanded a tool to visualize NiV spatio-temporal spread from a Bayesian continuous diffusion analysis. We observed that strains from Bangladesh segregated into two distinct clades that have intermingled geographically in Bangladesh over time and space. As these clades expanded geographically and temporally, we did not observe evidence for significant branch and site-specific selection, except for a single site in the Henipavirus L polymerase. However, the Bangladesh 1 and 2 clades are differentiated by mutations initially occurring in the polymerase, with additional mutations accumulating in the N, G, F, P, and L genes on external branches. Modeling the historic geographical and temporal spread demonstrates that while widespread, NiV does not exhibit significant genetic variation in Bangladesh. Thus, future public health measures should address whether NiV within in the bat population also exhibits comparable genetic variation, if zoonotic transmission results in a genetic bottleneck and if surveillance techniques are detecting only a subset of NiV.
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Affiliation(s)
- Shannon L M Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Michael K Lo
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Hossain M S Sazzad
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Sara Zufan
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Emily S Gurley
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sharmin Sultana
- Institute of Epidemiology, Disease Control and Research, Bangladesh
| | - Brian Amman
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Mohammed Ziaur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Stephanie Doan
- The Center for Global Health, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329
| | - Syed M Satter
- Institute of Epidemiology, Disease Control and Research, Bangladesh
| | - Meerjady S Flora
- Institute of Epidemiology, Disease Control and Research, Bangladesh
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - John D Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
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20
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Vrancken B, Zhao B, Li X, Han X, Liu H, Zhao J, Zhong P, Lin Y, Zai J, Liu M, Smith DM, Dellicour S, Chaillon A. Comparative Circulation Dynamics of the Five Main HIV Types in China. J Virol 2020; 94:e00683-20. [PMID: 32938762 PMCID: PMC7654276 DOI: 10.1128/jvi.00683-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023] Open
Abstract
The HIV epidemic in China accounts for 3% of the global HIV incidence. We compared the patterns and determinants of interprovincial spread of the five most prevalent circulating types. HIV pol sequences sampled across China were used to identify relevant transmission networks of the five most relevant HIV-1 types (B and circulating recombinant forms [CRFs] CRF01_AE, CRF07_BC, CRF08_BC, and CRF55_01B) in China. From these, the dispersal history across provinces was inferred. A generalized linear model (GLM) was used to test the association between migration rates among provinces and several measures of human mobility. A total of 10,707 sequences were collected between 2004 and 2017 across 26 provinces, among which 1,962 are newly reported here. A mean of 18 (minimum and maximum, 1 and 54) independent transmission networks involving up to 17 provinces were identified. Discrete phylogeographic analysis largely recapitulates the documented spread of the HIV types, which in turn, mirrors within-China population migration flows to a large extent. In line with the different spatiotemporal spread dynamics, the identified drivers thereof were also heterogeneous but are consistent with a central role of human mobility. The comparative analysis of the dispersal dynamics of the five main HIV types circulating in China suggests a key role of large population centers and developed transportation infrastructures as hubs of HIV dispersal. This advocates for coordinated public health efforts in addition to local targeted interventions.IMPORTANCE While traditional epidemiological studies are of great interest in describing the dynamics of epidemics, they struggle to fully capture the geospatial dynamics and factors driving the dispersal of pathogens like HIV as they have difficulties capturing linkages between infections. To overcome this, we used a discrete phylogeographic approach coupled to a generalized linear model extension to characterize the dynamics and drivers of the across-province spread of the five main HIV types circulating in China. Our results indicate that large urbanized areas with dense populations and developed transportation infrastructures are facilitators of HIV dispersal throughout China and highlight the need to consider harmonized country-wide public policies to control local HIV epidemics.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xingguang Li
- Department of Hospital Office, The First People's Hospital of Fangchenggang, Fangchenggang, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haizhou Liu
- Centre for Emerging Infectious Diseases, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Yi Lin
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Junjie Zai
- Immunology innovation Team, School of Medicine, Ningbo University, Ningbo, Zhejiang China
| | - Mingchen Liu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
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21
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Rubio-Garrido M, González-Alba JM, Reina G, Ndarabu A, Barquín D, Carlos S, Galán JC, Holguín Á. Current and historic HIV-1 molecular epidemiology in paediatric and adult population from Kinshasa in the Democratic Republic of Congo. Sci Rep 2020; 10:18461. [PMID: 33116151 PMCID: PMC7595211 DOI: 10.1038/s41598-020-74558-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/30/2020] [Indexed: 12/22/2022] Open
Abstract
HIV-1 diversity may impact monitoring and vaccine development. We describe the most recent data of HIV-1 variants and their temporal trends in the Democratic Republic of Congo (DRC) from 1976 to 2018 and in Kinshasa from 1983–2018. HIV-1 pol sequencing from dried blood collected in Kinshasa during 2016–2018 was done in 340 HIV-infected children/adolescents/adults to identify HIV-1 variants by phylogenetic reconstructions. Recombination events and transmission clusters were also analyzed. Variant distribution and genetic diversity were compared to historical available pol sequences from the DRC in Los Alamos Database (LANL). We characterized 165 HIV-1 pol variants circulating in Kinshasa (2016–2018) and compared them with 2641 LANL sequences from the DRC (1976–2012) and Kinshasa (1983–2008). During 2016–2018 the main subtypes were A (26.7%), G (9.7%) and C (7.3%). Recombinants accounted for a third of infections (12.7%/23.6% Circulant/Unique Recombinant Forms). We identified the first CRF47_BF reported in Africa and four transmission clusters. A significant increase of subtype A and sub-subtype F1 and a significant reduction of sub-subtype A1 and subtype D were observed in Kinshasa during 2016–2018 compared to variants circulating in the city from 1983 to 2008. We provide unique and updated information related to HIV-1 variants currently circulating in Kinshasa, reporting the temporal trends of subtypes/CRF/URF during 43 years in the DRC, and providing the most extensive data on children/adolescents.
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Affiliation(s)
- Marina Rubio-Garrido
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP, 28034, Madrid, Spain
| | - José María González-Alba
- Virology Section, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp, 28034, Madrid, Spain
| | - Gabriel Reina
- Microbiology Department, Clínica Universidad de Navarra, Navarra Institute for Health Research (IdiSNA), Institute of Tropical Health, Universidad de Navarra (ISTUN), 31008, Pamplona, Spain.
| | - Adolphe Ndarabu
- Monkole Hospital, Kinshasa, Democratic Republic of the Congo
| | - David Barquín
- Microbiology Department, Clínica Universidad de Navarra, Navarra Institute for Health Research (IdiSNA), Institute of Tropical Health, Universidad de Navarra (ISTUN), 31008, Pamplona, Spain
| | - Silvia Carlos
- Department of Preventive Medicine and Public Health, Navarra Institute for Health Research (IdiSNA), Institute of Tropical Health, Universidad de Navarra (ISTUN), Pamplona, 31008, Spain
| | - Juan Carlos Galán
- Virology Section, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp, 28034, Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP, 28034, Madrid, Spain.
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22
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Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nat Commun 2020; 11:5110. [PMID: 33037213 PMCID: PMC7547076 DOI: 10.1038/s41467-020-18877-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.
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Affiliation(s)
- Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium.
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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23
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Jin SW, Mwimanzi FM, Mann JK, Bwana MB, Lee GQ, Brumme CJ, Hunt PW, Martin JN, Bangsberg DR, Ndung’u T, Brumme ZL, Brockman MA. Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. PLoS Pathog 2020; 16:e1008813. [PMID: 32925973 PMCID: PMC7515180 DOI: 10.1371/journal.ppat.1008813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 09/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
HIV Nef counteracts cellular host restriction factors SERINC3 and SERINC5, but our understanding of how naturally occurring global Nef sequence diversity impacts these activities is limited. Here, we quantify SERINC3 and SERINC5 internalization function for 339 Nef clones, representing the major pandemic HIV-1 group M subtypes A, B, C and D. We describe distinct subtype-associated hierarchies for Nef-mediated internalization of SERINC5, for which subtype B clones display the highest activities on average, and of SERINC3, for which subtype B clones display the lowest activities on average. We further identify Nef polymorphisms that modulate its ability to counteract SERINC proteins, including substitutions in the N-terminal domain that selectively impair SERINC3 internalization. Our findings demonstrate that the SERINC antagonism activities of HIV Nef differ markedly among major viral subtypes and between individual isolates within a subtype, suggesting that variation in these functions may contribute to global differences in viral pathogenesis.
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Affiliation(s)
- Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Jaclyn K. Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mwebesa Bosco Bwana
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q. Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Peter W. Hunt
- School of Medicine, University of California, San Francisco, United States of America
| | - Jeff N. Martin
- School of Medicine, University of California, San Francisco, United States of America
| | - David R. Bangsberg
- School of Public Health, Oregon Health Science University, Portland, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, United States of America
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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24
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Jara M, Rasmussen DA, Corzo CA, Machado G. Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States. Transbound Emerg Dis 2020; 68:667-683. [PMID: 32657491 DOI: 10.1111/tbed.13728] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/25/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) remains widespread in the North American pig population. Despite improvements in virus characterization, it is unclear whether PRRSV infections are a product of viral circulation within production systems (local) or across production systems (external). Here, we examined the local and external dissemination dynamics of PRRSV and the processes facilitating its spread in three production systems. Overall, PRRSV genetic diversity has declined since 2018, while phylodynamic results support frequent external transmission. We found that PRRSV dissemination predominantly occurred mostly through transmission between farms of different production companies for several months, especially from November until May, a timeframe already established as PRRSV season. Although local PRRSV dissemination occurred mainly through regular pig flow (from sow to nursery and then to finisher farms), an important flux of PRRSV dissemination also occurred in the opposite direction, from finisher to sow and nursery farms, highlighting the importance of downstream farms as sources of the virus. Our results also showed that farms with pig densities of 500 to 1,000 pig/km2 and farms located at a range within 0.5 km and 0.7 km from major roads were more likely to be infected by PRRSV, whereas farms at an elevation of 41 to 61 meters and surrounded by denser vegetation were less likely to be infected, indicating their role as dissemination barriers. In conclusion, our results demonstrate that external dissemination was intense, and reinforce the importance of farm proximity on PRRSV spread. Thus, consideration of farm location, geographic characteristics and animal densities across production systems may help to forecast PRRSV collateral dissemination.
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Affiliation(s)
- Manuel Jara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Cesar A Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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25
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Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O’Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.22.165464. [PMID: 32596695 PMCID: PMC7315996 DOI: 10.1101/2020.06.22.165464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Spatiotemporal bias in genome sequence sampling can severely confound phylogeographic inference based on discrete trait ancestral reconstruction. This has impeded our ability to accurately track the emergence and spread of SARS-CoV-2, which is the virus responsible for the COVID-19 pandemic. Despite the availability of staggering numbers of genomes on a global scale, evolutionary reconstructions of SARS-CoV-2 are hindered by the slow accumulation of sequence divergence over its relatively short transmission history. When confronted with these issues, incorporating additional contextual data may critically inform phylodynamic reconstructions. Here, we present a new approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2, while also including global air transportation data. We demonstrate that including travel history data for each SARS-CoV-2 genome yields more realistic reconstructions of virus spread, particularly when travelers from undersampled locations are included to mitigate sampling bias. We further explore the impact of sampling bias by incorporating unsampled sequences from undersampled locations in the analyses. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts. Although further research is needed to fully examine the performance of our new data integration approaches and to further improve them, they represent multiple new avenues for directly addressing the colossal issue of sample bias in phylogeographic inference.
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Affiliation(s)
- Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Samuel Hong
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Verity Hill
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, F75012 Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, F75012 Paris, France
| | - Áine O’Toole
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - John T. McCrone
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andrew Rambaut
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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26
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Edoul G, Chia JE, Vidal N, Guichet E, Montavon C, Delaporte E, Mpoudi Ngole E, Ayouba A, Peeters M. High HIV burden and recent transmission chains in rural forest areas in southern Cameroon, where ancestors of HIV-1 have been identified in ape populations. INFECTION GENETICS AND EVOLUTION 2020; 84:104358. [PMID: 32439500 DOI: 10.1016/j.meegid.2020.104358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 11/18/2022]
Abstract
We studied HIV prevalence and genetic diversity in rural forest areas in Cameroon, where chimpanzee and gorilla populations infected with the ancestors of the different HIV-1 groups have been identified and transmitted to humans during the 20th century. A total of 2812 individuals were studied, 924 from south-central, 1116 from south-east and 772 from south-west Cameroon. Of 208 (7.4%) samples that were confirmed for HIV-1 infection all belong to HIV-1 group M. In all sites and in all age categories, HIV-1 prevalence was higher in women (160/1599 (10.0%)) as compared to men (48/1213 (4.0%)) with the highest prevalence in women aged between 25 and 34 years (>17%). For 188/208 (92.3%) HIV-1 positive individuals, a fragment of the pol gene was successfully amplified and sequenced. Phylogenetic analysis showed predominance of CRF02_AG (58%), a large diversity of subtypes (A, D, F2 and G), nine different CRFs and more than 12% URFs. Interestingly, 35/188 (18.6%) HIV-1 strains form 12 recent transmission chains. The majority of the clusters are composed of two (n = 8) or three (n = 3) sequences but one cluster included ten HIV-1 strains from women living in four different villages on a major road for logging concessions in the south-east (60 km distance). In the three regions of Cameroon where the ancestors of the four HIV-1 groups have been transmitted to humans, we observed a high HIV prevalence, especially in the southeast where HIV-1 M originated. Many factors allowing rapid establishment in the human population and subsequent rapid spread to urban areas of a new retrovirus or other pathogens of zoonotic origin are now present. Our study shows clearly that some rural areas should also be considered as hot-spots for HIV infection. Prevention efforts together with growing access to HIV diagnosis and antiretroviral treatment are urgently needed in these remote areas.
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Affiliation(s)
- Ginette Edoul
- Centre de Recherche sur les Maladies Emergentes et Reemergentes (CREMER), Virology Laboratory IMPM-IRD, IMPM, Yaoundé, Cameroon
| | - Julius Ebua Chia
- Centre de Recherche sur les Maladies Emergentes et Reemergentes (CREMER), Virology Laboratory IMPM-IRD, IMPM, Yaoundé, Cameroon
| | - Nicole Vidal
- TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM, Université de Montpellier, Montpellier, France
| | - Emilande Guichet
- Centre de Recherche sur les Maladies Emergentes et Reemergentes (CREMER), Virology Laboratory IMPM-IRD, IMPM, Yaoundé, Cameroon
| | - Celine Montavon
- TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM, Université de Montpellier, Montpellier, France
| | - Eric Delaporte
- TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM, Université de Montpellier, Montpellier, France
| | - Eitel Mpoudi Ngole
- Centre de Recherche sur les Maladies Emergentes et Reemergentes (CREMER), Virology Laboratory IMPM-IRD, IMPM, Yaoundé, Cameroon
| | - Ahidjo Ayouba
- TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM, Université de Montpellier, Montpellier, France
| | - Martine Peeters
- TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM, Université de Montpellier, Montpellier, France.
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Nduva GM, Hassan AS, Nazziwa J, Graham SM, Esbjörnsson J, Sanders EJ. HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya. Sci Rep 2020; 10:6775. [PMID: 32317722 PMCID: PMC7174422 DOI: 10.1038/s41598-020-63731-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/30/2020] [Indexed: 11/09/2022] Open
Abstract
HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005-2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.
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Affiliation(s)
- George M Nduva
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Amin S Hassan
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan M Graham
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Joakim Esbjörnsson
- Lund University, Lund, Sweden.
- The University of Oxford, Oxford, United Kingdom.
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The University of Oxford, Oxford, United Kingdom
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Gartner MJ, Roche M, Churchill MJ, Gorry PR, Flynn JK. Understanding the mechanisms driving the spread of subtype C HIV-1. EBioMedicine 2020; 53:102682. [PMID: 32114391 PMCID: PMC7047180 DOI: 10.1016/j.ebiom.2020.102682] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C (C-HIV) is the most prevalent form of HIV-1 globally, accounting for approximately 50% of infections worldwide. C-HIV is the predominant and near-exclusive subtype in the low resource regions of India and Southern Africa. Given the vast diversity of HIV-1 subtypes, it is curious as to why C-HIV constitutes such a large proportion of global infections. This enriched prevalence may be due to phenotypic differences between C-HIV isolates and other viral strains that permit enhanced transmission efficiency or, pathogenicity, or might due to the socio-demographics of the regions where C-HIV is endemic. Here, we compare the mechanisms of C-HIV pathogenesis to less prominent HIV-1 subtypes, including viral genetic and phenotypic characteristics, and host genetic variability, to understand whether evolutionary factors drove C-HIV to predominance.
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Affiliation(s)
- Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Melissa J Churchill
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; Department of Microbiology, Monash University, Melbourne, Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.
| | - Jacqueline K Flynn
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia; School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia.
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Matume ND, Tebit DM, Bessong PO. HIV-1 subtype C predicted co-receptor tropism in Africa: an individual sequence level meta-analysis. AIDS Res Ther 2020; 17:5. [PMID: 32033571 PMCID: PMC7006146 DOI: 10.1186/s12981-020-0263-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background Entry inhibitors, such as Maraviroc, hold promise as components of HIV treatment and/or pre-exposure prophylaxis in Africa. Maraviroc inhibits the interaction between HIV Envelope gp120 V3-loop and CCR5 coreceptor. HIV-1 subtype C (HIV-1-C) is predominant in Southern Africa and preferably uses CCR5 co-receptor. Therefore, a significant proportion of HIV-1-C CXCR4 utilizing viruses (X4) may compromise the effectiveness of Maraviroc. This analysis examined coreceptor preferences in early and chronic HIV-1-C infections across Africa. Methods African HIV-1-C Envelope gp120 V3-loop sequences sampled from 1988 to 2014 were retrieved from Los Alamos HIV Sequence Database. Sequences from early infections (< 186 days post infection) and chronic infections (> 186 days post infection) were analysed for predicted co-receptor preferences using Geno2Pheno [Coreceptor] 10% FPR, Phenoseq-C, and PSSMsinsi web tools. V3-loop diversity was determined, and viral subtype was confirmed by phylogenetic analysis. National treatment guidelines across Africa were reviewed for Maraviroc recommendation. Results Sequences from early (n = 6316) and chronic (n = 7338) HIV-1-C infected individuals from 10 and 15 African countries respectively were available for analyses. Overall, 518/6316 (8.2%; 95% CI 0.7–9.3) of early sequences were X4, with Ethiopia and Malawi having more than 10% each. For chronic infections, 8.3% (95% CI 2.4–16.2) sequences were X4 viruses, with Ethiopia, Tanzania, and Zimbabwe having more than 10% each. For sequences from early chronic infections (< 1 year post infection), the prevalence of X4 viruses was 8.5% (95% CI 2.6–11.2). In late chronic infections (≥ 5 years post infection), X4 viruses were observed in 36% (95% CI − 16.3 to 49.9), with two countries having relatively high X4 viruses: South Africa (43%) and Malawi (24%). The V3-loop amino acid sequence were more variable in X4 viruses in chronic infections compared to acute infections, with South Africa, Ethiopia and Zimbabwe showing the highest levels of V3-loop diversity. All sequences were phylogenetically confirmed as HIV-1-C and clustered according to their co-receptor tropism. In Africa, Maraviroc is registered only in South Africa and Uganda. Conclusions Our analyses illustrate that X4 viruses are present in significantly similar proportions in early and early chronic HIV-1 subtype C infected individuals across Africa. In contrast, in late chronic infections, X4 viruses increase 3–5 folds. We can draw two inferences from our observations: (1) to enhance the utility of Maraviroc in chronic HIV subtype C infections in Africa, prior virus co-receptor determination is needed; (2) on the flip side, research on the efficacy of CXCR4 antagonists for HIV-1-C infections is encouraged. Currently, the use of Maraviroc is very limited in Africa.
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The Impact of Human Mobility on Regional and Global Efforts to Control HIV Transmission. Viruses 2020; 12:v12010067. [PMID: 31935811 PMCID: PMC7019949 DOI: 10.3390/v12010067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
HIV prevention and control methods are implemented on different scales to reduce the spread of the virus amongst populations. However, despite such efforts, HIV continues to persist in populations with a global incidence rate of 1.8 million in 2017 alone. The introduction of new infections into susceptible regional populations promotes the spread of HIV, indicating a crucial need to study the impact of migration and mobility on regional and global efforts to prevent HIV transmission. Here we reviewed studies that assess the impact of human mobility on HIV transmission and spread. We found an important role for both travel and migration in driving the spread of HIV across regional and national borders. Combined, our results indicate that even in the presence of control and preventive efforts, if migration and travel are occurring, public health efforts will need to remain persistent to ensure that new infections do not grow into outbreaks.
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