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Rashid A, Kang L, Yi F, Getaneh Y, Chu Q, Shah SA, Abidi SH, Shao Y. Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan. Microbiol Spectr 2024; 12:e0052924. [PMID: 38771033 PMCID: PMC11218485 DOI: 10.1128/spectrum.00529-24] [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: 02/26/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiency virus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the pol gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses on them. The four NFLG sequences from our study and one DG unique recombinant form previously identified in the United Kingdom (GenBank accession: MF109700) formed a distinct monophyletic cluster with an Shimodaira-Hasegawa approximate likelihood ratio test node support value of 100%. Bootscan analyses of the five NFLG sequences of DG recombinants showed that all five NFLGs shared the same unique mosaic pattern of recombination breakpoints between D and G clades, with two D fragments in the pol and vif regions inserted into a G backbone. Subregion phylogenetic analyses confirmed these sequences to be a novel circulating recombinant form (CRF) composed of subtypes D and G. The DG recombinant sequences were eventually designated as CRF152_DG by the Los Alamos HIV Sequence Database staff. IMPORTANCE In Pakistan, the genetic diversity of human immunodeficiency virus type 1 (HIV-1) is becoming increasingly complex, compared to the early years of the epidemic that started after the detection of the first cases of HIV-1 in 1987 in Karachi. Based on the available molecular studies, two dominant HIV-1 clades, sub-subtype A1 and CRF02_AG, have been found to co-circulate with other clades, namely B, C, D, G, CRF01_AE, CRF35_A1D, and CRF56_cpx, in various urban areas of Pakistan. Several novel recombinant forms have also been detected. This first report of CRF152_DG highlights the complex nature of the HIV epidemic in Pakistan and emphasizes the importance of continual molecular surveillance (ideally based on whole-genome sequences) of HIV.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Feng Yi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Sciences, Nankai University, Tianjin, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Changping Laboratory, Beijing, China
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van de Klundert MAA, Antonova A, Di Teodoro G, Ceña Diez R, Chkhartishvili N, Heger E, Kuznetsova A, Lebedev A, Narayanan A, Ozhmegova E, Pronin A, Shemshura A, Tumanov A, Pfeifer N, Kaiser R, Saladini F, Zazzi M, Incardona F, Bobkova M, Sönnerborg A. Molecular Epidemiology of HIV-1 in Eastern Europe and Russia. Viruses 2022; 14:v14102099. [PMID: 36298654 PMCID: PMC9609922 DOI: 10.3390/v14102099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 12/04/2022] Open
Abstract
The HIV epidemic in Eastern Europe and Russia is large and not well-controlled. To describe the more recent molecular epidemiology of HIV-1, transmitted drug resistance, and the relationship between the epidemics in this region, we sequenced the protease and reverse transcriptase genes of HIV-1 from 812 people living with HIV from Ukraine (n = 191), Georgia (n = 201), and Russia (n = 420) before the initiation of antiretroviral therapy. In 190 Ukrainian patients, the integrase gene sequence was also determined. The most reported route of transmission was heterosexual contact, followed by intravenous drug use, and men having sex with men (MSM). Several pre-existing drug resistance mutations were found against non-nucleoside reverse transcriptase inhibitors (RTIs) (n = 103), protease inhibitors (n = 11), and nucleoside analogue RTIs (n = 12), mostly polymorphic mutations or revertants. In the integrase gene, four strains with accessory integrase strand transfer inhibitor mutations were identified. Sub-subtype A6 caused most of the infections (713/812; 87.8%) in all three countries, including in MSM. In contrast to earlier studies, no clear clusters related to the route of transmission were identified, indicating that, within the region, the exchange of viruses among the different risk groups may occur more often than earlier reported.
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Affiliation(s)
| | - Anastasiia Antonova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Giulia Di Teodoro
- EuResist Network, 00152 Rome, Italy
- Department of Computer Control and Management Engineering Antonio Ruberti, Sapienza University of Rome, 00185 Rome, Italy
| | - Rafael Ceña Diez
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, 14152 Stockholm, Sweden
| | - Nikoloz Chkhartishvili
- Infectious Diseases, AIDS and Clinical Immunology Research Center (IDACIRC), 0160 Tbilisi, Georgia
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
| | - Anna Kuznetsova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Aleksey Lebedev
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Aswathy Narayanan
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, 14152 Stockholm, Sweden
| | - Ekaterina Ozhmegova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Alexander Pronin
- Moscow Regional Center for Control and Prevention of AIDS and Infectious Diseases, 123098 Moscow, Russia
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia
| | - Alexandr Tumanov
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Nico Pfeifer
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
| | - Francesco Saladini
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | | | - Marina Bobkova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
- Correspondence: (M.B.); (A.S.)
| | - Anders Sönnerborg
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, 14152 Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
- Correspondence: (M.B.); (A.S.)
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First complete-genome documentation of HIV-1 intersubtype superinfection with transmissions of diverse recombinants over time to five recipients. PLoS Pathog 2021; 17:e1009258. [PMID: 33577588 PMCID: PMC7906459 DOI: 10.1371/journal.ppat.1009258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/25/2021] [Accepted: 12/22/2020] [Indexed: 11/19/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) recombinants in the world are believed to be generated through recombination between distinct HIV-1 strains among coinfection or superinfection cases. However, direct evidence to support transmission of HIV-1 recombinants from a coinfected/superinfected donor to putative recipient is lacking. Here, we report on the origin and evolutionary relationship between a set of recombinants from a CRF01_AE/CRF07_BC superinfected putative donor and diverse CRF01_AE/CRF07_BC recombinants from five putative recipients. Interviews on sociodemographic characteristics and sexual behaviors for these six HIV-1-infected men who have sex with men showed that they had similar ways of partner seeking: online dating sites and social circles. Phylogenetic and recombination analyses demonstrated that the near-full-length genome sequences from six patients formed a monophyletic cluster different from known HIV-1 genotypes in maximum likelihood phylogenetic trees, were all composed of CRF01_AE and CRF07_BC fragments with two common breakpoints on env, and shared 4-7 breakpoints with each other. Moreover, 3' half-genomes of recombinant strains from five recipients had identical/similar recombinant structures with strains at longitudinal samples from the superinfected donor. Recombinants from the donor were paraphyletic, whereas five recipients were monophyletic or polyphyletic in the maximum clade credibility tree. Bayesian analyses confirmed that the estimated time to the most recent common ancestor (tMRCA) of CRF01_AE and CRF07_BC strains of the donor was 2009.2 and 2010.7, respectively, and all were earlier than the emergence of recombinants from five recipients. Our results demonstrated that the closely related unique recombinant forms of HIV-1 might be the descendent of a series of recombinants generated gradually in a superinfected patient. This finding highlights the importance of early initiation of antiretroviral therapy as well as tracing and testing of partners in patients with multiple HIV-1 infection.
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Wolf JM, De Carli S, Pereira VRZB, Simon D, Lunge VR. Temporal evolution and global spread of hepatitis B virus genotype G. J Viral Hepat 2021; 28:393-399. [PMID: 33128240 DOI: 10.1111/jvh.13431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 09/09/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) infection is considered a major health problem in the world. HBV is classified into genotypes A to J disseminated worldwide. Genotypes A, D and F are the most frequent in the Western World, B and C are predominant in the East, and E, F, H and J are infrequent and restricted to specific regions. HBV-G is a rare genotype, but it has been detected in different continents. This study aimed to report the temporal evolution and global spread of HBV-G comparing whole-genome sequences of this genotype from different regions in the world. Bayesian coalescent analysis was performed to estimate the time to the most recent common ancestor (tMRCA) and the population dynamics in the last decades. The results demonstrated that tMRCA of all HBV-Gs dated back to 1855 (95% highest posterior density interval [HPD 95%]: 1778 - 1931). This genotype has a possible origin in North America and it was disseminated to other continents (South and Central America, Europe, Asia and Africa) more than one century later (around the 1970s). The viral population demonstrated constant spreading from 1855 to the 1980s, followed by an increase in the 1990s and reached a plateau after the 2000s. Wide spreading at the beginning of the 1990s was probably associated with the dissemination by highly sexual active groups and injecting drug users. In conclusion, the present study demonstrated that HBV-G was originated in the 19th century with main events of spread at the end of the 20th century.
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Affiliation(s)
- Jonas Michel Wolf
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, ULBRA, Universidade Luterana do Brasil, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | - Sílvia De Carli
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | | | - Daniel Simon
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, ULBRA, Universidade Luterana do Brasil, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | - Vagner Ricardo Lunge
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, ULBRA, Universidade Luterana do Brasil, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
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Pimentel V, Pingarilho M, Alves D, Diogo I, Fernandes S, Miranda M, Pineda-Peña AC, Libin P, Martins MRO, Vandamme AM, Camacho R, Gomes P, Abecasis A. Molecular Epidemiology of HIV-1 Infected Migrants Followed up in Portugal: Trends between 2001-2017. Viruses 2020; 12:v12030268. [PMID: 32121161 PMCID: PMC7150888 DOI: 10.3390/v12030268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
Migration is associated with HIV-1 vulnerability. Objectives: To identify long-term trends in HIV-1 molecular epidemiology and antiretroviral drug resistance (ARV) among migrants followed up in Portugal Methods: 5177 patients were included between 2001 and 2017. Rega, Scuel, Comet, and jPHMM algorithms were used for subtyping. Transmitted drug resistance (TDR) and Acquired drug resistance (ADR) were defined as the presence of surveillance drug resistance mutations (SDRMs) and as mutations of the IAS-USA 2015 algorithm, respectively. Statistical analyses were performed. Results: HIV-1 subtypes infecting migrants were consistent with the ones prevailing in their countries of origin. Over time, overall TDR significantly increased and specifically for Non-nucleoside reverse transcriptase inhibitor (NNRTIs) and Nucleoside reverse transcriptase inhibitor (NRTIs). TDR was higher in patients from Mozambique. Country of origin Mozambique and subtype B were independently associated with TDR. Overall, ADR significantly decreased over time and specifically for NRTIs and Protease Inhibitors (PIs). Age, subtype B, and viral load were independently associated with ADR. Conclusions: HIV-1 molecular epidemiology in migrants suggests high levels of connectivity with their country of origin. The increasing levels of TDR in migrants could indicate an increase also in their countries of origin, where more efficient surveillance should occur.
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Affiliation(s)
- Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Daniela Alves
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Andrea-Clemencia Pineda-Peña
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111321, Colombia
| | - Pieter Libin
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
- Artificial Intelligence lab, Department of computer science, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
| | - Ricardo Camacho
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- Correspondence:
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Crispim MAE, Reis MNDG, Abrahim C, Kiesslich D, Fraiji N, Bello G, Stefani MMA. Homogenous HIV-1 subtype B from the Brazilian Amazon with infrequent diverse BF1 recombinants, subtypes F1 and C among blood donors. PLoS One 2019; 14:e0221151. [PMID: 31498798 PMCID: PMC6733458 DOI: 10.1371/journal.pone.0221151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 07/31/2019] [Indexed: 11/18/2022] Open
Abstract
In the last decade a growing HIV/AIDS epidemic with increased incidence and AIDS-related mortality has been reported in Northern Brazil from which molecular data are scarce. Also, apparently healthy, adult blood donors, recently diagnosed with HIV-1 represent important sentinel populations for molecular studies. This cross-sectional study describes HIV-1 subtypes in blood donors from three reference public blood centers located in three States in Northern Brazil. HIV-1 pol sequencing (protease/PR, reverse transcriptase/RT) was performed on plasma samples of HIV-1 positive donors from HEMOAM, Manaus, Amazonas (n = 198), HEMERON, Porto Velho, Rondônia (n = 20) and HEMORAIMA, Boa Vista, Roraima (n = 9) collected from 2011-2017. HIV-1 subtypes were identified by REGA, phylogenetic inference; recombinant viruses were characterized by SIMPLOT. Young, single, males predominated, around half was first-time donors. Syphilis co-infection was detected in 17% (39 out of 227), 8% (18 out of 227) was anti-HBc positive. Subtype B represented ≥ 90% in Amazonas, Rondônia and Roraima, subtype C (3.1%) was found in Amazonas and Rondônia; subtype F1 (0.9%) and BF1 recombinants (5.3%) were only detected in Amazonas. Subtype B sequences from Amazonas (n = 179), Rondônia (n = 18) and Roraima (n = 9) were combined with viral strains representative of the BPANDEMIC (n = 300) and BCARIBBEAN/BCAR (n = 200) lineages. The BPANDEMIC lineage predominated (78%) although BCAR lineages were frequent in Roraima (56%) and Amazonas (22%). Subtype C and subtype F1 sequences identified here clustered within Brazilian CBR and F1BR lineages, respectively. Twelve BF1 mosaics showed 11 different recombination profiles: six were singleton unique-recombinant-forms/URFs, one displays a CRF28/29_BF-like recombinant pattern and the remaining four BF1 isolates branched with other Brazilian BF1 viruses previously described and may represent putative new CRF_BF1 from Northern Brazil. Our study shows a highly homogeneous molecular pattern with prevalent subtype B, followed by BF1, and sporadic subtype C and F1 in blood donors from the Northern region. Surveillance studies are important to monitor HIV-1 diversity which can reveal patterns of viral dissemination, especially in a highly endemic, remote and geographically isolated region as Northern Brazil.
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Affiliation(s)
| | - Mônica Nogueira da Guarda Reis
- Instituto de Patologia Tropical e Saúde Pública, Laboratório de Imunologia da AIDS e da Hanseniase, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Claudia Abrahim
- Fundação de Hematologia e Hemoterapia do Amazonas/HEMOAM, Amazonas, Manaus, Brazil
| | - Dagmar Kiesslich
- Fundação de Hematologia e Hemoterapia do Amazonas/HEMOAM, Amazonas, Manaus, Brazil
| | - Nelson Fraiji
- Fundação de Hematologia e Hemoterapia do Amazonas/HEMOAM, Amazonas, Manaus, Brazil
| | - Gonzalo Bello
- Instituto Oswaldo Cruz, FIOCRUZ, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariane Martins Araújo Stefani
- Instituto de Patologia Tropical e Saúde Pública, Laboratório de Imunologia da AIDS e da Hanseniase, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- * E-mail:
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Esashika Crispim MA, da Guarda Reis MN, Fraiji N, Bello G, Stefani MMA. Detection of human immunodeficiency virus Type 1 phylogenetic clusters with multidrug resistance mutations among 2011 to 2017 blood donors from the highly endemic Northern Brazilian Amazon. Transfusion 2019; 59:2593-2601. [PMID: 31119759 DOI: 10.1111/trf.15347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/19/2019] [Accepted: 04/21/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND This study describes transmitted drug resistance (TDR) in blood donors diagnosed with human immunodeficiency virus Type 1 (HIV-1) infection from 2011 to 2017 in three reference public blood centers from the Northern Brazilian Amazon. STUDY DESIGN AND METHODS This was a cross-sectional study on HIV-positive blood donors from HEMOAM, Manaus, Amazonas, AM (n = 198); HEMERON, Porto Velho, Rondônia, RO (n = 20); and HEMORAIMA, Boa Vista, Roraima, RR (n = 9). HIV-1 pol sequences (protease, reverse transcriptase) were analyzed for drug resistance mutations (DRMs) using the Calibrated Population Resistance tool (Stanford). TDR/DRM clusters were investigated by phylogenetic analysis after removing positions associated with drug resistance of Subtype B sequences from untreated and treated subjects from Northern Brazil. RESULTS Transmitted drug resistance/DRM in blood donors was 11% (25 of 227), all of them from HEMOAM. Most blood donors with TDR/DRM had multiple and similar DRMs. Nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations predominated (10.1%), followed by nucleoside reverse transcriptase inhibitor (NRTI) mutations (5.3%) and protease inhibitor mutations (0.4%). Dual-class NNRTI/NRTI mutations represented 4.8%. Three highly supported Subtype B monophyletic clades mostly composed by individuals from Amazonas with TDR/DRM mutations were identified. The largest transmission cluster contained 10 sequences, eight from HEMOAM and two sequences described previously (one from a treated subject from Amazonas and the other one from Roraima). This cluster was characterized by NRTI (D67N, T69D, T215S/F/L, K219Q) and NNRTI (K101H, K103 N, G190A) mutations. The other two transmission clades comprised only three and two sequences from HEMOAM sharing the E138A NNRTI mutation. CONCLUSIONS The identification of transmission clusters of multidrug-resistant viruses in blood donors from Amazonas highlight the need of continued monitoring of TDR/DRM and the importance of pretreatment genotyping in the highly endemic Amazonas state.
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Affiliation(s)
| | - Mônica Nogueira da Guarda Reis
- Laboratório de Imunologia da AIDS e da Hanseniase, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Nelson Fraiji
- Fundação de Hematologia e Hemoterapia do Amazonas, HEMOAM, Manaus, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariane Martins Araújo Stefani
- Laboratório de Imunologia da AIDS e da Hanseniase, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
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Antiretroviral resistance, genotypic characterization and origin of Human Immunodeficiency Virus among the infected wives of Intravenous drug users in Manipur. Sci Rep 2018; 8:15183. [PMID: 30315192 PMCID: PMC6185977 DOI: 10.1038/s41598-018-33636-z] [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: 04/03/2018] [Accepted: 10/03/2018] [Indexed: 11/08/2022] Open
Abstract
Increasing incidence of drug resistance is ascertained to be the main obstacles in limiting the virus among the human immunodeficiency virus (HIV) infected individuals. This study investigates the drug resistance mutations (DRMs), genetic variants and origin of transmitted drug resistance of HIV-1 among the HIV-1 infected wives of intravenous drug users (IDUs) in Manipur. 44 HIV pol gene sequences were generated from 56 blood samples by viral gene amplification and sequencing. Sequences were then analysed for drug resistance, genetic variants and origin. The result revealed that among the treatment naive cases, 35.7% had Transmitted Drug Resistance Mutations (TDRMs) while among treatment experienced cases, 50% had Acquired Drug Resistant Mutations (ADRMs). These TDRMs and ADRMs conferred resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and/or protease inhibitors (PIs). Majority of the isolated HIV-1 sequences (77.3%) were subtype C while 9.1% was discordant subtype, 6.8% was subtype B, 4.5% was CRF_01AE and 2.3% was URF_BC. TDRM strains were found to be introduced from Myanmar, Vietnam and mainland India. This study also reveals the appearance of CRF_01AE for the first time in Manipur. The finding of this study indicates high prevalence of drug resistant mutations and complex molecular epidemiology in Manipur.
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9
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Deng H, Liang S, Liu H, Xu M, Zhuo L, Gao H. Genetic characterization of a novel unique recombinant form of HIV-1 originating from subtype A1 and C in Guangdong Province, China. Arch Virol 2018; 164:285-290. [PMID: 30291501 DOI: 10.1007/s00705-018-4051-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/17/2018] [Indexed: 11/26/2022]
Abstract
The dominant human immunodeficiency virus type 1 (HIV-1) subtypes are CRF01_AE, CRF07_BC and CRF08_BC in Guangdong Province, China. In this study, we report a unique recombinant form (URF) of HIV-1 that was identified in an HIV/hepatitis B virus (HBV)/hepatitis C virus (HCV) triple-infected patient who was an intravenous drug user (IDU) in Heyuan City, Guangdong Province. The near full-length genome was amplified, and the PCR products were sequenced by Sanger's method. The Recombination Identification Program (RIP 3.0) and jpHMM online tools showed that four subtype C fragments were inserted into the A1 backbone genome in the gag, pol, vpr and nef gene regions. In the phylogenetic tree analysis, the subtype A1 and C fragments clustered with HIV-1 A1 and C reference sequences, respectively. No similar breakpoints between our strain and the other strains in the Los Alamos HIV database were observed. The results of evolutionary analysis using BEAST software showed that the subtype A1 fragment originated from Guangzhou City, China; however, the subtype C fragment originated from East Africa. This is the first report of HIV-1 URF A1C in Guangdong Province, China. The identification of this URF suggested that further dynamic surveillance of new recombinant forms is needed.
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Affiliation(s)
- Haohui Deng
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, No. 627, East of Dongfeng Road, Guangzhou, Guangdong, China
| | - Shuzhen Liang
- Lin He Street Community Health Service Center, No. 382, North of Tianhe Road, Guangzhou, Guangdong, China
| | - Huiyuan Liu
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, No. 627, East of Dongfeng Road, Guangzhou, Guangdong, China
| | - Min Xu
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, No. 627, East of Dongfeng Road, Guangzhou, Guangdong, China
| | - Li Zhuo
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, No. 627, East of Dongfeng Road, Guangzhou, Guangdong, China
| | - Hongbo Gao
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, No. 627, East of Dongfeng Road, Guangzhou, Guangdong, China.
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López P, De Jesús O, Yamamura Y, Rodríguez N, Arias A, Sánchez R, Rodríguez Y, Tamayo-Agrait V, Cuevas W, Rivera-Amill V. Molecular Epidemiology of HIV-1 Virus in Puerto Rico: Novel Cases of HIV-1 Subtype C, D, and CRF-24BG. AIDS Res Hum Retroviruses 2018; 34:507-516. [PMID: 29658302 DOI: 10.1089/aid.2017.0305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype B virus is the most prevalent subtype in Puerto Rico (PR), accounting for about 90% of infection in the island. Recently, other subtypes and circulating recombinant forms (CRFs), including F(12_BF), A (01_BF), and CRF-39 BF-like, have been identified. The purpose of this study is to assess the distribution of drug resistance mutations and subtypes in PR. A total of 846 nucleotide sequences from the period comprising 2013 through 2017 were obtained from our "HIV Genotyping" test file. Phylogenetic and molecular epidemiology analyses were performed to evaluate the evolutionary dynamics and prevalence of drug resistance mutations. According to our results, we detected a decrease in the prevalence of protease inhibitor, nucleoside reverse transcriptase inhibitor (NRTI), and non-NRTI (NNRTI) resistance mutations over time. In addition, we also detected recombinant forms and, for the first time, identified subtypes C, D, and CRF-24BG in PR. Recent studies suggest that non-subtypes B are associated with a high risk of treatment failure and disease progression. The constant monitoring of viral evolution and drug resistance mutation dynamics is important to establish appropriate efforts for controlling viral expansion.
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Affiliation(s)
- Pablo López
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Omayra De Jesús
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Yasuhiro Yamamura
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Nayra Rodríguez
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Andrea Arias
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Raphael Sánchez
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Yadira Rodríguez
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Vivian Tamayo-Agrait
- Puerto Rico Community Network for Clinical Research on AIDS, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Wilfredo Cuevas
- HIV Clinic Outpatient Department, Ryder Memorial Hospital, Humacao, Puerto Rico
| | - Vanessa Rivera-Amill
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
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11
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Guo J, Yan Y, Zhang J, Ji J, Ge Z, Ge R, Zhang X, Wang H, Chen Z, Luo J. Genetic characterization and antiretroviral resistance mutations among treatment-naive HIV-infected individuals in Jiaxing, China. Oncotarget 2017; 8:18271-18279. [PMID: 28407682 PMCID: PMC5392326 DOI: 10.18632/oncotarget.15382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022] Open
Abstract
The aim of this study was to characterize HIV-1 genotypes and antiretroviral resistance mutations among treatment-naive HIV-infected individuals in Jiaxing, China. The HIV-1 partial polymerase (pol) genes in 93 of the 99 plasma samples were successfully amplified and analyzed. Phylogenetic analysis revealed the existence of five HIV-1 genotypes, of which the most prevalent genotype was CRF01_AE (38.7%), followed by CRF07_BC (34.4%), CRF08_BC (16.1%), subtype B/B' (5.4%), and CRF55_01B (2.1%). Besides, three types of unique recombination forms (URFs) were also observed, including C/F2/A1, CRF01_AE/B, and CRF08_BC/CRF07_BC. Among 93 amplicons, 46.2% had drug resistance-associated mutations, including 23.7% for protease inhibitors (PIs) mutations, 1.1% for nucleoside reverse transcriptase inhibitors (NRTIs) mutations, and 20.4% for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations. Six (6.5%) out of 93 treatment-naive subjects were identified to be resistant to one or more NNRTIs, while resistance to NRTIs or PIs was not observed. Our study showed the genetic diversity of HIV-1 strains circulating in Jiaxing and a relative high proportion of antiretroviral resistance mutations among treatment-naive patients, indicating a serious challenge for HIV prevention and treatment program.
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Affiliation(s)
- Jinlei Guo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Jiafeng Zhang
- Institute of AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, PR China
| | - Jimei Ji
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Zhijian Ge
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Rui Ge
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Xiaofei Zhang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Jianyong Luo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
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Jia M, Shaw T, Zhang X, Liu D, Shen Y, Ezeamama AE, Yang C, Zhang M. Decoding noises in HIV computational genotyping. Virology 2017; 511:249-255. [PMID: 28918303 DOI: 10.1016/j.virol.2017.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
Abstract
Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings.
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Affiliation(s)
- MingRui Jia
- Department of Pain Management, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Jinan, Shandong Province 250021, China; Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA
| | - Timothy Shaw
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA
| | - Xing Zhang
- Diagnostic Imaging center, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dong Liu
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA; Laboratory of Ichthyology, Shanghai Ocean University, Shanghai 201306, China
| | - Ye Shen
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA
| | - Amara E Ezeamama
- Department of Psychiatry, Michigan State University, MI 48824, USA
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/TB, Center for Global Health, Centers for Diseases Control and Prevention, GA 30333, USA
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA.
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13
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Hakre S, Jagodzinski LL, Liu Y, Pham PT, Kijak GH, Tovanabutra S, McCutchan FE, Scoville SL, Cersovsky SB, Michael NL, Scott PT, Peel SA. Characteristics of HIV-infected U.S. Army soldiers linked in molecular transmission clusters, 2001-2012. PLoS One 2017; 12:e0182376. [PMID: 28759645 PMCID: PMC5536263 DOI: 10.1371/journal.pone.0182376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/17/2017] [Indexed: 11/18/2022] Open
Abstract
Objective Recent surveillance data suggests the United States (U.S.) Army HIV epidemic is concentrated among men who have sex with men. To identify potential targets for HIV prevention strategies, the relationship between demographic and clinical factors and membership within transmission clusters based on baseline pol sequences of HIV-infected Soldiers from 2001 through 2012 were analyzed. Methods We conducted a retrospective analysis of baseline partial pol sequences, demographic and clinical characteristics available for all Soldiers in active service and newly-diagnosed with HIV-1 infection from January 1, 2001 through December 31, 2012. HIV-1 subtype designations and transmission clusters were identified from phylogenetic analysis of sequences. Univariate and multivariate logistic regression models were used to evaluate and adjust for the association between characteristics and cluster membership. Results Among 518 of 995 HIV-infected Soldiers with available partial pol sequences, 29% were members of a transmission cluster. Assignment to a southern U.S. region at diagnosis and year of diagnosis were independently associated with cluster membership after adjustment for other significant characteristics (p<0.10) of age, race, year of diagnosis, region of duty assignment, sexually transmitted infections, last negative HIV test, antiretroviral therapy, and transmitted drug resistance. Subtyping of the pol fragment indicated HIV-1 subtype B infection predominated (94%) among HIV-infected Soldiers. Conclusion These findings identify areas to explore as HIV prevention targets in the U.S. Army. An increased frequency of current force testing may be justified, especially among Soldiers assigned to duty in installations with high local HIV prevalence such as southern U.S. states.
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Affiliation(s)
- Shilpa Hakre
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- * E-mail:
| | - Linda L. Jagodzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Ying Liu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Peter T. Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Gustavo H. Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Francine E. McCutchan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Stephanie L. Scoville
- U.S. Army Public Health Center, Aberdeen Proving Ground, Maryland, United States of America
| | - Steven B. Cersovsky
- U.S. Army Public Health Center, Aberdeen Proving Ground, Maryland, United States of America
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Paul T. Scott
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sheila A. Peel
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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14
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Cunningham E, Chan YT, Aghaizu A, Bibby DF, Murphy G, Tosswill J, Harris RJ, Myers R, Field N, Delpech V, Cane PA, Gill ON, Mbisa JL. Enhanced surveillance of HIV-1 drug resistance in recently infected MSM in the UK. J Antimicrob Chemother 2016; 72:227-234. [PMID: 27742812 DOI: 10.1093/jac/dkw404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 08/19/2016] [Accepted: 08/26/2016] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the prevalence of inferred low-frequency HIV-1 transmitted drug resistance (TDR) in MSM in the UK and its predicted effect on first-line therapy. METHODS The HIV-1 pol gene was amplified from 442 newly diagnosed MSM identified as likely recently infected by serological avidity testing in 2011-13. The PCR products were sequenced by next-generation sequencing with a mutation frequency threshold of >2% and TDR mutations defined according to the 2009 WHO surveillance drug resistance mutations list. RESULTS The majority (75.6%) were infected with subtype B and 6.6% with rare complex or unique recombinant forms. At a mutation frequency threshold of >20%, 7.2% (95% CI 5.0%-10.1%) of the sequences had TDR and this doubled to 15.8% (95% CI 12.6%-19.6%) at >2% mutation frequency (P < 0.0001). The majority (26/42, 62%) of low-frequency variants were against PIs. The most common mutations detected at >20% and 2%-20% mutation frequency differed for each drug class, these respectively being: L90M (n = 7) and M46IL (n = 10) for PIs; T215rev (n = 9) and D67GN (n = 4) for NRTIs; and K103N (n = 5) and G190E (n = 2) for NNRTIs. Combined TDR was more frequent in subtype B than non-B (OR = 0.38; 95% CI = 0.17-0.88; P = 0.024) and had minimal predicted effect on recommended first-line therapies. CONCLUSIONS The data suggest differences in the types of low-frequency compared with majority TDR variants that require a better understanding of the origins and clinical significance of low-frequency variants. This will better inform diagnostic and treatment strategies.
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Affiliation(s)
- Emma Cunningham
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Yuen-Ting Chan
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Adamma Aghaizu
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - David F Bibby
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Gary Murphy
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Jennifer Tosswill
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Ross J Harris
- Statistics, Modelling and Economics Department, National Infection Service, Public Health England, London, UK
| | - Richard Myers
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Nigel Field
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - Valerie Delpech
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Patricia A Cane
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - O Noel Gill
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Jean L Mbisa
- Virus Reference Department, National Infection Service, Public Health England, London, UK .,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
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15
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Bártolo I, Calado R, Borrego P, Leitner T, Taveira N. Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola. AIDS Res Hum Retroviruses 2016; 32:822-8. [PMID: 27098898 DOI: 10.1089/aid.2016.0084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Angola has an extremely diverse HIV-1 epidemic fueled in part by the frequent interchange of people with the Democratic Republic of Congo (DRC) and Republic of Congo (RC). Characterization of HIV-1 strains circulating in Angola should help to better understand the origin of HIV-1 subtypes and recombinant forms and their transmission dynamics. In this study we characterize the first near full-length HIV-1 genomic sequences from HIV-1 infected individuals from Angola. Samples were obtained in 1993 from three HIV-1 infected patients living in Cabinda, Angola. Near full-length genomic sequences were obtained from virus isolates. Maximum likelihood phylogenetic tree inference and analyses of potential recombination patterns were performed to evaluate the sequence classifications and origins. Phylogenetic and recombination analyses revealed that one virus was a pure subtype J, another mostly subtype J with a small uncertain region, and the final virus was classified as a H/U/CRF02_AG recombinant. Consistent with their epidemiological data, the subtype J sequences were more closely related to each other than to other J sequences previously published. Based on the env gene, taxa from Angola occur throughout the global subtype J phylogeny. HIV-1 subtypes J and H are present in Angola at low levels since at least 1993. Low transmission efficiency and/or high recombination potential may explain their limited epidemic success in Angola and worldwide. The high diversity of rare subtypes in Angola suggests that Angola was part of the early establishment of the HIV-1 pandemic.
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Affiliation(s)
- Inês Bártolo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Rita Calado
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Borrego
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Nuno Taveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
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Hraber PT, Leach RW, Reilly LP, Thurmond J, Yusim K, Kuiken C. Los Alamos Hepatitis C Virus Sequence and Human Immunology Databases: An Expanding Resource for Antiviral Research. ACTA ACUST UNITED AC 2016; 18:113-23. [PMID: 17626595 DOI: 10.1177/095632020701800301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The hepatitis C virus (HCV) resource at Los Alamos (hcv.lanl.gov) provides access to multiple databases: one containing annotated sequences and the other a repository of immunogenic epitopes. They are derived from databases originally developed for HIV research (hiv.lanl.gov). HCV and HIV are RNA viruses with relatively compact genomes (around 10 kb) that are extraordinarily variable, both within and between hosts. This diversity requires methods to track and exclude variants from an individual infection or from epidemiologically related infections, and tools to analyse the variation. The HCV immunology database contains a curated inventory of immunogenic epitopes and information about their interaction with the host immune system, with associated retrieval and analysis tools. This interactive resource provides flexible retrieval tools for sequences, epitopes, clinical information, and metadata, as well as utilities for scientific data analysis, to investigators with internet access and a web browser. This paper describes the types of data and the services that these databases offer, the tools they provide, and their configuration and use. Examples of applications to clonal analysis for drug-resistance mutations are shown.
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Affiliation(s)
- Peter T Hraber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA.
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17
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Zolt SD, Thermann R, Bangsow T, Pichl L, Müller B, Jork C, Weber-Schehl M, Hedges D, Schupp I, Unverzagt P, de Rue K, Roth WK. Implementation of an HIV-1 Triple-Target NAT Assay in the Routine Screening at Three German Red Cross Blood Centres. Transfus Med Hemother 2016; 43:183-9. [PMID: 27403090 DOI: 10.1159/000446290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Blood product safety was significantly improved by the introduction of NAT testing in the late 1990s, resulting in a strong decrease of transfusion-transmitted infections (TTIs). Due to the occurrence of HIV-1 NAT test failures as a consequence of mismatch mutations in the amplicon regions of mono-target NAT assays, the Paul Ehrlich Institute mandated the implementation of multi-target NAT assays for HIV-1 in 2014. Commercial suppliers mostly developed dual-target NAT assays, with only one implementing a triple-target NAT assay. METHODS The HIV-1 triple-target NAT assay v3 (GFE Blut) was tested on mutated specimens and synthetic DNA bearing mutations that resulted in sample underquantification or false-negative test results. In addition, data from 2 years routine testing at three German Red Cross Blood centres were analysed. RESULTS The HIV-1 triple-target PCR could compensate for all mutations tested and could compensate the loss of one amplicon without a significant loss of sensitivity. Data from 2 years routine testing showed a solid performance. CONCLUSION The HIV-1 triple-target v3 assay (GFE Blut) can compensate mutations in target sequences better than a dual-target assay and is applicable to high-throughput screening, thus increasing blood product safety.
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Affiliation(s)
- Silke De Zolt
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Rolf Thermann
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Thorsten Bangsow
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Lutz Pichl
- DRK Blutspendedienst West, Hagen, Germany
| | | | | | | | - Doris Hedges
- Blutspendedienst des Bayerischen Roten Kreuzes, Wiesentheid, Germany
| | - Ingo Schupp
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Patrick Unverzagt
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Katrin de Rue
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - W Kurt Roth
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
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Geographic origin and evolutionary history of China's two predominant HIV-1 circulating recombinant forms, CRF07_BC and CRF08_BC. Sci Rep 2016; 6:19279. [PMID: 26763952 PMCID: PMC4725877 DOI: 10.1038/srep19279] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/09/2015] [Indexed: 11/08/2022] Open
Abstract
To determine the origin and evolutionary history of two predominant and closely-related circulating recombinant forms (CRF07_BC and CRF08_BC), recombinant structures and phylogenies of 7 unique recombinant forms comprised of subtypes of B’ (Thai B linage) and C (designated URFs_BC) from archival specimens of injection drug users (IDUs) collected in 1996 to 1998 from western Yunnan and 4 circulating recombinant forms with B’/C recombinants recently identified (designated nCRFs_BC) in China were compared with those of CRF07_BC and CRF08_BC. The results showed that 5 of 7 URFs_BC and all the nCRFs_BC shared recombination breakpoints with CRF07_BC and/or CRF08_BC. Yunnan URFs_BC consistently occupied the basal branch positions compared with CRF07_BC, CRF08_BC, and nCRFs_BC in phylogenetic trees. The estimated most recent common ancestors (tMRCA) for Yunnan URFs_BC were from ~1987, approximately half a decade earlier than those for CRF07_BC (~1994) and CRF08_BC (~1992). Discrete phylogeographic and spatial diffusion analysis revealed that both CRF07_BC and CRF08 BC came from western Yunnan in the early 1990s. Our results provide compelling evidence for western Yunnan as the geographic origin of CRF07_BC and CRF08_BC, which emerged from a swarm of URFs_BC by a series of recombination events in western Yunnan in the early 1990s.
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Li L, Sun G, Zhong P, Han J, Li T, Jia D, Liu Y, Sun C, Wang Z, Li H, Wang X, Li J. HIV-1 Thai B strain has spread out of former plasma donors into general population through sexual contact in Henan, China. J Med Virol 2015; 88:614-21. [PMID: 26381060 DOI: 10.1002/jmv.24383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 11/05/2022]
Abstract
Henan, China is characterized by the outbreak of HIV epidemic of Thai B strain in former plasma donors in 1990s. After the forbidden of paid blood donation, whether Thai B strain will spread out of former plasma donors into sexual transmitted population is unknown. To answer the question, phylogenetic analysis was used to explore relationships of HIV strains circulating in those two populations in the study. HIV-1 sero-positive drug-naïve patients infected through sexual contact were enrolled into the study. Full length gag and pol genes were amplified with nested RT-PCR followed by sequencing and phylogenetic analysis. The genotypes of anti-HIV drug resistance were also analyzed with available pol genes. HIV subtypes were determined in 249 individuals from 288 participants. Subtype B was dominant (202/249, 81.1%), followed by CRF01_AE (25/249, 10.0%), CRF07_BC (14/249, 5.6%), C (4/249, 1.6%), URF (3/249, 1.2%), and CRF08_BC (1/249, 0.4%). Most of subtype B strains belong to Thailand B lineage. All of Thai B strains identified in sexual transmitted population intermixed with those from former blood donors in phylogenetic tree, suggesting close phylogenetic relationship between strains epidemic in those two populations. TDR was identified in 9.9% individuals. Thai B strain has spread out of former blood donors in Henan province. The finding will contribute to understanding the distribution and evolution of HIV-1 in Henan province and also provide clue to behavior change intervention.
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Affiliation(s)
- Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Guoqing Sun
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Ping Zhong
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dijing Jia
- Anhui Medical University, Changsha, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Changrong Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Wang
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Griffin TZ, Kang W, Ma Y, Zhang M. The HAND Database: a gateway to understanding the role of HIV in HIV-associated neurocognitive disorders. BMC Med Genomics 2015; 8:70. [PMID: 26510927 PMCID: PMC4625622 DOI: 10.1186/s12920-015-0143-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 10/16/2015] [Indexed: 11/17/2022] Open
Abstract
Background Despite an augmented research effort and scale-up of highly active antiretroviral therapy, a high prevalence of HIV-1-associated neurocognitive disorders (HAND) persists in the HIV-infected population. Nearly 50 % of all HIV-1-infected individuals suffer from a neurocognitive disorder due to neural and synaptodendritic damage. Challenges in HAND research, including limited availability of brain tissue from HIV patients, variation in HAND study protocols, and virus genotyping inconsistency and errors, however, have resulted in studies with insufficient power to delineate molecular mechanisms underlying HAND pathogenesis. There exists, therefore, a great need for a reliable and centralized resource specific to HAND research, particularly for epidemiological study and surveillance in resource-limited countries where severe forms of HAND persist. Description To address the aforementioned imperative need, here we present the HAND Database, a resource containing well-curated and up-to-date HAND virus information and associated clinical and epidemiological data. This database provides information on 5,783 non-redundant HIV-1 sequences from global HAND research published to date, representing a total of 163 unique individuals that have been assessed for HAND. A user-friendly interface allows for flexible searching, filtering, browsing, and downloading of data. The most comprehensive database of its kind, the HAND Database not only bolsters current HAND research by increasing sampling power and reducing study biases caused by protocol variation and genotyping inconsistency, it allows for comparison between HAND studies across different dimensions. Development of the HAND Database has also revealed significant knowledge gaps in HIV-driven neuropathology. These gaps include inadequate sequencing of viral genes beyond env, lack of HAND viral data from HIV epidemiologically important regions including Asian and Sub-Saharan African countries, and biased sampling toward the male gender, all factors that impede efforts toward providing an improved quality of life to HIV-infected individuals, and toward elimination of viruses in the brain. Conclusion Our aim with the HAND database is to provide researchers in both the HIV and neuroscience fields a comprehensive and rigorous data source toward better understanding virus compartmentalization and to help in design of improved strategies against HAND viruses. We also expect this resource, which will be updated on a regular basis, to be useful as a reliable reference for further HAND epidemiology studies. The HAND Database is freely available and accessible online at http://www.handdatabase.org.
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Affiliation(s)
- Tess Z Griffin
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, 30602, USA. .,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
| | - Weiliang Kang
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, 30602, USA. .,Present address: College of Pharmacy, University of Illinois, Chicago, IL, 60612, USA.
| | - Yongjie Ma
- Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key laboratory of Cancer Prevention and Therapy, Tianjin, 300060, PR China.
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, 30602, USA.
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Gui T, Zhao J, Sun C, Chen L, Liu Y, Zheng C, Li H, Li T, Bao Z, Wang X, Li J, Li L. Genetic Characterization of a Unique Recombinant Originating from CRF55_01B, CRF01_AE, and CRF07_BC in Shenzhen, China. AIDS Res Hum Retroviruses 2015; 31:559-63. [PMID: 25748656 DOI: 10.1089/aid.2014.0337] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple subtypes were found to be epidemic in the Shenzhen men who have sex with men (MSM) population, which always predicts the emergence of a unique recombinant. In 2012, CRF55_01B was first reported, which later was proven to have originated in MSM in Shenzhen city. In this study, we reported a unique recombinant form (URF) of HIV-1 identified in a man who has had sex with men in Shenzhen city. The strain showed a genomic schematic map similar to CRF55_01B with subtype C segments inserted in the gag and pol genes. The full-length genome was amplified in two halves with 1-kb overlap regions. The PCR products were cloned and sequenced. A recombination detection program showed that two subtype C fragments and two subtype B fragments were inserted into the CRF01_AE backbone genome in the gag and pol regions. In the phylogenetic tree, the subtype C fragments clustered with CRF07_BC variants and the other segments grouped with CRF55_01B strains except for one segment that clustered with CRF01_AE. Similar breakpoints between our strain and CRF65_cpx were also observed. The data suggested that the URF strain might be the recombinant form of CRF55_01B, CRF01_AE, and CRF07_BC. This is the first report of a third generation of recombination of HIV-1 that originated from CRF55_01B in China. The identification of the URF indicated the severity of the HIV epidemic in Shenzhen MSM and the urgent need for epidemiological surveillance of the new recombination.
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Affiliation(s)
- Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Changrong Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Wilkinson E, Holzmayer V, Jacobs GB, de Oliveira T, Brennan CA, Hackett J, van Rensburg EJ, Engelbrecht S. Sequencing and phylogenetic analysis of near full-length HIV-1 subtypes A, B, G and unique recombinant AC and AD viral strains identified in South Africa. AIDS Res Hum Retroviruses 2015; 31:412-20. [PMID: 25492033 PMCID: PMC4378615 DOI: 10.1089/aid.2014.0230] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
By the end of 2012, more than 6.1 million people were infected with HIV-1 in South Africa. Subtype C was responsible for the majority of these infections and more than 300 near full-length genomes (NFLGs) have been published. Currently very few non-subtype C isolates have been identified and characterized within the country, particularly full genome non-C isolates. Seven patients from the Tygerberg Virology (TV) cohort were previously identified as possible non-C subtypes and were selected for further analyses. RNA was isolated from five individuals (TV047, TV096, TV101, TV218, and TV546) and DNA from TV016 and TV1057. The NFLGs of these samples were amplified in overlapping fragments and sequenced. Online subtyping tools REGA version 3 and jpHMM were used to screen for subtypes and recombinants. Maximum likelihood (ML) phylogenetic analysis (phyML) was used to infer subtypes and SimPlot was used to confirm possible intersubtype recombinants. We identified three subtype B (TV016, TV047, and TV1057) isolates, one subtype A1 (TV096), one subtype G (TV546), one unique AD (TV101), and one unique AC (TV218) recombinant form. This is the first NFLG of subtype G that has been described in South Africa. The subtype B sequences described also increased the NFLG subtype B sequences in Africa from three to six. There is a need for more NFLG sequences, as partial HIV-1 sequences may underrepresent viral recombinant forms. It is also necessary to continue monitoring the evolution and spread of HIV-1 in South Africa, because understanding viral diversity may play an important role in HIV-1 prevention strategies.
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Affiliation(s)
- Eduan Wilkinson
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Academic Hospital, Tygerberg, Cape Town, South Africa
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
| | | | - Graeme B. Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Academic Hospital, Tygerberg, Cape Town, South Africa
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa
| | | | | | | | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Academic Hospital, Tygerberg, Cape Town, South Africa
- National Health Laboratory Services (NHLS), Western Cape Region, Tygerberg Hospital (Coastal), Cape Town, South Africa
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Li X, Zang X, Ning C, Feng Y, Xie C, He X, Takebe Y, Sun L, Guo Q, Xing H, Kalish ML, Shao Y. Molecular epidemiology of HIV-1 in Jilin province, northeastern China: emergence of a new CRF07_BC transmission cluster and intersubtype recombinants. PLoS One 2014; 9:e110738. [PMID: 25356726 PMCID: PMC4214716 DOI: 10.1371/journal.pone.0110738] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/17/2014] [Indexed: 11/25/2022] Open
Abstract
Objective To investigate the HIV-1 molecular epidemiology among newly diagnosed HIV-1 infected persons living in the Jilin province of northeastern China. Methods Plasma samples from 189 newly diagnosed HIV-1 infected patients were collected between June 2010 and August 2011 from all nine cities of Jilin province. HIV-1 nucleotide sequences of gag P17–P24 and env C2–C4 gene regions were amplified using a multiplex RT-PCR method and sequenced. Phylogenetic and recombination analyses were used to determine the HIV-1 genotypes. Results Based on all sequences generated, the subtype/CFR distribution was as follows: CRF01_AE (58.1%), CRF07_BC (13.2%), subtype B’ (13.2%), recombinant viruses (8.1%), subtype B (3.7%), CRF02_AG (2.9%), subtype C (0.7%). In addition to finding CRF01_AE strains from previously reported transmission clusters 1, 4 and 5, a new transmission cluster was described within the CRF07_BC radiation. Among 11 different recombinants identified, 10 contained portions of gene regions from the CRF01_AE lineage. CRF02_AG was found to form a transmission cluster of 4 in local Jilin residents. Conclusions Our study presents a molecular epidemiologic investigation describing the complex structure of HIV-1 strains co-circulating in Jilin province. The results highlight the critical importance of continuous monitoring of HIV-infections, along with detailed socio-demographic data, in order to design appropriate prevention measures to limit the spread of new HIV infections.
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Affiliation(s)
- Xingguang Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
- HIV Molecular Epidemiology and Virology Research Group, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xihui Zang
- Jilin Provincial Center for Disease Control and Prevention, Changchun, Jilin, China
| | - Chuanyi Ning
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Cunxin Xie
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Xiang He
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Yutaka Takebe
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Liuyan Sun
- Jilin Provincial Center for Disease Control and Prevention, Changchun, Jilin, China
| | - Qi Guo
- Jilin Provincial Center for Disease Control and Prevention, Changchun, Jilin, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Marcia L. Kalish
- Vanderbilt Institute for Global Health, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
- * E-mail:
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Bulla I, Schultz AK, Chesneau C, Mark T, Serea F. A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection. BMC Bioinformatics 2014; 15:205. [PMID: 24946781 PMCID: PMC4230192 DOI: 10.1186/1471-2105-15-205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. RESULTS To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. CONCLUSIONS We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.
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Affiliation(s)
- Ingo Bulla
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Straße 47, 17487 Greifswald, Germany.
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Li X, Ning C, He X, Yang Y, Xing H, Hong K, Shao Y, Yang R. Near full-length genome sequence of a novel HIV type 1 second-generation recombinant form (CRF01_AE/CRF07_BC) identified among men who have sex with men in Jilin, China. AIDS Res Hum Retroviruses 2013; 29:1604-8. [PMID: 23809010 DOI: 10.1089/aid.2013.0116] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report here a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) composed of CRF01_AE and CRF07_BC, identified among men who have sex with men (MSM) in Jilin, with four breakpoints observed in the pol, vif, and vpr genes. The CRF01_AE regions of the recombinant were clustered with the CRF01_AE lineage, which is mainly circulating among MSM in northern China, with the support of 100% bootstrap value, indicating that the parental origin of the CRF01_AE regions was from MSM, in which recombination events may be more likely to occur. To the best of our knowledge, this is the first detection of a novel HIV-1 second-generation recombinant form (CRF01AE/CRF07_BC) in Jilin, which indicates active transmission networks of HIV-1 infection among MSM in the region. Therefore, it is necessary to continue monitoring the molecular epidemiology of HIV-1 among MSM in Jilin to obtain a better understanding of the transmission and potential public health impact of HIV-1 among MSM in the region.
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Affiliation(s)
- Xingguang Li
- HIV Molecular Epidemiology and Virology Research Group, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chuanyi Ning
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiang He
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Yang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kunxue Hong
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Rongge Yang
- HIV Molecular Epidemiology and Virology Research Group, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
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26
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Andernach IE, Hunewald OE, Muller CP. Bayesian inference of the evolution of HBV/E. PLoS One 2013; 8:e81690. [PMID: 24312336 PMCID: PMC3843692 DOI: 10.1371/journal.pone.0081690] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 10/21/2013] [Indexed: 12/16/2022] Open
Abstract
Despite its wide spread and high prevalence in sub-Saharan Africa, hepatitis B virus genotype E (HBV/E) has a surprisingly low genetic diversity, indicating an only recent emergence of this genotype in the general African population. Here, we performed extensive phylogeographic analyses, including Bayesian MCMC modeling. Our results indicate a mutation rate of 1.9×10−4 substitutions per site and year (s/s/y) and confirm a recent emergence of HBV/E, most likely within the last 130 years, and only after the transatlantic slave-trade had come to an end. Our analyses suggest that HBV/E originated from the area of Nigeria, before rapidly spreading throughout sub-Saharan Africa. Interestingly, viral strains found in Haiti seem to be the result of multiple introductions only in the second half of the 20th century, corroborating an absence of a significant number of HBV/E strains in West Africa several centuries ago. Our results confirm that the hyperendemicity of HBV(E) in today's Africa is a recent phenomenon and likely the result of dramatic changes in the routes of viral transmission in a relatively recent past.
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Affiliation(s)
- Iris E. Andernach
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Oliver E. Hunewald
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Claude P. Muller
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
- * E-mail:
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Pandey S, Tripathy S, Paranjape R. Molecular characterization of unique intersubtype HIV type 1 A1/C recombinant strain circulating in Pune, India. AIDS Res Hum Retroviruses 2013; 29:1245-53. [PMID: 23742670 DOI: 10.1089/aid.2013.0150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
An increasing number of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) all over the world has necessitated being vigilant about new recombinants. Since the first report of a recombinant virus with an A1/C mosaic in 1998 more and more B/C and A/C recombinant viruses are being reported from India. Here we report the identification and characterization of a unique HIV-1 A1/C recombinant circulating in Western India. Analysis of the full-length genome using RIP, SimPlot, and jpHMM@Gobics has confirmed its mosaic structure with insertion of subtype A1 in the backbone of subtype C at three positions: gag-pol (1973±15-2617±47), pol-vif (4879±37-5582±32), and gp41 (8437±106-8811±8); however, RIP and SimPlot showed one more small insertion in integrase (4343-4519). Phylogenetic analysis confirmed that the recombinant virus has an insertion of clade A1 in the backbone of subtype C, which has come from Indian subtype C.
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Affiliation(s)
- Sudhanshu Pandey
- Division of Immunology, National AIDS Research Institute (ICMR), Pune, India
| | - Srikanth Tripathy
- Central JALMA Institute for Leprosy and other Mycobacterial Diseases, Agra, India
| | - Ramesh Paranjape
- Division of Immunology, National AIDS Research Institute (ICMR), Pune, India
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Li L, Chen L, Yang S, Li T, Li J, Liu Y, Jia L, Yang B, Bao Z, Li H, Wang X, Zhuang D, Liu S, Li J. Recombination form and epidemiology of HIV-1 unique recombinant strains identified in Yunnan, China. PLoS One 2012; 7:e46777. [PMID: 23056447 PMCID: PMC3467292 DOI: 10.1371/journal.pone.0046777] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
Several studies identified HIV-1 recombination in some distinct areas in Yunnan, China. However, no comprehensive studies had been fulfilled in the whole province up to now. To illustrate the epidemiology and recombination form of Unique Recombinant Forms (URFs) circulating in Yunnan, 788 HIV-1 positive individuals residing in 15 prefectures of Yunnan were randomly enrolled into the study. Full-length gag and pol genes were amplified and sequenced. Maximum likelihood tree was constructed for phylogenetic analysis. Recombinant breakpoints and genomic schematics were identified with online software jpHMM. 63 (10.2%) unique recombinant strains were identified from 617 strains with subtypes. The URFs distributed significantly differently among prefectures (Pearson chi-square test, P<0.05). IDUs contained more URFs than sexual transmitted population (Pearson chi-square test, P<0.05). Two main recombinant forms were identified by considering the presence of CRF01_AE segments in full length gag-pol genes, which were B′/C and B′/C/CRF01-AE recombinants. Three clusters were identified in the ML tree which contained more than three sequences and supported by high bootstrap values. One CRF was identified. Many of URFs contained identical breakpoints. The results will contribute to our understanding on HIV recombination and provide clues to the identification of potential CRFs in China.
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Affiliation(s)
- Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lili Chen
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Urumqi General Hospital of Lanzhou Military Area Command, Urumqi, Xinjiang, China
| | - Shaomin Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianjian Li
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bihui Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail:
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Melo FL, Jamal LF, Zanotto PMDA. Characterization of primary isolates of HIV type 1 CRF28_BF, CRF29_BF, and unique BF recombinants circulating in São Paulo, Brazil. AIDS Res Hum Retroviruses 2012; 28:1082-8. [PMID: 22176121 PMCID: PMC3423645 DOI: 10.1089/aid.2011.0123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report for the first time the genetic and biological characterization of 10 HIV-1 primary isolates representing CRF28_BF and CRF29_BF together with additional unique BF recombinant forms (URFs) obtained by PBMC cocultivation. Recombination is an important factor promoting the increase in the genetic diversity of HIV-1. Notably, more than 20% of HIV-1 sequences worldwide were recombinants. Several recombinant viruses were reported in Brazil, and six circulating recombinant forms (CRFs) have been identified (CRF28_BF, CRF29_BF, CRF31_BC, CRF39_BF, CRF40_BF, and CRF46_BF). CRF28_BF and CRF29_BF were found to infect almost 30% of the patients in São Paulo State. The near full-length genomes of these 10 primary isolates were amplified by nested PCR in three overlapping segments, purified, and sequenced. Three samples were related to CRF28_BF, three to CRF29_BF, and four were unique recombinant forms (URFs), as determined by their breakpoint profile determined with the jpHMM program. Additionally, the coreceptor usage of these isolates was investigated in vitro using GHOST assays, which revealed three dual-tropic (X4/R5) viruses, four lymphotropic (X4) viruses, and three macrophage-tropic (R5) viruses with different V3-loop motifs, which challenges the notion that GWGR-carrying viruses are macrophage-tropic only. In sum, we report a much-anticipated well-characterized panel of viruses representing CRF28_BF, CRF29_BF, and URFs from São Paulo State, Brazil.
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Affiliation(s)
- Fernando Lucas Melo
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute-ICBII, University of São Paulo, Brazil
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Bolcic F, Laufer N, Trinchero J, Jones LR, Quarleri J. A clustering phenomenon among HCV-1a strains among patients coinfected with HIV from Buenos Aires, Argentina. J Med Virol 2012; 84:570-81. [PMID: 22337295 DOI: 10.1002/jmv.23243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The human immunodeficiency virus (HIV) and hepatitis C virus (HCV) share the same transmission routes which lead to high coinfection rates. Among HIV-infected individuals such rates reached 21% in Argentina, being HCV-1a the most predominant subtype. In this work, 25 HCV subtype 1a (HCV-1a) strains from Argentinean patients coinfected with HIV were studied based on E2 and NS5A sequences. Phylogenetic analyses indicated that 12 strains were highly related to each other, constituting a highly supported (posterior probability = 0.95) monophyletic group that we called "M." The remaining HCV strains (group dispersed or "D") were interspersed along the phylogenetic trees. When comparing both groups of HCV-1a, 10 amino acid differences were located in functional domains of E2 and NS5A proteins that appeared to affect eventually the peptides binding to MHC-I molecules thus favoring immune escape and contributing to the divergence of HCV genotypes. Bayesian coalescent analyses for HCV-1a cluster M isolates indicated that the time to the most recent common ancestor (tMRCA) overlaps with the age estimated recently for the HIV-BF epidemic in Argentina. Furthermore, the genomic characterization based on pol gene analysis from HIV viremic patients showed that most HIV isolates from patients coinfected with HCV-1a cluster M were BF recombinants with identical recombination patterns. In conclusion, these results suggest the presence of an HCV-1a monophyletic cluster with a potential HIV co-transmission by phylogenetic analyses.
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Affiliation(s)
- Federico Bolcic
- Microbiology Department, National Reference Center for AIDS Research, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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Schultz AK, Bulla I, Abdou-Chekaraou M, Gordien E, Morgenstern B, Zoaulim F, Dény P, Stanke M. jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. Nucleic Acids Res 2012; 40:W193-8. [PMID: 22600739 PMCID: PMC3394342 DOI: 10.1093/nar/gks414] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
jpHMM is a very accurate and widely used tool for recombination detection in genomic sequences of HIV-1. Here, we present an extension of jpHMM to analyze recombinations in viruses with circular genomes such as the hepatitis B virus (HBV). Sequence analysis of circular genomes is usually performed on linearized sequences using linear models. Since linear models are unable to model dependencies between nucleotides at the 5'- and 3'-end of a sequence, this can result in inaccurate predictions of recombination breakpoints and thus in incorrect classification of viruses with circular genomes. The proposed circular jpHMM takes into account the circularity of the genome and is not biased against recombination breakpoints close to the 5'- or 3'-end of the linearized version of the circular genome. It can be applied automatically to any query sequence without assuming a specific origin for the sequence coordinates. We apply the method to genomic sequences of HBV and visualize its output in a circular form. jpHMM is available online at http://jphmm.gobics.de for download and as a web server for HIV-1 and HBV sequences.
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Affiliation(s)
- Anne-Kathrin Schultz
- Abteilung für Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany.
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Iamarino A, de Melo FL, Braconi CT, Zanotto PMDA. BF integrase genes of HIV-1 circulating in São Paulo, Brazil, with a recurrent recombination region. PLoS One 2012; 7:e34324. [PMID: 22485165 PMCID: PMC3317518 DOI: 10.1371/journal.pone.0034324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 02/25/2012] [Indexed: 11/19/2022] Open
Abstract
Although some studies have shown diversity in HIV integrase (IN) genes, none has focused particularly on the gene evolving in epidemics in the context of recombination. The IN gene in 157 HIV-1 integrase inhibitor-naïve patients from the São Paulo State, Brazil, were sequenced tallying 128 of subtype B (23 of which were found in non-B genomes), 17 of subtype F (8 of which were found in recombinant genomes), 11 integrases were BF recombinants, and 1 from subtype C. Crucially, we found that 4 BF recombinant viruses shared a recurrent recombination breakpoint region between positions 4900 and 4924 (relative to the HXB2) that includes 2 gRNA loops, where the RT may stutter. Since these recombinants had independent phylogenetic origin, we argue that these results suggest a possible recombination hotspot not observed so far in BF CRF in particular, or in any other HIV-1 CRF in general. Additionally, 40% of the drug-naïve and 45% of the drug-treated patients had at least 1 raltegravir (RAL) or elvitegravir (EVG) resistance-associated amino acid change, but no major resistance mutations were found, in line with other studies. Importantly, V151I was the most common minor resistance mutation among B, F, and BF IN genes. Most codon sites of the IN genes had higher rates of synonymous substitutions (dS) indicative of a strong negative selection. Nevertheless, several codon sites mainly in the subtype B were found under positive selection. Consequently, we observed a higher genetic diversity in the B portions of the mosaics, possibly due to the more recent introduction of subtype F on top of an ongoing subtype B epidemics and a fast spread of subtype F alleles among the B population.
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Affiliation(s)
| | | | | | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute-ICB II, University of São Paulo, São Paulo, Brazil
- * E-mail:
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Unterthiner T, Schultz AK, Bulla J, Morgenstern B, Stanke M, Bulla I. Detection of viral sequence fragments of HIV-1 subfamilies yet unknown. BMC Bioinformatics 2011; 12:93. [PMID: 21481263 PMCID: PMC3086866 DOI: 10.1186/1471-2105-12-93] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 04/11/2011] [Indexed: 11/25/2022] Open
Abstract
Background Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI), has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments. Results We have developed Unknown Subtype Finder (USF), an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM) for each known subtype and an additional pHMM for an unknown subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise) probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI. Conclusions Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.
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Affiliation(s)
- Thomas Unterthiner
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr, 1, 37077 Göttingen, Germany.
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Oyaro M, Mbithi J, Oyugi F, Laten A, Anzala O, Engelbrecht S. Molecular characterization of HIV type 1 among HIV-infected respondents in a cohort being prepared for HIV Phase III vaccine clinical trials, Western Kenya. AIDS Res Hum Retroviruses 2011; 27:257-64. [PMID: 20950148 DOI: 10.1089/aid.2010.0061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Kenya is one of the sub-Saharan African countries affected by HIV-1 infection and AIDS. We investigated HIV-1 genetic diversity in 130 individuals from Busia, Bungoma, and Kakamega in western Kenya as part of an HIV-1 vaccine feasibility study in preparation for Phase III efficacy clinical trials. After RNA extraction the partial gag (484 bp) and env (1297 bp) regions were amplified and directly sequenced. Phylogenetic analysis was done using MEGA version 4 and recombinants were identified using the jpHMM tool and phylogenetic analysis. HIV-1 sequences were amplified from 122 of the 130 samples, 118 (90.8%) from the gag region and 78 (60 %) from the env region and 74 samples (56.9%) from both the gag and env regions. Of these sequenced on both regions, 51.4% were subtype A, 9.4% subtype D, 1.4% subtype C, 4.1% subtype G, and 33.7% were discordant and thus possible recombinants, including A1/C, A1/D, A1/A2, and A2/C. The jpHMM tool indicated a further two samples with CD and BD breakpoints within the env gene and one within the gag gene (A1C). An additional sample had an A1D breakpoint in the gag gene, but the envelope was not amplified. HIV-1 subtype diversity in western Kenya should be considered in vaccines designed for clinical trials in this region and this genetic diversity should be continuously monitored.
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Affiliation(s)
- Micah Oyaro
- Kenyatta University, Department of Biological Sciences, Nairobi, Kenya
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - John Mbithi
- Kenyatta University, Department of Biological Sciences, Nairobi, Kenya
| | - Fred Oyugi
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Annette Laten
- Division of Medical Virology, National Health Laboratory Services (NHLS) and University of Stellenbosch, Tygerberg, South Africa
| | - Omu Anzala
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Susan Engelbrecht
- Division of Medical Virology, National Health Laboratory Services (NHLS) and University of Stellenbosch, Tygerberg, South Africa
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Kim J, Ahn Y, Lee K, Park SH, Kim S. A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis. BMC Bioinformatics 2010; 11:434. [PMID: 20727194 PMCID: PMC2936400 DOI: 10.1186/1471-2105-11-434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 08/21/2010] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Accurate classification into genotypes is critical in understanding evolution of divergent viruses. Here we report a new approach, MuLDAS, which classifies a query sequence based on the statistical genotype models learned from the known sequences. Thus, MuLDAS utilizes full spectra of well characterized sequences as references, typically of an order of hundreds, in order to estimate the significance of each genotype assignment. RESULTS MuLDAS starts by aligning the query sequence to the reference multiple sequence alignment and calculating the subsequent distance matrix among the sequences. They are then mapped to a principal coordinate space by multidimensional scaling, and the coordinates of the reference sequences are used as features in developing linear discriminant models that partition the space by genotype. The genotype of the query is then given as the maximum a posteriori estimate. MuLDAS tests the model confidence by leave-one-out cross-validation and also provides some heuristics for the detection of 'outlier' sequences that fall far outside or in-between genotype clusters. We have tested our method by classifying HIV-1 and HCV nucleotide sequences downloaded from NCBI GenBank, achieving the overall concordance rates of 99.3% and 96.6%, respectively, with the benchmark test dataset retrieved from the respective databases of Los Alamos National Laboratory. CONCLUSIONS The highly accurate genotype assignment coupled with several measures for evaluating the results makes MuLDAS useful in analyzing the sequences of rapidly evolving viruses such as HIV-1 and HCV. A web-based genotype prediction server is available at http://www.muldas.org/MuLDAS/.
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Affiliation(s)
- Jiwoong Kim
- Department of Bioinformatics & Life Sciences, Soongsil University, Seoul, Korea
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Bulla I, Schultz AK, Schreiber F, Zhang M, Leitner T, Korber B, Morgenstern B, Stanke M. HIV classification using the coalescent theory. ACTA ACUST UNITED AC 2010; 26:1409-15. [PMID: 20400454 DOI: 10.1093/bioinformatics/btq159] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns. RESULTS We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. It reconstructs ancestral recombination graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov chain Monte Carlo approach. ARGUS was able to distinguish the correct classification with a low error rate from plausible alternative classifications in simulation studies with realistic parameters. We applied our algorithm to decide between two recently debated alternatives in the classification of CRF02 of HIV-1 and find that CRF02 is indeed a recombinant of Subtypes A and G. AVAILABILITY ARGUS is implemented in C++ and the source code is available at http://gobics.de/software.
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Affiliation(s)
- Ingo Bulla
- Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
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Zhang M, Foley B, Schultz AK, Macke JP, Bulla I, Stanke M, Morgenstern B, Korber B, Leitner T. The role of recombination in the emergence of a complex and dynamic HIV epidemic. Retrovirology 2010; 7:25. [PMID: 20331894 PMCID: PMC2855530 DOI: 10.1186/1742-4690-7-25] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 03/23/2010] [Indexed: 12/11/2022] Open
Abstract
Background Inter-subtype recombinants dominate the HIV epidemics in three geographical regions. To better understand the role of HIV recombinants in shaping the current HIV epidemic, we here present the results of a large-scale subtyping analysis of 9435 HIV-1 sequences that involve subtypes A, B, C, G, F and the epidemiologically important recombinants derived from three continents. Results The circulating recombinant form CRF02_AG, common in West Central Africa, appears to result from recombination events that occurred early in the divergence between subtypes A and G, followed by additional recent recombination events that contribute to the breakpoint pattern defining the current recombinant lineage. This finding also corrects a recent claim that G is a recombinant and a descendant of CRF02, which was suggested to be a pure subtype. The BC and BF recombinants in China and South America, respectively, are derived from recent recombination between contemporary parental lineages. Shared breakpoints in South America BF recombinants indicate that the HIV-1 epidemics in Argentina and Brazil are not independent. Therefore, the contemporary HIV-1 epidemic has recombinant lineages of both ancient and more recent origins. Conclusions Taken together, we show that these recombinant lineages, which are highly prevalent in the current HIV epidemic, are a mixture of ancient and recent recombination. The HIV pandemic is moving towards having increasing complexity and higher prevalence of recombinant forms, sometimes existing as "families" of related forms. We find that the classification of some CRF designations need to be revised as a consequence of (1) an estimated > 5% error in the original subtype assignments deposited in the Los Alamos sequence database; (2) an increasing number of CRFs are defined while they do not readily fit into groupings for molecular epidemiology and vaccine design; and (3) a dynamic HIV epidemic context.
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Affiliation(s)
- Ming Zhang
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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38
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Jacobs G, Loxton A, Laten A, Robson B, van Rensburg EJ, Engelbrecht S. Emergence and diversity of different HIV-1 subtypes in South Africa, 2000-2001. J Med Virol 2009; 81:1852-9. [DOI: 10.1002/jmv.21609] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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HIV-1 pol phylogenetic diversity and antiretroviral resistance mutations in treatment naïve patients from Central West Brazil. J Clin Virol 2009; 46:134-9. [DOI: 10.1016/j.jcv.2009.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 07/03/2009] [Accepted: 07/15/2009] [Indexed: 11/23/2022]
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40
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Bruselles A, Rozera G, Bartolini B, Prosperi M, Del Nonno F, Narciso P, Capobianchi MR, Abbate I. Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV Type 1 BF recombinant associated with a fatal primary infection. AIDS Res Hum Retroviruses 2009; 25:937-42. [PMID: 19751146 DOI: 10.1089/aid.2009.0083] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Near full length genome characterization of a BF recombinant from a patient who died from multiorgan failure during HIV-1 seroconversion is reported. Massive parallel pyrosequencing was used with the shotgun approach. Intrahost genetic variability along the whole genome was calculated and coreceptor usage of viral quasispecies was predicted. A consensus sequence was established to perform subtype assignment, phylogenetic analysis, and recombination tests. The sequence clustered with two recently described BF unique recombinant forms from Brazil, consistent with the recombination pattern, yielding breakpoints located at the same positions, with the exception of the second env breakpoint. The actual prevalence of recombinant forms is probably underestimated if partial genomic regions are considered. Here the first full length BF recombinant from Italy is described, together with an evaluation of quasispecies heterogeneity. Our data provide evidence that next generation sequencing may provide a major contribution to HIV-1 molecular epidemiology and to the comprehension of intrapatient heterogeneity.
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Schultz AK, Zhang M, Bulla I, Leitner T, Korber B, Morgenstern B, Stanke M. jpHMM: improving the reliability of recombination prediction in HIV-1. Nucleic Acids Res 2009; 37:W647-51. [PMID: 19443440 PMCID: PMC2703979 DOI: 10.1093/nar/gkp371] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of ‘uncertainty’ regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/.
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Affiliation(s)
- Anne-Kathrin Schultz
- Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
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Lemey P, Lott M, Martin DP, Moulton V. Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics 2009; 10:126. [PMID: 19397803 PMCID: PMC2684544 DOI: 10.1186/1471-2105-10-126] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 04/27/2009] [Indexed: 12/02/2022] Open
Abstract
Background Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences. Results Analysis of phylogenetic simulations reveal that identifying the descendents of relatively old recombination events is a challenging task for all methods available, and that quartet scanning performs relatively well compared to the triplet based methods. The use of quartet scanning is further demonstrated by analyzing both well-established and putative HIV-1 recombinant strains. In agreement with recent findings, we provide evidence that the presumed circulating recombinant CRF02_AG is a 'pure' lineage, whereas the presumed parental lineage subtype G has a recombinant origin. We also demonstrate HIV-1 intrasubtype recombination, confirm the hybrid origin of SIV in chimpanzees and further disentangle the recombinant history of SIV lineages in a primate immunodeficiency virus data set. Conclusion Quartet scanning makes a valuable addition to triplet-based methods for identifying recombinant sequences without prior specifications of either query and reference sequences. The new method is available in the VisRD v.3.0 package .
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Affiliation(s)
- Philippe Lemey
- Rega Institute, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Ntemgwa M, Gill MJ, Brenner BG, Moisi D, Wainberg MA. Discrepancies in assignment of subtype/recombinant forms by genotyping programs for HIV type 1 drug resistance testing may falsely predict superinfection. AIDS Res Hum Retroviruses 2008; 24:995-1002. [PMID: 18593348 DOI: 10.1089/aid.2008.0064] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
With the growing diversity of the HIV pandemic, routine genotyping is an important tool for monitoring viral subtype as well as drug resistance. In this regard, numerous subtyping tools and drug resistance algorithms are available online. However, there are discrepancies in the use of these online tools in the designation of HIV-1 subtypes or recombinant forms that may have an impact on drug susceptibility profiles. Indeed, inconsistencies in some of these tools may lead to a false designation of dual infection and/or superinfection. In this case study, we evaluated the sequence diversity of an infection that was referred to us as a potential case of superinfection as a result of variations in designation of subtype. We evaluated sequences using five different online tools and finally determined by phylogenetic analysis that the sequence was a unique A1/C intersubtype recombinant at baseline and not a case of superinfection.
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Affiliation(s)
- Michel Ntemgwa
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - M. John Gill
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Bluma G. Brenner
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
| | - Daniela Moisi
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A. Wainberg
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
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Ntemgwa M, Toni TD, Brenner BG, Routy JP, Moisi D, Oliveira M, Wainberg MA. Near full-length genomic analysis of a novel subtype A1/C recombinant HIV type 1 isolate from Canada. AIDS Res Hum Retroviruses 2008; 24:655-9. [PMID: 18366312 DOI: 10.1089/aid.2007.0282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The rapid introduction of non-B HIV-1 subtypes into Quebec, mostly from persons from regions where HIV prevalence is high and where different variants circulate, means that recombination must now be an important consideration in the epidemiologic surveillance of HIV infection. No circulating recombinant form (CRF), currently involving exclusively subtypes A1 and C, exists in the Los Alamos HIV database. This study presents a near full-length genomic analysis of a novel HIV-1 recombinant involving subtypes A1 and C. Bootscanning revealed that the recombinant structure involves three breakpoints that separate the genome into four regions, alternating between subtypes A1 and C. The intersubtype recombinant breakpoint in the pol gene was at midpoint between the protease and reverse transcriptase open reading frames. This is the first report of a recombinant involving subtypes A1 and C in Canada, the epidemiologic significance of which is not yet known.
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Affiliation(s)
- Michel Ntemgwa
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H3A 2T5, Canada
| | - Thomas D'Aquin Toni
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, Quebec H3A 2T5, Canada
| | - Bluma G. Brenner
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Jean-Pierre Routy
- Immunodeficiency Service and Division of Hematology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Daniela Moisi
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Mark A. Wainberg
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H3A 2T5, Canada
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Schultz AK, Zhang M, Leitner T, Kuiken C, Korber B, Morgenstern B, Stanke M. A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. BMC Bioinformatics 2006; 7:265. [PMID: 16716226 PMCID: PMC1525204 DOI: 10.1186/1471-2105-7-265] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 05/22/2006] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events. RESULTS We developed a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach. Given a partition of the aligned input sequence family into known sequence subtypes, our model can jump between states corresponding to these different subtypes, depending on which subtype is locally most similar to a database sequence. Jumps between different subtypes are indicative of intersubtype recombinations. We applied our method to a large set of genome sequences from human immunodeficiency virus (HIV) and hepatitis C virus (HCV) as well as to simulated recombined genome sequences. CONCLUSION Our results demonstrate that jumps in our jumping profile HMM often correspond to recombination breakpoints; our approach can therefore be used to detect recombinations in genomic sequences. The recombination breakpoints identified by jpHMM were found to be significantly more accurate than breakpoints defined by traditional methods based on comparing single representative sequences.
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Affiliation(s)
- Anne-Kathrin Schultz
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
| | - Ming Zhang
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Thomas Leitner
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Carla Kuiken
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- The Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Burkhard Morgenstern
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
| | - Mario Stanke
- Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
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