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Ismael N, Wilkinson E, Mahumane I, Gemusse H, Giandhari J, Bauhofer A, Vubil A, Mambo P, Singh L, Mabunda N, Bila D, Engelbrecht S, Gudo E, Lessells R, de Oliveira T. Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999–2018. Viruses 2022; 14:v14091992. [PMID: 36146798 PMCID: PMC9505726 DOI: 10.3390/v14091992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
HIV drug resistance (HIVDR) can become a public health concern, especially in low- and middle-income countries where genotypic testing for people initiating antiretroviral therapy (ART) is not available. For first-line regimens to remain effective, levels of transmitted drug resistance (TDR) need to be monitored over time. To determine the temporal trends of TDR in Mozambique, a search for studies in PubMed and sequences in GenBank was performed. Only studies covering the pol region that described HIVDR and genetic diversity from treatment naïve patients were included. A dataset from seven published studies and one novel unpublished study conducted between 1999 and 2018 were included. The Calibrated Population Resistance tool (CPR) and REGA HIV-1 Subtyping Tool version 3 for sequences pooled by sampling year were used to determine resistance mutations and subtypes, respectively. The prevalence of HIVDR amongst treatment-naïve individuals increased over time, reaching 14.4% in 2018. The increase was most prominent for non-nucleoside reverse transcriptase inhibitors (NNRTIs), reaching 12.7% in 2018. Subtype C was predominant in all regions, but a higher genetic variability (19% non-subtype C) was observed in the north region of Mozambique. These findings confirm a higher diversity of HIV in the north of the country and an increased prevalence of NNRTI resistance among treatment naïve individuals over time.
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Affiliation(s)
- Nalia Ismael
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
- Correspondence: (N.I.); (T.d.O.)
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Isabel Mahumane
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Hernane Gemusse
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Adilson Bauhofer
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Adolfo Vubil
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Pirolita Mambo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Dulce Bila
- Elizabeth Glaser Pediatric AIDS Foundation in Mozambique, Avenida Agostinho Neto, Maputo 620, Mozambique
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Eduardo Gudo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Túlio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
- Correspondence: (N.I.); (T.d.O.)
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Adeniyi OV, Obi CL, Ter Goon D, Iweriebor B, Chitha W, Okoh A. Genetic Characterization of HIV-1 Subtype A1/C/D/B/K Unique Recombinant Form from Eastern Cape, South Africa. AIDS Res Hum Retroviruses 2021; 37:162-168. [PMID: 33076679 DOI: 10.1089/aid.2020.0160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype C is the predominant circulating virus in South Africa. There are reports of non-C subtypes emerging in different regions of the country, however, very little information exists on the genetic diversity of HIV in the Eastern Cape Province, despite having the third largest HIV epidemic in the country. In the current study, a near full-length genomic sequence obtained from a heterosexual woman in the Eastern Cape (ADE/CMH/0032), was analyzed using two rapid online subtyping tools; REGA and the jumping Profile Hidden Markov Model (jpHMM). There was agreement between the two tools in the assignment of the pol, Vif, and vpr regions, identified as a C/D recombinant (pol) and subtype C (vif and vpr). Some degree of agreement existed in the assignment of the Gag region, as recombinant: A1/C/B/D by REGA, and A1/C/D by jPHMM, respectively. There was disparity between the two online tools in the subtype assignment of the remaining gene regions. Phylogenetic analysis with pure subtype reference sequences showed that the query sequence clustered with a subtype C reference strain, with a low bootstrap value of 43%. This is the first report from South Africa of a putative unique recombinant as classified by rapid online subtyping tools, involving subtype A1, C, D, B, and K. However, the clinical and epidemiological implications of this variant remain unclear. Further studies are needed to fully understand the genetic diversity of HIV in the Eastern Cape.
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Affiliation(s)
- Oladele Vincent Adeniyi
- Department of Family Medicine & Rural Health, Faculty of Health Sciences, Walter Sisulu University/Cecilia Makiwane Hospital/East London Hospital Complex, East London, South Africa
| | - Chikwelu Larry Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Daniel Ter Goon
- Department of Public Health, Faculty of Health Sciences, University of Fort Hare, East London, South Africa
| | - Benson Iweriebor
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Wezile Chitha
- Health Systems Enablement & Innovation Uni, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anthony Okoh
- SAMRC Microbial Water Quality Monitoring Centre, Faculty of Science and Agriculture, University of Fort Hare, Alice, South Africa
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Digban TO, Iweriebor BC, Obi LC, Nwodo U, Okoh AI. Molecular Genetics and the Incidence of Transmitted Drug Resistance Among Pre-Treatment HIV-1 Infected Patients in the Eastern Cape, South Africa. Curr HIV Res 2020; 17:335-342. [PMID: 31584370 DOI: 10.2174/1570162x17666191004093433] [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: 05/25/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Transmitted drug resistance (TDR) remains a significant threat to Human immunodeficiency virus (HIV) infected patients that are not exposed to antiretroviral treatment. Although, combined antiretroviral therapy (cART) has reduced deaths among infected individuals, emergence of drug resistance is gradually on rise. OBJECTIVE To determine the drug resistance mutations and subtypes of HIV-1 among pre-treatment patients in the Eastern Cape of South Africa. METHODS Viral RNA was extracted from blood samples of 70 pre-treatment HIV-1 patients while partial pol gene fragment amplification was achieved with specific primers by RT-PCR followed by nested PCR and positive amplicons were sequenced utilizing ABI Prism 316 genetic sequencer. Drug resistance mutations (DRMs) analysis was performed by submitting the generated sequences to Stanford HIV drug resistance database. RESULTS Viral DNA was successful for 66 (94.3%) samples of which 52 edited sequences were obtained from the protease and 44 reverse transcriptase sequences were also fully edited. Four major protease inhibitor (PI) related mutations (I54V, V82A/L, L76V and L90M) were observed in seven patients while several other minor and accessory PIs were also identified. A total of 11(25.0%) patients had NRTIs related mutations while NNRTIs were observed among 14(31.8%) patients. K103N/S, V106M and M184V were the most common mutations identified among the viral sequences. Phylogenetic analysis of the partial pol gene indicated all sequences clustered with subtype C. CONCLUSION This study indicates that HIV-1 subtype C still predominates and responsible for driving the epidemic in the Eastern Cape of South Africa with slow rise in the occurrence of transmitted drug resistance.
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Affiliation(s)
- Tennison Onoriode Digban
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Benson Chucks Iweriebor
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Larry Chikwelu Obi
- Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Uchechuwku Nwodo
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Anthony Ifeanyi Okoh
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
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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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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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Murzakova A, Kireev D, Baryshev P, Lopatukhin A, Serova E, Shemshura A, Saukhat S, Kolpakov D, Matuzkova A, Suladze A, Nosik M, Eremin V, Shipulin G, Pokrovsky V. Molecular Epidemiology of HIV-1 Subtype G in the Russian Federation. Viruses 2019; 11:E348. [PMID: 30995717 PMCID: PMC6521041 DOI: 10.3390/v11040348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023] Open
Abstract
Although HIV-1 subtype A has predominated in Russia since the end of the 20th century, other viral variants also circulate in this country. The dramatic outbreak of HIV-1 subtype G in 1988-1990 represents the origin of this variant spreading in Russia. However, full genome sequencing of the nosocomial viral variant and an analysis of the current circulating variants have not been conducted. We performed near full-length genome sequencing and phylogenetic and recombination analyses of 11 samples; the samples were determined to be subtype G based on an analysis of the pol region. Three samples were reliably obtained from patients infected during the nosocomial outbreak. The other 8 samples were obtained from patients who were diagnosed in 2010-2015. Phylogenetic analysis confirmed that a man from the Democratic Republic of the Congo was the origin of the outbreak. We also found that currently circulating viral variants that were genotyped as subtype G according to their pol region are in fact unique recombinant forms. These recombinant forms are similar to the BG-recombinants from Western Europe, particularly Spain and Portugal. The limitations of subtyping based on the pol region suggest that these viral variants are more widespread in Europe than is currently supposed.
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Affiliation(s)
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
| | - Pavel Baryshev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
| | | | - Ekaterina Serova
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia.
| | - Sergey Saukhat
- Department of Epidemiology, Rostov State Medical University, 344022 Rostov-on-Don, Russia.
| | - Dmitry Kolpakov
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Anna Matuzkova
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Alexander Suladze
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Marina Nosik
- Ilya Ilyich Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia.
| | - Vladimir Eremin
- Republican Research and Practical Center for Epidemiology and Microbiology, 220114 Minsk, Belarus.
| | - German Shipulin
- Center of Strategical Planning and Management of Biomedical Health Risks of the Ministry of Health, 119121 Moscow, Russia.
| | - Vadim Pokrovsky
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
- Department of infectious diseases with courses of epidemiology and phthisiology, RUDN University, 117198 Moscow, Russia.
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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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8
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Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management. J Int AIDS Soc 2015; 18:20035. [PMID: 26115688 PMCID: PMC4482814 DOI: 10.7448/ias.18.1.20035] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/08/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022] Open
Abstract
Introduction HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Methods Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. Results After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Conclusions Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.
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