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HIV/AIDS Global Epidemic. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, Struck D, Vercauteren J, Wensing AMJ, Alexiev I, Åsjö B, Balotta C, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej S, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Boucher CAB, Kaplan L, Vandamme AM, Paraskevis D. Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia. J Infect Dis 2014; 211:1735-44. [PMID: 25512631 DOI: 10.1093/infdis/jiu666] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/24/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype CRF01_AE originated in Africa and then passed to Thailand, where it established a major epidemic. Despite the global presence of CRF01_AE, little is known about its subsequent dispersal pattern. METHODS We assembled a global data set of 2736 CRF01_AE sequences by pooling sequences from public databases and patient-cohort studies. We estimated viral dispersal patterns, using statistical phylogeographic analysis run over bootstrap trees estimated by the maximum likelihood method. RESULTS We show that Thailand has been the source of viral dispersal to most areas worldwide, including 17 of 20 sampled countries in Europe. Japan, Singapore, Vietnam, and other Asian countries have played a secondary role in the viral dissemination. In contrast, China and Taiwan have mainly imported strains from neighboring Asian countries, North America, and Africa without any significant viral exportation. DISCUSSION The central role of Thailand in the global spread of CRF01_AE can be probably explained by the popularity of Thailand as a vacation destination characterized by sex tourism and by Thai emigration to the Western world. Our study highlights the unique case of CRF01_AE, the only globally distributed non-B clade whose global dispersal did not originate in Africa.
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Affiliation(s)
- Konstantinos Angelis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor, and Cell Biology Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece Department of Zoology, University of Oxford, United Kingdom
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | | | | | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium
| | | | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Ricardo J Camacho
- Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | | | | | | | | | | | - Snjezana Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases Dr F. Mihaljevic, Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases Prof Dr Matei Bals, Bucharest, Romania
| | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Center, University of Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Division of Infectious Diseases Division of Clinical Virology, Karolinska Institute Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | - Lauren Kaplan
- Alcohol Research Group, University California, Berkeley
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
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Cross-border sexual transmission of the newly emerging HIV-1 clade CRF51_01B. PLoS One 2014; 9:e111236. [PMID: 25340817 PMCID: PMC4207770 DOI: 10.1371/journal.pone.0111236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/30/2014] [Indexed: 11/19/2022] Open
Abstract
A novel HIV-1 recombinant clade (CRF51_01B) was recently identified among men who have sex with men (MSM) in Singapore. As cases of sexually transmitted HIV-1 infection increase concurrently in two socioeconomically intimate countries such as Malaysia and Singapore, cross transmission of HIV-1 between said countries is highly probable. In order to investigate the timeline for the emergence of HIV-1 CRF51_01B in Singapore and its possible introduction into Malaysia, 595 HIV-positive subjects recruited in Kuala Lumpur from 2008 to 2012 were screened. Phylogenetic relationship of 485 amplified polymerase gene sequences was determined through neighbour-joining method. Next, near-full length sequences were amplified for genomic sequences inferred to be CRF51_01B and subjected to further analysis implemented through Bayesian Markov chain Monte Carlo (MCMC) sampling and maximum likelihood methods. Based on the near full length genomes, two isolates formed a phylogenetic cluster with CRF51_01B sequences of Singapore origin, sharing identical recombination structure. Spatial and temporal information from Bayesian MCMC coalescent and maximum likelihood analysis of the protease, gp120 and gp41 genes suggest that Singapore is probably the country of origin of CRF51_01B (as early as in the mid-1990s) and featured a Malaysian who acquired the infection through heterosexual contact as host for its ancestral lineages. CRF51_01B then spread rapidly among the MSM in Singapore and Malaysia. Although the importation of CRF51_01B from Singapore to Malaysia is supported by coalescence analysis, the narrow timeframe of the transmission event indicates a closely linked epidemic. Discrepancies in the estimated divergence times suggest that CRF51_01B may have arisen through multiple recombination events from more than one parental lineage. We report the cross transmission of a novel CRF51_01B lineage between countries that involved different sexual risk groups. Understanding the cross-border transmission of HIV-1 involving sexual networks is crucial for effective intervention strategies in the region.
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Impact of clade, geography, and age of the epidemic on HIV-1 neutralization by antibodies. J Virol 2014; 88:12623-43. [PMID: 25142591 DOI: 10.1128/jvi.01705-14] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Neutralizing antibodies (nAbs) are a high priority for vaccines that aim to prevent the acquisition of HIV-1 infection. Vaccine effectiveness will depend on the extent to which induced antibodies neutralize the global diversity of circulating HIV-1 variants. Using large panels of genetically and geographically diverse HIV-1 Env-pseudotyped viruses and chronic infection plasma samples, we unambiguously show that cross-clade nAb responses are commonly induced in response to infection by any virus clade. Nonetheless, neutralization was significantly greater when the plasma clade matched the clade of the virus being tested. This within-clade advantage was diminished in older, more-diverse epidemics in southern Africa, the United States, and Europe compared to more recent epidemics in Asia. It was most pronounced for circulating recombinant form (CRF) 07_BC, which is common in China and is the least-divergent lineage studied; this was followed by the slightly more diverse Asian CRF01_AE. We found no evidence that transmitted/founder viruses are generally more susceptible to neutralization and are therefore easier targets for vaccination than chronic viruses. Features of the gp120 V1V2 loop, in particular, length, net charge, and number of N-linked glycans, were associated with Env susceptibility and plasma neutralization potency in a manner consistent with neutralization escape being a force that drives viral diversification and plasma neutralization breadth. The overall susceptibility of Envs and potencies of plasma samples were highly predictive of the neutralization outcome of any single virus-plasma combination. These findings highlight important considerations for the design and testing of candidate HIV-1 vaccines that aim to elicit effective nAbs. IMPORTANCE An effective HIV-1 vaccine will need to overcome the extraordinary variability of the virus, which is most pronounced in the envelope glycoproteins (Env), which are the sole targets for neutralizing antibodies (nAbs). Distinct genetic lineages, or clades, of HIV-1 occur in different locales that may require special consideration when designing and testing vaccines candidates. We show that nAb responses to HIV-1 infection are generally active across clades but are most potent within clades. Because effective vaccine-induced nAbs are likely to share these properties, optimal coverage of a particular clade or combination of clades may require clade-matched immunogens. Optimal within-clade coverage might be easier to achieve in regions such as China and Thailand, where the epidemic is more recent and the virus less diverse than in southern Africa, the United States, and Europe. Finally, features of the first and second hypervariable regions of gp120 (V1V2) may be critical for optimal vaccine design.
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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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Ng KT, Ng KY, Khong WX, Chew KK, Singh PK, Yap JK, Tan MT, Leo YS, Laeyendecker O, Quinn TC, Kamarulzaman A, Tee KK, Ng OT. Phylodynamic profile of HIV-1 subtype B, CRF01_AE and the recently emerging CRF51_01B among men who have sex with men (MSM) in Singapore. PLoS One 2013; 8:e80884. [PMID: 24312505 PMCID: PMC3846621 DOI: 10.1371/journal.pone.0080884] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/17/2013] [Indexed: 12/04/2022] Open
Abstract
HIV-1 subtype B and CRF01_AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and the recently characterized CRF51_01B strains circulating among the MSM population in Singapore. A total of 105 (49.5%) newly-diagnosed treatment-naïve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 – 2629), gp120 (HXB2: 6942 – 7577) and gp41 (HXB2: 7803 – 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01_AE and one within CRF51_01B lineages) of different sizes (involving 3 – 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01_AE. Exponential increase in effective population size for both subtype B and CRF01_AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51_01B lineages were probably generated through series of recombination events involving CRF01_AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and CRF51_01B viral strains circulating among MSM in Singapore.
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Affiliation(s)
- Kim Tien Ng
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kah Ying Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Wei Xin Khong
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Kuan Kiat Chew
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Palvinder Kaur Singh
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Joe Kwan Yap
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Mei Ting Tan
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Yee Sin Leo
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Oliver Laeyendecker
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland United States of America
| | - Thomas C. Quinn
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland United States of America
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
| | - Oon Tek Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
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HIV/AIDS Global Epidemic. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Ng OT, Munshaw S, Lamers SL, Chew KK, Lin L, Redd AD, Manucci J, Quinn TC, Ray SC, Chua A, Leo YS, Laeyendecker O. Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms. AIDS Res Hum Retroviruses 2011; 27:1135-7. [PMID: 21235306 DOI: 10.1089/aid.2010.0364] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To investigate HIV-1 molecular epidemiology in Singapore, we sequenced portions of three regions of the HIV-1 genome (protease HXB2: 2163 to 2620, gp120 HXB2: 6904 to 7628, and gp41 HXB2: 7817 to 8264) from 212 plasma samples collected between February 2008 and August 2009. From these samples, 109 (51.4%) generated interpretable data in all regions. Sixty-one (56.0%) were identified as CRF01_AE, 26 (23.9%) as subtype B and 14 (12.8%) as possible novel recombinant forms. The main novel recombinant pattern, detected in 13 sequences, had subtype B in protease and gp41 and CRF01_AE in gp120. There was intermixing of subtypes within transmission risk groups. However, 85% of subjects infected with the novel recombinant forms self-identified as men who have sex with men or bisexuals compared with only 41% of individuals infected with CRF01_AE and 62% infected with subtype B (p = 0.001).
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Affiliation(s)
- Oon Tek Ng
- Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | | | | | - Kuan Kiat Chew
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Li Lin
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
| | - Jordyn Manucci
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
| | - Thomas C. Quinn
- Johns Hopkins School of Medicine, Baltimore, Maryland
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
| | - Stuart C. Ray
- Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Arlene Chua
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee Sin Leo
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Oliver Laeyendecker
- Johns Hopkins School of Medicine, Baltimore, Maryland
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
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Demma LJ, Vanderford TH, Logsdon JM, Feinberg MB, Staprans SI. Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host. Retrovirology 2006; 3:19. [PMID: 16549011 PMCID: PMC1431560 DOI: 10.1186/1742-4690-3-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Accepted: 03/20/2006] [Indexed: 12/02/2022] Open
Abstract
Background The ability of emerging pathogens to infect new species is likely related to the diversity of pathogen variants present in existing reservoirs and their degree of genomic plasticity, which determines their ability to adapt to new environments. Certain simian immunodeficiency viruses (SIVcpz, SIVsm) have demonstrated tremendous success in infecting new species, including humans, resulting in the HIV-1 and HIV-2 epidemics. Although SIV diversification has been studied on a population level, the essential substrates for cross-species transmission, namely SIV sequence diversity and the types and extent of viral diversification present in individual reservoir animals have not been elucidated. To characterize this intra-host SIV diversity, we performed sequence analyses of clonal viral envelope (env) V1V2 and gag p27 variants present in individual SIVsm-infected sooty mangabeys over time. Results SIVsm demonstrated extensive intra-animal V1V2 length variation and amino acid diversity (le38%), and continual variation in V1V2 N-linked glycosylation consensus sequence frequency and location. Positive selection was the predominant evolutionary force. Temporal sequence shifts suggested continual selection, likely due to evolving antibody responses. In contrast, gag p27 was predominantly under purifying selection. SIVsm V1V2 sequence diversification is at least as great as that in HIV-1 infected humans, indicating that extensive viral diversification in and of itself does not inevitably lead to AIDS. Conclusion Positive diversifying selection in this natural reservoir host is the engine that has driven the evolution of the uniquely adaptable SIV/HIV envelope protein. These studies emphasize the importance of retroviral diversification within individual host reservoir animals as a critical substrate in facilitating cross-species transmission.
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Affiliation(s)
- LJ Demma
- Program in Population Biology, Evolution and Ecology, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Centers for Disease Control and Prevention, Division of Bacterial and Mycotic Diseases, 1600 Clifton Road, Mailstop D-63, Atlanta, GA 30333, USA
| | - TH Vanderford
- Program in Population Biology, Evolution and Ecology, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - JM Logsdon
- Department of Biology, Emory University, Atlanta, GA. Current address: University of Iowa, Department of Biological Sciences, Roy J. Carver Center for Comparative Genomics, 301 Biology Building, Iowa City, IA 52242, USA
| | - MB Feinberg
- Departments of Medicine and Microbiology and Immunology, and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Merck Vaccine Division, Merck and Company, Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - SI Staprans
- Departments of Medicine and Microbiology and Immunology, and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, 954 Gatewood Rd., Atlanta, GA, 30329, USA
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Blay WM, Gnanakaran S, Foley B, Doria-Rose NA, Korber BT, Haigwood NL. Consistent patterns of change during the divergence of human immunodeficiency virus type 1 envelope from that of the inoculated virus in simian/human immunodeficiency virus-infected macaques. J Virol 2006; 80:999-1014. [PMID: 16379001 PMCID: PMC1346845 DOI: 10.1128/jvi.80.2.999-1014.2006] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have analyzed changes to proviral Env gp120 sequences and the development of neutralizing antibodies (NAbs) during 1 year of simian/human immunodeficiency virus SHIV-89.6P infection in 11 Macaca nemestrina macaques. Seven macaques had significant env divergence from that of the inoculum, and macaques with greater divergence had higher titers of homologous NAbs. Substitutions in sequons encoding potential N-linked glycosylation sites (PNGs) were among the first to be established, although overall the total number of sequons did not increase significantly. The majority (19 of 23) of PNGs present in the inoculum were conserved in the sequences from all macaques. Statistically significant variations in PNGs occurred in multiple macaques within constrained regions we term "hot spots," resulting in the selection of sequences more similar to the B consensus. These included additions on V1, the N-terminal side of V4, and the outer region of C2. Complex mutational patterns resulted in convergent PNG shifts in V2 and V5. Charge changes in Env V1V2, resulting in a net acidic charge, and a proline addition in V5 occurred in several macaques. Molecular modeling of the 89.6P sequence showed that the conserved glycans lie on the silent face of Env and that many are proximal to disulfide bonds, while PNG additions and shifts are proximal to the CD4 binding site. Nonsynonymous-to-synonymous substitution ratios suggest that these changes result from selective pressure. This longitudinal and cross-sectional study of mutations in human immunodeficiency virus (HIV) env in the SHIV background provides evidence that there are more constraints on the configuration of the glycan shield than were previously appreciated.
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Affiliation(s)
- W M Blay
- Department of Pathobiology, University of Washington, Seattle, WA 98195, USA
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Hsu LY, Subramaniam R, Bacheler L, Paton NI. Characterization of Mutations in CRF01_AE Virus Isolates From Antiretroviral Treatment-Naive and -Experienced Patients in Singapore. J Acquir Immune Defic Syndr 2005; 38:5-13. [PMID: 15608517 DOI: 10.1097/00126334-200501010-00002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To determine the frequency of drug resistance mutations among antiretroviral treatment-naive and -experienced patients infected with CRF01_AE virus. DESIGN Prospective observational study. METHODS We recruited antiretroviral-experienced HIV-infected patients with suspected drug resistance and consecutive newly diagnosed drug-naive patients. Viral sequencing was performed using standard methods. Frequencies of mutations in CRF01_AE virus isolates were compared with reference data for subtype B virus. RESULTS Sequences were obtained for CRF01_AE virus isolates from 69 patients with treatment exposure and 35 treatment-naive patients. Treatment-naive patients had numerous polymorphisms but no major drug resistance mutations. There were differences between CRF01_AE and subtype B viruses in several drug resistance mutations including the following: D67N, L210F, K101E, V106M, V179I/D, G190A/S/E, and G48V (which were more common in CRF01_AE virus) and M41L, T215Y, and V82A (which were less common in CRF01_AE virus). CONCLUSIONS The pattern of treatment-related mutations in CRF01_AE virus differs from that in subtype B virus at a number of positions determining drug resistance. Understanding these differences is important for interpreting results of resistance tests and determining treatment choices.
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Affiliation(s)
- Li-Yang Hsu
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
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Meloni ST, Sankalé JL, Hamel DJ, Eisen G, Guéye-Ndiaye A, Mboup S, Kanki PJ. Molecular epidemiology of human immunodeficiency virus type 1 sub-subtype A3 in Senegal from 1988 to 2001. J Virol 2004; 78:12455-61. [PMID: 15507632 PMCID: PMC525044 DOI: 10.1128/jvi.78.22.12455-12461.2004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The global human immunodeficiency virus (HIV)epidemic is characterized by significant genetic diversity in circulating viruses. We have recently characterized a group of viruses that form a distinct sub-subtype within the subtype A radiation, which we have designated HIV type 1 (HIV-1) sub-subtype A, circulating in West Africa. A prospective study of a cohort of female sex workers (FSW) in Dakar, Senegal over an 18-year period indicated that an A3-specific sequence in the C2-V3 region of the env gene was found in 46 HIV-1-infected women. HIV-1 sub-subtype A3 appeared in the FSW population as early as 1988 and continued to be transmitted as of 2001. We also found that HIV-1 A3 is not confined to the FSW cohort in Senegal but is also circulating in the general population in Dakar. Furthermore, analyses of viral sequences from a few other West and Central African countries also demonstrated evidence of HIV-1 A3 sequence in isolates from HIV-1-infected people in Ivory Coast, Nigeria, Niger, Guinea Bissau, Benin, and Equatorial Guinea. Overall, because of the evidence of sub-subtype A3 in the general population in Senegal, as well as in a few neighboring West and Central African countries, along with the increasing incidence of infection with A3-containing viruses in the Dakar high-risk FSW population, we feel that HIV-1 sub-subtype A3 viruses are important to distinguish and monitor.
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Affiliation(s)
- Seema Thakore Meloni
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
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