1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Kwon EH, Musema GMA, Boelter J, Townsend S, Tshala-Katumbay D, Kayembe PK, West J, Wood C. HIV-1 subtypes and drug resistance mutations among female sex workers varied in different cities and regions of the Democratic Republic of Congo. PLoS One 2020; 15:e0228670. [PMID: 32045455 PMCID: PMC7012409 DOI: 10.1371/journal.pone.0228670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/20/2020] [Indexed: 01/16/2023] Open
Abstract
Background Complex mosaic structures of HIV-1 were found in the Democratic Republic of Congo (DRC). Currently, there is limited information on the circulating HIV-1 strains, the distribution of these strains and antiretroviral (ART) resistant viruses in different regions of the country, and the HIV-1 strains harbored by the high-risk groups like female sex workers (FSW) reported to be the source of recombinant and ART resistant viruses. Methods Dried Blood Spots (DBS), collected from 325 infected FSWs in ten cities from 2012 DRC HIV/STI Integrated Biological and Behavioral Surveillance Survey, were tested for HIV-1 genotypes and antiretroviral resistance mutations. Regional segregation of HIV-1 clades was detected using phylogenetics. The significance for differences in HIV-1 subtype and drug resistance mutations were evaluated using Chi-square tests. Results There were 145 (env) and 93 (pol) sequences analyzed. Based on env sequences, the predominant subtype was A1 (44%), and recombinants as defined pol sequences comprised 35% of the total sample. Paired sequences of pol and env from DRC FSW revealed mosaic recombinant in 54% of the sequences. Distinct geographic distributions of different HIV-1 subtypes and recombinants were observed. Subtype A1 was prevalent (40%) in Goma located in the East and significantly higher than in Mbuji-Mayi (p<0.05) in the South-central region, or in Lubumbashi in the South. Antiretroviral resistance was detected in 21.5% of 93 pol sequences analyzed, with the M184I/V and K103N mutations that confer high-level resistance to NRTI and NNRTI, respectively, being the most frequent mutations. However, the K103N mutant viruses were found only in the East. Conclusion HIV-1 variants found in DRC FSW reflect those reported to circulate in the general population from the corresponding geographical locations. HIV-1 mosaic genetics were readily detected in FSW. Importantly, ART resistance mutations to NNRTI and NRTI were common in the DRC sex workers.
Collapse
Affiliation(s)
- Eun Hee Kwon
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | | | - Jessica Boelter
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Sydney Townsend
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Désiré Tshala-Katumbay
- Department of Neurology, School of Medicine and School of Public Health, Oregon Health & Science University, Portland, Oregon, United States of America
- Department of Neurology, University of Kinshasa, Kinshasa, Democratic Republic of Congo
- Institut National de Recherches Biomédicales, Kinshasa, Democratic Republic of Congo
| | - Patrick K. Kayembe
- School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - John West
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Charles Wood
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
| |
Collapse
|
3
|
Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA. A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution. Syst Biol 2018; 66:299-319. [PMID: 27798403 DOI: 10.1093/sysbio/syw093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 10/10/2016] [Indexed: 12/26/2022] Open
Abstract
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes. Here, we relax one of the major restrictions of standard Brownian diffusion by incorporating a nontrivial estimable mean into the process. We introduce a relaxed directional random walk (RDRW) model for the evolution of multivariate continuously varying traits along a phylogenetic tree. Notably, the RDRW model accommodates branch-specific variation of directional trends while preserving model identifiability. Furthermore, our development of a computationally efficient dynamic programming approach to compute the data likelihood enables scaling of our method to large data sets frequently encountered in phylogenetic comparative studies and viral evolution. We implement the RDRW model in a Bayesian inference framework to simultaneously reconstruct the evolutionary histories of molecular sequence data and associated multivariate continuous trait data, and provide tools to visualize evolutionary reconstructions. We demonstrate the performance of our model on synthetic data, and we illustrate its utility in two viral examples. First, we examine the spatiotemporal spread of HIV-1 in central Africa and show that the RDRW model uncovers a clearer, more detailed picture of the dynamics of viral dispersal than standard Brownian diffusion. Second, we study antigenic evolution in the context of HIV-1 resistance to three broadly neutralizing antibodies. Our analysis reveals evidence of a continuous drift at the HIV-1 population level towards enhanced resistance to neutralization by the VRC01 monoclonal antibody over the course of the epidemic. [Brownian Motion; Diffusion Processes; Phylodynamics; Phylogenetics; Phylogeography; Trait Evolution.].
Collapse
Affiliation(s)
- Mandev S Gill
- Department of Statistics, Columbia University, New York, NY 10027, USA
| | - Lam Si Tung Ho
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium
| | - Marc A Suchard
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Universtiy of California, Los Angeles, CA, USA
| |
Collapse
|
4
|
Niama FR, Vidal N, Diop-Ndiaye H, Nguimbi E, Ahombo G, Diakabana P, Bayonne Kombo ÉS, Mayengue PI, Kobawila SC, Parra HJ, Toure-Kane C. HIV-1 genetic diversity and primary drug resistance mutations before large-scale access to antiretroviral therapy, Republic of Congo. BMC Res Notes 2017; 10:243. [PMID: 28679441 PMCID: PMC5498887 DOI: 10.1186/s13104-017-2550-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/19/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In this work, we investigated the genetic diversity of HIV-1 and the presence of mutations conferring antiretroviral drug resistance in 50 drug-naïve infected persons in the Republic of Congo (RoC). Samples were obtained before large-scale access to HAART in 2002 and 2004. METHODS To assess the HIV-1 genetic recombination, the sequencing of the pol gene encoding a protease and partial reverse transcriptase was performed and analyzed with updated references, including newly characterized CRFs. The assessment of drug resistance was conducted according to the WHO protocol. RESULTS Among the 50 samples analyzed for the pol gene, 50% were classified as intersubtype recombinants, charring complex structures inside the pol fragment. Five samples could not be classified (noted U). The most prevalent subtypes were G with 10 isolates and D with 11 isolates. One isolate of A, J, H, CRF05, CRF18 and CRF37 were also found. Two samples (4%) harboring the mutations M230L and Y181C associated with the TAMs M41L and T215Y, respectively, were found. CONCLUSION This first study in the RoC, based on WHO classification, shows that the threshold of transmitted drug resistance before large-scale access to antiretroviral therapy is 4%.
Collapse
Affiliation(s)
- Fabien Roch Niama
- Laboratoire National de Santé Publique, Unité de Biologie Moléculaire, BP 120 Avenue du Général De Gaule, Brazzaville, Republic of Congo. .,Laboratoire de Bactériologie et Virologie, Hôpital Le Dantec, Dakar, Sénégal. .,Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of Congo.
| | - Nicole Vidal
- IRD_UMI 233 TransVIHMI, Délégation Régionale Occitanie 911 avenue Agropolis, Montpellier, France
| | | | - Etienne Nguimbi
- Laboratoire National de Santé Publique, Unité de Biologie Moléculaire, BP 120 Avenue du Général De Gaule, Brazzaville, Republic of Congo
| | - Gabriel Ahombo
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of Congo
| | - Philippe Diakabana
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of Congo
| | | | - Pembe Issamou Mayengue
- Laboratoire National de Santé Publique, Unité de Biologie Moléculaire, BP 120 Avenue du Général De Gaule, Brazzaville, Republic of Congo.,Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of Congo
| | - Simon-Charles Kobawila
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of Congo
| | - Henri Joseph Parra
- Laboratoire National de Santé Publique, Unité de Biologie Moléculaire, BP 120 Avenue du Général De Gaule, Brazzaville, Republic of Congo
| | - Coumba Toure-Kane
- Laboratoire de Bactériologie et Virologie, Hôpital Le Dantec, Dakar, Sénégal
| |
Collapse
|
5
|
Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, Prosperi MCF. Phylodynamic applications in 21 st century global infectious disease research. Glob Health Res Policy 2017; 2:13. [PMID: 29202081 PMCID: PMC5683535 DOI: 10.1186/s41256-017-0034-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/31/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21st century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics. RESULTS The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework. These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus. CONCLUSIONS Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.
Collapse
Affiliation(s)
- Brittany D Rife
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Carla Mavian
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Xinguang Chen
- Department of Epidemiology, University of Florida, Gainesville, FL USA
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
- Unit of Clinical Pathology and Microbiology, University Campus Biomedico of Rome, Rome, Italy
| | - Marco Salemi
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Jae Min
- Department of Epidemiology, University of Florida, Gainesville, FL USA
| | | |
Collapse
|
6
|
Sharma AL, Singh TR, Devi KR, Singh LS. Molecular epidemiology of HIV-1 among the HIV infected people of Manipur, Northeastern India: Emergence of unique recombinant forms. J Med Virol 2016; 89:989-999. [PMID: 27869320 DOI: 10.1002/jmv.24738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/12/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022]
Abstract
According to the Joint National Programme on HIV/AIDS (UNAIDS), the northeastern region of India has the highest HIV prevalence in the country. This study was conducted to determine the current HIV-1 molecular epidemiology of Manipur, a state in northeast India. Blood samples from HIV-1 seropositive subjects were collected between June 2011 and February 2014. The partial regions of HIV-1 genes; pol and tat-vpu-env were independently amplified, sequenced, analyzed, and genotyped. Based on all sequences generated from 110 samples using pol and/or tat-vpu-env gene, the overall HIV-1 genotypes distribution of Manipur was as follows: 65.45% (72/110) subtype C, 32.73% (36/110) unique recombinant forms (URFs), and 1.82% (2/110) subtype B. The distribution of HIV-1 genotypes among the risk groups was: heterosexual: 58.33% (35/60) subtype C, 38.33% (23/60) URFs, and 3.34% (2/60) subtype B; intravenous drug users (IDUs): 85.36% (35/41) subtype C, 9.76% (4/41) URFs, and 4.88% (2/41) subtype B; mother to child (MTC): 50% (3/6) URFs and 50% (3/6) subtype C and blood transfusion: 100% (3/3) subtype C. The findings for the first time revealed the emergence of URFs of HIV-1 in Manipur which is predominant among the sexual and MTC risk groups as compared to IDUs. Taking together, this study illustrated that Manipur is the "recombinant hotspot of HIV" of India. The results will provide the clinical importance for continuous monitoring of HIV-infections in order to design appropriate prevention measures to limit the spread of new HIV infections.
Collapse
Affiliation(s)
| | - Thiyam Ramsing Singh
- Cancer and Molecular Biology Division, Department of Biotechnology, Manipur University, Imphal, Manipur, India
| | - Khuraijam Ranjana Devi
- Department of Microbiology, Regional Institute of Medical Sciences, Imphal, Manipur, India
| | - Lisam Shanjukumar Singh
- Cancer and Molecular Biology Division, Department of Biotechnology, Manipur University, Imphal, Manipur, India
| |
Collapse
|
7
|
The sexually driven epidemic in youths in China's southwestern border region was caused by dynamic emerging multiple recombinant HIV-1 strains. Sci Rep 2015; 5:11323. [PMID: 26133091 PMCID: PMC4489098 DOI: 10.1038/srep11323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/01/2015] [Indexed: 11/25/2022] Open
Abstract
Dehong prefecture, Yunnan province on China’s southwestern border was the gateway of the country’s AIDS epidemic. Studies on HIV-1 molecular epidemiology will provide key information on virus transmission dynamics and help to inform HIV prevention strategies. HIV-1 infected youths (age 16–25 years) diagnosed in the continuous 3 months in 2009 to 2012 were enrolled. By means of phylogenetic and statistical analyses, It was showed that two thirds (133/205) of youths in Dehong, of which 74.1% were infected sexually, were infected by uncharacterized recombinant HIV-1 strains. Among them about 59.4% (79/131) were unique recombinant forms (URFs) and 40.6% (54/131) formed 11 transmission clusters, termed potential circulating recombinant forms (pCRFs). The emergence of recombinants was statistically significant related with people of low education, residents outside the capital city of Dehong and being Myanmar residents. It was the first report with ongoing HIV-1 recombinant strains in a sexually driven epidemic area in China. Great efforts should be put on reducing multiple risk exposures behavior in local young people, containing the spread of pCRFs to other regions, and preventing the URFs from evolving into future CRFs. Collaborative prevention across border is needed to better control the local AIDS epidemic.
Collapse
|
8
|
Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science 2014; 346:56-61. [PMID: 25278604 PMCID: PMC4254776 DOI: 10.1126/science.1256739] [Citation(s) in RCA: 368] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.
Collapse
Affiliation(s)
- Nuno R Faria
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK. Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Marc A Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-1766, USA. Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095-1766, USA
| | - Guy Baele
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa J Ward
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Andrew J Tatem
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Department of Geography and Environment, University of Southampton, Highfield, Southampton, UK
| | - João D Sousa
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium. Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | | | - Jacques Pépin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, CHUS, 3001, 12ème Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| | - Martine Peeters
- Laboratoire Retrovirus, UMI233, Institut de Recherche pour le Développement and University of Montpellier, 911 Avenue Agropolis, BP5045, 34032 Montpellier, France
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| | - Philippe Lemey
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
| |
Collapse
|
9
|
Faria NR, Suchard MA, Abecasis A, Sousa JD, Ndembi N, Bonfim I, Camacho RJ, Vandamme AM, Lemey P. Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2012; 12:453-60. [PMID: 21565285 PMCID: PMC4677783 DOI: 10.1016/j.meegid.2011.04.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 12/18/2022]
Abstract
Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XX century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to investigate the spatiotemporal patterns of the CRF02_AG clade. By explicitly integrating prevalence counts and genetic population size estimates we date the epidemic emergence of CRF02_AG at 1973.1 (1972.1, 1975.3, 95% CI). To infer the phylogeographic signature of this clade at a regional scale, we analyze pol and env time-stamped sequence data from 10 countries using a Bayesian phylogeographic approach based on an asymmetric discretized diffusion model. Our data confirms a spatial origin of CRF02_AG in the Democratic Republic of Congo (DRC) and suggests that viral dissemination to Cameroon occurred at an early stage of the evolutionary history of CRF02_AG. We find considerable support for epidemiological linkage between neighbour countries. Compilation of ethnographic data suggested that well-supported viral migration did not reflect sustained human migratory flows. Finally, using sequence data from 15 locations in Cameroon, we use relaxed random walk models to explore the spatiotemporal dynamics of CRF02_AG at a finer geographical detail. Phylogeographic dispersal in continuous space reveals that at least two distinct CRF02_AG lineages are circulating in overlapping regions that are evolving at different evolutionary and diffusion rates. In conclusion, by combining molecular and epidemiological data, our results provide a time scale for CRF02_AG, early 70s, place its spatial root in the DRC within the putative root of group-M diversity and propose a scenario of chance-exportation events for the spatiotemporal patterns of a successful HIV-1 lineage both at a regional and country-scale.
Collapse
Affiliation(s)
- Nuno R Faria
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Kousiappa I, Achilleos C, Hezka J, Lazarou Y, Othonos K, Demetriades I, Kostrikis LG. Molecular characterization of HIV type 1 strains from newly diagnosed patients in Cyprus (2007-2009) recovers multiple clades including unique recombinant strains and lack of transmitted drug resistance. AIDS Res Hum Retroviruses 2011; 27:1183-99. [PMID: 21453134 DOI: 10.1089/aid.2011.0060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
HIV-1 evolution generates substantial genetic diversity among isolates, the majority of which are represented in areas where multiple strains cocirculate. A heterogeneous genetic HIV-1 pool has been found in Cyprus, directing us to determine the dynamics of the local HIV-1 infection by characterizing strains isolated from 74 subjects during 2007-2009, representing 88% of the known-living HIV-1-infected population, of whom 53 are newly diagnosed therapy-naive patients and 21 are chronic patients, according to the European HIV Resistance guidelines. Near full-length genome sequences were amplified by RT-nested PCR using diluted RNA from all HIV-1 seropositives and sequenced using a newly designed assay. Resistant mutations were not found among the population of the newly diagnosed therapy-naive patients either to protease, reverse transcriptase, or integrase inhibitors. Phylogenetic analyses indicated subtype B as the main subtype (48.6%), followed by subtype A (18.9%), subtype C (10.8%), CRF02_AG (8.1%), CRF11_cpx (2.7%), and (sub)subtype F1 and CRF37_cpx (1.4% each). Six HIV-1 isolates (8.1%) were not classified in any pure (sub)subtype or circulating recombinant form (CRF). Complete phylogenetic and bootscanning analyses revealed that each isolate had a new, unique recombinant pattern and is distinct from all other CRFs or unique recombinant forms (URFs) reported so far. Two of the six isolates have the same mosaic pattern. Analogous to results of the earlier epidemiological studies, this study expands on the HIV-1 sequence database and reveals the high degree of diversity of HIV-1 infection in Cyprus.
Collapse
Affiliation(s)
- Ioanna Kousiappa
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Charis Achilleos
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Johana Hezka
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Yiota Lazarou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Katerina Othonos
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | | |
Collapse
|
11
|
Djoko CF, Rimoin AW, Vidal N, Tamoufe U, Wolfe ND, Butel C, LeBreton M, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Pike BL, Fair JN, Mbacham WF, Saylors KE, Mpoudi-Ngole E, Delaporte E, Grillo M, Peeters M. High HIV type 1 group M pol diversity and low rate of antiretroviral resistance mutations among the uniformed services in Kinshasa, Democratic Republic of the Congo. AIDS Res Hum Retroviruses 2011; 27:323-9. [PMID: 20954909 DOI: 10.1089/aid.2010.0201] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For the first time the genetic diversity among the uniformed personnel in Kinshasa, the capital city of the Democratic Republic of Congo (DRC), a country that has experienced military conflicts since 1998 and in which the global HIV-1/M pandemic started, has now been documented. A total of 94 HIV-1-positive samples, collected in 2007 in Kinshasa garrison settings from informed consenting volunteers, were genetically characterized in the pol region (protease and RT). An extensive diversity was observed, with 51% of the strains corresponding to six pure subtypes (A 23%, C 13.8%, D, G, H, J, and untypable), 15% corresponding to nine different CRFs (01, 02, 11, 13, 25, 26, 37, 43, and 45), and 34% being unique recombinants with one-third being complex mosaic viruses involving three or more different subtypes/CRFs. Only one strain harbored a single mutation, I54V, associated with drug resistance to protease inhibitors. Due to their high mobility and potential risk behavior, HIV infections in military personnel can lead to an even more complex epidemic in the DRC and to a possible increase of subtype C.
Collapse
Affiliation(s)
- Cyrille F. Djoko
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
- Biotechnology Center and Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Nicole Vidal
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
| | - Ubald Tamoufe
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Nathan D. Wolfe
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
- Stanford University, Program in Human Biology, Stanford, California
| | - Christelle Butel
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
| | - Matthew LeBreton
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Felix M. Tshala
- Military Health Services, Ministry of Defence, Kinshasa, Democratic Republic of the Congo
| | - Patrick K. Kayembe
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Jean Jacques Muyembe
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Samuel Edidi-Basepeo
- National AIDS Control Program Laboratory, Kinshasa, Democratic Republic of the Congo
| | - Brian L. Pike
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Joseph N. Fair
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Wilfred F. Mbacham
- Biotechnology Center and Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Karen E. Saylors
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | | | - Eric Delaporte
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
- Department of Infectious Diseases, CHU, Montpellier, France
| | - Michael Grillo
- Department of Defense HIV AIDS Prevention Program (DHAPP), San Diego, California
| | - Martine Peeters
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
| |
Collapse
|
12
|
Yamaguchi J, Vallari A, Ngansop C, Makamche F, Ndembi N, Mbanya D, Kaptué L, Gürtler LG, Devare SG, Brennan CA. Near full-length sequence of HIV type 1 subtype J strain 04CMU11421 from Cameroon. AIDS Res Hum Retroviruses 2010; 26:693-7. [PMID: 20518650 DOI: 10.1089/aid.2009.0305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although Cameroon, in west central Africa, has a relatively low HIV prevalence of 5-6%, all HIV-1 groups (M, N, O, and P), nearly all HIV-1 group M subtypes, and numerous intersubtype recombinant forms have been identified in Cameroon. In this report, we describe the near full-length sequence of 04CMU11421, an HIV-1 group M subtype J strain collected in Cameroon in 2004. Phylogenetic analysis of the genome sequence shows high bootstrap support with three subtype J reference sequences in the HIV Sequence database. Therefore, 04CMU11421 represents a fourth pure subtype J isolate and the first reported in Cameroon.
Collapse
Affiliation(s)
| | | | | | | | - Nicaise Ndembi
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- Université des Montagnes, Bangangté, Cameroon
| | | | - Lazare Kaptué
- Université de Yaoundé, Yaoundé, Cameroon
- Université des Montagnes, Bangangté, Cameroon
| | | | | | | |
Collapse
|
13
|
Kousiappa I, Van De Vijver DA, Kostrikis LG. Near full-length genetic analysis of HIV sequences derived from Cyprus: evidence of a highly polyphyletic and evolving infection. AIDS Res Hum Retroviruses 2009; 25:727-40. [PMID: 19619035 DOI: 10.1089/aid.2008.0239] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular epidemiology of HIV-1 infection was previously studied in Cyprus but the degree of HIV-1 diversity has remained indefinable. The main objective of the present study is to examine HIV-1 strains isolated from 77 HIV-1-infected individuals representing 38% of the known infected population in Cyprus in the period 1986 to 2006. DNA of the near full-length genome encoding gag, pol, vif, vpr, vpu, tat, rev, env, and 5'-end of nef was amplified by nested PCR/RT-PCR from all HIV-1 seropositives and sequenced using a newly designed assay. Detailed phylogenetic and bootscanning analyses were performed to determine phylogenetic associations and subtype assignments. Phylogenetic analyses of the obtained viral sequences indicated that subtype B was the dominant subtype (61%), followed by subtype A (23.3%), subtype C (5.2%), CRF02_AG (3.9%), and subtype D, CRF01_AE, and CRF04_cpx (1.3% each). Two HIV-1 isolates (2.6%), originating from the Democratic Republic of Congo (DRC), were not classified in any pure (sub)subtype or circulating recombinant form (CRF). Complete phylogenetic and bootscanning analyses revealed that one of these isolates had a new, unique recombinant pattern, comprising segments of subtypes D and G, and is distinct from any other CRFs or URFs reported so far. Detailed analyses of the sequence of the second isolate, which could not be classified, reveal that it is close to subtype K reference sequences but clusters near the root of the clade. At least two epidemiologically unrelated HIV-1 seropositives with an HIV-1 variant similar to this isolate are required to designate this variant as a novel HIV-1 subtype or subsubtype of subtype K. Analogous to results of the earlier epidemiological studies, these data exhibit the extensive heterogeneity of HIV-1 infection in Cyprus, which is being fueled by a continuous entry of new strains from other countries, creating an evolving and polyphyletic infection.
Collapse
Affiliation(s)
- Ioanna Kousiappa
- Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - David A.M.C. Van De Vijver
- Department of Virology, Erasmus MC, University Medical Centre Rotterdam, 3000 CA Rotterdam, The Netherlands
| | | |
Collapse
|
14
|
Marechal V, Jauvin V, Selekon B, Leal J, Pelembi P, Fikouma V, Gabrie P, Heredeibona LS, Goumba C, Serdouma E, Ayouba A, Fleury H. Increasing HIV type 1 polymorphic diversity but no resistance to antiretroviral drugs in untreated patients from Central African Republic: a 2005 study. AIDS Res Hum Retroviruses 2006; 22:1036-44. [PMID: 17067275 DOI: 10.1089/aid.2006.22.1036] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
As the HIV-1 pandemic becomes increasingly complex and as new countries acceed to antiretroviral drugs, the molecular characterization of HIV-1 strains circulating has important implications for vaccine research and for the efficacy of treatments. To follow the evolution of HIV-1 diversity in African countries, we have carried out a molecular analysis of HIV-1 strains collected from 150 HIV-1-positive pregnant women recruited in Bangui, Central African Republic (CAR). We have sequenced reverse transcriptase (RT) and protease (PROT) genes to (1) characterize the subtypes and CRFs, (2) describe the polymorphism of RT and PROT, particularly at the positions of drug resistance mutations in subtype B, and (3) observe potential drug resistance mutations and evaluate the prevalence of isolates bearing such mutations in this untreated population. The results showed that there is a very high and increasing diversity of HIV-1 strains circulating in CAR; out of 117 samples sequenced, we have observed 45 CRF11_cpx, 22 subtypes A1, 13 subtypes G, 7 subtypes CRF01_AE, 3 subtypes B, 3 subtypes CRF02_AG, 2 of each subtype F2 and CRF09_cpx, and one of each subtype D, J, C, H, CRF06_cpx, CRF13_cpx, and CRF19_cpx; the remaining 13 strains showed discordant genomic results suggesting multiple recombinations leading to mosaic viruses. The polymorphism of RT and PROT was high compared to subtype B, particularly at some positions that have been involved in antiretroviral resistance in subtype B, but we could not observe any major resistance mutation in this sample of untreated patients. The prevalence of drug resistance mutations in this population was therefore clearly under the WHO 5% threshold.
Collapse
|
15
|
Niama FR, Toure-Kane C, Vidal N, Obengui P, Bikandou B, Ndoundou Nkodia MY, Montavon C, Diop-Ndiaye H, Mombouli JV, Mokondzimobe E, Diallo AG, Delaporte E, Parra HJ, Peeters M, Mboup S. HIV-1 subtypes and recombinants in the Republic of Congo. INFECTION GENETICS AND EVOLUTION 2006; 6:337-43. [PMID: 16473564 DOI: 10.1016/j.meegid.2005.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 11/15/2005] [Accepted: 12/29/2005] [Indexed: 10/25/2022]
Abstract
To document the actual genetic diversity of HIV-1 strains in the Republic of Congo, 114 HIV-1 positives persons were sampled in 2003 and 2004 after their informed consent. They were attending the teaching hospital, the reference health center in Makelekele, Brazzaville and the regional hospital centers in Pointe-Noire, Gamboma and Ouesso. A total of 104 samples were genetically characterized by direct sequencing of the p24 gag region and 80 were also subtyped in the V3-V5 env region. The genetic subtype distribution of the Congolese strains showed the predominance of subtype A (36.5% and 32.5% in gag and env, respectively) and G (30.8% and 21.25%), whereas subtype D strains represented 12.5% and 15%. Subtypes C, F, H, J, K and the CRFs-01, -02, -05 -06, and also the recently characterized CRF18 were seen at lower rates. Finally, 4.8% (gag) and 6.25% (env) of the strains could not be classified. Moreover, a high intra-subtype diversity was observed in our study. Among 70 strains which have been characterized in the two genomic regions, 14 (20%) appeared to be unique recombinants. These data show a high genetic variability in the Republic of Congo, where all the subtypes have been documented together with certain subsubtypes and several CRFs.
Collapse
Affiliation(s)
- Fabien Roch Niama
- Laboratoire de Bactériologie et Virologie, Hôpital Le Dantec, Dakar, Senegal
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Vidal N, Mulanga C, Bazepeo SE, Lepira F, Delaporte E, Peeters M. Identification and molecular characterization of subsubtype A4 in central Africa. AIDS Res Hum Retroviruses 2006; 22:182-7. [PMID: 16478401 DOI: 10.1089/aid.2006.22.182] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic analysis on partial env sequences of HIV-1-positive samples obtained from sentinel population groups in HIV serosurveillance studies in 1997 and 2002 in the Democratic Republic of Congo (DRC) revealed a high genetic diversity in the number of cocirculating subtypes/CRFs as well as intrasubtype diversity. A cluster of three strains that formed a distinct and well-separated group within the subtype A radiation was observed. To determine a more precise structure of these viruses, the full-length genomes were sequenced. Phylogenetic tree and bootscan analysis showed that all three newly characterized viruses formed a new nonrecombinant lineage that was more closely related to subtype A. The SUDI (Subtype Distance) program showed that the distances of the newly derived HIV-1 sequences to subtype A references fell in the range of distances previously characterized for subsubtypes. According to current nomenclature rules, we have thus designated this new lineage as subsubtype A4. Analysis of viral sequences from other African countries suggests that the A4 strains seem restricted to DRC where they already circulated at the onset of the HIV/AIDS epidemic.
Collapse
Affiliation(s)
- N Vidal
- UMR145, Laboratoire Retrovirus, IRD, BP 64501, 34394 Montpellier Cedex 1, France
| | | | | | | | | | | |
Collapse
|
17
|
Vidal N, Mulanga C, Bazepeo SE, Mwamba JK, Tshimpaka J, Kashi M, Mama N, Valéa D, Delaporte E, Lepira F, Peeters M. HIV type 1 pol gene diversity and antiretroviral drug resistance mutations in the Democratic Republic of Congo (DRC). AIDS Res Hum Retroviruses 2006; 22:202-6. [PMID: 16478404 DOI: 10.1089/aid.2006.22.202] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To study recombination and the natural polymorphism in pol of HIV-1 strains in the Democratic Republic of Congo (DRC) we sequenced the protease and RT genes for 70 HIV-1 strains previously characterized in the env V3-V5 region from a sentinel surveillance study in 2002. For 41 of the 70 (58.6%) strains, the same subtype/ CRF designations were observed in pol and env. Twenty-three (32.9%) of 70 pol sequences were complex recombinants involving two to five subtypes as well as fragments that could not be classified into any of the known subtypes. All subtypes were involved in recombination events. Unclassified (U) and env subtype H strains were very likely to be recombinant strains. Overall, many minor mutations were identified in the protease sequences. Although at the time of our study ARV use was not yet widespread in DRC, three strains were identified with one major mutation associated with drug resistance: L90M and M46L in protease and K103N in RT.
Collapse
Affiliation(s)
- N Vidal
- UMR145, Laboratoire Retrovirus, IRD, BP 64501, 34394 Montpellier Cedex 1, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Kijak GH, McCutchan FE. HIV diversity, molecular epidemiology, and the role of recombination. Curr Infect Dis Rep 2005; 7:480-8. [PMID: 16225787 DOI: 10.1007/s11908-005-0051-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The magnitude of the HIV pandemic and its extensive genetic variation may earn it a unique place among infectious agents. A high mutation rate and a rampant recombination are driving HIV's evolution. Nine subtypes and a variety of recombinant forms of HIV now exist. The source of recombinant forms is the multiple infection of target cells, which becomes highly significant when individuals become infected with two or more divergent strains. In the current paper, we re-examine the role of dual infection and recombination in the generation of HIV-1 diversity, both in individuals and on a global scale. The current molecular epidemiology of HIV-1 is reviewed, emphasizing the latest reports from regional epidemics.
Collapse
Affiliation(s)
- Gustavo H Kijak
- US Military HIV Research Program, Henry M. Jackson Foundation, 1600 East Gude Drive, Rockville, MD 20850, USA.
| | | |
Collapse
|