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Antiretroviral (ARV) Drug Resistance and HIV-1 Subtypes among Injecting Drug Users in the Coastal Region of Kenya. Adv Virol 2022; 2022:3217749. [PMID: 35186083 PMCID: PMC8853818 DOI: 10.1155/2022/3217749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 11/21/2022] Open
Abstract
HIV-1 genetic diversity results into the development of widespread drug-resistant mutations (DRMs) for the first-line retroviral therapy. Nevertheless, few studies have investigated the relationship between DRMs and HIV-1 subtypes among HIV-positive injecting drug users (IDUs). This study therefore determined the association between HIV-1 genotypes and DRMs among the 200 IDUs. Stanford HIV Drug Resistance Database was used to interpret DRMs. The five HIV-1 genotypes circulating among the IDUs were A1 (25 (53.2%)), A2 (2 (4.3%)), B (2 (4.3%)), C (9 (19.1%)), and D (9 (19.1%)). The proportions of DRMs were A1 (12 (52.2%)), A2 (1 (4.3%)), B (0 (0.0%)), C (5 (21.7%)), and D (5 (21.7%)). Due to the large proportion of drug resistance across all HIV-1 subtypes, surveillance and behavioral studies need to be explored as IDUs may be spreading the drug resistance to the general population. In addition, further characterization of DRMs including all the relevant clinical parameters among the larger population of IDUs is critical for effective drug resistance surveillance.
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Ekpenyong ME, Adegoke AA, Edoho ME, Inyang UG, Udo IJ, Ekaidem IS, Osang F, Uto NP, Geoffery JI. Collaborative Mining of Whole Genome Sequences for Intelligent HIV-1 Sub-Strain(s) Discovery. Curr HIV Res 2022; 20:163-183. [PMID: 35142269 DOI: 10.2174/1570162x20666220210142209] [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: 08/24/2021] [Revised: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Effective global antiretroviral vaccines and therapeutic strategies depend on the diversity, evolution, and epidemiology of their various strains as well as their transmission and pathogenesis. Most viral disease-causing particles are clustered into a taxonomy of subtypes to suggest pointers toward nucleotide-specific vaccines or therapeutic applications of clinical significance sufficient for sequence-specific diagnosis and homologous viral studies. These are very useful to formulate predictors to induce cross-resistance to some retroviral control drugs being used across study areas. OBJECTIVE This research proposed a collaborative framework of hybridized (Machine Learning and Natural Language Processing) techniques to discover hidden genome patterns and feature predictors, for HIV-1 genome sequences mining. METHOD 630 human HIV-1 genome sequences above 8500 bps were excavated from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov) for 21 countries across different continents, Antarctica exempt. These sequences were transformed and learned using a self-organizing map (SOM). To discriminate emerging/new sub-strain(s), the HIV-1 reference genome was included as part of the input isolates/samples during the training. After training the SOM, component planes defining pattern clusters of the input datasets were generated, for cognitive knowledge mining and subsequent labelling of the datasets. Additional genome features including dinucleotide transmission recurrences, codon recurrences, and mutation recurrences, were finally extracted from the raw genomes to construct output classification targets for supervised learning. RESULTS SOM training explains the inherent pattern diversity of HIV-1 genomes as well as inter- and intra-country transmissions in which mobility might play an active role, as corroborated by literature. Nine sub-strains were discovered after disassembling the SOM correlation hunting matrix space attributed to disparate clusters. Cognitive knowledge mining separated similar pattern clusters bounded by a certain degree of correlation range, discovered by the SOM. A Kruskal-Wallis rank-sum test and Wilcoxon rank-sum test showed statistically significant variations in dinucleotide, codon, and mutation patterns. CONCLUSION Results of the discovered sub-strains and response clusters visualizations corroborate existing literature, with significant haplotype variations. The proposed framework would assist in the development of decision support systems for easy contact tracing, infectious disease surveillance, and studying the progressive evolution of the reference HIV-1 genome.
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Affiliation(s)
- Moses E Ekpenyong
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
- Centre for Research and Development, University of Uyo, Uyo, Nigeria
| | - Anthony A Adegoke
- Department of Microbiology, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Mercy E Edoho
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Udoinyang G Inyang
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Ifiok J Udo
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Itemobong S Ekaidem
- Department of Chemical Pathology, College of Health Sciences, University of Uyo, Uyo, Nigeria
| | - Francis Osang
- Department of Computer Science, Faculty of Science, National Open University, Abuja, Nigeria
| | - Nseobong P Uto
- School of Mathematics and Statistics, University of St Andrews, Scotland, United Kingdom
| | - Joseph I Geoffery
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
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Kusagawa S, Tatsumi M, Sakamoto-Umeki Y, Takekawa N, Matsubayashi K, Ishimaru K, Kawana-Tachikawa A. Nucleotide Sequence of HIV-1-Positive Specimen Reference Panel for Evaluation of HIV In Vitro Diagnostics in Japan. AIDS Res Hum Retroviruses 2021; 37:994-997. [PMID: 34652965 DOI: 10.1089/aid.2021.0160] [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/circulating recombinant form (CRF) distribution of HIV-1-positive specimens for evaluating HIV in vitro diagnostics (IVDs) was examined and compared with the HIV-1 epidemic in Japan. The nucleotide sequences of the gag-pol region of 173 plasma specimens (84, provided in 2007, and 89 in 2013-2015) were determined. HIV-1 subtype/CRF classification was performed based on the phylogenetic analyses of the sequences. The subtype/CRF distribution resulting in this study was similar to that of a previous epidemiological report. Three CRF02_AG and one unique recombinant form, including subtype G and A regions, were observed in the 2013 and 2014 specimens, except in the 2007 specimens. The reference panel consisting of these specimens was practical for the evaluation of HIV IVDs in Japan.
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Affiliation(s)
- Shigeru Kusagawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masashi Tatsumi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuko Sakamoto-Umeki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Naho Takekawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keiji Matsubayashi
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Ken Ishimaru
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Phylodynamic analysis reveals changing transmission dynamics of HIV-1 CRF01_AE in Japan from heterosexuals to men who have sex with men. Int J Infect Dis 2021; 108:397-405. [PMID: 34082091 DOI: 10.1016/j.ijid.2021.05.066] [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: 04/06/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND HIV-1 circulating recombinant form (CRF) 01_AE is the second major subtype in Japan. Our previous study indicated that CRF01_AE was predominantly circulating in heterosexuals/injecting drug users (IDUs). With implications of increased CRF01_AE infections among men who have sex with men (MSM), this study sought to investigate whether the transmission dynamics of CRF01_AE infections in Japan have changed. METHODS Sequences from 8032 newly diagnosed HIV-1-infected individuals were analysed. For 614 (7.6%) of CRF01_AE cases, clusters were identified and categorised by transmission risks. Median times to the most recent common ancestors (tMRCA) were estimated. RESULTS The individuals were predominantly Japanese (64%) and male (72%). MSM became the predominant transmission risk from 2014. Thirty transmission clusters (TCs) and 48 pairs, including 40% of individuals, were identified. MSM were approximately five times more likely to be in a TC compared to heterosexuals, and were the major contributors to TCs. tMRCA data suggest that MSM TCs emerged from 1996 and became predominant around 2000. CONCLUSIONS CRF01_AE has spread among MSM, with frequent and continuous cluster formations, and MSM has become the predominant transmission risk. Our study suggested that CRF01_AE transmission has shifted from heterosexuals/IDUs to MSM. Prevention measures targeting key populations should be considered for controlling CRF01_AE spread.
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Waheed U, Noor FA, Saba N, Wazeer A, Qasim Z, Arshad M, Karimi S, Farooq A, Usman J, Zaheer HA. Genetic Diversity of Human Immunodeficiency Virus Type 1 in Asymptomatic Blood Donors in Islamabad, Pakistan. J Lab Physicians 2020; 12:92-97. [PMID: 32905360 PMCID: PMC7467833 DOI: 10.1055/s-0040-1716593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective
The serological testing of human immunodeficiency virus (HIV) is mandatory under the blood safety legislation of Pakistan; hence, data exist on the prevalence of HIV in blood donors. However, little is known about the molecular epidemiology of HIV in the blood donor population. Therefore, the current study was designed to study the genetic diversity of HIV-1 infection in a population of apparently healthy treatment-naive blood donors in Islamabad, Pakistan.
Material and Methods
A total of 85,736 blood donors were tested for HIV by the chemiluminescence immunoassay. All positive donor samples were analyzed for the presence of various HIV genotypes (types and subtypes). Viral ribonucleic acid was extracted from blood samples of HIV positive donors and reverse transcribed into complementary deoxyribonucleic acid (cDNA). The cDNA of all positive donors was then analyzed for the presence of various HIV genotypes (types and subtypes) by employing subtype-specific primers in a nested polymerase chain reaction. The amplified products were run on ethidium bromide-stained 2% agarose gel and visualized using a ultraviolet transilluminator. A particular subtype was assigned to a sample if the subtype-specific reaction made a band 20% highly intense compared with the band made by the subtype-independent reaction.
Results
A total of 85,736 blood donors were screened for the presence of antibodies to HIV. Out of them, 114 were initially found reactive for HIV. The repeat testing resulted in 112 (0.13%) positive donors, 95% confidence interval 0.0014 (0.0011–0.0018). These 112 samples were analyzed for molecular typing of HIV-1. The predominant HIV-1 subtype was A (
n
= 101) (90.1%) followed by subtype B (
n
= 11) (9.9%).
Conclusion
These findings are key to understand the diversified HIV epidemic at the molecular level and should assist public health workers in implementing measures to lessen the further dissemination of these viruses in the country.
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Affiliation(s)
- Usman Waheed
- Department of Pathology and Transfusion Medicine, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.,Islamabad Blood Transfusion Authority, Ministry of National Health Services, Government of Pakistan, Islamabad, Pakistan
| | - Farooq Ahmed Noor
- Department of Pathology and Transfusion Medicine, Divisional Headquarters Teaching Hospital, Mirpur, Azad Jammu and Kashmir, Pakistan
| | - Noore Saba
- Department of Health, Peshawar Regional Blood Centre, Khyber Pakhtunkhwa, Pakistan
| | - Akhlaaq Wazeer
- Department of Pathology and Transfusion Medicine, Divisional Headquarters Teaching Hospital, Mirpur, Azad Jammu and Kashmir, Pakistan
| | - Zahida Qasim
- Department of Pathology and Transfusion Medicine, Divisional Headquarters Teaching Hospital, Mirpur, Azad Jammu and Kashmir, Pakistan
| | - Muhammad Arshad
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Saira Karimi
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Ahmad Farooq
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Javaid Usman
- Department of Pathology, Army Medical College, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Hasan Abbas Zaheer
- Department of Pathology and Transfusion Medicine, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.,Safe Blood Transfusion Programme, Ministry of National Health Services, Government of Pakistan, Islamabad, Pakistan
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Ali M, Nadeem M, Numan M, Khalil AT, Maqbool K, Yousaf MZ, Shinwari ZK, Idrees M. Thirty years of HIV in Pakistan: a systematic review of prevalence and current scenario. Future Virol 2017. [DOI: 10.2217/fvl-2017-0009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: HIV infection was first reported in Pakistan in 1987. Since then it has been a point of concern in the country. Materials & methods: We searched the literature on HIV in Pakistan using different keywords in Google, Pubmed, PakMediNet and GoogleScholar, and found a total of 64 articles dating from 1987 to 2016. Results: Total 4,882,450 individuals from Pakistan have been screened for HIV since last 30 years. The estimated overall prevalence was 0.041% (95% CI: 0.0–6.79). The highest infection rates of 15.05% (SE = 4.27%) were observed in injection drug users, followed by refugees (2.63%), sex workers (2.21%) and prisoners (1.32%). Conclusion: Awareness and medical surveillance programs in the high-risk population are required to decrease future burden of HIV in Pakistan.
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Affiliation(s)
- Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Muhammad Nadeem
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Muhammad Numan
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Ali Talha Khalil
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Khurram Maqbool
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Muhammad Zubair Yousaf
- Centers of Excellence in Science & Applied Technologies, Islamabad, Pakistan
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, 54600 Pakistan
| | - Zabta Khan Shinwari
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Muhammad Idrees
- Hazara University Mansehra, Khyber Pakhtunkhwa, 21120 Pakistan-
- Center for Applied Molecular Biology (CAMB), University of the Punjab, 53700 Lahore
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Matsumoto C, Shinohara N, Sobata R, Uchida S, Satake M, Tadokoro K. Genetic Analysis of HIV-1 in Japan: a Comprehensive Analysis of Donated Blood. Jpn J Infect Dis 2016; 70:136-142. [PMID: 27357980 DOI: 10.7883/yoken.jjid.2015.504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Japan, the number of human immunodeficiency virus (HIV)-1 infections remains relatively low; nevertheless, the annual incidence of HIV-1 infection has not decreased. New infections remain a great concern, and an improved understanding of epidemiological trends is critical for public health. The env C2V3 and pol sequences of HIV-1 RNA from 240 early (1996-2001) and 223 more recent (2010-2012) blood donations were used to compare the distribution of virus subtypes and to generate phylogenetic trees. Subtype B was clearly predominant in both early and more recent donations (both were 88.3%), and CRF01_AE was the second most common subtype. Phylogenetic analysis revealed a peculiar epidemiological transition. Compared to early subtype B isolates from 2 major endemic areas (Tokyo and Osaka), the more recent subtype B isolates formed fewer tight clusters in phylogenetic trees (from 8 to 2 clusters in Tokyo and 5 to zero clusters in Osaka). Furthermore, mixing of HIV-1 infections between these 2 endemic areas appear to increase. Analysis of phylogenetic trees suggested that local outbreaks have become smaller in Japan; however, intermixing of viral types between these 2 areas was more evident in the more recent samples.
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Affiliation(s)
- Chieko Matsumoto
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society
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8
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Junqueira DM, Almeida SEDM. HIV-1 subtype B: Traces of a pandemic. Virology 2016; 495:173-84. [PMID: 27228177 DOI: 10.1016/j.virol.2016.05.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/01/2016] [Accepted: 05/03/2016] [Indexed: 11/18/2022]
Abstract
Human migration is a major process that shaped the origin and dissemination of HIV. Within HIV-1, subtype B (HIV-1B) is the most disseminated variant and it is assumed to be the causative agent in approximately 11% of all cases of HIV worldwide. Phylogenetic studies have revealed that HIV-1B emerged in Kinshasa (Africa) and was introduced into the Caribbean region via Haiti in or around 1966 by human migration. After localized dispersion, the virus was brought to the United States of America via homosexual/bisexual contact around 1969. Inside USA, the incidence of HIV-1B infection increased exponentially and it became established in the population, affecting not only homosexual individuals but also heterosexual individuals and injecting drug users. Soon after, the virus was disseminated and became established in other regions, including Europe, Asia, Latin America, and Australia. Recent studies suggest that, in addition to this pandemic clade, several lineages have emerged from Haiti and reached other Caribbean and Latin American countries via short-distance dissemination. Different subtype B genetic variants have also been detected in these epidemics. Four genetic variants have been described to date: subtype B', which mainly circulates in Thailand and other Asian countries; a specific variant mainly found in Trinidad and Tobago; the GPGS variant, which is primarily detected in Korea; and the GWGR variant, which is mainly detected in Brazil. This paper reviews the evolution of HIV-1B and its impact on the human population.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Centro Universitário Ritter dos Reis - UniRitter, Departamento de Ciências da Saúde, Avenida Orfanotrófio, 555 - Teresópolis, Porto Alegre, RS, Brazil.
| | - Sabrina Esteves de Matos Almeida
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Instituto de Ciências da Saúde, Universidade FEEVALE, Rodovia RS 239, 2755 - Vila Nova, Novo Hamburgo, RS, Brazil.
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Cashin K, Gray LR, Harvey KL, Perez-Bercoff D, Lee GQ, Sterjovski J, Roche M, Demarest JF, Drummond F, Harrigan PR, Churchill MJ, Gorry PR. Reliable genotypic tropism tests for the major HIV-1 subtypes. Sci Rep 2015; 5:8543. [PMID: 25712827 PMCID: PMC4894445 DOI: 10.1038/srep08543] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/23/2015] [Indexed: 01/21/2023] Open
Abstract
Over the past decade antiretroviral drugs have dramatically improved the prognosis for HIV-1 infected individuals, yet achieving better access to vulnerable populations remains a challenge. The principal obstacle to the CCR5-antagonist, maraviroc, from being more widely used in anti-HIV-1 therapy regimens is that the pre-treatment genotypic "tropism tests" to determine virus susceptibility to maraviroc have been developed primarily for HIV-1 subtype B strains, which account for only 10% of infections worldwide. We therefore developed PhenoSeq, a suite of HIV-1 genotypic tropism assays that are highly sensitive and specific for establishing the tropism of HIV-1 subtypes A, B, C, D and circulating recombinant forms of subtypes AE and AG, which together account for 95% of HIV-1 infections worldwide. The PhenoSeq platform will inform the appropriate use of maraviroc and future CCR5 blocking drugs in regions of the world where non-B HIV-1 predominates, which are burdened the most by the HIV-1 pandemic.
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Affiliation(s)
- Kieran Cashin
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010
| | - Lachlan R Gray
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - Katherine L Harvey
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010
| | | | - Guinevere Q Lee
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada Y6Z 1Y6
| | - Jasminka Sterjovski
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - Michael Roche
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - James F Demarest
- ViiV Healthcare, Research Triangle Park, North Carolina, USA 27709-3398
| | | | | | - Melissa J Churchill
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Medicine, Monash University, Melbourne, Australia 3800 [3] Department of Microbiology, Monash University, Melbourne, Australia 3800
| | - Paul R Gorry
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010 [3] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800 [4] School of Applied Sciences, College of Science, Engineering and Health, RMIT University, Melbourne, Australia 3001
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Phylodynamic analysis reveals CRF01_AE dissemination between Japan and neighboring Asian countries and the role of intravenous drug use in transmission. PLoS One 2014; 9:e102633. [PMID: 25025900 PMCID: PMC4099140 DOI: 10.1371/journal.pone.0102633] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 06/21/2014] [Indexed: 11/30/2022] Open
Abstract
Background One major circulating HIV-1 subtype in Southeast Asian countries is CRF01_AE, but little is known about its epidemiology in Japan. We conducted a molecular phylodynamic study of patients newly diagnosed with CRF01_AE from 2003 to 2010. Methods Plasma samples from patients registered in Japanese Drug Resistance HIV-1 Surveillance Network were analyzed for protease-reverse transcriptase sequences; all sequences undergo subtyping and phylogenetic analysis using distance-matrix-based, maximum likelihood and Bayesian coalescent Markov Chain Monte Carlo (MCMC) phylogenetic inferences. Transmission clusters were identified using interior branch test and depth-first searches for sub-tree partitions. Times of most recent common ancestor (tMRCAs) of significant clusters were estimated using Bayesian MCMC analysis. Results Among 3618 patient registered in our network, 243 were infected with CRF01_AE. The majority of individuals with CRF01_AE were Japanese, predominantly male, and reported heterosexual contact as their risk factor. We found 5 large clusters with ≥5 members and 25 small clusters consisting of pairs of individuals with highly related CRF01_AE strains. The earliest cluster showed a tMRCA of 1996, and consisted of individuals with their known risk as heterosexual contacts. The other four large clusters showed later tMRCAs between 2000 and 2002 with members including intravenous drug users (IVDU) and non-Japanese, but not men who have sex with men (MSM). In contrast, small clusters included a high frequency of individuals reporting MSM risk factors. Phylogenetic analysis also showed that some individuals infected with HIV strains spread in East and South-eastern Asian countries. Conclusions Introduction of CRF01_AE viruses into Japan is estimated to have occurred in the 1990s. CFR01_AE spread via heterosexual behavior, then among persons connected with non-Japanese, IVDU, and MSM. Phylogenetic analysis demonstrated that some viral variants are largely restricted to Japan, while others have a broad geographic distribution.
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11
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Evaluating immunologic response and clinical deterioration in treatment-naive patients initiating first-line therapies infected with HIV-1 CRF01_AE and subtype B. J Acquir Immune Defic Syndr 2013; 62:293-300. [PMID: 23138836 DOI: 10.1097/qai.0b013e31827a2e8f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND HIV-1 group M viruses diverge 25%-35% in envelope, important for viral attachment during infection, and 10%-15% in the pol region, under selection pressure from common antiretrovirals. In Asia, subtypes B and CRF01_AE are common genotypes. Our objectives were to determine whether clinical, immunological, or virological treatment responses differed by genotype in treatment-naive patients initiating first-line therapy. METHODS Prospectively collected longitudinal data from patients in Thailand, Hong Kong, Malaysia, Japan, Taiwan, and South Korea were provided for analysis. Covariates included demographics, hepatitis B and C coinfections, baseline CD4 T lymphocyte count, and plasma HIV-1 RNA levels. Clinical deterioration (a new diagnosis of Centers for Disease Control and Prevention category B/AIDS-defining illness or death) was assessed by proportional hazards models. Surrogate endpoints were 12-month change in CD4 cell count and virologic suppression post therapy, evaluated by linear and logistic regression, respectively. RESULTS Of 1105 patients, 1036 (93.8%) infected with CRF01_AE or subtype B were eligible for inclusion in clinical deterioration analyses and contributed 1546.7 person-years of follow-up (median: 413 days, interquartile range: 169-672 days). Patients >40 years demonstrated smaller immunological increases (P = 0.002) and higher risk of clinical deterioration (hazard ratio = 2.17; P = 0.008). Patients with baseline CD4 cell counts >200 cells per microliter had lower risk of clinical deterioration (hazard ratio = 0.373; P = 0.003). A total of 532 patients (48.1% of eligible) had CD4 counts available at baseline and 12 months post therapy for inclusion in immunolgic analyses. Patients infected with subtype B had larger increases in CD4 counts at 12 months (P = 0.024). A total of 530 patients (48.0% of eligible) were included in virological analyses with no differences in response found between genotypes. CONCLUSIONS Results suggest that patients infected with CRF01_AE have reduced immunologic response to therapy at 12 months, compared with subtype B-infected counterparts. Clinical deterioration was associated with low baseline CD4 counts and older age. The lack of differences in virologic outcomes suggests that all patients have opportunities for virological suppression.
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Emergence in Japan of an HIV-1 variant associated with transmission among men who have sex with men (MSM) in China: first indication of the International Dissemination of the Chinese MSM lineage. J Virol 2013; 87:5351-61. [PMID: 23365432 DOI: 10.1128/jvi.02370-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A survey of HIV-1 strains circulating in the Tokyo-Kanagawa metropolitan area of Japan during 2004 to 2011 (n = 477) identified six Japanese males (patients 1 to 6), who harbored viruses with genome segments derived from a distinct CRF01_AE variant uniquely found among men who have sex with men (MSM) in China (designated CN.MSM.01-1). These six HIV infections were diagnosed in 2010 and 2011 among MSM (3 of 75) and men with unknown risk factors (3 of 63) and differed from the vast majority of HIV infections among MSM in Japan, which are overwhelmingly characterized by subtype B (239 of 246 [97.2%]). Approximately one-third (91 of 239 [38.1%]) of subtype B strains from MSM in Japan belong to a large monophyletic cluster (designated JP.MSM.B-1). In addition, we identified a smaller subtype B cluster (n = 8) (designated JP.MSM.B-2) that also contains strains from two Chinese MSM living in Japan. Interestingly, patients 5 and 6 were found to be coinfected with CRF01_AE (CN.MSM.01-1) and subtype B (JP.MSM.B-2 or JP.MSM.B-1) variants that are unique to the HIV-1 epidemics among MSM in China and Japan, respectively. Our study demonstrates for the first time the effect of the expanding HIV epidemic among MSM in China on transmission in neighboring countries and shows the ongoing mixing of CRF01_AE and subtype B lineages unique to HIV-1 that cocirculate in MSM populations in East Asia. This finding highlights the importance of strengthening epidemiological surveillance in the region and the need for effective measures to limit transmission among MSM in East Asia.
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Hemelaar J. Implications of HIV diversity for the HIV-1 pandemic. J Infect 2012; 66:391-400. [PMID: 23103289 DOI: 10.1016/j.jinf.2012.10.026] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/21/2012] [Indexed: 11/17/2022]
Abstract
HIV-1 genetic variability within individuals and populations plays a central role in the HIV pandemic. Multiple zoonotic transmissions of SIV to humans have resulted in distinct HIV lineages in humans which have further diversified within the population over time. High rates of mutation and recombination during HIV reverse transcription create a genetic diversity in the host which is subject to selection pressures by the immune response and antiretroviral treatment. The global distribution of HIV genetic variants and the impact of HIV diversity on pathogenesis, transmission and clinical management are reviewed. Finally, the key role of escape mutations in the immune response to HIV is discussed as well as the major challenge which HIV-1 diversity poses to HIV vaccine development.
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Affiliation(s)
- Joris Hemelaar
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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Sanabani SS, Pastena ÉRDS, da Costa AC, Martinez VP, Kleine-Neto W, de Oliveira ACS, Sauer MM, Bassichetto KC, Oliveira SMS, Tomiyama HTI, Sabino EC, Kallas EG. Characterization of partial and near full-length genomes of HIV-1 strains sampled from recently infected individuals in São Paulo, Brazil. PLoS One 2011; 6:e25869. [PMID: 22022460 PMCID: PMC3193532 DOI: 10.1371/journal.pone.0025869] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 09/13/2011] [Indexed: 12/03/2022] Open
Abstract
Background Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in São Paul, Brazil. Methodology HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. The NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. The data were phylogenetically analyzed. Results Of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. Of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. The proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%). Conclusions Our results confirm the existence of various HIV-1 subtypes circulating in São Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. The proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations.
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Affiliation(s)
- Sabri Saeed Sanabani
- Division of Clinical Immunology and Allergy, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
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Tovanabutra S, Sanders EJ, Graham SM, Mwangome M, Peshu N, McClelland RS, Muhaari A, Crossler J, Price MA, Gilmour J, Michael NL, McCutchan FM. Evaluation of HIV type 1 strains in men having sex with men and in female sex workers in Mombasa, Kenya. AIDS Res Hum Retroviruses 2010; 26:123-31. [PMID: 20156095 DOI: 10.1089/aid.2009.0115] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We compared HIV-1 strains in incident and prevalent infections in a cohort of men having sex with men (MSM) and female sex workers (FSW) near Mombasa, Kenya and conducted a cross-sectional study of viral isolates from a sample of HIV-1-infected MSM and FSW in Kilifi, Coast Province, Kenya. RNA extracted from plasma of 13 MSM, 9 FSW, and one heterosexual male was amplified by nested RT-PCR and the products were directly sequenced. HIV-1 strains from 21 individuals were characterized with one or more complete genome sequences, and two were sequenced in the Nef gene. The envelope quasispecies was also studied in one individual. Among MSM, eight strains were subtype A and five were recombinant. There were two epidemiologically linked pairs of sequences; one pair was subtype A and the other pair was a complex AA2CD recombinant of identical structure. Another MSM was dually infected with DG recombinant strains of related, but nonidentical, structure. MSM also harbored AC and AD recombinant strains. The FSW harbored seven subtype A strains, an AD recombinant, and an AA2D strain related to CRF16_A2D. The one heterosexual male studied had a subtype A infection. This MSM epidemic in Kenya appears to be of local origin, harboring many strains typical of the broader Kenyan epidemic. Characteristics of a close social network were identified, with extended chains of transmission, novel recombinant strains possibly generated within the network, and a relatively high proportion of recombinant and dual infections.
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Affiliation(s)
- Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | - Eduard J. Sanders
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Susan M. Graham
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
- University of Washington, Seattle, Washington 98109
| | - Mary Mwangome
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
| | - Norbert Peshu
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
| | | | - Allan Muhaari
- Centre for Geographic Medicine Research–Coast, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
| | - Jacqueline Crossler
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | - Matt A. Price
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Jill Gilmour
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | - Francine M. McCutchan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland 20850
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Giuliani M, Montieri S, Palamara G, Latini A, Alteri C, Perno C, Santoro M, Rezza G, Ciccozzi M. Non-B HIV type 1 subtypes among men who have sex with men in Rome, Italy. AIDS Res Hum Retroviruses 2009; 25:157-64. [PMID: 19108689 DOI: 10.1089/aid.2008.0175] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
An increase in the circulation of HIV-1 non-B subtypes has been observed in recent years in Western European countries. Due to the lack of data on the circulation of HIV-1 non-B subtypes among European HIV-1-infected men who have sex with men (MSM), a biomolecular study was conducted in Rome, Italy. HIV-1 partial pol gene sequences from 111 MSM individuals (76 drug naive and 35 drug experienced) were collected during the years 2004-2006. All these sequences were analyzed using the REGA HIV-1 Subtyping Tool, and aligned using CLUSTAL X followed by manual editing using the Bioedit software. A BLAST search for non-B subtype sequences was also performed. Twenty-six (23.4%) MSM were not Italians. Eight individuals (7.2%) were diagnosed as HIV infected before 1991, 20 (18.0%) between 1991 and 1999, and 83 (74.8%) from 2000 to 2006. Fifteen (15/111, 13.5%) individuals were infected with the non-B subtype. The percentage of infection with HIV-1 non-B subtypes was 8.2% (7/85) among Italian MSM and 30.8% (8/26) among the non-Italians (OR = 4.95 95% IC: 1.40-17.87). Individuals infected with the non-B subtype were significantly younger than those infected with the HIV-1 B subtype (28 years vs. 34 years, p = 0.003). The CRFs were more prevalent (8.1%) than pure subtypes (5.4%), which were distributed as follows: subtype C (2.6%), subtype A1 (1.7%), and subtype F1 (0.9%). Major mutations conferring resistance to antiretroviral drugs (ARV) were not found among HIV-1 non-B subtype drug-naive patients but were found in two ARV-experienced individuals. The data show that viral diversity is likely increasing in a population group that had been previously characterized by the circulation of HIV-1 subtype B.
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Affiliation(s)
- M. Giuliani
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - S. Montieri
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
| | - G. Palamara
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - A. Latini
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - C. Alteri
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - C.F. Perno
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - M.M. Santoro
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - G. Rezza
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
| | - M. Ciccozzi
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
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Khoja S, Ojwang P, Khan S, Okinda N, Harania R, Ali S. Genetic analysis of HIV-1 subtypes in Nairobi, Kenya. PLoS One 2008; 3:e3191. [PMID: 18784834 PMCID: PMC2527130 DOI: 10.1371/journal.pone.0003191] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 08/18/2008] [Indexed: 01/17/2023] Open
Abstract
Background Genetic analysis of a viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, in vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution. Objective In this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya. Methodology 69 blood samples were collected from a diverse subject population attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Polymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database. Results Blood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C. Conclusion Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections.
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Affiliation(s)
- Suhail Khoja
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan
| | - Peter Ojwang
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Saeed Khan
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan
| | - Nancy Okinda
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Reena Harania
- Department of Medicine, Aga Khan University Hospital, Nairobi, Kenya
| | - Syed Ali
- Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan
- * E-mail:
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Salemi M, Goodenow MM, Montieri S, de Oliveira T, Santoro MM, Beshkov D, Alexiev I, Elenkov I, Elenkov I, Yakimova T, Varleva T, Rezza G, Ciccozzi M. The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries. AIDS Res Hum Retroviruses 2008; 24:771-9. [PMID: 18544022 DOI: 10.1089/aid.2007.0181] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little is known about the HIV-1 epidemic in Balkan countries. To fill the gap, we investigated the viral genetic diversity in Bulgaria, by sequencing and phylogenetic characterization of 86 plasma samples collected between 2002 and 2006 from seropositive individuals diagnosed within 1986-2006. Analysis of pol gene sequences assigned 51% of the samples to HIV-1 subtype B and 27% to subtype A1. HIV-1 subtype C, F, G, H, and a few putative recombinant forms were also found. Phylogenetic and molecular clock analysis showed a continuous exchange of subtype A and B between Bulgaria and Western as well as other Eastern European countries. At least three separate introductions of HIV-1 subtype A and four of HIV-1 subtype B have occurred within the past 25 years in Bulgaria. The central geographic location of Bulgaria, the substantial genetic heterogeneity of the epidemic with multiple subtypes, and the significant viral flow observed to and from the Balkan countries have the potential to modify the current HIV-1 epidemiological structure in Europe and highlight the importance of more extensive and continuous monitoring of the epidemic in the Balkans.
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Affiliation(s)
- Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610
| | - Maureen M. Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610
| | - Stefania Montieri
- Epidemiology Unit, Department of Infectious Parasitic and Immunomediate Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Tulio de Oliveira
- MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of Western Cape, Cape Town, South Africa
| | | | - Danail Beshkov
- National HIV Confirmatory Laboratory—National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivailo Alexiev
- National HIV Confirmatory Laboratory—National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Ivan Elenkov
- Faculty of Biology, University of Sofia, Sofia, Bulgaria
| | - Tsvetana Yakimova
- Ministry of Health, Program of “Prevention and Control of HIV/AIDS,” Sofia, Bulgaria
| | - Tonka Varleva
- Ministry of Health, Program of “Prevention and Control of HIV/AIDS,” Sofia, Bulgaria
| | - Giovanni Rezza
- Epidemiology Unit, Department of Infectious Parasitic and Immunomediate Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious Parasitic and Immunomediate Diseases, Istituto Superiore di Sanità, Rome, Italy
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Abstract
The enormous genetic diversity of HIV-1 is a major challenge to vaccine development and may have important clinical consequences. HIV-1 group M predominates globally, with nine subtypes, several sub-subtypes and over 30 circulating recombinant forms that may exhibit differences with respect to transmissibility, pathogenicity and development of antiretroviral resistance. Subtype D appears to be more virulent than other subtypes, in particular subtype A. Subtype C may be less virulent and more transmissible, although the evidence for this is inconclusive. All group M non-B subtypes appear to be equally susceptible to combination antiretroviral therapy, but development of resistance mutations may vary significantly between subtypes. Further research into the clinical implications of HIV-1 diversity is crucial for effective HIV-1 prevention and treatment.
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Affiliation(s)
- Susan M Graham
- University of Washington, Box 359909, 325 Ninth Avenue, Seattle, WA 98104, USA
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Hamatake M, Nishizawa M, Yamamoto N, Kato S, Sugiura W. A simple competitive RT-PCR assay for quantitation of HIV-1 subtype B and non-B RNA in plasma. J Virol Methods 2007; 142:113-7. [PMID: 17367872 DOI: 10.1016/j.jviromet.2007.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 12/21/2006] [Accepted: 01/17/2007] [Indexed: 11/22/2022]
Abstract
An easy, inexpensive competitive RT-PCR assay for HIV-1 RNA quantitation was constructed. A 138-bp sequence in the HIV-1 gag p24 region was selected as the target and co-amplified with competitor RNA containing an internal 44-bp deletion. Quantitation of serial dilutions of control RNA samples prepared from the LAI isolate demonstrated a good linearity (R(2)=0.991) within the range between 10 and 250 copies/sample. The detection limit of the assay was determined to be 3.8 copies/sample by Probit analysis and corresponded to 110 copies/ml in plasma. The intra-assay CV value was 9.1%, and the inter-assay value was 25.9%. Both were comparable to those obtained with commercially available HIV-1 RNA quantitation kits. The correlation efficient for the results obtained in 47 plasma samples from HIV-1-infected individuals (subtype A in 1, subtype B in 25, subtype C in 4, subtype F in 1, and CRF01 AE in 16) with the competitive RT-PCR and Cobas Amplicor HIV-1 Monitor test v1.5 was 0.956 for subtype B and 0.947 for subtype non-B. The assay devised is a good alternative for monitoring antiretroviral therapy in resource-poor countries.
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Affiliation(s)
- Makiko Hamatake
- Department of Molecular Virology, Tokyo Medical Dental University, Bunkyo, Tokyo 1138510, Japan
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Khan S, Rai MA, Khanani MR, Khan MN, Ali SH. HIV-1 subtype A infection in a community of intravenous drug users in Pakistan. BMC Infect Dis 2006; 6:164. [PMID: 17105667 PMCID: PMC1654165 DOI: 10.1186/1471-2334-6-164] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 11/14/2006] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Data on the subtypes of HIV in a population help in predicting the potential foci of epidemic, tracking the routes of infection and following the patterns of the virus' genetic divergence. Globally, the most prevalent HIV infection is the HIV-1 subtype C. In Asia, predominant subtypes of HIV-1 are B, C, and CRF-01AE. During the last few years, HIV prevalence in Pakistan has taken the form of a concentrated epidemic in at least two high risk groups, namely, Intravenous Drug Users (IDUs) and Male Sex Workers (MSWs). Factors that have facilitated the proliferation of HIV infection include transmission through a large number of repatriates and needle-sharing intravenous drug users, unscreened blood transfusions, and sexual illiteracy. The HIV subtypes infecting Pakistani populations have not been explored to date. In this study, we analyzed HIV-1 subtypes from in a high-risk community of IDUs in Karachi, the largest city of Pakistan. METHODS Samples were collected from 34 IDUs after their informed consent. In addition, the study subjects were administered a questionnaire regarding their sexual behavior and travel history. For HIV analysis, DNA was extracted from the samples and analyzed for HIV types and subtypes using subtype-specific primers in a nested polymerase chain reaction (PCR). The results from this PCR were further confirmed using the Heteroduplex Mobility Assay (HMA). RESULTS We found HIV-1 subtype A in all the 34 samples analyzed. A few of the study subjects were found to have a history of travel and stay in the United Arab Emirates. The same subjects also admitted to having contact with commercial sex workers during their stay abroad. CONCLUSION Our study therefore shows clade A HIV-1 to be prevalent among the IDUs in Karachi. As the prevalence of HIV in Pakistan continues to rise, more work needs to be done to track the infection, and to analyze the strains of HIV spreading through the country.
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Affiliation(s)
- Saeed Khan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Mohammad A Rai
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Muhammad N Khan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Syed H Ali
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
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