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Wan Z, Zhang C. How to report and make sense of a new HIV-1 circulating recombinant form? Front Microbiol 2024; 15:1343143. [PMID: 38450164 PMCID: PMC10915052 DOI: 10.3389/fmicb.2024.1343143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024] Open
Abstract
Co-circulation of multiple HIV-1 subtypes in the same high-risk groups leads to the on-going generation of various inter-subtype recombinants, including unique (URFs) and circulating (CRFs) recombinant forms, which brings a new challenge for the prevention and eradication of HIV/AIDS. Identification and prompt reporting of new CRFs will provide not only new insights into the understanding of genetic diversity and evolution of HIV-1, but also an early warning of potential prevalence of these variants. Currently, 140 HIV-1 CRFs have been described; however, their prevalence and clinical importance are less concerned. Apart from the mosaic genomic maps, less other valuable information, including the clinical and demographic data, genomic sequence characteristics, origin and evolutionary dynamics, as well as representative genomic fragments for determining the variants, are available for most of these CRFs. Accompanied with the growing increase of HIV-1 full-length genomic sequences, more and more CRFs will be identified in the near future due to the high recombination potential of HIV-1. Here, we discuss the prevalence and clinical importance of various HIV-1 CRFs and propose how to report and make sense of a new HIV-1 CRF.
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Affiliation(s)
- Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Polotan FGM, Salazar CRP, Morito HLE, Abulencia MFB, Pantoni RAR, Mercado ES, Hué S, Ditangco RA. Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018. Virus Evol 2023; 9:vead073. [PMID: 38131006 PMCID: PMC10735293 DOI: 10.1093/ve/vead073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The Philippines has had a rapidly growing human immunodeficiency virus (HIV) epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing the history of HIV-1 CRF01_AE transmissions in the Philippines through molecular epidemiology. Partial polymerase sequences (n = 1144) collected between 2008 and 2018 from three island groups were collated from the Research Institute for Tropical Medicine drug resistance genotyping database. Estimation of the time to the most recent common ancestor (tMRCA), effective reproductive number (Re), effective viral population size (Ne), relative migration rates, and geographic spread of CRF01_AE was performed with BEAST. Re and Ne were compared between CRF01_AE and B. Most CRF01_AE sequences formed a single clade with a tMRCA of June 1996 [95 per cent highest posterior density (HPD): December 1991, October 1999]. An increasing CRF01_AE Ne was observed from the tMRCA to 2013. The CRF01_AE Re reached peaks of 2.46 [95 per cent HPD: 1.76, 3.27] in 2007 and 2.52 [95 per cent HPD: 1.83, 3.34] in 2015. A decrease of CRF01_AE Re occurred in the intervening years of 2007 to 2011, reaching as low as 1.43 [95 per cent HPD: 1.06, 1.90] in 2011, followed by a rebound. The CRF01_AE epidemic most likely started in Luzon and then spread to the other island groups of the country. Both CRF01_AE and Subtype B exhibited similar patterns of Re fluctuation over time. These results characterize the subtype-specific phylodynamic history of the largest CRF01_AE cluster in the Philippines, which contextualizes and may inform past, present, and future public health measures toward controlling the HIV epidemic in the Philippines.
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Affiliation(s)
- Francisco Gerardo M Polotan
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Carl Raymund P Salazar
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6700 EH, The Netherlands
| | - Hannah Leah E Morito
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Miguel Francisco B Abulencia
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Roslind Anne R Pantoni
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Edelwisa S Mercado
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
| | - Stéphane Hué
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, Camden WC1E 7HT , UK
| | - Rossana A Ditangco
- AIDS Research Group, Research Institute for Tropical Medicine, 9002, Research Drive, Filinvest Corporate City, Alabang, Muntinlupa City, Metro Manila 1781, The Philippines
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Ostankova YV, Shchemelev AN, Thu HHK, Davydenko VS, Reingardt DE, Serikova EN, Zueva EB, Totolian AA. HIV Drug Resistance Mutations and Subtype Profiles among Pregnant Women of Ho Chi Minh City, South Vietnam. Viruses 2023; 15:2008. [PMID: 37896785 PMCID: PMC10612098 DOI: 10.3390/v15102008] [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: 09/03/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
According to the latest data released by UNAIDS, the global number of people living with HIV (PLHIV) in 2021 was 38.4 million, with 1.5 million new HIV infections. In different countries, a significant proportion of these cases occur in the adult fertile population aged 15-49 years. According to UNAIDS, Vietnam had a national HIV prevalence of 0.3% of the total population at the end of 2019, with approximately 230,000 PLHIV. The most effective way to prevent mother-to-child transmission of HIV is ART to reduce maternal viral load. HIV-infected pregnant women should undergo monthly monitoring, especially before the expected date of delivery. The aim of our work was to analyze subtypic structure and drug-resistant variants of HIV in pregnant women in Ho Chi Minh City. The study material was blood plasma samples from HIV-infected pregnant women: 31 women showed virological failure of ART, and 30 women had not previously received therapy. HIV-1 genotyping and mutation detection were performed based on analysis of the nucleotide sequences of the pol gene region. More than 98% of sequences genotyped as HIV-1 sub-subtype CRF01_AE. When assessing the occurrence of drug resistance mutations, genetic resistance to any drug was detected in 74.41% (95% CI: 62.71-85.54%) of patients. These included resistance mutations to protease inhibitors in 60.66% (95% CI: 47.31-72.93%) of patients, to NRTIs in 8.20% (95% CI: 2.72-18.10%), and to NNRTIs in 44.26% (95% CI: 31.55-57.52%). Mutations associated with NRTI (2) and NNRTI (8) resistance as well as PI mutations (12), including minor ones, were identified. The high prevalence of drug resistance mutations found in this study among pregnant women, both in therapeutically naive individuals and in patients with virological failure of ART, indicates that currently used regimens in Vietnam are insufficient to prevent vertical HIV infection.
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Affiliation(s)
- Yulia V. Ostankova
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | | | | | | | - Diana E. Reingardt
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | - Elena N. Serikova
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | - Elena B. Zueva
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | - Areg A. Totolian
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
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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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Alexiev I, Campbell EM, Knyazev S, Pan Y, Grigorova L, Dimitrova R, Partsuneva A, Gancheva A, Kostadinova A, Seguin-Devaux C, Elenkov I, Yancheva N, Switzer WM. Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria. Viruses 2021; 13:116. [PMID: 33467166 PMCID: PMC7829743 DOI: 10.3390/v13010116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
HIV-1 subtype CRF01_AE is the second most predominant strain in Bulgaria, yet little is known about the molecular epidemiology of its origin and transmissibility. We used a phylodynamics approach to better understand this sub-epidemic by analyzing 270 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1995 and 2019. Using network analyses at a 1.5% genetic distance threshold (d), we found a large 154-member outbreak cluster composed mostly of persons who inject drugs (PWID) that were predominantly men. At d = 0.5%, which was used to identify more recent transmission, the large cluster dissociated into three clusters of 18, 12, and 7 members, respectively, five dyads, and 107 singletons. Phylogenetic analysis of the Bulgarian sequences with publicly available global sequences showed that CRF01_AE likely originated from multiple Asian countries, with Vietnam as the likely source of the outbreak cluster between 1988 and 1990. Our findings indicate that CRF01_AE was introduced into Bulgaria multiple times since 1988, and infections then rapidly spread among PWID locally with bridging to other risk groups and countries. CRF01_AE continues to spread in Bulgaria as evidenced by the more recent large clusters identified at d = 0.5%, highlighting the importance of public health prevention efforts in the PWID communities.
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Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Ellsworth M. Campbell
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
| | - Sergey Knyazev
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
- Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Yi Pan
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
| | - Lyubomira Grigorova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Aleksandra Partsuneva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Luxembourg, Luxembourg;
| | - Ivaylo Elenkov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria; (I.E.); (N.Y.)
| | - Nina Yancheva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria; (I.E.); (N.Y.)
| | - William M. Switzer
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
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Paraskevis D, Kostaki EG. An evolving genetic tapestry of HIV-1 recombinants. Lancet HIV 2020; 7:e733-e734. [PMID: 33128900 DOI: 10.1016/s2352-3018(20)30272-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
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