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Ng QR, Tee KK, Binley JM, Tong T. Cross-Neutralizing CRF01_AE-Infected Plasma from Malaysia Targets CD4-Binding Site of Human Immunodeficiency Virus Type-1 Envelope Glycoprotein. AIDS Res Hum Retroviruses 2022; 38:162-172. [PMID: 34006141 PMCID: PMC9206480 DOI: 10.1089/aid.2020.0299] [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: 02/03/2023] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) antigenic variation poses a great challenge for vaccine immunogen design to elicit broadly neutralizing antibodies (bNAbs). Over the last 10-15 years, great progress has been made to understand the conserved sites of sensitivity on HIV envelope glycoprotein spikes targeted by bNAbs. Plasma neutralization mapping and monoclonal antibody isolation efforts have revealed five major conserved epitope clusters. Most of this work has focused on subtype B and C-infected Caucasian or African donors. It is not clear if the same epitopes and epitope rank order preferences are also true in donors infected with different HIV-1 subtypes and with different racial backgrounds. To investigate this point, in this study we report the first attempt to profile the bNAb specificities of CRF01_AE-infected Malaysian plasmas. We first measured neutralization titers of 21 plasmas against a subtype A, B, and AE pseudovirus panel. This revealed that 14% (3 of 21) plasmas had cross-clade breadth. Focusing on the cross-neutralizing plasma P9, we used AE and JR-FL mutant pseudoviruses, gp120 monomer interference, and native polyacrylamide gel electrophoresis to better understand the neutralization specificity. P9 demonstrates CD4-binding-site specificity with trimer dependence and D368 independence.
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Affiliation(s)
- Qi Ron Ng
- Department of Biological Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - James M. Binley
- HIV and Coronavirus Vaccine Development, San Diego Biomedical Research Institute, San Diego, California, USA
| | - Tommy Tong
- Department of Biological Sciences, Sunway University, Bandar Sunway, Malaysia.,Address correspondence to: Tommy Tong, Department of Biological Sciences, Sunway University, Bandar Sunway 47500, Malaysia
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Zhou YH, Chen X, Liang YB, Pang W, Qin WH, Zhang C, Zheng YT. Near Full-Length Identification of a Novel HIV-1 CRF01_AE/B/C Recombinant in Northern Myanmar. AIDS Res Hum Retroviruses 2015; 31:845-50. [PMID: 25970165 DOI: 10.1089/aid.2015.0021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Myanmar-China border appears to be the "hot spot" region for the occurrence of HIV-1 recombination. The majority of the previous analyses of HIV-1 recombination were based on partial genomic sequences, which obviously cannot reflect the reality of the genetic diversity of HIV-1 in this area well. Here, we present a near full-length characterization of a novel HIV-1 CRF01_AE/B/C recombinant isolated from a long-distance truck driver in Northern Myanmar. It is the first description of a near full-length genomic sequence in Myanmar since 2003, and might be one of the most complicated HIV-1 chimeras ever detected in Myanmar, containing four CRF01_AE, six B segments, and five C segments separated by 14 breakpoints throughout its genome. The discovery and characterization of this new CRF01_AE/B/C recombinant indicate that intersubtype recombination is ongoing in Myanmar, continuously generating new forms of HIV-1. More work based on near full-length sequence analyses is urgently needed to better understand the genetic diversity of HIV-1 in these regions.
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Affiliation(s)
- Yan-Heng Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yue-Bo Liang
- Yunnan International Travel Healthcare Center, Kunming, Yunnan, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei-Hong Qin
- Yunnan International Travel Healthcare Center, Kunming, Yunnan, China
| | - Chiyu Zhang
- Pathogen Diagnostic Center, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Diverse forms of HIV-1 among Burmese long-distance truck drivers imply their contribution to HIV-1 cross-border transmission. BMC Infect Dis 2014; 14:463. [PMID: 25158600 PMCID: PMC4152572 DOI: 10.1186/1471-2334-14-463] [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: 02/19/2014] [Accepted: 08/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The China-Myanmar border is a particularly interesting region that has very high prevalence of and considerable diversity of HIV-1 recombinants. Due to the transient nature of their work, long-distance truck drivers (LDTDs) have a comparatively high potential to become infected with HIV-1 and further spread virus to other individuals in the area they travel within. In this study, we hypothesized that Burmese LDTDs crossing the China-Myanmar border frequently may potentially be involved in the cross-border transmission of HIV, and contribute to the extremely high prevalence of HIV-1 inter-subtype recombinants in this border region. METHODS A molecular epidemiology study was conducted among 105 Burmese LDTDs between 2008 and 2010. HIV-1 genetic fragments including p17, pol, vif-vpr, vpr-env, and C2V3 were amplified and sequenced. The subtype characterization and HIV-1 transmission were determined by both phylogenetic and phylogeographic analyses. RESULTS Diverse forms of HIV-1, including subtypes CRF01_AE (41.9%), C (8.6%), B (4.8%), CRF02_AG (1.0%), and inter-subtype recombinants (33.3%), as well as dual infection (10.5%), were detected among the tested LDTDs. Phylogeographic analyses based on pure subtype revealed that 77.8% Burmese LDTDs acquired HIV-1 infection in Yunnan, and the others in Myanmar. Both the C-related and CRF01_AE-related recombinants from these LDTDs appeared to have close genetic relationship with those from IDUs in Myanmar and Dehong. CONCLUSIONS Burmese LDTDs may contribute to HIV-1 transmission along the China-Myanmar border. The results may provide some new perspective for understanding the on-going generation and prevalence of HIV-1 recombinants in the border region.
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Kaur P, Khong WX, Wee SY, Tan EL, Pipper J, Koay E, Ng KY, Yap JK, Chew KK, Tan MT, Leo YS, Inoue M, Ng OT. Clinical evaluation of a low cost, in-house developed real-time RT-PCR human immunodeficiency virus type 1 (HIV-1) quantitation assay for HIV-1 infected patients. PLoS One 2014; 9:e89826. [PMID: 24603460 PMCID: PMC3945479 DOI: 10.1371/journal.pone.0089826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/26/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES HIV-1 viral quantitation is essential for treatment monitoring. An in-house assay would decrease financial barriers to access. MATERIALS AND METHODS A real-time competitive RT-PCR in house assay (Sing-IH) was developed in Singapore. Using HXB2 as reference, the assay's primers and probes were designed to generate a 183-bp product that overlaps a portion of the LTR region and gag region. A competitive internal control (IC) was included in each assay to monitor false negative results due to inhibition or human error. Clinical evaluation was performed on 249 HIV-1 positive patient samples in comparison with the commercially available Generic HIV Viral Load assay. Correlation and agreement of results were assessed for plasma HIV-1 quantification with both assays. RESULTS The assay has a lower limit of detection equivalent to 126 copies/mL of HIV-1 RNA and a linear range of detection from 100-1000000 copies/mL. Comparative analysis with reference to the Generic assay demonstrated good agreement between both assays with a mean difference of 0.22 log10 copies/mL and 98.8% of values within 1 log10 copies/mL range. Furthermore, the Sing-IH assay can quantify HIV-1 group M subtypes A-H and group N isolates adequately, making it highly suitable for our region, where subtype B and CRF01_AE predominate. CONCLUSIONS With a significantly lower running cost compared to commercially available assays, the broadly sensitive Sing-IH assay could help to overcome the cost barriers and serve as a useful addition to the currently limited HIV viral load assay options for resource-limited settings.
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Affiliation(s)
- Palvinder Kaur
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Wei Xin Khong
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sue Yuen Wee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, Singapore
| | - Eng Lee Tan
- Centre for Biomedical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
- Department of Paediatrics, University Children's Medical Institute, National University Hospital, Singapore
| | - Juergen Pipper
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore, Singapore
| | - Evelyn Koay
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kah Ying Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Joe Kwan Yap
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kuan Kiat Chew
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Mei Ting Tan
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee Sin Leo
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Lee Kong Chian School Of Medicine, Nanyang Technological University, Singapore
| | - Masafumi Inoue
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, Singapore
| | - Oon Tek Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
- * E-mail:
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Dey SK, Zahan N, Afrose S, Islam T, Shajahan M, Saha S, Mahmud SA, Talukder AA, Mizuguchi M, Ushijima H. Molecular epidemiology of HIV in Asia. HIV & AIDS REVIEW 2014. [DOI: 10.1016/j.hivar.2014.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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7
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Han X, An M, Zhao B, Duan S, Yang S, Xu J, Zhang M, McGoogan JM, Takebe Y, Shang H. High prevalence of HIV-1 intersubtype B'/C recombinants among injecting drug users in Dehong, China. PLoS One 2013; 8:e65337. [PMID: 23741489 PMCID: PMC3669332 DOI: 10.1371/journal.pone.0065337] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Objective To examine the distribution of HIV-1 genotypes among injecting drug users (IDUs) from Dehong, Yunnan province. Materials and Methods Blood samples from a total of 95 HIV-positive IDUs were retrospectively analyzed. Samples were collected between 2005 and 2009 from four cities in Dehong prefecture, western Yunnan province, the geographical origin of the HIV epidemic in China. HIV-1 gag, partial pol, vpr-env fragment, half-genome, or near-full-length sequences were analyzed to determine the HIV-1 genotypes of each subject. Results were compared with findings from past studies of IDUs in Dehong and in neighboring Myanmar. Results We observed a high prevalence of B′/C recombinants (82.4%) among IDUs in Dehong, the structural profiles of which do not match those previously reported in Dehong or in Myanmar. Furthermore, statistically significant differences in geographical and temporal distributions of HIV-1 genotypes were characterized by a predominance of HIV-1 B′/C recombinant forms among older subjects(p = 0.034), subjects from Longchuan district (p = 0.022), and subjects diagnosed between 2000 and 2004 (p = 0.004). Conclusions The increasing prevalence of multiple, new B′/C recombinant forms suggest that HIV-1 intersubtype recombination is substantial and ongoing in western Yunnan. This reflects the high-risk behavior of IDUs in this region and argues the need for stronger monitoring and prevention measures in Dehong and other high-prevalence areas around China.
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Affiliation(s)
- Xiaoxu Han
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Minghui An
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Bin Zhao
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Song Duan
- Dehong Prefecture Center for Disease Control and Prevention, Mangshi, Yunnan Province, China
| | - Shaomin Yang
- AIDS Care Center, Yunnan Provincial Hospital Infectious Disease, Kunming, Yunnan, China
| | - Junjie Xu
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Min Zhang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Jennifer M. McGoogan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yutaka Takebe
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hong Shang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
- * E-mail:
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Travers SA. Conservation, Compensation, and Evolution of N-Linked Glycans in the HIV-1 Group M Subtypes and Circulating Recombinant Forms. ISRN AIDS 2012; 2012:823605. [PMID: 24052884 PMCID: PMC3765798 DOI: 10.5402/2012/823605] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/25/2012] [Indexed: 01/17/2023]
Abstract
The “glycan shield” exposed on the surface of the HIV-1 gp120 env glycoprotein has been previously proposed as a novel target for anti-HIV treatments. While such targeting of these glycans provides an exciting prospect for HIV treatment, little is known about the conservation and variability of glycosylation patterns within and between the various HIV-1 group M subtypes and circulating recombinant forms. Here, we present evidence of strong strain-specific glycosylation patterns and show that the epitope for the 2G12 neutralising antibody is poorly conserved across HIV-1 group M. The unique glycosylation patterns within the HIV-1 group M subtypes and CRFs appear to explain their varying susceptibility to neutralisation by broadly cross-neutralising (BCN) antibodies. Compensatory glycosylation at linearly distant yet three-dimensionally proximal amino acid positions appears to maintain the integrity of the glycan shield while conveying resistance to neutralisation by BCN antibodies. We find that highly conserved clusters of glycosylated residues do exist on the gp120 trimer surface and suggest that these positions may provide an exciting target for the development of BCN anticarbohydrate therapies.
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Affiliation(s)
- Simon A Travers
- Medical Research Council Unit for Bioinformatics Capacity Development, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Belville 7535, South Africa
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Liu J, Jia Y, Xu Q, Zheng YT, Zhang C. Phylodynamics of HIV-1 unique recombinant forms in China-Myanmar border: implication for HIV-1 transmission to Myanmar from Dehong, China. INFECTION GENETICS AND EVOLUTION 2012; 12:1944-8. [PMID: 22917657 DOI: 10.1016/j.meegid.2012.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 07/18/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
Abstract
China-Myanmar border plays a crucial role in HIV-1 transmission in Asia. Here, we performed Bayesian phylodynamics analyses on p17 gene using BEAST to investigate HIV-1 transmission in this region. Maximum clade credibility trees of subtype C and CRF01_AE show that majority of unique recombinant forms (URFs) and pure subtype strains from Dehong and Myanmar cluster together, forming large clades with ancestral geographical states of Dehong. Bayes factor tests support the statistically significant geographic diffusion link between Dehong and Myanmar. The estimated time to the most recent common ancestor of Myanmar URFs_BC (1999.2) was later than that of Dehong URFs_BC (1998.0), but earlier than that of Myanmar URFs_01BC (2004.3). Since 1998, HIV-1 recombination between subtypes B, C and CRF01_AE has been continuously occurring in China-Myanmar border region. These results suggest that HIV-1 subtypes B, C and CRF01_AE were most likely transmitted from Dehong to Myanmar, and predict that URFs_01BC should be also prevalent in Dehong, Yunnan.
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Affiliation(s)
- Jun Liu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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10
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Extensive and complex HIV-1 recombination between B', C and CRF01_AE among IDUs in south-east Asia. AIDS 2012; 26:1121-9. [PMID: 22333750 DOI: 10.1097/qad.0b013e3283522c97] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
OBJECTIVE To investigate the subtype characterization of HIV-1 among IDUs in northern Myanmar. DESIGN A molecular epidemiological investigation was conducted among IDUs in Laza and Maizayang cities of northern Myanmar. METHODS A total of 83 HIV-1-positive serums were collected from consenting IDUs during June to August 2009. HIV-1 p17, pol, vif-env, C2V3 fragments were amplified and sequenced. Phylogenetic and bootscanning analyses were performed. RESULTS A very high proportion (86.1%) of HIV-1 intersubtype recombinants and very low proportion of subtypes B' (3.8%), C (7.6%) and CRF01_AE (1.3%) were found in this HIV-infected IDUs cohort. These recombinants cover all four kinds of recombination forms formed among CRF01_AE, B and C. The B/C and CRF01_AE/B/C recombinants are the two most dominant recombinants, accounting for 54.4 and 42.6% of all cases, respectively, and indicating the ongoing generation of extensive and complex HIV-1 recombination among CRF01_AE, B' and C in northern Myanmar. Intriguingly, most recombinants have different chimeric patterns from each other, forming 64 unique recombination forms (URFs) that are quite distinct from any previously identified circulating recombinant forms (CRFs) and URFs in Asia. CONCLUSION The extremely high proportion of intersubtype recombinants, especially CRF01_AE/B'/C recombinants (42.6%), strongly suggests that northern Myanmar is a big forge for HIV-1 recombination among CRF01_AE, B' and C.
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Zhou YH, Liu FL, Yao ZH, Duo L, Li H, Sun Y, Zheng YT. Comparison of HIV-, HBV-, HCV- and co-infection prevalence between Chinese and Burmese intravenous drug users of the China-Myanmar border region. PLoS One 2011; 6:e16349. [PMID: 21283696 PMCID: PMC3025010 DOI: 10.1371/journal.pone.0016349] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Accepted: 12/14/2010] [Indexed: 12/13/2022] Open
Abstract
Background Co-infection with HIV and HCV and/or HBV is highly prevalent in intravenous drug users (IDUs). Because of the proximity to the “Golden Triangle”, HIV prevalence among the IDUs is very high in the China-Myanmar border region. However, there are few studies about co-infection with HIV and HCV and/or HBV, especially in the region that belongs to Myanmar. Methods 721 IDUs, including 403 Chinese and 318 Burmese, were investigated for their HIV, hepatitis B virus (HBV), and hepatitis C virus (HCV) serological status. Statistical analysis was performed to evaluate the differences of the epidemic situation between the Chinese IDUs and the Burmese IDUs. Results Among the Chinese IDUs and the Burmese IDUs, HCV infection was the most prevalent (69.0% vs 48.1%, P<0.001), followed by HBV (51.6% vs 43.1%, P<0.05) and HIV (33.7% vs 27.0%, P>0.05). Besides, there were more HIV-HBV co-infected IDUs (20.1% vs 11.3%, P<0.005), and HIV-HCV co-infected IDUs (31.8% vs 23.9%, P<0.05) in China than in Myanmar, as well as HIV-HBV-HCV triple infection (19.1% vs 10.4%, P<0.005). Conclusion Co-infection with HIV and HCV and/or HBV is highly prevalent among the IDUs in the China-Myanmar border region. The HIV epidemic appears to be in a downward trend, compared with previous reports. However, all infections were more prevalent among the Chinese IDUs than among the Burmese.
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Affiliation(s)
- Yan-Heng Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- The Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Feng-Liang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- The Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Zhi-Hong Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- The Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Lin Duo
- The Second People's Hospital of Yunnan Province, Kunming, China
| | - Hong Li
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Yi Sun
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- The First People's Hospital of Yunnan Province, Kunming, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail:
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SahBandar IN, Takahashi K, Motomura K, Djoerban Z, Firmansyah I, Kitamura K, Sato H, Pohan HT, Sato S. The indonesian variants of CRF33_01B: Near-full length sequence analysis. AIDS Res Hum Retroviruses 2011; 27:97-102. [PMID: 20958201 DOI: 10.1089/aid.2010.0163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cocirculation of subtype B and CRF01_AE in Southeast Asia has led to the establishment of new recombinant forms. In our previous study, we found five samples suspected of being recombinants between subtype B and CRF01_AE, and here, we analyzed near full-length sequences of two samples and compared them to known CRFs_01B, subtype B, and CRF01_AE. Five overlapped segments were amplified with nested PCR from PBMC DNA, sequenced, and analyzed for genome mosaicism. The two Indonesian samples, 07IDJKT189 and 07IDJKT194, showed genome-mosaic patterns similar to CRF33_01B references from Malaysia, with one short segment in the 3' end of the p31 integrase-coding region, which was rather more similar to subtype B than CRF01_AE, consisting of unclassified sequences. These results suggest gene-specific continuous diversification and spread of the CRF33_01B genomes in Southeast Asia.
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Affiliation(s)
- Ivo N. SahBandar
- Department of Microbiology, School of Medicine, Iwate Medical University, Morioka, Japan
- Department of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Kiyomi Takahashi
- Department of Microbiology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Kazushi Motomura
- Center for Genomic Pathogen, National Institute of Infectious Diseases, Tokyo, Japan
| | - Zubairi Djoerban
- Department of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Iman Firmansyah
- Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia
| | | | - Hironori Sato
- Center for Genomic Pathogen, National Institute of Infectious Diseases, Tokyo, Japan
| | - Herdiman T. Pohan
- Department of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Shigehiro Sato
- Department of Microbiology, School of Medicine, Iwate Medical University, Morioka, Japan
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Habekova M, Takacova M, Lysy J, Mokras M, Camacho R, Truska P, Stanekova D. Genetic subtypes of HIV type 1 circulating in Slovakia. AIDS Res Hum Retroviruses 2010; 26:1103-7. [PMID: 20849303 DOI: 10.1089/aid.2009.0220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Slovakia belongs to the group of European countries with a low prevalence of HIV infection. The major proportion of HIV-positive cases in Slovakia is still represented by MSM, followed by heterosexuals infected through unprotected sexual intercourse. This study was conducted to update the description of HIV subtypes circulating in Slovakia. HIV-1 partial pol gene sequences from 143 individuals were prospectively collected from 2004 to 2008 and analyzed. Phylogenetic analysis based on HIV-1 partial pol gene sequences revealed the highest prevalence of HIV-1 B subtype (93.0 %), predominantly associated with the MSM group. Ten (7.0%) individuals were infected with HIV-1 non-B subtypes. The pure subtypes were more frequent (7; 4.9%) than CRFs (3; 2.1%) and their occurrence was as follows: subtype C (3; 2, 1%), subtype A (2; 1.4%), subtype F (2; 1.4%), CRF_01AE (1; 0.7%), CRF_02AG (1; 0.7%), and CRF08_BC (1; 0.7%). Data show slightly increasing HIV-1 subtype diversity, with HIV-1 subtype B still having the highest prevalence in the Slovak-infected population.
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Affiliation(s)
- M. Habekova
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
| | - M. Takacova
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
| | - J. Lysy
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
| | - M. Mokras
- Medical faculty of Commenius University, Derer Hospital, Bratislava, Slovakia
| | - R. Camacho
- Laboratório de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal
| | - P. Truska
- Institute of Public Health of the Capital of Slovakia, Bratislava, Slovakia
| | - D. Stanekova
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
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14
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Zhao J, Tang S, Ragupathy V, Carr JK, Wolfe ND, Awazi B, Hewlett I. Identification and genetic characterization of a novel CRF22_01A1 recombinant form of HIV type 1 in Cameroon. AIDS Res Hum Retroviruses 2010; 26:1033-45. [PMID: 20812894 DOI: 10.1089/aid.2009.0197] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cameroon is a country in West Central Africa in which all four groups of HIV-1 (M, N, O, and P), some circulating recombinant forms (CRFs) and unique recombinant forms (URFs) are prevalent. The CRF22 was initially identified through a novel URF strain, 01CM53122, and later defined from two additional sequences; however, the genomic properties of CRF22 have never been demonstrated in detail. In this study, we describe the characterization of five CRF22_01A1 strains, 02CMLT72, 01CM1867LE, 01CM001BBY, 02CM3097MN, and 02CM1917LE, identified in Cameroon without apparent epidemiological links. A typical CRF22_01A1 strain contains five fragments that can be assigned to the CRF01_AE and subsubtype A1 radiations. Forty-eight percent of the genome is classified as CRF01_AE, spanning the entire region of the gag gene, part of the pol gene, and accessory genes as well as the beginning and the end of the env gene and nef gene. Fifty-two percent of the genome is subsubtype A1 including regions mostly in the pol, vif, and env genes. The five CRF22_01A1 viruses formed a deep branch outside the groups of CRF01_AE and displayed similar mosaic structure but were moderately different from the original strain of CRF22_01A1, 01CM53122. Further analysis of the 01CM53122 genome showed that this virus represents a diverse set of mosaic genomes from CRF22_01A1, including a 446-nt segment of 01CM53122 in the env region, but unlike other CRF22 strains, clustered with CRF01_AE rather than the A1 sequence, suggesting that the 01CM53122 strain is a recombinant of CRF22_01A1 and CRF01_AE.
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Affiliation(s)
- Jiangqin Zhao
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland
| | - Shixing Tang
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland
| | - Viswanath Ragupathy
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland
| | - Jean K. Carr
- Division of Epidemiology and Prevention, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Nathan D. Wolfe
- Global Viral Forecasting Initiative, San Francisco, California 94104 and Stanford University, Program in Human Biology, Stanford, California
| | - Bih Awazi
- Mobile Laboratory, Sanitation and Hygiene, Administration of Health, Cameroon
| | - Indira Hewlett
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland
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15
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Sahbandar IN, Takahashi K, Djoerban Z, Firmansyah I, Naganawa S, Motomura K, Sato H, Kitamura K, Pohan HT, Sato S. Current HIV type 1 molecular epidemiology profile and identification of unique recombinant forms in Jakarta, Indonesia. AIDS Res Hum Retroviruses 2009; 25:637-46. [PMID: 19621986 DOI: 10.1089/aid.2008.0266] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV infection is a major problem in Indonesia. The number of people living with HIV has been increasing from year to year, especially among injecting drug users (IDUs). Since there were only limited data about molecular epidemiology profiles of HIV/AIDS in Indonesia, a cross-sectional study involving 208 HIV-1-seropositive individuals was conducted in 2007 in Jakarta. The majority of participants were 16-30 years of age (64.9%) and 74.5% were male. The most frequent risk factor was injecting drug use (IDU) (45.7%) followed by heterosexual transmission (34.1%). Phylogenetic analysis of gag (p17 and p6) and env C2V3 regions showed 200 (96.2%) of 208 DNA samples were CRF01_AE and only 3 (1.4%) were subtype B. Five samples (2.4%) indicated discordant subtypes between the three aforementioned regions: three of them showed unique CRF01_AE/B recombination patterns in 2.3-kbp nucleotide sequences (from p17 to part of RT), including one sample showing similarity to CRF33_01B, reported previously in Malaysia. This study shows the current predominant subtype is CRF01_AE in every risk group, with a decreasing number of pure subtype B, and the first identification of CRF01_AE/B recombinant forms among HIV-1-seropositive Indonesians.
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Affiliation(s)
- Ivo N. Sahbandar
- Department of Microbiology, School of Medicine, Iwate Medical University, Morioka, Japan
- Department of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Kiyomi Takahashi
- Department of Microbiology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Zubairi Djoerban
- Department of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Iman Firmansyah
- Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia
| | | | - Kazushi Motomura
- Center for Genomic Pathogen, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hironori Sato
- Center for Genomic Pathogen, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Herdiman T. Pohan
- Department of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Shigehiro Sato
- Department of Microbiology, School of Medicine, Iwate Medical University, Morioka, Japan
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16
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Motomura K. [Analysis of genetic recombination between human immunodeficiency virus type 1 (HIV-1) and HIV-2]. KANSENSHOGAKU ZASSHI. THE JOURNAL OF THE JAPANESE ASSOCIATION FOR INFECTIOUS DISEASES 2009; 83:81-93. [PMID: 19364034 DOI: 10.11150/kansenshogakuzasshi.83.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
It is estimated that one million people are dually infected with Human Immunodeficiency Virus type-I (HIV-1) and type-II (HIV-2) in West Africa and parts of India. HIV-1 and HIV-2 use the same receptor and coreceptors for entry into cells, and thus target the same cell populations in the host. Additionally, we first examined whether RNAs from HIV-1 and HIV-2 can be copackaged into the same virion. Therefore these properties suggest that in the dually infected population, it is likely that some cells can be infected by both HIV-1 and HIV-2, thereby providing opportunities for these two viruses to interact with each other. We constructed recombination assay system for measurement recombination frequencies and analyzed recombination rate between HIV-1 and HIV-2. We used modified near-full-length viruses that each contained a green fluorescent protein gene (gfp) with a different inactivating mutation. Thus, a functional gfp could be reconstituted via recombination, which was used to detect copackaging of HIV-1 and HIV-2 RNAs. In this study, approximately 0.2% of infection events generated the GFP phenotype. Therefore, the appearance of the GFP+ phenotype in the current system is approximately 35-fold lower than that between two homologous HIV-1 or HIV-2 viruses. We then mapped the general structures of the recombinant viruses and characterized the recombination junctions by DNA sequencing. We observed several different recombination patterns including those only had crossovers in gfp. The most common hybrid genomes had heterologous LTRs. Although infrequent, crossovers were also identified in the viral sequences. Such chimeric HIV-1 and HIV-2 viruses have yet to be observed in the infected population. It is unclear whether the lack of observed chimeras is due to the divergence between HIV-1 and HIV-2 being too great for such an event to occur, or whether such events could occur but have not yet been observed. Given the number of coinfected people, the potential for interactions between HIV-1 and HIV-2 should not be ignored.
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Affiliation(s)
- Kazushi Motomura
- HIV Drug Resistance Program, National Cancer Institute-Frederick, NIH, U.S.A
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17
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Jones KL, Sonza S, Mak J. Primary T-lymphocytes rescue the replication of HIV-1 DIS RNA mutants in part by facilitating reverse transcription. Nucleic Acids Res 2008; 36:1578-88. [PMID: 18216043 PMCID: PMC2275147 DOI: 10.1093/nar/gkm1149] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The dimerization initiation site (DIS) stem-loop within the HIV-1 RNA genome is vital for the production of infectious virions in T-cell lines but not in primary cells. In comparison to peripheral blood mononuclear cells (PBMCs), which can support the replication of both wild type and HIV-1 DIS RNA mutants, we have found that DIS RNA mutants are up to 100 000-fold less infectious than wild-type HIV-1 in T-cell lines. We have also found that the cell-type-dependent replication of HIV-1 DIS RNA mutants is largely producer cell-dependent, with mutants displaying a greater defect in viral cDNA synthesis when viruses were not derived from PBMCs. While many examples exist of host–pathogen interplays that are mediated via proteins, analogous examples which rely on nucleic acid triggers are limited. Our data provide evidence to illustrate that primary T-lymphocytes rescue, in part, the replication of HIV-1 DIS RNA mutants through mediating the reverse transcription process in a cell-type-dependent manner. Our data also suggest the presence of a host cell factor that acts within the virus producer cells. In addition to providing an example of an RNA-mediated cell-type-dependent block to viral replication, our data also provides evidence which help to resolve the dilemma of how HIV-1 genomes with mismatched DIS sequences can recombine to generate chimeric viral RNA genomes.
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Affiliation(s)
- Kate L Jones
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Australia
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18
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Global molecular epidemiology of HIV: understanding the genesis of AIDS pandemic. ADVANCES IN PHARMACOLOGY 2008; 56:1-25. [PMID: 18086407 DOI: 10.1016/s1054-3589(07)56001-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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19
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20
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Crotti A, Chiara GD, Ghezzi S, Lupo R, Jeeninga RE, Liboi E, Lievens PMJ, Vicenzi E, Bovolenta C, Berkhout B, Poli G. Heterogeneity of signal transducer and activator of transcription binding sites in the long-terminal repeats of distinct HIV-1 subtypes. Open Virol J 2007; 1:26-32. [PMID: 19440456 PMCID: PMC2675545 DOI: 10.2174/1874357900701010026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 09/06/2007] [Accepted: 09/17/2007] [Indexed: 01/25/2023] Open
Abstract
HIV-1 can be subdivided into distinct subtypes; the consequences of such a genomic variability remain largely speculative. The long terminal repeats (LTR) control HIV transcription and reflect the major differences of distinct viral subtypes. Three regions in the HIV-1 subtype B LTR are close matches to the Signal Transducer and Activator of Transcription (STAT) consensus sequence. Here, we show heterogeneity in these putative STAT binding sites among HIV-1 LTR subtypes A through G. Transfection of constitutively activated STAT5 lead to transcriptional activation of HIV-1 expression in 293T cells transfected with a reporter assay driven by HIV-1 LTR subtype B. Constitutively activated STAT5 transactivated the LTR of various subtypes in U937 cells with different potency. These findings support and expand the potential relevance of STAT5 activation in HIV infection and may bear relevance for a differential regulation of latency and expression of different subtypes of HIV-1.
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Affiliation(s)
- Andrea Crotti
- AIDS Immunopathogenesis, San Raffaele Scientific Institute, Milano, Italy.
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21
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Buonaguro L, Tornesello ML, Buonaguro FM. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol 2007; 81:10209-19. [PMID: 17634242 PMCID: PMC2045484 DOI: 10.1128/jvi.00872-07] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- L Buonaguro
- Laboratory of Viral Oncogenesis and Immunotherapy & AIDS Reference Center, Ist. Naz. Tumori Fond. G. Pascale, Via Mariano Semmola, 1, 80131 Naples, Italy.
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22
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Sanders-Buell E, Saad MD, Abed AM, Bose M, Todd CS, Strathdee SA, Botros BA, Safi N, Earhart KC, Scott PT, Michael N, McCutchan FE. A nascent HIV type 1 epidemic among injecting drug users in Kabul, Afghanistan is dominated by complex AD recombinant strain, CRF35_AD. AIDS Res Hum Retroviruses 2007; 23:834-9. [PMID: 17604548 DOI: 10.1089/aid.2006.0299] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Injecting drug use (IDU), common in global centers of heroin production, confers significant risk for HIV-1 infection. Once introduced into IDU networks, an explosive rise in HIV-1 infection typically occurs, fueled principally by needle sharing. New HIV-1 epidemics in IDUs have occurred in Russia, China, Thailand, Spain, Iran, and in other countries, and some have spread into other risk groups in their respective countries. In Afghanistan, the introduction of HIV-1 into IDU networks has begun, but a recent report of 3% HIV-1 prevalence suggests that the epidemic is still at an early stage. Here we establish, by complete genome sequencing and phylogenetic analysis of four viral strains from Afghan IDUs, that all are the same complex recombinant strain, combining HIV-1 subtypes A and D and herein termed CRF35_AD. Published partial HIV-1 sequences from an HIV-1 epidemic among IDUs in Iran, already at 23.2% HIV-1 prevalence, are either CRF35_AD or a related recombinant. Voluntary HIV-1 screening and harm reduction programs in Afghanistan, applied now, could limit the spread of HIV-1, both in IDUs and in other social networks.
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Affiliation(s)
- E Sanders-Buell
- US Military HIV Research Program/Division of Retrovirology, Walter Reed Army Institute of Research, Rockville Maryland 20850, USA.
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23
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Moncany MLJ, Dalet K, Courtois PRR. Identification of conserved lentiviral sequences as landmarks of genomic flexibility. C R Biol 2006; 329:751-64. [PMID: 17027636 PMCID: PMC7172886 DOI: 10.1016/j.crvi.2006.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 06/29/2006] [Accepted: 07/05/2006] [Indexed: 11/25/2022]
Abstract
Considering that recombinations produce quasispecies in lentivirus spreading, we identified and localized highly conserved sequences that may play an important role in viral ontology. Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). They were located mainly in the structural genes forming hot spots particularly in the gag and pol genes and to a lesser extent in LTRs and regulatory genes. The CLS pattern was the same throughout the different HIV-1 subtypes, except for some HIV-1-O strains. Only CLS 3 and 4 were detected in both negative control HTLV-1 oncornaviruses and D-particle-forming simian viruses, which are not immunodeficiency inducers and display a genetic stability. CLSs divided the virus genomes into domains allowing us to distinguish sequence families leading to the notion of ‘species self’ besides that of ‘lentiviral self’. Most of acutely localized CLSs in HIV-1s (82%) corresponded to wide recombination segments being currently reported. To cite this article: M.L.J. Moncany et al., C. R. Biologies 329 (2006).
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Affiliation(s)
- Maurice L J Moncany
- Laboratoire de biologie cellulaire et moléculaire, UFR de sciences, Université de La Rochelle, av. Michel-Crépeau, 17042 La Rochelle cedex 1, France.
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24
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Watanaveeradej V, Benenson MW, Souza MD, Sirisopana N, Nitayaphan S, Tontichaivanich C, Amphaipit R, Renzullo PO, Brown AE, McNeil JG, Robb ML, Birx DL, Tovanabutra S, Carr JK, McCutchan FE. Molecular epidemiology of HIV Type 1 in preparation for a Phase III prime-boost vaccine trial in Thailand and a new approach to HIV Type 1 genotyping. AIDS Res Hum Retroviruses 2006; 22:801-7. [PMID: 16910837 DOI: 10.1089/aid.2006.22.801] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To characterize HIV-1 genotypes in candidate populations for a prime-boost phase III vaccine trial in Thailand, specimens from prevalent and incident HIV-1 infections from a family planning clinic population in Rayong Province and a community cohort in Chon Buri Province, collected from 1998 to 2001, were genotyped. A new multiregion hybridization assay, MHAbce, capable of distinguishing HIV-1 CRF01_AE, subtype B, and subtype C and their recombinants, was developed and applied to prevalent infections. Most incident and selected prevalent infections were studied by complete genome sequencing. By MHAbce, 168 of 194 prevalent infections were genotyped. Of these, 90.5% were CRF01_AE, 2.4% were subtype B, and 7.2% showed discordant or dual probe reactivity, indicative of recombination or dual infection, respectively. Among 23 incident infections, 20 were sequenced. Eighteen CRF01_AE, one subtype B, and one CRF01/B recombinant strains were seen. Two CRF01/B and one CRF01/C recombinant were identified among selected prevalent infections. These results indicate that incident and prevalent HIV-1 infections in Rayong and Chon Buri during 1998-2001 were 90% CRF01_AE, 3% subtype B, and 7% either recombinant or dual. This study frames the genetic diversity of HIV-1 in these cohorts in their preparatory phase for the ongoing ALVACHIV (vCP1521) prime, AIDSVAX B/E boost, phase III vaccine trial and will provide a benchmark for interpretation and analysis.
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25
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Abstract
Human immunodeficiency virus (HIV) is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS). HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.
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Affiliation(s)
- Henry I Z Requejo
- Seção de Imunologia, Instituto Adolfo Lutz, Av. Dr. Arnaldo 351, 01246-902 São Paulo, SP, Brazil.
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26
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Siddappa NB, Dash PK, Mahadevan A, Desai A, Jayasuryan N, Ravi V, Satishchandra P, Shankar SK, Ranga U. Identification of unique B/C recombinant strains of HIV-1 in the southern state of Karnataka, India. AIDS 2005; 19:1426-9. [PMID: 16103776 DOI: 10.1097/01.aids.0000180795.49016.89] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We characterized the molecular nature of a large number of primary HIV-1 isolates in the four southern states of India. In addition to confirming a predominance of subtype C infection, for the first time we identified three B/C recombinant viruses in a subset of 115 samples. Unexpectedly, env sequences of two of the three B/C recombinants phylogenetically clustered with subtype B strains of the USA. The determination of the real incidence of the recombinant viruses is of importance.
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Affiliation(s)
- Nagadenahalli Byrareddy Siddappa
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, India
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27
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Bhanja P, Sengupta S, Singh NY, Sarkar K, Bhattacharya SK, Chakrabarti S. Determination of gag and env subtypes of HIV-1 detected among injecting drug users (IDUs) in Manipur, India: evidence for intersubtype recombination. Virus Res 2005; 114:149-53. [PMID: 16054722 DOI: 10.1016/j.virusres.2005.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 06/16/2005] [Accepted: 06/16/2005] [Indexed: 11/23/2022]
Abstract
The majority of HIV-1 transmission in Manipur, one of the northeastern states of India, is through the sharing of needles and syringes among the injecting drug users (IDUs). A total of 28 HIV seropositive samples were used to determine the HIV-1 subtypes with respect to both gag and envelope genes. The specific regions within gag and envelope genes were amplified from PBMC DNA by nested PCR using appropriate primers. These amplicons were used in heteroduplex mobility assay followed by DNA sequencing. Phylogenetic analysis of the nucleotide sequences of respective regions showed that 89% of samples (25/28) were infected with subtype C with respect to both gag and envelope genes; however, 11% of the samples (3/28) showed subtype discordance with respect to the envelope (C2-V3) and gag (p24-p7) genomic regions. Simplot analysis of the discordant samples showed the presence of intersubtype recombination between subtype C and Thai B; two samples were found to be subtype C in envelope but Thai B in gag, whereas, one sample was found to be subtype Thai B in envelope and 'C' in gag region.
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MESH Headings
- Adult
- DNA, Viral/analysis
- Gene Products, env/chemistry
- Gene Products, env/genetics
- Gene Products, gag/chemistry
- Gene Products, gag/genetics
- Genes, env/genetics
- Genes, gag/genetics
- HIV Infections/virology
- HIV-1/classification
- HIV-1/genetics
- Heteroduplex Analysis
- Humans
- India
- Male
- Molecular Sequence Data
- Recombination, Genetic
- Sequence Analysis, DNA
- Substance Abuse, Intravenous/complications
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Affiliation(s)
- Payel Bhanja
- National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Calcutta 700010, India
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28
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Chin MPS, Rhodes TD, Chen J, Fu W, Hu WS. Identification of a major restriction in HIV-1 intersubtype recombination. Proc Natl Acad Sci U S A 2005; 102:9002-7. [PMID: 15956186 PMCID: PMC1157039 DOI: 10.1073/pnas.0502522102] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic recombination increases diversity in HIV-1 populations, thereby allowing variants to escape from host immunity or antiviral therapies. In addition to the currently described nine subtypes of HIV-1, many of the circulating strains are intersubtype recombinants. In this study, we determined the recombination rate between two HIV-1 subtype C viruses and between a subtype B virus and a subtype C virus during a single round of virus replication. Although HIV-1 subtype C recombines at a high rate, similar to that of HIV-1 subtype B, the recombination rate between a subtype B virus and a subtype C virus is much lower than the intrasubtype recombination rate. A 3-nt sequence difference in the dimerization initiation signal (DIS) region between HIV-1 subtypes B and C accounts for most of the reduction of intersubtype recombination. By matching the DIS sequences, the B/C intersub-type recombination rate was elevated 4-fold; by introducing mismatches in the 3-nt sequences, the B/B intrasubtype recombination rate was reduced 4-fold. Further analyses showed that the intermolecular template-switching frequency was unaffected by the sequence identity of the DIS region. These results support the hypothesis that mismatched sequences in the DIS region alter the formation of heterozygous virions, thereby lowering the observable recombination rate. Here, we present the discovery of a major restriction in HIV-1 intersubtype recombination. These results have important implications for virus evolution, the mechanism of HIV-1 RNA packaging, high negative interference in recombination, and the generation of circulating intersubtype recombinants within the infected population.
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Affiliation(s)
- Mario P S Chin
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
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29
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Buonaguro L, Tagliamonte M, Tornesello ML, Pilotti E, Casoli C, Lazzarin A, Tambussi G, Ciccozzi M, Rezza G, Buonaguro FM. Screening of HIV-1 Isolates by Reverse Heteroduplex Mobility Assay and Identification of Non-B Subtypes in Italy. J Acquir Immune Defic Syndr 2004; 37:1295-306. [PMID: 15385738 DOI: 10.1097/01.qai.0000123273.76723.04] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The increasing prevalence of HIV-1 transmission through heterosexual contacts and the growing number of immigrants from non-Western countries, where non-B subtypes and recombinant forms are prevalent, suggest the possible emergence in Italy of a new epidemic wave of HIV-1 non-B subtypes as well as recombinant forms. METHODS The distribution of HIV-1 subtypes has been evaluated in 63 seropositive individuals residing in Italy, most of whom were infected through a sexual route during the last 5 years. A modified heteroduplex mobility assay (HMA) strategy, reverse HMA (rHMA), has been developed in our laboratory, allowing rapid identification of divergent-from-B-subtype isolates, which have been subsequently characterized by detailed molecular and phylogenetic analyses. RESULTS Five samples show, on rHMA, an electrophoretic pattern compatible with a non-B subtype classification. Their phylogenetic analysis, performed on both env and gag regions, confirms the rHMA subtyping prediction, given that 3 samples fall into the "A-family" subtype and 2 into the G subtype. The 5 non-B-subtype HIV-1 isolates have been identified among 23 variants (prevalence, 21.74%) isolated during the 2000 to 2001 period in heterosexuals. In parallel, B-subtype isolates show high levels of intrasubtype nucleotide divergence, compatible with a constant HIV-1 molecular diversification. CONCLUSION The Italian HIV-1 epidemic is still mostly attributable to the B subtype, which shows an increasing nucleotide heterogeneity. Heterosexual transmission and the interracial blending, however, are slowly introducing novel HIV-1 subtypes, and the data indicate that rHMA represents a powerful tool for HIV-1 biomolecular screening in epidemics characterized by a mono-/dual-subtype predominance.
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Affiliation(s)
- Luigi Buonaguro
- Viral Oncology and AIDS Refer. Center, Ist. Naz. Tumori Fond. G. Pascale, Naples, Italy
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Derebail SS, DeStefano JJ. Mechanistic analysis of pause site-dependent and -independent recombinogenic strand transfer from structurally diverse regions of the HIV genome. J Biol Chem 2004; 279:47446-54. [PMID: 15342633 DOI: 10.1074/jbc.m408927200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retroviral recombinants are generated by strand transfers occurring within internal regions of the viral genome and are a major source of genetic variability. Strand transfer has been linked to "pausing" occurring at secondary structures during synthesis by reverse transcriptase. Yet, weakly structured templates lacking strong pause sites also undergo efficient transfer. In this report, transfer crossover sites on high and low structured templates from the gag-pol frameshift region (GagPol) and the env (Env) regions, respectively, were determined by using a reconstituted in vitro strand transfer assay. The assay tested transfers occurring between a donor and acceptor template over a 150-nucleotide homologous region. The majority of crossovers were in a small 23-nucleotide region near a major pause site on GagPol, clearly indicating a pause-driven mechanism. In contrast, on Env, transfers were more dispersed clustering toward the end of the homologous region. Slowing down polymerization on Env by decreasing the dNTP concentration resulted in crossovers shifting toward the beginning of the homologous region. Removal of a small 38-nucleotide region at the 3'-end of the Env acceptor had a large effect on the level of strand transfer despite very few crossovers mapping to this region. This implicated this part of the acceptor in transfers occurring at downstream positions. For Env the results support a mechanism where the acceptor rapidly binds nascent DNA, then "zippers" downstream catching up with the donor-DNA hybrid and displacing the donor. Such a mechanism may be important to recombination in low structure regions of the HIV genome.
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MESH Headings
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Fusion Proteins, gag-pol/genetics
- Genes, env
- Genome, Viral
- HIV-1/genetics
- Humans
- Models, Genetic
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombination, Genetic
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Affiliation(s)
- Suchitra S Derebail
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland 20742, USA
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31
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Troyer JL, Pecon-Slattery J, Roelke ME, Black L, Packer C, O'Brien SJ. Patterns of feline immunodeficiency virus multiple infection and genome divergence in a free-ranging population of African lions. J Virol 2004; 78:3777-91. [PMID: 15016897 PMCID: PMC371036 DOI: 10.1128/jvi.78.7.3777-3791.2004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Feline immunodeficiency virus (FIV) is a lentivirus that causes AIDS-like immunodeficiency disease in domestic cats. Free-ranging lions, Panthera leo, carry a chronic species-specific strain of FIV, FIV-Ple, which so far has not been convincingly connected with immune pathology or mortality. FIV-Ple, harboring the three distinct strains A, B, and C defined by pol gene sequence divergences, is endemic in the large outbred population of lions in the Serengeti ecosystem in Tanzania. Here we describe the pattern of variation in the three FIV genes gag, pol-RT, and pol-RNase among lions within 13 prides to assess the occurrence of FIV infection and coinfection. Genome diversity within and among FIV-Ple strains is shown to be large, with strain divergence for each gene approaching genetic distances observed for FIV between different species of cats. Multiple in fections with two or three strains were found in 43% of the FIV-positive individuals based on pol-RT sequence analysis, which may suggest that antiviral immunity or interference evoked by one strain is not consistently protective against infection by a second. This comprehensive study of FIV-Ple in a free-ranging population of lions reveals a dynamic transmission of virus in a social species that has historically adapted to render the virus benign.
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Affiliation(s)
- Jennifer L Troyer
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick. IRSP Program, SAIC-Frederick, Frederick, Maryland 21702, USA
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Abstract
BACKGROUND Human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) epidemic is a global threat to maternal and child health, especially in developing countries. It is estimated that 800 000 children are infected and 580 000 children die of AIDS-related illnesses every year. Molecular epidemiology has been a useful tool in analyzing the origin of HIV and tracking the course of global HIV spread. This article provides an overview of recent advances in the field of molecular epidemiology of HIV across the world, and discuss the biological implications. METHODS Based on the near full-length or partial nucleotide sequence information, the phylogeny and recombinant structure of HIV strains are analyzed. Using genotype classification of HIV as a molecular marker, the origin and the genesis of HIV epidemic are investigated. RESULTS The HIV-1 group M, a major HIV group responsible for current AIDS pandemic, began its expansion in human population approximately 70 years ago and diversified rapidly over time, now comprising a number of different subtypes and circulating recombinant forms (CRF). Of note, recent studies revealed that new recombinant strains are arising continually, becoming a powerful force in the spread of HIV-1 across the globe. CONCLUSIONS Global dissemination of HIV is a dramatic and deadly example of recent genome emergence and expansion. Molecular epidemiological investigation is expected to provide information critical for prevention and future vaccine strategies.
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Affiliation(s)
- Yutaka TakebE
- Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan.
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Takebe Y, Motomura K, Tatsumi M, Lwin HH, Zaw M, Kusagawa S. High prevalence of diverse forms of HIV-1 intersubtype recombinants in Central Myanmar: geographical hot spot of extensive recombination. AIDS 2003; 17:2077-87. [PMID: 14502011 DOI: 10.1097/00002030-200309260-00009] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To investigate the molecular epidemiology and genetic structure of HIV-1s causing the epidemic in Central Myanmar and to explore the genesis of HIV epidemic in this area. DESIGN A molecular epidemiological investigation was conducted in 1999-2000 in the city of Mandalay among high-risk populations and the structural features of circulating HIV-1s were analyzed. METHODS HIV-1 genotypes of 59 specimens were screened based on gag (p17) and env (C2/V3) regions. Near full-length nucleotide sequences of HIV-1 isolates with subtype discordance were determined and their recombinant structures were characterized. RESULTS Three lineages of HIV-1 strains, including CRF01_AE (27, 45.8%), subtype B' (Thailand variant of subtype B) (15, 25.4%) and subtype C (8, 13.6%), were distributed in Mandalay, while substantial portions (9, 15.3%) of specimens showed various patterns of subtype discordance in different regions of HIV-1 genomes. The study on six HIV-1 isolates with subtype discordance revealed that they were highly diverse types of unique recombinant forms (URFs) comprised of various combinations of three circulating subtypes. One URF was a particularly complex mosaic that contained 13 recombination breakpoints between three HIV-1 subtypes. Approximately half of recombinants showed 'pseudotype' virion structures, in which the external portions of envelope glycoproteins were exchanged with different lineages of HIV-1 strains, suggesting the potential selective advantage of 'pseudotype' viruses over parental strains. CONCLUSION The study revealed the unique geographical hot spot in Central Myanmar where extensive recombination events appeared to be taking place continually. This reflects the presence of highly exposed individuals and social networks of HIV-1 transmission.
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Affiliation(s)
- Yutaka Takebe
- Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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Nájera R, Delgado E, Pérez-Alvarez L, Thomson MM. Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS 2003; 16 Suppl 4:S3-16. [PMID: 12698994 DOI: 10.1097/00002030-200216004-00002] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rafael Nájera
- Department of Viral Patogénesis, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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Abstract
A pressing problem in studying the evolution of microbial pathogens is to determine the extent to which these genomes recombine. This information is essential for locating pathogenicity loci by using association studies or population genetic approaches. Recombination also complicates the use of phylogenetic approaches to estimate evolutionary parameters such as selection pressures. Reliable methods that detect and estimate the rate of recombination are, therefore, vital. This article reviews the approaches that are available for detecting and estimating recombination in microbial pathogens and how they can be used to understand pathogen evolution and to identify medically relevant loci.
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Affiliation(s)
- Philip Awadalla
- Section of Evolution and Ecology, University of California at Davis, California 95616, USA.
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37
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Yang R, Kusagawa S, Zhang C, Xia X, Ben K, Takebe Y. Identification and characterization of a new class of human immunodeficiency virus type 1 recombinants comprised of two circulating recombinant forms, CRF07_BC and CRF08_BC, in China. J Virol 2003; 77:685-95. [PMID: 12477871 PMCID: PMC140648 DOI: 10.1128/jvi.77.1.685-695.2003] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified a new class of human immunodeficiency virus type 1 (HIV-1) recombinants (00CN-HH069 and 00CN-HH086) in which further recombination occurred between two established circulating recombinant forms (CRFs). These two isolates were found among 57 HIV-1 samples from a cohort of injecting drug users in eastern Yunnan Province of China. Informative-site analysis in conjunction with bootscanning plots and exploratory tree analysis revealed that these two strains were closely related mosaics comprised of CRF07_BC and CRF08_BC, which are found in China. The genotype screening based on gag-reverse transcriptase sequences of 57 samples from eastern Yunnan identified 47 CRF08_BC specimens (82.5%), 5 CRF07_BC specimens (8.8%), and 3 additional specimens with the novel recombinant structure. These new "second-generation" recombinants thus constitute a substantial proportion (5 of 57; 8.8%) of HIV-1 strains in this population and may belong to a new but yet-undefined class of CRF. This might be the first example of CRFs recombining with each other, leading to the evolution of second-generation inter-CRF recombinants.
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Affiliation(s)
- Rongge Yang
- Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
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Myint L, Ariyoshi K, Yan H, Frater AJ, Auwanit W, Pathipvanith P, Yamada K, Matsuda M, Chiba T, Fujita K, McClure M, Weber JN, Sugiura W. Mutagenically separated PCR assay for rapid detection of M41L and K70R zidovudine resistance mutations in CRF01_AE (subtype E) human immunodeficiency virus type 1. Antimicrob Agents Chemother 2002; 46:3861-8. [PMID: 12435689 PMCID: PMC132767 DOI: 10.1128/aac.46.12.3861-3868.2002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A rapid zidovudine (ZDV) resistance genotypic assay was developed based on the mutagenically separated PCR (MS-PCR) technique to detect two ZDV-resistant mutations, M41L and K70R in CRF01_AE (subtype E). Endpoint dilution analysis revealed that the newly constructed MS-PCR assay could successfully detect three to nine copies of human immunodeficiency virus type 1 template RNA. The test against wild-type and mutant template mixtures in different ratios demonstrated that the assay could detect 10% minor population, at least. Fifty-one subtype E clinical samples were analyzed by the newly constructed MS-PCR assay and direct nucleotide sequencing. The concordance of the two assays was 92 and 100% in codons 41 and 70, respectively. The MS-PCR assay is a rapid, simple, and inexpensive assay that is highly sensitive in detecting mutant targets, including minor populations. Thus, it could be used as a powerful tool for epidemiological surveillance of drug-resistant mutations in developing countries.
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Affiliation(s)
- Lay Myint
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Mandal D, Jana S, Bhattacharya SK, Chakrabarti S. HIV type 1 subtypes circulating in eastern and northeastern regions of India. AIDS Res Hum Retroviruses 2002; 18:1219-27. [PMID: 12494921 DOI: 10.1089/08892220260387968] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic subtyping has been a powerful tool in tracking the global spread of HIV. To determine the HIV-1 subtypes circulating in eastern and northeastern regions of India blood samples were collected from female sex workers in Calcutta and intravenous drug users (IDUs) in Manipur. Fifty-four samples from Calcutta and 25 samples from Manipur were analyzed for HIV-1 subtyping by heteroduplex mobility assay (HMA). Twenty-six samples from these regions were sequenced. HMA and sequencing of the samples from these regions revealed subtype C as the major subtype, circulating within both eastern and northeastern regions. In Manipur, subtype ThaiB was also detected as the second major subtype. Some of the IDUs from Manipur were found to be dual infected with subtype C and ThaiB.
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Affiliation(s)
- Dibyakanti Mandal
- National Institute of Cholera and Enteric Diseases, ICMR, Calcutta, India
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40
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Yang R, Xia X, Kusagawa S, Zhang C, Ben K, Takebe Y. On-going generation of multiple forms of HIV-1 intersubtype recombinants in the Yunnan Province of China. AIDS 2002; 16:1401-7. [PMID: 12131217 DOI: 10.1097/00002030-200207050-00012] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To investigate the molecular epidemiology of HIV in China's Yunnan Province, where the initial HIV-1 outbreak among injecting drug users (IDU) occurred in 1989, and to analyse the genesis and interrelationship of the epidemic with that in surrounding areas. DESIGN A molecular epidemiological investigation was conducted among IDU in three prefectures in Yunnan Province, including Wenshan (east), Honghe (southeast) and Dehong (west). METHODS Thirty-nine specimens were collected from consenting IDU in 2000-2001. The nucleotide sequences of 2.6 kb gag-RT and 340 base pair (bp) env (C2/V3) regions were determined. Phylogenetic tree and recombination breakpoint analyses were performed. RESULTS The circulating recombinant form (CRF), CRF08_BC, predominated in east Yunnan near Guangxi Province (89% in Wenshan and 81% in Honghe), whereas it was not detected in Dehong (0/14) in the west. In contrast, 71% (10/14) of the Dehong isolates were unique recombinant forms (URF), mostly between subtypes B' (Thailand variant of subtype B) and C, with distinct profiles of recombination breakpoints. The subtype B' accounts for the remaining 29% (4/14) of Dehong isolates. Interestingly, two Honghe isolates (2/16) shared some of the precise B'/C recombination breakpoints with CRF07_BC. CONCLUSION New recombinant strains are arising continually in west Yunnan near the Myanmar border. Some appeared to be secondary recombinants derived from CRF07_BC that had further recombined with other strains. The uneven distribution of subtypes, CRF and URF, suggests the presence of independent transmission networks and clusters among IDU in Yunnan.
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Affiliation(s)
- Rongge Yang
- Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
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41
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Affiliation(s)
- I D Tatt
- Sexually Transmitted and Blood Borne Virus Laboratory, Central Public Health Laboratory, Public Health Laboratory Service, London, UK
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42
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Thomson MM, Delgado E, Herrero I, Villahermosa ML, Vázquez-de Parga E, Cuevas MT, Carmona R, Medrano L, Pérez-Álvarez L, Cuevas L, Nájera R. Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences. J Gen Virol 2002; 83:107-119. [PMID: 11752707 DOI: 10.1099/0022-1317-83-1-107] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near full-length proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.
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MESH Headings
- Argentina
- Base Sequence
- DNA, Viral
- Female
- Gene Products, gag/genetics
- Gene Products, gag/physiology
- Gene Products, rev/genetics
- Gene Products, rev/physiology
- Genetic Variation
- Genome, Viral
- HIV Antigens/genetics
- HIV Antigens/physiology
- HIV Envelope Protein gp41/genetics
- HIV Envelope Protein gp41/physiology
- HIV Infections/virology
- HIV Reverse Transcriptase/genetics
- HIV Reverse Transcriptase/physiology
- HIV-1/classification
- HIV-1/genetics
- Human Immunodeficiency Virus Proteins
- Humans
- Male
- Molecular Sequence Data
- Mosaicism
- Phylogeny
- Protein Structure, Tertiary
- Recombination, Genetic
- Sequence Analysis, Protein
- Sequence Analysis, RNA
- Viral Proteins
- Viral Regulatory and Accessory Proteins/genetics
- Viral Regulatory and Accessory Proteins/physiology
- gag Gene Products, Human Immunodeficiency Virus
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Michael M Thomson
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Elena Delgado
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Isabel Herrero
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - María Luisa Villahermosa
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Elena Vázquez-de Parga
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - María Teresa Cuevas
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Rocío Carmona
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Leandro Medrano
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Lucía Pérez-Álvarez
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Laureano Cuevas
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Rafael Nájera
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
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