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Billings E, Sanders-Buell E, Bose M, Bradfield A, Lei E, Kijak GH, Arroyo MA, Kibaya RM, Scott PT, Wasunna MK, Sawe FK, Shaffer DN, Birx DL, McCutchan FE, Michael NL, Robb ML, Kim JH, Tovanabutra S. The Number and Complexity of Pure and Recombinant HIV-1 Strains Observed within Incident Infections during the HIV and Malaria Cohort Study Conducted in Kericho, Kenya, from 2003 to 2006. PLoS One 2015; 10:e0135124. [PMID: 26287814 PMCID: PMC4543584 DOI: 10.1371/journal.pone.0135124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/18/2015] [Indexed: 11/18/2022] Open
Abstract
Characterization of HIV-1 subtype diversity in regions where vaccine trials are conducted is critical for vaccine development and testing. This study describes the molecular epidemiology of HIV-1 within a tea-plantation community cohort in Kericho, Kenya. Sixty-three incident infections were ascertained in the HIV and Malaria Cohort Study conducted in Kericho from 2003 to 2006. HIV-1 strains from 58 of those individuals were full genome characterized and compared to two previous Kenyan studies describing 41 prevalent infections from a blood bank survey (1999–2000) and 21 infections from a higher-risk cohort containing a mix of incident and prevalent infections (2006). Among the 58 strains from the community cohort, 43.1% were pure subtypes (36.2% A1, 5.2% C, and 1.7% G) and 56.9% were inter-subtype recombinants (29.3% A1D, 8.6% A1CD, 6.9% A1A2D, 5.2% A1C, 3.4% A1A2CD, and 3.4% A2D). This diversity and the resulting genetic distance between the observed strains will need to be addressed when vaccine immunogens are chosen. In consideration of current vaccine development efforts, the strains from these three studies were compared to five candidate vaccines (each of which are viral vectored, carrying inserts corresponding to parts of gag, pol, and envelope), which have been developed for possible use in sub-Saharan Africa. The sequence comparison between the observed strains and the candidate vaccines indicates that in the presence of diverse recombinants, a bivalent vaccine is more likely to provide T-cell epitope coverage than monovalent vaccines even when the inserts of the bivalent vaccine are not subtype-matched to the local epidemic.
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Affiliation(s)
- Erik Billings
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Eric Sanders-Buell
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Meera Bose
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Andrea Bradfield
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Esther Lei
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Gustavo H. Kijak
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Miguel A. Arroyo
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Rukia M. Kibaya
- The Kenya Medical Research Institute/Walter Reed Project Clinical Research Center, Kericho, Kenya
| | - Paul T. Scott
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Monique K. Wasunna
- The Kenya Medical Research Institute, Kericho, Kenya
- The Kenya Medical Research Institute, Nairobi, Kenya
| | - Frederick K. Sawe
- The Kenya Medical Research Institute/Walter Reed Project HIV Program, Kericho, Kenya
| | - Douglas N. Shaffer
- United States Army Medical Research Unit-Kenya/Walter Reed Project HIV Program, Kericho, Kenya
| | - Deborah L. Birx
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Francine E. McCutchan
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Nelson L. Michael
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Merlin L. Robb
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Jerome H. Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Sodsai Tovanabutra
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
- * E-mail:
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Chang CH, Kist NC, Stuart Chester TL, Sreenu VB, Herman M, Luo M, Lunn D, Bell J, Plummer FA, Ball TB, Katzourakis A, Iversen AKN. HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression. Sci Rep 2015; 5:11253. [PMID: 26082240 PMCID: PMC4469978 DOI: 10.1038/srep11253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/11/2015] [Indexed: 11/15/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL) responses against the HIV Gag protein are associated with lowering viremia; however, immune control is undermined by viral escape mutations. The rapid viral mutation rate is a key factor, but recombination may also contribute. We hypothesized that CTL responses drive the outgrowth of unique intra-patient HIV-recombinants (URFs) and examined gag sequences from a Kenyan sex worker cohort. We determined whether patients with HLA variants associated with effective CTL responses (beneficial HLA variants) were more likely to carry URFs and, if so, examined whether they progressed more rapidly than patients with beneficial HLA-variants who did not carry URFs. Women with beneficial HLA-variants (12/52) were more likely to carry URFs than those without beneficial HLA variants (3/61) (p < 0.0055; odds ratio = 5.7). Beneficial HLA variants were primarily found in slow/standard progressors in the URF group, whereas they predominated in long-term non-progressors/survivors in the remaining cohort (p = 0.0377). The URFs may sometimes spread and become circulating recombinant forms (CRFs) of HIV and local CRF fragments were over-represented in the URF sequences (p < 0.0001). Collectively, our results suggest that CTL-responses associated with beneficial HLA variants likely drive the outgrowth of URFs that might reduce the positive effect of these CTL responses on disease progression.
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Affiliation(s)
- Chih-Hao Chang
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicolaas C Kist
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Tammy L Stuart Chester
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada
| | - Vattipally B Sreenu
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Melissa Herman
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Ma Luo
- 1] National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada [2] Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel Lunn
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - John Bell
- Office of the Regius Professor of Medicine, The Richard Doll Building, University of Oxford, Oxford, United Kingdom
| | - Francis A Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - T Blake Ball
- 1] National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada [2] Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada [3] Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Astrid K N Iversen
- 1] Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom [2] Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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3
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Jia L, Li L, Li H, Liu S, Wang X, Bao Z, Li T, Zhuang D, Liu Y, Li J. Recombination pattern reanalysis of some HIV-1 circulating recombination forms suggest the necessity and difficulty of revision. PLoS One 2014; 9:e107349. [PMID: 25203725 PMCID: PMC4159329 DOI: 10.1371/journal.pone.0107349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 08/09/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Recombination is one of the major mechanisms underlying the generation of HIV-1 variability. Currently 61 circulating recombinant forms of HIV-1 have been identified. With the development of recombination detection techniques and accumulation of HIV-1 reference stains, more accurate mosaic structures of circulating recombinant forms (CRFs), like CRF04 and CRF06, have undergone repeated analysis and upgrades. Such revisions may also be necessary for other CRFs. Unlike previous studies, whose results are based primarily on a single recombination detection program, the current study was based on multiple recombination analysis, which may have produced more impartial results. METHODS Representative references of 3 categories of intersubtype recombinants were selected, including BC recombinants (CRF07 and CRF08), BG recombinants (CRF23 and CRF24), and BF recombinants (CRF38 and CRF44). They were reanalyzed in detail using both the jumping profile hidden Markov model and RDP3. RESULTS The results indicate that revisions and upgrades are very necessary and the entire re-analysis suggested 2 types of revision: (i) length of inserted fragments; and (ii) number of inserted fragments. The reanalysis also indicated that determination of small regions of about 200 bases or fewer should be performed with more caution. CONCLUSION Results indicated that the involvement of multiple recombination detection programs is very necessary. Additionally, results suggested two major challenges, one involving the difficulty of accurately determining the locations of breakpoints and the second involving identification of small regions of about 200 bases or fewer with greater caution. Both indicate the complexity of HIV-1 recombination. The resolution would depend critically on development of a recombination analysis algorithm, accumulation of HIV-1 stains, and a higher sequencing quality. With the changes in recombination pattern, phylogenetic relationships of some CRFs may also change. All these results may be critical to understand the role of recombination in a complex and dynamic HIV evolution.
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Affiliation(s)
- Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
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4
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Safiullah Sarker M, Rahman M, Urmi AZ, Al-Mamun F, Islam LN, Azim T. Detection of a Rare HIV Type 1 Strain CRF16_A2D in Bangladesh. AIDS Res Hum Retroviruses 2011; 27:435-8. [PMID: 20929347 DOI: 10.1089/aid.2010.0209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Circulating recombinant form (CRF) 16_A2D is a rare HIV strain among the most recently identified subsubtype A2. Samples taken from an HIV-seropositive married couple who attended a voluntary counseling and testing unit in Dhaka, Bangladesh showed two rare CRF16_A2D isolates. Further genetic analyses targeting three HIV genes (gag, pol, and env) showed that the two isolates from the couple were closely related making it likely that one of them acquired the virus and transferred it to the other. The husband admitted that he had contact with sex workers and both wife and husband had never traveled outside the country. This indicates that the husband might have acquired the virus from sex workers and that this rare strain is already circulating in the country. Detecting unusual isolates is important to determine the true diversity of HIV strains in the country. Monitoring of such strains will help in identifying transmission patterns and possible interventions to prevent the spread of HIV infection.
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Affiliation(s)
- M. Safiullah Sarker
- Virology Laboratory, ICDDR,B, Mohakhali, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | | | - Feroz Al-Mamun
- Virology Laboratory, ICDDR,B, Mohakhali, Dhaka, Bangladesh
| | - Laila N. Islam
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tasnim Azim
- Virology Laboratory, ICDDR,B, Mohakhali, Dhaka, Bangladesh
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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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6
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Singh A, Page T, Moore PL, Allgaier RL, Hiramen K, Coovadia HM, Walker BD, Morris L, Ndung’u T. Functional and genetic analysis of coreceptor usage by dualtropic HIV-1 subtype C isolates. Virology 2009; 393:56-67. [PMID: 19695656 PMCID: PMC3492694 DOI: 10.1016/j.virol.2009.07.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Revised: 05/19/2009] [Accepted: 07/15/2009] [Indexed: 11/25/2022]
Abstract
It is widely documented that a complete switch from the predominant CCR5 (R5) to CXCR4 (X4) phenotype is less common for HIV-1 subtype C (HIV-1C) compared to other major subtypes. We investigated whether dualtropic HIV-1C isolates represented dualtropic, mixed R5 and X4 clones or both. Thirty of 35 functional HIV-1 env clones generated by bulk PCR amplification from peripheral blood mononuclear cells (PBMCs) infected with seven dualtropic HIV-1C isolates utilized CXCR4 exclusively. Five of 35 clones displayed dualtropism. Endpoint dilution of one isolate did not yield a substantial proportion of R5-monotropic env clones. Sequence-based predictive algorithms showed that env sequences from PBMCs, CXCR4 or CCR5-expressing cell lines were indistinguishable and all possessed X4/dualtropic characteristics. We describe HIV-1C CXCR4-tropic env sequence features. Our results suggest a dramatic loss of CCR5 monotropism as dualtropism emerges in HIV-1C which has important implications for the use of coreceptor antagonists in therapeutic strategies for this subtype.
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MESH Headings
- Amino Acid Sequence
- Cells, Cultured
- Cluster Analysis
- DNA, Viral/chemistry
- DNA, Viral/genetics
- HIV-1/classification
- HIV-1/genetics
- HIV-1/physiology
- Humans
- Leukocytes, Mononuclear/virology
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction/methods
- Receptors, CCR5/analysis
- Receptors, CXCR5/analysis
- Receptors, HIV/analysis
- Receptors, HIV/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology
- Virus Internalization
- env Gene Products, Human Immunodeficiency Virus/genetics
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Affiliation(s)
- Ashika Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Taryn Page
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Penny L. Moore
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Rachel L. Allgaier
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Charlestown, MA, USA
| | - Keshni Hiramen
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Hoosen M. Coovadia
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Department of Paediatrics and Child Heath, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Bruce D. Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Charlestown, MA, USA
| | - Lynn Morris
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Charlestown, MA, USA
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7
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Land AM, Ball TB, Luo M, Rutherford J, Sarna C, Wachihi C, Kimani J, Plummer FA. Full-length HIV type 1 proviral sequencing of 10 highly exposed women from Nairobi, Kenya reveals a high proportion of intersubtype recombinants. AIDS Res Hum Retroviruses 2008; 24:865-72. [PMID: 18544023 DOI: 10.1089/aid.2007.0200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analysis has revealed that the current HIV/AIDS pandemic consists of a multitude of different viral clades and recombinant viruses. The predominant circulating HIV-1 clade in Kenya is A1; however, Kenya borders countries where different subtypes are prominent, making Kenya a likely location for recombination. Previous studies have reported significant differences in the proportions of sequences in Kenya that are intersubtype recombinants. Studies that performed sequence-based typing on multiple HIV-1 genomic regions or full-length sequences found higher rates of recombination than those that examined a single gene or gene fragment. In this study, we describe full-length HIV-1 proviral sequence-based genotyping after limited peripheral blood mononuclear cell (PBMC) coculture. Ten subjects from a highly exposed cohort located in Nairobi, Kenya were examined. Pairwise comparison found minimal difference between sequences generated directly from patient PBMC DNA compared to sequences from cocultured PBMC DNA. Of the 10 full-length HIV-1 sequences examined, five were nonrecombinant clade A1, while the other five were unique intersubtype recombinants. Although this frequency of recombination is higher than previously described in Kenya, this finding is in agreement with previous full-length sequence data. Interestingly, although all the nonrecombinant sequences were clade A1, not all the recombinant sequences contained a clade A1 sequence.
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Affiliation(s)
- Allison M. Land
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - T. Blake Ball
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - John Rutherford
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Caitlin Sarna
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Charles Wachihi
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Francis A. Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
- Public Health Agency of Canada, Winnipeg, Canada
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8
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Chin MP, Lee SK, Chen J, Nikolaitchik OA, Powell DA, Fivash MJ, Hu WS. Long-range recombination gradient between HIV-1 subtypes B and C variants caused by sequence differences in the dimerization initiation signal region. J Mol Biol 2008; 377:1324-33. [PMID: 18314135 PMCID: PMC2706499 DOI: 10.1016/j.jmb.2008.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 01/23/2008] [Accepted: 02/01/2008] [Indexed: 11/26/2022]
Abstract
HIV-1 intersubtype recombinants have an increasingly important role in shaping the AIDS pandemic. We sought to understand the molecular mechanisms that generate intersubtype HIV-1 recombinants. We analyzed recombinants of HIV-1 subtypes B and C, and identified their crossover junctions in the viral genome from the 5' long terminal repeat (LTR) to the end of pol. We identified 56 recombination events in 56 proviruses; the distribution of these events indicated an apparent recombination gradient: there were significantly more crossover junctions in the 3' half than in the 5' half of the region analyzed. HIV-1 subtypes B and C have different dimerization initiation signal (DIS). We hypothesized that the inability of subtype B and C RNAs to form perfect base-pairing of the DIS affects the dimeric RNA structure and causes a decrease in recombination events at the 5' end of the viral genome. To test this hypothesis, we examined recombinants generated from a subtype C virus and a modified subtype B virus containing a subtype C DIS. In the 56 proviruses analyzed, we identified 96 recombination events, which are significantly more frequent than in the B/C recombinants. Furthermore, these crossover junctions were distributed evenly throughout the region analyzed, indicating that the recombination gradient was corrected by matching the DIS. Therefore, base-pairing at the DIS has an important function during HIV-1 reverse transcription, most likely in maintaining nucleic-acid structure in the complex. These findings reveal elements important to retroviral recombination and provide insights into the generation of HIV-1 intersubtype recombinants that are important to the AIDS epidemic.
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Affiliation(s)
- Mario P.S. Chin
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702
| | - Sook-Kyung Lee
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702
| | - Jianbo Chen
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702
| | | | - Douglas A. Powell
- Data Management Services Inc., National Cancer Institute, Frederick, MD 21702
| | - Mathew J. Fivash
- Data Management Services Inc., National Cancer Institute, Frederick, MD 21702
| | - Wei-Shau Hu
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702
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9
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Finnefrock AC, Liu X, Opalka DW, Shiver JW, Casimiro DR, Condra JH. HIV type 1 vaccines for worldwide use: predicting in-clade and cross-clade breadth of immune responses. AIDS Res Hum Retroviruses 2007; 23:1283-92. [PMID: 17961117 DOI: 10.1089/aid.2007.0098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the greatest challenges in HIV vaccine development is accommodating the worldwide sequence diversity of the HIV-1 virus. To understand how viral sequence diversity may affect the potential breadth of HIV-1 vaccines designed to elicit antiviral T cell immunity, we have developed novel approaches to assess sequence conservation at the amino acid level, where vaccine effects are exerted. Taking each sequence from the LANL 2004 amino acid alignments as a potential vaccine or as a challenge virus, all pairwise combinations of sequences were evaluated by two methods: first, a traditional comparison of aligned sequences, and second, by a new walking 9-mer algorithm chosen to emphasize the typical length of an MHC-I epitope. The rules for comparing mismatched 9-mer pairs between vaccine and challenge sequences were empirically deduced from an experiment on Nef-specific CD8 epitopes and the viral sequences from naturally HIV-1-infected patients. Results were weighted such that each clade contributed in proportion to its global prevalence. Cross-clade breadth of response is best maintained for vaccines encoding Pol and Gag, while commonly proposed Env- and Tat-based vaccines would be more clade sensitive. We evaluated the additional breadth that could be expected from multiclade vaccines including consensus and ancestral sequences. For more diverse proteins, adding a second strain can add a significant increase in breadth, although for three or more strains the intrinsic diversity of the protein leads to diminishing improvement.
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Affiliation(s)
- Adam C. Finnefrock
- Vaccine and Biologics Research, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Xiaomei Liu
- Vaccine and Biologics Research, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - David W. Opalka
- Vaccine and Biologics Research, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - John W. Shiver
- Vaccine and Biologics Research, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Danilo R. Casimiro
- Vaccine and Biologics Research, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Jon H. Condra
- Vaccine and Biologics Research, Merck Research Laboratories, West Point, Pennsylvania 19486
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