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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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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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Maksimenko LV, Totmenin AV, Gashnikova MP, Astakhova EM, Skudarnov SE, Ostapova TS, Yaschenko SV, Meshkov IO, Bocharov EF, Maksyutov RА, Gashnikova NM. Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9057541. [PMID: 32964045 PMCID: PMC7501552 DOI: 10.1155/2020/9057541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/28/2019] [Indexed: 12/31/2022]
Abstract
More than a quarter of HIV-infected individuals registered in Russia live in Siberia. Unlike Central Russia where HIV-1 subtype A6 is predominant, in most Siberian regions since 2012, a new HIV-1 CRF63_02A1 genetic variant has spread, with the share of this variant attaining 75-85% among newly identified HIV cases. Krasnoyarsk Krai is considered to be a high-risk territory according to morbidity rate and HIV infection incidence among the population. The current paper aims to study the molecular epidemiologic characteristics of HIV-1 spreading in Krasnoyarsk Krai. Phylogenetic and recombination analyses of pol (PR-RT, IN) and env regions of the virus were used for genotyping 159 HIV-1 isolated in Krasnoyarsk Krai. 57.2% of the isolates belonged to subtype A (A6) specific to Russia, 12.6% to CRF63_02A1, and 0.6% to CRF02_AGСА, and in 29.6% HIV-1 URFs were detected, including URF63/А (23.9%), URFА/В (4.4%), and URF02/А (1.3%). In 6 of 7, HIV-1 URFА/В identical recombination model was detected; the origin of 38 URF63/А was proven to be the result of individual recombination events. Since 2015, a share of the population with newly diagnosed HIV who were infected with HIV-1 URF reached an exceptionally high rate of 38.6%. As distinct from adjacent Siberian regions, the HIV-1 CRF63_02A1 prevalence rate in Krasnoyarsk Krai is within 16%; however, the increased contribution of new HIV-1 into the regional epidemic development was observed due to the recombination of viruses of subtypes А, В, and CRF63_02A1. The difference between the described molecular epidemiologic picture in Krasnoyarsk Krai and in adjacent areas is likely caused by differences in predominant routes of HIV transmission and by more recent HIV-1 CRF63_02A1 transmission in the PWID group, which had a high prevalence of HIV-1 subtype A by the time of the new virus transmission, resulting in increased possibility of coinfection with various HIV-1 genetic variants.
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Affiliation(s)
- Lada V. Maksimenko
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Aleksey V. Totmenin
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Mariya P. Gashnikova
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | | | - Sergey E. Skudarnov
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Tatyana S. Ostapova
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Svetlana V. Yaschenko
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Ivan O. Meshkov
- Novosibirsk Tuberculosis Research Institute, Novosibirsk 630040, Russia
| | - Evgeniy F. Bocharov
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Rinat А. Maksyutov
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
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Lunar MM, Mlakar J, Zorec TM, Poljak M. HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing. Viruses 2020; 12:v12010063. [PMID: 31947872 PMCID: PMC7019782 DOI: 10.3390/v12010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 11/30/2022] Open
Abstract
Surveillance of HIV circulating recombinant forms (CRFs) is important because HIV diversity can affect various aspects of HIV infection from prevention to diagnosis and patient management. A comprehensive collection of pol sequences obtained from individuals diagnosed with HIV-1 from 2000 to 2016 in Slovenia was subtyped to identify possible unique recombinant forms (URFs). Selected samples were subjected to near full-length genome (NFLG) sequencing and detailed recombination analyses. Discordant subtyping results were observed for 68/387 (17.6%) sequences and 20 sequences were identified as the most probable URFs and selected for NFLG characterization. Further, 11 NFLGs and two sequences of >7000 base pairs were obtained. Seven sequences were identified as “pure” subtypes or already characterized CRFs: subtype B (n = 5), sub-subtype A6 (n = 1), and CRF01_AE (n = 1). The remaining six sequences were determined to be URFs; four displayed a single recombination event and two exhibited a complex recombination pattern involving several subtypes or CRFs. Finally, three HIV strains were recognized as having epidemic potential and could be further characterized as new CRFs. Our study shows that the identification of new CRFs is possible, even in countries where HIV diversity is considered limited, emphasizing the importance of the surveillance of HIV recombinant forms.
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Bavaro DF, Di Carlo D, Rossetti B, Bruzzone B, Vicenti I, Pontali E, Zoncada A, Lombardi F, Di Giambenedetto S, Borghi V, Pecorari M, Milini P, Meraviglia P, Monno L, Saracino A. Pretreatment HIV drug resistance and treatment failure in non-Italian HIV-1-infected patients enrolled in ARCA. Antivir Ther 2020; 25:61-71. [PMID: 32118584 DOI: 10.3851/imp3349] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND An increase in pretreatment drug resistance (PDR) to first-line antiretroviral therapy (ART) in low-income countries has been recently described. Herein we analyse the prevalence of PDR and risk of virological failure (VF) over time among migrants to Italy enrolled in ARCA. METHODS HIV-1 sequences from ART-naive patients of non-Italian nationality were retrieved from ARCA database from 1998 to 2017. PDR was defined by at least one mutation from the reference 2009 WHO surveillance list. RESULTS Protease/reverse transcriptase sequences from 1,155 patients, mainly migrants from sub-Saharan Africa (SSA; 42%), followed by Latin America (LA; 25%) and Western countries (WE; 21%), were included. PDR was detected in 8.6% of sequences (13.1% versus 5.8% for B and non-B strains, respectively; P<0.001). 2.1% of patients carried a PDR for protease inhibitors (PIs; 2.1% versus 2.3%; P=0.893), 3.9% for nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs; 6.8% versus 2.1%; P<0.001) and 4.3% for non-nucleoside/nucleotide reverse transcriptase inhibitors (NNRTIs; 6.3% versus 3.1%; P=0.013). Overall, prevalence of PDR over the years remained stable, while it decreased for PIs in LA (P=0.021) and for NRTIs (P=0.020) among migrants from WE. Having more than one class of PDR (P=0.015 versus absence of PDR), higher viral load at diagnosis (P=0.008) and being migrants from SSA (P=0.001 versus WE) were predictive of VF, while a recent calendar year of diagnosis (P<0.001) was protective for VF. CONCLUSIONS PDR appeared to be stable over the years in migrants to Italy enrolled in ARCA; however, it still remains an important cause of VF together with viral load at diagnosis.
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Affiliation(s)
- Davide Fiore Bavaro
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari Medical School, Bari, Italy.,These authors equally contributed to this work
| | - Domenico Di Carlo
- Pediatric Clinical Research Center 'Romeo and Enrica Invernizzi', University of Milan, Milan, Italy.,These authors equally contributed to this work
| | - Barbara Rossetti
- Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università di Siena, Siena, Italy
| | | | | | - Francesca Lombardi
- Università Cattolica del Sacro Cuore, Roma Italia, Istituto di Clinica Malattie Infettive, Rome, Italy
| | - Simona Di Giambenedetto
- Università Cattolica del Sacro Cuore, Roma Italia, Istituto di Clinica Malattie Infettive, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma Italia, UOC malattie infettive, Rome, Italy
| | - Vanni Borghi
- Clinica Malattie infettive, Azienda Ospedaliero Universitaria di Modena, Modena, Italy
| | - Monica Pecorari
- SSD Virologia, Azienda Ospedaliero-Univeristaria Policlinico Modena, Modena, Italy
| | - Paola Milini
- Infectious Diseases Unit, Macerata Hospital, Macerata, Italy
| | - Paola Meraviglia
- 1st Division of Infectious Diseases, ASST Fatebenefratelli-Sacco, Milan, Italy
| | - Laura Monno
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari Medical School, Bari, Italy
| | - Annalisa Saracino
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari Medical School, Bari, Italy
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Rhee SY, Shafer RW. Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. Sci Data 2018; 5:180148. [PMID: 30063225 PMCID: PMC6067049 DOI: 10.1038/sdata.2018.148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 05/21/2018] [Indexed: 12/11/2022] Open
Abstract
Accurate classification of HIV-1 group M lineages, henceforth referred to as subtyping, is essential for understanding global HIV-1 molecular epidemiology. Because most HIV-1 sequencing is done for genotypic resistance testing pol gene, we sought to develop a set of geographically-stratified pol sequences that represent HIV-1 group M sequence diversity. Representative pol sequences differ from representative complete genome sequences because not all CRFs have pol recombination points and because complete genome sequences may not faithfully reflect HIV-1 pol diversity. We developed a software pipeline that compiled 6,034 one-per-person complete HIV-1 pol sequences annotated by country and year belonging to 11 pure subtypes and 70 CRFs and selected a set of sequences whose average distance to the remaining sequences is minimized for each subtype/CRF and country to generate a Geographically-Stratified set of 716 Pol Subtype/CRF (GSPS) reference sequences. We provide extensive data on pol diversity within each subtype/CRF and country combination. The GSPS reference set will also be useful for HIV-1 pol subtyping.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94301, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94301, USA
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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
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