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Chen M, Chen H, Dai J, Dong L, Ma Y, Jia M. Identification of a Novel HIV-1 Circulating Recombinant Form (CRF150_Cpx) Among Men Who Have Sex with Men in China. AIDS Res Hum Retroviruses 2024. [PMID: 39113542 DOI: 10.1089/aid.2024.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024] Open
Abstract
Recent studies have reported increasing complexity in human immunodeficiency virus 1 (HIV-1) genotypes among men who have sex with men (MSM) in China. In an HIV-1 molecular epidemiological study conducted among MSM in Yunnan Province, China, we discovered that four samples could potentially represent a circulating recombinant form (CRF). In this study, we conducted further analysis on their nearly full-length genome (NFLG) sequences. The NFLG sequences formed a distinct monophyletic clade in the phylogenetic tree. Recombination analysis indicated that the four sequences were constructed upon the backbone of CRF149_01B, with the insertion of three CRF07_BC fragments. Consequently, they were designated as CRF150_cpx. Evolutionary analyses suggested that CRF150_cpx emerged between approximately 2014 and 2015. The identification of new CRFs not only deepens our understanding of HIV recombination but also aids in comprehending the prevalence and transmission history of HIV among specific populations.
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Affiliation(s)
- Min Chen
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Health Laboratory Center, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Huichao Chen
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Jie Dai
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Lijuan Dong
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Yanling Ma
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Manhong Jia
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
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Raymond S, Jeanne N, Vellas C, Nicot F, Saune K, Ranger N, Latour J, Carcenac R, Harter A, Delobel P, Izopet J. HIV-1 genotypic resistance testing using single molecule real-time sequencing. J Clin Virol 2024; 174:105717. [PMID: 39068746 DOI: 10.1016/j.jcv.2024.105717] [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: 04/26/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND HIV-1 resistance testing is recommended in clinical management and next-generation sequencing (NGS) methods are now available in many virology laboratories. OBJECTIVES To evaluate the diagnostic performance of Long-Read Single Molecule Real-time (SMRT) sequencing (Sequel, PacBio) for HIV-1 polymerase genotyping. STUDY DESIGN 111 prospective clinical samples (83 plasma and 28 leukocyte-enriched blood fraction) were analyzed for routine HIV-1 resistance genotyping using Sanger sequencing, Vela NGS, and SMRT sequencing. We developed a SMRT sequencing protocol and a bio-informatics pipeline to infer antiretroviral resistance on both haplotype and variant calling approaches. RESULTS The polymerase was successfully sequenced by the three platforms in 98 % of plasma RNA samples for viral loads above 4 log copies/mL. The success rate decreased to 83 % using Sanger or Vela sequencing and to 67 % using SMRT sequencing for viral loads of 3 to 4 log copies/mL. Sensitivities of 50 %, 54 % and 61 % were obtained using SMRT, Vela, and Sanger sequencing, respectively, in cellular DNA from patients with prolonged undetectable plasma HIV-1 RNA. Ninety-eight percent of resistance-associated mutations (RAMs) identified with Sanger sequencing were detected using SMRT sequencing. Furthermore, 91 % of RAMs (> 5 % threshold) identified with Vela NGS were detected using SMRT sequencing. RAM quantification using Vela and SMRT sequencing was well correlated (Spearman correlation ρ = 0.82; P < 0.0001). CONCLUSIONS SMRT sequencing of the full-length HIV-1 polymerase appeared performant for characterizing HIV-1 genotypic resistance on both RNA and DNA clinical samples. Long-read sequencing is a new tool for mutation haplotyping and resistance analysis.
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Affiliation(s)
- Stéphanie Raymond
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France.
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Camille Vellas
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Karine Saune
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Noémie Ranger
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Justine Latour
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Pierre Delobel
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
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3
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Khairunisa SQ, Indriati DW, Megasari NLA, Ueda S, Kotaki T, Fahmi M, Ito M, Rachman BE, Hidayati AN, Nasronudin, Kameoka M. Spatial-temporal transmission dynamics of HIV-1 CRF01_AE in Indonesia. Sci Rep 2024; 14:9917. [PMID: 38730038 PMCID: PMC11087524 DOI: 10.1038/s41598-024-59820-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) remains a serious health threat in Indonesia. In particular, the CRF01_AE viruses were the predominant HIV-1 strains in various cities in Indonesia. However, information on the dynamic transmission characteristics and spatial-temporal transmission of HIV-1 CRF01_AE in Indonesia is limited. Therefore, the present study examined the spatial-temporal transmission networks and evolutionary characteristics of HIV-1 CRF01_AE in Indonesia. To clarify the epidemiological connection between CRF01_AE outbreaks in Indonesia and the rest of the world, we performed phylogenetic studies on nearly full genomes of CRF01_AE viruses isolated in Indonesia. Our results showed that five epidemic clades, namely, IDN clades 1-5, of CRF01_AE were found in Indonesia. To determine the potential source and mode of transmission of CRF01_AE, we performed Bayesian analysis and built maximum clade credibility trees for each clade. Our study revealed that CRF01_AE viruses were commonly introduced into Indonesia from Southeast Asia, particularly Thailand. The CRF01_AE viruses might have spread through major pandemics in Asian countries, such as China, Vietnam, and Laos, rather than being introduced directly from Africa in the early 1980s. This study has major implications for public health practice and policy development in Indonesia. The contributions of this study include understanding the dynamics of HIV-1 transmission that is important for the implementation of HIV disease control and prevention strategies in Indonesia.
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Affiliation(s)
- Siti Qamariyah Khairunisa
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Dwi Wahyu Indriati
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Health, Vocational Faculty, Universitas Airlangga, Surabaya, Indonesia
| | - Ni Luh Ayu Megasari
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Postgraduate School, Universitas Airlangga, Surabaya, Indonesia
| | - Shuhei Ueda
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan
| | - Tomohiro Kotaki
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Muhamad Fahmi
- Research Department, Research Institute for Humanity and Nature, Kyoto, Japan
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Brian Eka Rachman
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Afif Nurul Hidayati
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Nasronudin
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.
| | - Masanori Kameoka
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan.
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Halikov MR, Ekushov VE, Totmenin AV, Gashnikova NM, Antonets ME, Tregubchak TV, Skliar LP, Solovyova NP, Gorelova IS, Beniova SN. Identification of a novel HIV-1 circulating recombinant form CRF157_A6C in Primorsky Territory, Russia. J Infect 2024; 88:180-182. [PMID: 37981217 DOI: 10.1016/j.jinf.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Affiliation(s)
- Maksim R Halikov
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", ABK 12A, Koltsovo, Novosibirsk 630559, Russia
| | - Vasily E Ekushov
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", ABK 12A, Koltsovo, Novosibirsk 630559, Russia.
| | - Alexei V Totmenin
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", ABK 12A, Koltsovo, Novosibirsk 630559, Russia
| | - Natalya M Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", ABK 12A, Koltsovo, Novosibirsk 630559, Russia
| | - Mariya E Antonets
- Department of Molecular Virology, State Research Center of Virology and Biotechnology "Vector", ABK 12A, Koltsovo, Novosibirsk 630559, Russia
| | - Tatyana V Tregubchak
- Department of Molecular Virology, State Research Center of Virology and Biotechnology "Vector", ABK 12A, Koltsovo, Novosibirsk 630559, Russia
| | - Lidiia P Skliar
- Regional Clinical Hospital No 2 - Center for Prevention and Control of AIDS and Infectious Diseases, Vladivostok 690011, Russia
| | - Natalia P Solovyova
- Regional Clinical Hospital No 2 - Center for Prevention and Control of AIDS and Infectious Diseases, Vladivostok 690011, Russia
| | - Irina S Gorelova
- Regional Clinical Hospital No 2 - Center for Prevention and Control of AIDS and Infectious Diseases, Vladivostok 690011, Russia
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5
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Li Y, Chang W, Liang J, Liu Y, Li L, Liu L, Wang JY, Feng RL, Liao B, Feng Y. Characterization of a new HIV-1 second-generation circulating recombinant form (CRF170_0107) among men who have sex with men in Yunnan, China. J Infect 2024; 88:206-209. [PMID: 38135162 DOI: 10.1016/j.jinf.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Affiliation(s)
- Yi Li
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Wei Chang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Liang
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Yang Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li Li
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jing-Ying Wang
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Rui-Lin Feng
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Bin Liao
- Kunming Center for Disease Control and Prevention, Kunming, China.
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
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6
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Dong Z, Xu Z, Zhou Y, Tian R, Zhou K, Wang D, Ya X, Shen Q. Genetic characterization of HIV-1 viruses among cases with antiretroviral therapy failure in Suzhou City, China. AIDS Res Ther 2023; 20:41. [PMID: 37381002 PMCID: PMC10303762 DOI: 10.1186/s12981-023-00540-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND This retrospective study aimed to characterize the distribution of HIV-1 genotypes and the prevalence of drug resistance mutations in people with antiretroviral treatment (ART) failure in Suzhou City, China. METHODS Pol gene of HIV-1 viruses in blood samples of EDTA anticoagulants from 398 patients with failed antiviral treatment was successfully amplified by using an in-house assay. Drug resistance mutations were analyzed by using the Stanford HIV Drug Resistance Database system ( https://hivdb.stanford.edu/hivdb/by-mutations/ ). HIV-1 genotypes were determined by the REGA HIV subtyping tool (version 3.46, https://www.genomedetective.com/app/typingtool/hiv ). Near full-length genomes (NFLG) of HIV-1 viruses were obtained by next generation sequencing method. RESULTS Sequences analysis of the pol gene revealed that CRF 01_AE (57.29%, 228/398) was the dominant subtype circulating in Suzhou City, followed by CRF 07_BC (17.34%, 69/398), subtype B (7.54%, 30/398), CRF 08_BC (6.53%, 26/398), CRF 67_01B (3.02%, 12/398) and CRF55_01B (2.51%, 10/398). The overall prevalence of drug-resistant mutations in cases with ART failure was 64.57% (257/398), including 45.48% (181/398) for nucleotide reverse transcriptase inhibitors (NRTIs) mutations, 63.32% (252/398) for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations, and 3.02% (12/398) for protease inhibitors (PIs) mutations. Ten near full-length genomes (NFLG) of HIV-1 viruses were identified, including six recombinants of CRF 01_AE and subtype B, two recombinants of CRF 01_AE, subtype B and subtype C sequences, one recombinant of CRF 01_AE and subtype C and one recombinant of CRF 01_AE, subtype A1 and subtype C. CONCLUSIONS The high prevalence of drug-resistant HIV-1 viruses was a serious challenge for HIV prevention and treatment of people with HIV infection. Treatment regimens for ART failure patients should be adjusted over time based on the outcome of drug resistance tests. NFLG sequencing facilitates the identification of new recombinants of HIV-1.
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Affiliation(s)
- Zefeng Dong
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Zhihui Xu
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Ying Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210003, China
| | - Runfang Tian
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Kai Zhou
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Di Wang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Xuerong Ya
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
| | - Qiang Shen
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
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7
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Manyana S, Pillay M, Gounder L, Khan A, Moodley P, Naidoo K, Chimukangara B. Affordable drug resistance genotyping of HIV-1 reverse transcriptase, protease and integrase genes, for resource limited settings. AIDS Res Ther 2023; 20:9. [PMID: 36759801 PMCID: PMC9912687 DOI: 10.1186/s12981-023-00505-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND As use of dolutegravir (DTG) becomes more common in resource limited settings (RLS), the demand for integrase resistance testing is increasing. Affordable methods for genotyping all relevant HIV-1 pol genes (i.e., protease (PR), reverse transcriptase (RT) and integrase (IN)) are required to guide choice of future antiretroviral therapy (ART). We designed an in-house HIV-1 drug resistance (HIVDR) genotyping method that is affordable and suitable for use in RLS. METHODS We obtained remnant plasma samples from CAPRISA 103 study and amplified HIV-1 PR, RT and IN genes, using an innovative PCR assay. We validated the assay using remnant plasma samples from an external quality assessment (EQA) programme. We genotyped samples by Sanger sequencing and assessed HIVDR mutations using the Stanford HIV drug resistance database. We compared drug resistance mutations with previous genotypes and calculated method cost-estimates. RESULTS From 96 samples processed, we obtained sequence data for 78 (81%), of which 75 (96%) had a least one HIVDR mutation, with no major-IN mutations observed. Only one sample had an E157Q INSTI-accessory mutation. When compared to previous genotypes, 18/78 (23%) had at least one discordant mutation, but only 2/78 (3%) resulted in different phenotypic predictions that could affect choice of subsequent regimen. All CAPRISA 103 study sequences were HIV-1C as confirmed by phylogenetic analysis. Of the 7 EQA samples, 4 were HIV-1C, 2 were HIV-1D, and 1 was HIV-1A. Genotypic resistance data generated using the IDR method were 100% concordant with EQA panel results. Overall genotyping cost per sample was estimated at ~ US$43-$US49, with a processing time of ~ 2 working days. CONCLUSIONS We successfully designed an in-house HIVDR method that is suitable for genotyping HIV-1 PR, RT and IN genes, at an affordable cost and shorter turnaround time. This HIVDR genotyping method accommodates changes in ART regimens and will help to guide HIV-1 treatment decisions in RLS.
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Affiliation(s)
- Sontaga Manyana
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Melendhran Pillay
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Lilishia Gounder
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Aabida Khan
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Pravi Moodley
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Benjamin Chimukangara
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, 800 Vusi Mzimela Road, Durban, 4058, South Africa.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA.
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8
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Fan Q, Liu J, Chai C, Zhu S, Fang Q, Guo Z, Xia Y, Ding X, Zhang J. Identification and genomic characterization of a novel HIV-1 unique recombinant form (CRF01_AE/CRF07_BC) in Zhejiang Province, China. Virus Genes 2023; 59:142-147. [PMID: 36301459 PMCID: PMC9832081 DOI: 10.1007/s11262-022-01945-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/07/2022] [Indexed: 01/14/2023]
Abstract
Mutation and recombination are important mechanisms leading to the frequent evolution and genetic diversity of viruses as HIV-1. In this study, we identified the near full-length genomic characterization of a novel HIV-1 unique recombinant form (URF) strain (Sample ID: ZJ20202195/ZJ/CHN/2020, hereafter referred to as ZJ20202195) isolated during the HIV-1 molecular surveillance in 2020 in Zhejiang Province, China, through different recombination analysis tools and phylogenetic analysis. Our results amply proved that the near full-length genome (NFLG) sequence of ZJ20202195 was a novel HIV-1 unique recombinant form (URF) consisting of CRF01_AE and CRF07_BC subtype, and delimited three recombinant segments, of which the Segment I (HXB2:776-5559 nucleotide (nt)) and Segment III (HXB2:6224-9412 nt) were mainly originated from CRF01_AE cluster g4a strains prevalent in China and Segment II (HXB2:5560-6223 nt) was from CRF07_BC subtype. Overall, our findings provide insight and a scientific basis in the genetic diversity and accurate determination of HIV-1 recombinant strains in China.
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Affiliation(s)
- Qin Fan
- Department of HIV/AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No.3399, Binsheng Road, Hangzhou, 310051 People’s Republic of China
| | - Jing Liu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035 People’s Republic of China
| | - Chengliang Chai
- Department of HIV/AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No.3399, Binsheng Road, Hangzhou, 310051 People’s Republic of China
| | - Shuying Zhu
- Department of Microbiological Analysis, Jinhua Municipal Center for Disease Control and Prevention, Jinhua, 321002 People’s Republic of China
| | - Qionglou Fang
- Department of Microbiological Analysis, Jinhua Municipal Center for Disease Control and Prevention, Jinhua, 321002 People’s Republic of China
| | - Zhihong Guo
- Department of HIV/AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No.3399, Binsheng Road, Hangzhou, 310051 People’s Republic of China
| | - Yan Xia
- Department of HIV/AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No.3399, Binsheng Road, Hangzhou, 310051 People’s Republic of China
| | - Xiaobei Ding
- Department of HIV/AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No.3399, Binsheng Road, Hangzhou, 310051 People’s Republic of China
| | - Jiafeng Zhang
- Department of HIV/AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No.3399, Binsheng Road, Hangzhou, 310051 People’s Republic of China
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Zhang J, Fan Q, Ye L, Liu J, Chen X, Li X, Chai C. Tracing the origin of an imported HIV-1 sub-subtype A6 strain first identified in Zhejiang Province, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105388. [PMID: 36403919 DOI: 10.1016/j.meegid.2022.105388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Human migration and mobility have been identified as key drivers of HIV dissemination among nations, which increases the problem of genetic diversity. Here, we report the near full-length genome of HIV-1 A6 identified in a female patient in the remote mountain area of Lishui, Zhejiang Province, which is the first time A6 has been reported in China. The near full-length genome was amplified with two large amplicons of 5.5 kb and 3.7 kb, and then target PCR products were sequenced by Sanger sequencing. The A6 strain was confirmed by the Basic Local Alignment Search Tool (BLAST) and a maximum-likelihood (ML) phylogenetic tree. The time to the most recent common ancestor (tMRCA) was inferred to be 2004 (95% HPD interval: 2003-2006). The sequence harbored the L74I mutation, which is a key characteristic genetic marker of A6. Combining the above evidence with epidemiological investigations, this A6 strain was determined to be from Ukraine, which was supported by phylogenetic analysis. This study identified a foreign imported strain, indicating a trend of increasing complication in the HIV-1 epidemic in Zhejiang, China.
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Affiliation(s)
- Jiafeng Zhang
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Qin Fan
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ling Ye
- Lishui Prefectural Center for Disease Control and Prevention, Lishui, China
| | - Jing Liu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xiaolei Chen
- Lishui Prefectural Center for Disease Control and Prevention, Lishui, China
| | - Xingguang Li
- Department of Technology R&D, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China; Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Chengliang Chai
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.
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10
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Abstract
Genetically-characterizing full-length HIV-1 RNA is critical for identifying genetically-intact genomes and for comparing these RNA genomes to proviral DNA. We have developed a method for sequencing plasma-derived RNA using long-range sequencing (PRLS assay; ∼8.3 kb from gag to the 3′ end or ∼5 kb from integrase to the 3′ end). We employed the gag-3′ PRLS assay to sequence HIV-1 RNA genomes from ART-naive participants during acute/early infection (n = 6) or chronic infection (n = 2). On average, only 65% of plasma-derived genomes were genetically-intact. Defects were found in all genomic regions but were concentrated in env and pol. We compared these genomes to near-full-length proviral sequences from paired peripheral blood mononuclear cell (PBMC) samples for the acute/early group and found that near-identical (>99.98% identical) sequences were identified only during acute infection. For three participants who initiated therapy during acute infection, we used the int-3′ PRLS assay to sequence plasma-derived genomes from an analytical treatment interruption and identified 100% identical genomes between pretherapy and rebound time points. The PRLS assay provides a new level of sensitivity for understanding the genetic composition of plasma-derived HIV-1 RNA from viremic individuals either pretherapy or after treatment interruption, which will be invaluable in assessing possible HIV-1 curative strategies. IMPORTANCE We developed novel plasma-derived RNA using long-range sequencing assays (PRLS assay; 8.3 kb, gag-3′, and 5.0 kb, int-3′). Employing the gag-3′ PRLS assay, we found that 26% to 51% of plasma-derived genomes are genetically-defective, largely as a result of frameshift mutations and deletions. These genetic defects were concentrated in the env region compared to gag and pol, likely a reflection of viral immune escape in env during untreated HIV-1 infection. Employing the int-3′ PRLS assay, we found that analytical treatment interruption (ATI) plasma-derived sequences were identical and genetically-intact. Several sequences from the ATI plasma samples were identical to viral sequences from pretherapy plasma and PBMC samples, indicating that HIV-1 reservoirs established prior to therapy contribute to viral rebound during an ATI. Therefore, near-full-length sequencing of HIV-1 particles is required to gain an accurate picture of the genetic landscape of plasma HIV-1 virions in studies of HIV-1 replication and persistence.
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11
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Rahman S, Sarker MS, Aralaguppe SG, Sarwar G, Khan SI, Rahman M. Drug resistance pattern among ART-naive clients attending an HIV testing and counseling center in Dhaka, Bangladesh. J Med Virol 2021; 94:787-790. [PMID: 34636431 DOI: 10.1002/jmv.27387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022]
Abstract
In Bangladesh, antiretroviral therapy (ART) is provided without screening drug resistance-associated mutations (DRM) among people living with HIV, while DRM might emerge and transmit to the newly infected individual. The present study was aimed to identify DRM among ART-naive clients from an HIV testing and counseling (HTC) center in the initial stages of ART programs. Randomly selected (n = 64) archived plasma samples were used for the pol gene amplification and sequencing by sanger technology. Recovered sequences (n = 10) were genotyped using HIV genotyping tools of NCBI and analyzed using the Stanford University HIV drug resistance database (hivdb.stanford.edu). Various genotypes with a number of DRM were identified in HTC clients, who belonged to different risk groups based on behavioral data. The drug resistance algorithm showed that all samples were fully resistant to tipranavir/ritonavir drugs except for one intermediate resistance. Despite the small sample size, our understanding from this study warrants an ART policy with a DRM monitoring system for the country.
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Affiliation(s)
- Sezanur Rahman
- Virology Laboratory, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md S Sarker
- Virology Laboratory, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Golam Sarwar
- HIV Programme, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sharful I Khan
- HIV Programme, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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12
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Rahman M, Rahman S, Reza MM, Khan SI, Sarker MS. HIV-1 drug resistance and genotypes circulating among HIV-positive key populations in Bangladesh: 2016 update. Int J Infect Dis 2021; 104:150-158. [DOI: https:/doi.org/10.1016/j.ijid.2020.12.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
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13
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Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea. Sci Rep 2021; 11:4122. [PMID: 33602986 PMCID: PMC7892834 DOI: 10.1038/s41598-021-82872-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 01/25/2021] [Indexed: 11/08/2022] Open
Abstract
In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.
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14
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Rahman M, Rahman S, Reza MM, Khan SI, Sarker MS. HIV-1 drug resistance and genotypes circulating among HIV-positive key populations in Bangladesh: 2016 update. Int J Infect Dis 2020; 104:150-158. [PMID: 33359062 DOI: 10.1016/j.ijid.2020.12.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE HIV-1 subtyping data of Bangladeshi strains are available in global HIV Sequence Database up to 2007, and there is no sequence of drug resistance profile based on the pol gene segment. This study aimed to update HIV genotyping data and describe the drug resistance mutations for the first time from Bangladesh using specimens from the latest HIV sero-surveillance conducted in 2016. STUDY DESIGN AND METHODS During HIV sero-surveillance, a total of 1268 people who inject drugs (PWID) and 3765 female sex workers (FSW) were screened and among them, 230 (18.1%) PWID and 7 (0.2%) FSW were HIV positive. Among HIV positives, randomly selected 74 specimens (60 male-PWID, 7 female-PWID, and 7 FSW) were subjected to gag, pol, and env gene sequencing using gene-specific primers. Genotyping was decided based on the partial gag and env genes while transmission dynamics was based on the gag sequence (n = 237). Drug resistance profiles were obtained by using the algorithm of the established available drug resistance database. RESULTS HIV subtype C and C-related recombinants have remained the major circulating genotypes in Bangladesh. Although the recurring transmission of subtype C occurred among PWID, we identified possible transmission to other key populations (KPs), which suggests spillover from PWID through the sexual route. The prevalence of drug-resistant mutation was low, and all strains were susceptible to NRTIs and NNRTIs drugs. Unique recombination forms (URF) with genotype C for gag-pol and A1 for env was also identified. CONCLUSIONS The study findings warrant continuous monitoring of HIV-positive individuals and future investigation to identify social networks within and between KPs to halt the transmission and prevent new infections.
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Affiliation(s)
- Mustafizur Rahman
- icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh.
| | - Sezanur Rahman
- icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh
| | - Md Masud Reza
- icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh
| | - Sharful Islam Khan
- icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh
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15
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Soares RRG, Varela JC, Neogi U, Ciftci S, Ashokkumar M, Pinto IF, Nilsson M, Madaboosi N, Russom A. Sub-attomole detection of HIV-1 using padlock probes and rolling circle amplification combined with microfluidic affinity chromatography. Biosens Bioelectron 2020; 166:112442. [PMID: 32755809 DOI: 10.1016/j.bios.2020.112442] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
Abstract
Despite significant progress in diagnostics and disease management during the past decades, human immunodeficiency virus (HIV) infections are still responsible for nearly 1 million deaths every year, mostly in resource-limited settings. Thus, novel, accurate and cost-effective tools for viral load monitoring become crucial to allow specific diagnostics and the effective monitoring of the associated antiviral therapies. Herein, we report an effective combination of a (1) padlock probe (PLP)-mediated rolling circle amplification (RCA) bioassay and an (2) agarose bead-based microfluidic device for the affinity chromatography-based capture and detection of RCA products (RCPs) pre-labelled simultaneously with biotin and an organic fluorophore. This method allowed the efficient capture of ~1 μm-sized RCPs followed by their quantification either as discrete signals or an average fluorescence signal, thus being compatible with both high-resolution imaging for maximum sensitivity as well as simpler optical detection setups. A limit of detection < 30 fM was obtained for HIV-1 synthetic target with just a single round of RCA, comparable to recently reported procedures requiring technically complex amplification strategies such as hyperbranching and/or enzymatic digestion/amplification. Furthermore, targeting a set of five conserved regions in the HIV-1 gag gene, the method could specifically detect HIV-1 in 293T cell culture supernatants, as well as a set of 11 HIV-1 NIH reference samples with four different subtypes. The reported method provides simplicity of operation, unique versatility of signal transduction (i.e. average or discrete signals), and potential coupling with previously reported miniaturized photodetectors. These combined features hold promise for bringing RCA-based molecular diagnostics closer to the point-of-care.
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Affiliation(s)
- Ruben R G Soares
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden; Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - João C Varela
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Sibel Ciftci
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Manickam Ashokkumar
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Inês F Pinto
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - Narayanan Madaboosi
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - Aman Russom
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
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16
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Gibson KM, Steiner MC, Rentia U, Bendall ML, Pérez-Losada M, Crandall KA. Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Viruses 2020; 12:E758. [PMID: 32674515 PMCID: PMC7412389 DOI: 10.3390/v12070758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.
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Affiliation(s)
- Keylie M. Gibson
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Margaret C. Steiner
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Uzma Rentia
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Matthew L. Bendall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4169-007 Vairão, Portugal
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
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17
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Njenda DT, Aralaguppe SG, Singh K, Rao R, Sönnerborg A, Sarafianos SG, Neogi U. Antiretroviral potency of 4'-ethnyl-2'-fluoro-2'-deoxyadenosine, tenofovir alafenamide and second-generation NNRTIs across diverse HIV-1 subtypes. J Antimicrob Chemother 2019; 73:2721-2728. [PMID: 30053052 DOI: 10.1093/jac/dky256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Objectives 4'-Ethnyl-2'-fluoro-2'-deoxyadenosine (EFdA) is a novel translocation-defective reverse transcriptase inhibitor. We investigated the virological and biochemical inhibitory potentials of EFdA against a broad spectrum of subtype-specific chimeric viruses and compared it with tenofovir alafenamide, nevirapine, efavirenz, rilpivirine and etravirine. Methods pNL4.3 chimeric viruses encoding gag-pol from treatment-naive patients (n = 24) and therapy-failure patients (n = 3) and a panel of reverse transcriptase inhibitor-resistant strains (n = 7) were used to compare the potency of reverse transcriptase inhibitor drugs. The phenotypic drug susceptibility assay was performed using TZM-bl cells. In vitro inhibition assays were done using patient-derived reverse transcriptase. IC50 values of NNRTIs were calculated using a PicoGreen-based spectrophotometric assay. Steady-state kinetics were used to determine the apparent binding affinity (Km.dNTP) of triphosphate form of EFdA (EFdA-TP) and dATP. Results Among the chimeric treatment-naive viruses, EFdA had an ex vivo antiretroviral activity [median (IQR) EC50 = 1.4 nM (0.6-2.1 nM)] comparable to that of tenofovir alafenamide [1.6 nM (0.5-3.6 nM)]. Subtype-specific differences were found for etravirine (P = 0.004) and rilpivirine (P = 0.017), where HIV-1C had the highest EC50 values. EFdA had a greater comparative efficiency [calculated by dividing the efficiency of monophosphate form of EFdA (EFdA-MP) incorporation (kcat.EFdA-TP/Km.EFdA-TP) over the efficiency of dATP incorporation (kcat.dATP/Km.dATP)] compared with the natural substrate dATP, with a fold change of between 1.6 and 3.2. Ex vivo analysis on reverse transcriptase inhibitor-resistant strains showed EFdA to have a higher potency. Despite the presence of rilpivirine DRMs, some non-B strains showed hypersusceptibility to rilpivirine. Conclusions Our combined virological and biochemical data suggest that EFdA inhibits both WT and reverse transcriptase inhibitor-resistant viruses efficiently in a subtype-independent manner. In contrast, HIV-1C is least susceptible to etravirine and rilpivirine.
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Affiliation(s)
- Duncan T Njenda
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Rohit Rao
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
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18
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Ueda S, Witaningrum AM, Khairunisa SQ, Kotaki T, Motomura K, Nasronudin, Kameoka M. Transmission dynamics of HIV-1 subtype B strains in Indonesia. Sci Rep 2019; 9:13986. [PMID: 31562375 PMCID: PMC6764962 DOI: 10.1038/s41598-019-50491-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/13/2019] [Indexed: 11/09/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) and acquired immunodeficiency syndrome (AIDS) represent a major public health concern in Indonesia. Although circulating recombinant form (CRF) 01_AE is a predominant subtype in Indonesia, HIV-1 subtype B (HIV-1B) is also widely prevalent. However, the viral genetic evolution, spatial origins, and patterns of transmission of HIV-1B in Indonesia remain unclear. In the present study, we described the evolutionary characteristics and spatial-temporal transmission networks of HIV-1B in Indonesia. To elucidate the epidemiological link between HIV-1B epidemics in Indonesia and those in the remainder of the world, we conducted phylogenetic analyses of HIV-1B strains in Indonesia. Based on the results obtained, at least three epidemic clades [the Indonesia, United States (US), and China clades] of HIV-1B were found to be prevalent in Indonesia. In order to identify the potential source and transmission route of Indonesian HIV-1B strains, we performed Bayesian analyses and constructed Maximum clade credibility trees of each clade. Although some HIV-1B strains in Indonesia were introduced from Thailand, the prevalent HIV-1B strains appeared to have been directly introduced from Europe or America. Indonesian HIV-1B may have spread via the main dispersal of pandemic HIV-1B strains via the US from the Caribbean region rather than being directly introduced from Africa.
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Affiliation(s)
- Shuhei Ueda
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan.,Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan.,Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Adiana Mutamsari Witaningrum
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Siti Qamariyah Khairunisa
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Tomohiro Kotaki
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan.,Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | | | - Nasronudin
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Airlangga Hospital, Surabaya, Indonesia
| | - Masanori Kameoka
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan. .,Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan.
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19
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Hebberecht L, Vancoillie L, Schauvliege M, Staelens D, Demecheleer E, Hardy J, Mortier V, Verhofstede C. Single genome sequencing of near full-length HIV-1 RNA using a limiting dilution approach. J Virol Methods 2019; 274:113737. [PMID: 31562885 DOI: 10.1016/j.jviromet.2019.113737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 11/18/2022]
Abstract
Sequencing very long stretches of the HIV-1 genome can advance studies on virus evolution and in vivo recombination but remains technically challenging. We developed an efficient procedure to sequence near full-length HIV-1 RNA using a two-amplicon approach. The whole genome was successfully amplified for 107 (88%) of 121 plasma samples including samples from patients infected with HIV-1 subtype A1, B, C, D, F1, G, H, CRF01_AE and CRF02_AG. For the 17 samples with a viral load below 1000 c/ml and the 104 samples with a viral load above 1000 c/ml, the amplification efficiency was respectively 53% and 94%. The sensitivity of the method was further evaluated using limiting dilution of RNA extracted from a plasma pool containing an equimolar mixture of three HIV-1 subtypes (B, C and CRF02_AG) and diluted before and after cDNA generation. Both RNA and cDNA dilution showed comparable sensitivity and equal accuracy in reflecting the subtype distribution of the plasma pool. One single event of in vitro recombination was detected amongst the 41 sequences obtained after cDNA dilution but no indications for in vitro recombination were found after RNA dilution. In conclusion, a two-amplicon strategy and limiting dilution of viral RNA followed by reverse transcription, nested PCR and Sanger sequencing, allows near full genome sequencing of individual HIV-1 RNA molecules. This method will be a valuable tool in the study of virus evolution and recombination.
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Affiliation(s)
- Laura Hebberecht
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
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20
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Telele NF, Kalu AW, Gebre-Selassie S, Fekade D, Marrone G, Grossmann S, Neogi U, Tegbaru B, Sönnerborg A. A viral genome wide association study and genotypic resistance testing in patients failing first line antiretroviral therapy in the first large countrywide Ethiopian HIV cohort. BMC Infect Dis 2019; 19:569. [PMID: 31262272 PMCID: PMC6604127 DOI: 10.1186/s12879-019-4196-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 06/17/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Antiretroviral therapy (ART) was rolled-out in Ethiopia in 2005, but there are no reports on outcome of ART and human immunodeficiency virus drug resistance (HIVDR) at national level. We described acquired drug resistance mutations in pol gene and performed a viral genome wide association study in virologic treatment failure patients who started first line ART during 2009-2011 in the first large countrywide HIV cohort in Ethiopia. METHODS The outcome of tenofovir (TDF)- and zidovudine (ZDV)-based ART was defined in 874 ART naïve patients using the on-treatment (OT) and intention-to-treat (ITT) analyses. Genotypic resistance testing was done in patients failing ART (> 1000 copies/ml) at month 6 and 12. Near full-length genome sequencing (NFLG) was used to assess amino acid changes in HIV-1 gag, pol, vif, vpr, tat, vpu, and nef genes between paired baseline and month 6 samples. RESULTS High failure rates were found in ITT analysis at month 6 and 12 (23.3%; 33.9% respectively). Major nucleoside and non-nucleoside reverse transcriptase (NRTI/NNRTI) drug resistance mutations were detected in most failure patients at month 6 (36/47; 77%) and month 12 (20/30; 67%). A high rate of K65R was identified only in TDF treated patients (35.7%; 50.0%, respectively). No significant difference was found in failure rate or extent of HIVDR between TDF- and ZDV- treated patients. All target regions of interest for HIVDR were described by NFLG in 16 patients tested before initiation of ART and at month 6. CONCLUSION In this first Ethiopian national cohort, a high degree of HIVDR was seen among ART failure patients, independent on whether TDF- or ZDV was given. However, the major reason to ART failure was lost-to-follow-up rather than virologic failure. Our NFLG assay covered all relevant target genes for antiretrovirals and is an attractive alternative for HIVDR surveillance.
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Affiliation(s)
- Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebre-Selassie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gaetano Marrone
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sebastian Grossmann
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Wellcome Trust Sanger Institute, Cancer, Ageing and Somatic Mutation Programme, Cambridge, UK
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
| | - Belete Tegbaru
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Genetic characterization and recombinant history of a novel HIV-1 circulating recombinant form (CRF101_01B) identified in Yunnan, China. INFECTION GENETICS AND EVOLUTION 2019; 73:109-112. [PMID: 31028881 DOI: 10.1016/j.meegid.2019.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/29/2019] [Accepted: 04/23/2019] [Indexed: 11/20/2022]
Abstract
The high frequency of multiple HIV-1 recombinant events among the B, C and CRF01_AE were constantly occurring in Yunnan China. Here, we characterized a novel HIV-1 circulating recombinant form (CRF) consisting of CRF01_AE and subtype B (CRF101_01B) from three epidemiologically unlinked individuals. Phylogenetic analysis based on near full length genome (NFLG) sequences revealed that CRF101_01B formed a distinct monophyletic cluster supported by a high bootstrap value of 100%, distantly related to all known HIV-1 CRFs. CRF101_01B had a CRF01_AE backbone with two B segments inserted, respectively, in the gag and pol region. Further, subregion tree analysis showed that CRF01_AE backbone and subtype B segment inserted originated from a Thailand lineage. In addition, our study found that CRF101_01B originated around the year 1996-1998. This findings described a novel HIV-1 CRF, and highlighted the importance of continual monitoring of genetic diversity and complexity of HIV-1 strains in Yunnan, China.
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22
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Banerjee I, Aralaguppe SG, Lapins N, Zhang W, Kazemzadeh A, Sönnerborg A, Neogi U, Russom A. Microfluidic centrifugation assisted precipitation based DNA quantification. LAB ON A CHIP 2019; 19:1657-1664. [PMID: 30931470 DOI: 10.1039/c9lc00196d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleic acid amplification methods are increasingly being used to detect trace quantities of DNA in samples for various diagnostic applications. However, quantifying the amount of DNA from such methods often requires time consuming purification, washing or labeling steps. Here, we report a novel microfluidic centrifugation assisted precipitation (μCAP) method for single-step DNA quantification. The method is based on formation of a visible precipitate, which can be quantified, when an intercalating dye (GelRed) is added to the DNA sample and centrifuged for a few seconds. We describe the mechanism leading to the precipitation phenomenon. We utilize centrifugal microfluidics to precisely control the formation of the visible and quantifiable mass. Using a standard CMOS sensor for imaging, we report a detection limit of 45 ng μl-1. Furthermore, using an integrated lab-on-DVD platform we recently developed, the detection limit is lowered to 10 ng μl-1, which is comparable to those of current commercially available instruments for DNA quantification. As a proof of principle, we demonstrate the quantification of LAMP products for a HIV-1B type genome containing plasmid on the lab-on-DVD platform. The simple DNA quantification system could facilitate advanced point of care molecular diagnostics.
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Affiliation(s)
- I Banerjee
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Sweden.
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23
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Obasa AE, Engelbrecht S, Jacobs GB. Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985. Sci Rep 2019; 9:6227. [PMID: 30996293 PMCID: PMC6470202 DOI: 10.1038/s41598-019-42417-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/06/2019] [Indexed: 11/09/2022] Open
Abstract
HIV-1 subtype C is the most prevalent subtype in South Africa. Although subtype B was previously detected in South Africa, there is limited sequence information available. We characterized near full-length HIV-1 subtype B sequences from samples collected at the start of the South African HIV-1 epidemic, in the 1980s. Five samples were analysed by PCR amplification, Sanger DNA sequencing and phylogenetic analyses. The viral genomes were amplified in two overlapping fragments of 5.5 kb and 3.7 kb. The sequences were subtyped using REGA version 3.0, RIP version 3.0 and jpHMM. Maximum Likelihood phylogenetic trees were inferred with MEGA version 6. Four HIV-1 patient sequences were subtyped as pure HIV-1 subtype B. One sequence was characterized as a novel HIV-1 subtype B and D recombinant. The sequences clustered phylogenetically with other HIV-1 subtype B sequences from South Africa, Europe and the USA. We report the presence of an HIV-1 subtype B and D recombinant strain detected in the beginning of the epidemic. This indicates that viral recombination events were already happening in 1985, but could have been missed as sequence analyses were often limited to small genomic regions of HIV-1.
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Affiliation(s)
- Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.,National Health Laboratory Services (NHLS), Western Cape Region, Tygerberg Hospital, Cape Town, South Africa
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
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24
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Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [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] [Received: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
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Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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25
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Banin AN, Tuen M, Bimela JS, Tongo M, Zappile P, Khodadadi-Jamayran A, Nanfack AJ, Meli J, Wang X, Mbanya D, Ngogang J, Heguy A, Nyambi PN, Fokunang C, Duerr R. Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants. Viruses 2019; 11:E317. [PMID: 30939815 PMCID: PMC6520859 DOI: 10.3390/v11040317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/17/2022] Open
Abstract
Near full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic instrument to assist targeted therapeutic measures against viral components. There is still a lack of robust and adaptable techniques for efficient NFGS from miscellaneous HIV-1 subtypes. Using rational primer design, a broad primer set was developed for the amplification and sequencing of diverse HIV-1 group M variants from plasma. Using pure subtypes as well as diverse, unique recombinant forms (URF), variable amplicon approaches were developed for NFGS comprising all functional genes. Twenty-three different genomes composed of subtypes A (A1), B, F (F2), G, CRF01_AE, CRF02_AG, and CRF22_01A1 were successfully determined. The NFGS approach was robust irrespective of viral loads (≥306 copies/mL) and amplification method. Third-generation sequencing (TGS), single genome amplification (SGA), cloning, and bulk sequencing yielded similar outcomes concerning subtype composition and recombinant breakpoint patterns. The introduction of a simple and versatile near full genome amplification, sequencing, and cloning method enables broad application in phylogenetic studies of diverse HIV-1 subtypes and can contribute to personalized HIV therapy and diagnosis.
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Affiliation(s)
- Andrew N Banin
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Faculty of Medicine and Biomedical Sciences, Department of Biochemistry, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Michael Tuen
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Jude S Bimela
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Faculty of Science, Department of Biochemistry, BP 1364 Yaoundé, Cameroon.
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants, BP 906 Yaoundé, Cameroon.
| | - Paul Zappile
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories (ABL) and Genome Technology Center (GTC), Division of Advanced Research Technologies (DART), New York University Langone Medical Center, New York, NY 10016, USA.
| | - Aubin J Nanfack
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Medical Diagnostic Center, BP 15810 Yaoundé, Cameroon.
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, BP 3077 Messa Yaoundé, Cameroon.
| | | | - Xiaohong Wang
- Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, Department of Microbiology, Parasitology and Infectious Diseases, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Jeanne Ngogang
- Faculty of Medicine and Biomedical Sciences, Department of Biochemistry, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Adriana Heguy
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Phillipe N Nyambi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
| | - Charles Fokunang
- Faculty of Medicine and Biomedical Sciences, Department of Pharmacotoxicology & Pharmacokinetics, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Ralf Duerr
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
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26
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Zhang W, Svensson Akusjärvi S, Sönnerborg A, Neogi U. Characterization of Inducible Transcription and Translation-Competent HIV-1 Using the RNAscope ISH Technology at a Single-Cell Resolution. Front Microbiol 2018; 9:2358. [PMID: 30333813 PMCID: PMC6176121 DOI: 10.3389/fmicb.2018.02358] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/14/2018] [Indexed: 01/17/2023] Open
Abstract
Identifying the source and dynamics of persistent HIV-1 at single-cell resolution during cART is crucial for the design of strategies to eliminate the latent HIV-1 reservoir. An assay to measure latent HIV-1 that can distinguish inducible from defective proviruses with high precision is essential to evaluate the efficacy of HIV-1 cure efforts but is presently lacking. The primary aim of this study was therefore to identify transcription and translation competent latently infected cells through detection of biomolecules that are dependent on transcriptional activation of the provirus. We investigated the applicability of two commercially available assays; PrimeFlowTM RNA Assay (RNAflow) and RNAscope® ISH (RNAscope) for evaluation of the efficacy of latency reversal agents (LRAs) to reactivate the HIV-1 latent reservoir. The J-Lat cell model (clones 6.3, 9.3, and 10.6) and four LRAs was used to evaluate the sensitivity, specificity, and lower detection limit of the RNAflow and RNAscope assays for the detection and description of the translation-competent HIV-1 reservoir. We also checked for HIV-1 subtype specificity of the RNAscope assay using patient-derived subtype A1, B, C, and CRF01_AE recombinant plasmids following transfection in 293T cells and the applicability of the method in patient-derived peripheral blood mononuclear cells (PBMCs). The lower detection limit of RNAflow was 575 HIV-1 infected cells/million and 45 cells/million for RNAscope. The RNAscope probes, designed for HIV-1B, also detected other subtypes (A1, B, C, and CRF01_AE). RNAscope was applicable for the detection of HIV-1 in patient-derived PBMCs following LRA activation. In conclusion, our study showed that RNAscope can be used to quantify the number of directly observed individual cells expressing HIV-1 mRNA following LRA activation. Therefore, it can be a useful tool for characterization of translation-competent HIV-1 in latently infected cell at single-cell resolution in the fields of HIV-1 pathogenesis and viral persistence.
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Affiliation(s)
- Wang Zhang
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden.,Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Sweden
| | - Sara Svensson Akusjärvi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden.,Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
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Miao J, Ran J, Song Y, Liu Y, Gao L, Miao Z, Zhang C, Feng Y, Xia X. Characterization of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B'/C (CRF96_cpx), in Yunnan, China. AIDS Res Hum Retroviruses 2018; 34:393-397. [PMID: 29258320 DOI: 10.1089/aid.2017.0288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Currently, complex HIV-1 recombinations among the B', C, and CRF01_AE genotypes have frequently arisen in Yunnan, China. A novel HIV-1 complex circulating recombinant form (CRF) consisting of B', C, and CRF01_AE (CRF96_cpx) was recently characterized from three epidemiologically unlinked individuals. Two strains of them were isolated from the injecting drug users in this study, the remaining one strain (JL. RL01) was obtained from a previous report in Jilin province. Phylogenetic analysis based on near full-length genome revealed that CRF96_cpx formed a distinct monophyletic cluster supported by a high bootstrap value of 100%, distantly related to all known HIV-1 subtypes/CRFs. CRF96_cpx had a CRF01_AE backbone with three subtype B' and C segments inserted, respectively, in the gag and pol region. Furthermore, subregion tree analysis showed that CRF01_AE backbone and subtype B segment inserted originated from a Thai-CRF01_AE lineage, whereas subtype C fragment inserted was from an India C lineage. They are different from previously documented CRF01_AE/B/C forms in its distinct backbone, inserted fragment size, and breakpoints. This highlighted the importance of continual monitoring of genetic diversity and complexity of HIV-1 strains in Yunnan, China.
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Affiliation(s)
- Jing Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jieyu Ran
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yindi Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yang Liu
- Yunnan SCISPARK Genetic Testing Lab, Kunming SCISPARK Biotechnology Co., Ltd, Kunming, China
| | - Li Gao
- Department of Infectious Diseases, Yunnan Provincial Hospital of Infectious Diseases, Kunming, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Chunyue Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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Ex-vivo antiretroviral potency of newer integrase strand transfer inhibitors cabotegravir and bictegravir in HIV type 1 non-B subtypes. AIDS 2018; 32:469-476. [PMID: 29239896 DOI: 10.1097/qad.0000000000001726] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To determine the antiretroviral activity of the integrase strand transfer inhibitors (INSTIs), raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), cabotegravir (CAB) and bictegravir (BIC), against different subtypes as well as primary and acquired drug resistance mutations (DRMs) in a patient-cohort infected with diverse subtypes. DESIGN Biochemical and virological drug sensitivity analyses using patient-derived HIV type 1 (HIV-1) genes and cross-sectional/longitudinal clinical study. METHODS Assays for 50% inhibition of 3'-end processing (IC50-3EP), strand transfer (IC50-ST) and drug sensitivity for five INSTIs were done using patient-derived integrase or gag-pol genes from subtypes A1, B, C, 01_AE and 02_AG. Integrase from INSTI-naive (n = 270) and experienced (n = 96) patients were sequenced. RESULTS RAL had higher IC50-ST than the other INSTIs for all subtypes. EVG had higher IC50-ST for HIV 1 subtype C (P < 0.05) and 02_AG (P < 0.05) than HIV 1 subtype B (HIV-1B). DTG showed lower IC50-ST in HIV 1 subtype C than HIV-1B (P = 0.003). In CAB , the non-B subtypes showed lower IC50-ST (P < 0.05) than HIV-1B. In BIC, lower IC50-ST in 01_AE (P = 0.017) and 02_AG (P = 0.045) than HIV-1B. In drug sensitivity assay, inhibiting virus replication by 50% for DTG [median (IQR) 2.14 (1.3-2.56)], CAB [1.68 (1.34-2.55)] and BIC [1.07 (0.22-2.53)] were lower than RAL and EVG. One patient had a primary DRMs (0.3%, 1/270), but 17 (6.3%) had one major accessory DRM, of which 12 were E157Q. CONCLUSION The equal or higher potency in non-B subtypes of DTG, CAB and BIC compared with RAL and EVG confirms their suitability for use in countries dominated by non-B subtypes. Any impact of the high prevalence of major accessory mutations, especially E157Q, requires long-term follow-up studies.
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29
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Alampalli SV, Thomson MM, Sampathkumar R, Sivaraman K, U. K. J. AJ, Dhar C, D. Souza G, Berry N, Vyakarnam A. Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India. PLoS One 2017; 12:e0188603. [PMID: 29220350 PMCID: PMC5722309 DOI: 10.1371/journal.pone.0188603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/09/2017] [Indexed: 01/25/2023] Open
Abstract
India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics. Here we describe the development and implementation of approaches for HIV-1 NGS analysis in a southern Indian cohort. Plasma samples (n = 20) were obtained from HIV-1-confirmed individuals living in and around the city of Bengaluru. Near full-length genome recovery was obtained for 9 Indian HIV-1 patients, with recovery of full-length gag and env genes for 10 and 2 additional subjects, respectively. Phylogenetic analyses indicate the majority of sequences to be represented by subtype C viruses branching within a monophyletic clade, comprising viruses from India, Nepal, Myanmar and China and closely related to a southern African cluster, with a low prevalence of the A1C recombinant form also present. Development of algorithms for bespoke recovery and analysis at a local level will further aid clinical management of HIV-1 infected Indian subjects and delineate the progress of the HIV-1 pandemic in this and other geographical regions.
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Affiliation(s)
| | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Majadahonda, Madrid, Spain
| | - Raghavan Sampathkumar
- Centre for Infectious Disease Research (CIDR), Indian Institute of Science, Bengaluru, India
| | - Karthi Sivaraman
- Centre for Infectious Disease Research (CIDR), Indian Institute of Science, Bengaluru, India
| | | | - Chirag Dhar
- Department of Infectious Diseases, St John’s Research Institute, Bengaluru, India
| | - George D. Souza
- Department of Pulmonary Medicine & Department of Infectious Diseases, St John’s Research Institute, Bengaluru, India
| | - Neil Berry
- Division of Virology, NIBSC, South Mimms, United Kingdom
| | - Annapurna Vyakarnam
- Centre for Infectious Disease Research (CIDR), Indian Institute of Science, Bengaluru, India
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- * E-mail: ,
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30
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Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden. Sci Rep 2017; 7:6371. [PMID: 28744024 PMCID: PMC5527090 DOI: 10.1038/s41598-017-06860-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/19/2017] [Indexed: 11/08/2022] Open
Abstract
A temporal increase in non-B subtypes has earlier been described in Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex and unique recombinant forms (URFs) if the epidemics converge. In the present study, we performed subtyping using four automated tools and phylogenetic analysis by RAxML of pol gene sequences (n = 5246) and HIV-1 near full-length genome (HIV-NFLG) sequences (n = 104). A CD4+ T-cell decline trajectory algorithm was used to estimate time of HIV infection. Transmission clusters were identified using the family-joining method. The analysis of HIV-NFLG and pol gene described 10.6% (11/104) and 2.6% (137/5246) of the strains as URFs, respectively. An increasing trend of URFs was observed in recent years by both approaches (p = 0·0082; p < 0·0001). Transmission cluster analysis using the pol gene of all URFs identified 14 clusters with two to eight sequences. Larger transmission clusters of URFs (BF1 and 01B) were observed among MSM who mostly were sero-diagnosed in recent time. Understanding the increased appearance and transmission of URFs in recent years could have importance for public health interventions and the use of HIV-NFLG would provide better statistical support for such assessments.
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31
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Li Y, Miao J, Miao Z, Song Y, Wen M, Zhang Y, Guo S, Zhao Y, Feng Y, Xia X. Identification of a Novel HIV Type 1 Circulating Recombinant Form (CRF86_BC) Among Heterosexuals in Yunnan, China. AIDS Res Hum Retroviruses 2017; 33:279-283. [PMID: 27593341 DOI: 10.1089/aid.2016.0188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, multiple circulating recombinant forms (CRFs) and unique recombinant forms of human immunodeficiency virus type 1 (HIV-1) have been described in Yunnan, China. Here, we identified a novel HIV-1 CRF (CRF86_BC) isolated from three heterosexuals with no obvious epidemiologic linkage in western Yunnan (Baoshan prefecture) in China. CRF86_BC had a subtype C backbone with four subtype B fragments inserted into the pol, vpr, vpu, env, and nef gene regions, respectively. Furthermore, subregion tree analysis revealed that subtype C backbone originated from an Indian C lineage and subtype B segment inserted was from a Thai B lineage. They are different from previously documented B/C forms in its distinct backbone, inserted fragment size, and break points. This highlighted the importance of continual monitoring of genetic diversity and complexity of HIV-1 strains in this region.
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Affiliation(s)
- Yanping Li
- Pharmaceutical College, Guangxi Medical University, Guangxi, China
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Jing Miao
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Yindi Song
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Min Wen
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Ya Zhang
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Shimin Guo
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Yuan Zhao
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Yue Feng
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
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Aralaguppe SG, Siddik AB, Manickam A, Ambikan AT, Kumar MM, Fernandes SJ, Amogne W, Bangaruswamy DK, Hanna LE, Sonnerborg A, Neogi U. Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus. J Virol Methods 2016; 236:98-104. [PMID: 27448822 DOI: 10.1016/j.jviromet.2016.07.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 07/08/2016] [Accepted: 07/09/2016] [Indexed: 11/16/2022]
Abstract
Analysing the HIV-1 near full-length genome (HIV-NFLG) facilitates new understanding into the diversity of virus population dynamics at individual or population level. In this study we developed a simple but high-throughput next generation sequencing (NGS) protocol for HIV-NFLG using clinical specimens and validated the method against an external quality control (EQC) panel. Clinical specimens (n=105) were obtained from three cohorts from two highly conserved HIV-1C epidemics (India and Ethiopia) and one diverse epidemic (Sweden). Additionally an EQC panel (n=10) was used to validate the protocol. HIV-NFLG was performed amplifying the HIV-genome (Gag-to-nef) in two fragments. NGS was performed using the Illumina HiSeq2500 after multiplexing 24 samples, followed by de novo assembly in Iterative Virus Assembler or VICUNA. Subtyping was carried out using several bioinformatics tools. Amplification of HIV-NFLG has 90% (95/105) success-rate in clinical specimens. NGS was successful in all clinical specimens (n=45) and EQA samples (n=10) attempted. The mean error for mutations for the EQC panel viruses were <1%. Subtyping identified two as A1C recombinant. Our results demonstrate the feasibility of a simple NGS-based HIV-NFLG that can potentially be used in the molecular surveillance for effective identification of subtypes and transmission clusters for operational public health intervention.
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Affiliation(s)
- Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Abu Bakar Siddik
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ashokkumar Manickam
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Indian Council of Medical Research, Chennai, India
| | | | | | - Sunjay Jude Fernandes
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine & Science for Life Laboratories, Karolinska Institutet, Stockholm, Sweden
| | - Wondwossen Amogne
- Department of Internal Medicine, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Luke Elizabeth Hanna
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Indian Council of Medical Research, Chennai, India
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden; Department of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.
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Lee NY, Wang JC, Lin YC, Wu CJ, Li CW, Li MC, Wang SW, Tseng FC, Ko WC. Characterization of the Near Full-Length Genome of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant in an Injection Drug User from Southern Taiwan. AIDS Res Hum Retroviruses 2016; 32:588-94. [PMID: 26892740 DOI: 10.1089/aid.2015.0246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 CRF07_BC became prevalent in Taiwan after the epidemic among injection drug users (IDUs). We describe a unique recombinant form (URF) consisting of CRF01_AE and CRF07_BC (named URF_0107-H8) genes detected from an IDU. The 8.8 kb near full-length genome of URF_0107-H8 had a CRF01_AE backbone with two CRF07_BC fragments in the reverse transcriptase and integrase region [RT-Int; HXB2 nucleotide (nt) positions 2942-4709] and within the envelop (nt 8467-8722) gene. Phylogenetic analyses revealed that its 1.8 kb RT-Int sequence clustered with those of CRF07_BC strains from Taiwan, while sequences of CRF01_AE portions were more similar to those of Central African origin than contemporaneous CRF01_AE isolates in Taiwan or prevalent in East or Southeast Asia. Recombination breakpoints and phylogenetic relationships of URF_0107-H8 were different from those of CRF01_AE/CRF07_BC URFs previously reported from China. This highlighted the importance of continual monitoring of genetic evolution of HIV strains and the emergence of new recombinants.
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Affiliation(s)
- Nan-Yao Lee
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jui-Ching Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Yi-Ching Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Chi-Jung Wu
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Chia-Wen Li
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Ming-Chi Li
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Shainn-Wei Wang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Fan-Chen Tseng
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
- Department of Nursing, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Wen-Chien Ko
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
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Amogne W, Bontell I, Grossmann S, Aderaye G, Lindquist L, Sönnerborg A, Neogi U. Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster. AIDS Res Hum Retroviruses 2016; 32:471-4. [PMID: 26881451 DOI: 10.1089/aid.2015.0380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In this study, we characterize HIV-1 subtype C (HIV-1C) strains at the near full-length genome (NFLG) level and perform genotypic drug resistance testing (GRT) and genotypic tropism testing (GTT) from Ethiopia (HIV-1CET). Plasma samples (n = 150) were obtained from therapy-naive individuals residing in Addis Ababa, Ethiopia in 2008. HIV-NFLG was performed in a subset of patients (n = 30). GRT (pol) and GTT (V3 env) were performed using in-house methods. GTT was analyzed by PhenoSeq-C. The phylogenetic analysis of the NLFG identified two separate clusters of HIV-1CET, although all strains formed one large overarching cluster together. At NFLG, greater diversity was found among HIV-1CET strains compared to HIV-1C strains from other geographical locations. The geographic clustering was weak in the small subgenomic (pol and env) regions. The primary drug-resistant mutations were identified at a low level (<5%). GTT identified that 12% (12/102) of the patients were predicted to be harboring X4-tropic or both R5/X4-tropic viruses.
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Affiliation(s)
- Wondwossen Amogne
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Irene Bontell
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Grossmann
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Getachew Aderaye
- Department of Medicine, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lars Lindquist
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Ujjwal Neogi
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
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Neogi U, Häggblom A, Singh K, Rogers LC, Rao SD, Amogne W, Schülter E, Zazzi M, Arnold E, Sarafianos SG, Sönnerborg A. Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries. J Antimicrob Chemother 2015; 71:367-71. [PMID: 26518047 DOI: 10.1093/jac/dkv359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/02/2015] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES The use of the NNRTI rilpivirine in low- and middle-income countries (LMICs) is under debate. The main objective of this study was to provide further clinical insights and biochemical evidence on the usefulness of rilpivirine in LMICs. PATIENTS AND METHODS Rilpivirine resistance was assessed in 5340 therapy-naive and 13,750 first-generation NNRTI-failed patients from Europe and therapy-naive HIV-1 subtype C (HIV-1C)-infected individuals from India (n = 617) and Ethiopia (n = 127). Rilpivirine inhibition and binding affinity assays were performed using patient-derived HIV-1C reverse transcriptases (RTs). RESULTS Primary rilpivirine resistance was rare, but the proportion of patients with >100,000 HIV-1 RNA copies/mL pre-ART was high in patients from India and Ethiopia, limiting the usefulness of rilpivirine as a first-line drug in LMICs. In patients failing first-line NNRTI treatments, cross-resistance patterns suggested that 73% of the patients could benefit from switching to rilpivirine-based therapy. In vitro inhibition assays showed ∼ 2-fold higher rilpivirine IC50 for HIV-1C RT than HIV-1B RT. Pre-steady-state determination of rilpivirine-binding affinities revealed 3.7-fold lower rilpivirine binding to HIV-1C than HIV-1B RT. Structural analysis indicated that naturally occurring polymorphisms close to the NNRTI-binding pocket may reduce rilpivirine binding, leading to lower susceptibility of HIV-1C to rilpivirine. CONCLUSIONS Our clinical and biochemical findings indicate that the usefulness of rilpivirine has limitations in HIV-1C-dominated epidemics in LMICs, but the drug could still be beneficial in patients failing first-line therapy if genotypic resistance testing is performed.
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Affiliation(s)
- Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden
| | - Amanda Häggblom
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Kamalendra Singh
- Departments of Molecular Microbiology & Immunology and Biochemistry, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Leonard C Rogers
- Departments of Molecular Microbiology & Immunology and Biochemistry, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Shwetha D Rao
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden
| | | | - Eugen Schülter
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Eddy Arnold
- Department of Chemistry and Chemical Biology and Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Stefan G Sarafianos
- Departments of Molecular Microbiology & Immunology and Biochemistry, Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
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