1
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Rodgers MA, Gomathi S, Vallari A, Saravanan S, Lucas GM, Mehta S, Solomon SS, Cloherty GA. Diverse HCV Strains And HIV URFS Identified Amongst People Who Inject Drugs In India. Sci Rep 2020; 10:7214. [PMID: 32350342 PMCID: PMC7190742 DOI: 10.1038/s41598-020-64309-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/27/2020] [Indexed: 12/22/2022] Open
Abstract
Although the prevalences of HIV and HCV are significantly higher amongst PWID in India compared to the general population, the strains circulating within this group have not been well-characterized. Through subgenomic sequencing of viruses present in residual plasma from an HIV/HCV prevalence study conducted amongst PWID across five cities in India in 2016-2017, a total of N = 498 HCV and N = 755 HIV strains were classified from N = 975 study participants. Considerable HCV diversity was identified, with different strains predominating in each region of the country. Overall, the most common strain was genotype 3a (39.0%), with genotypes 1a (26.9%), 1b (3.0%), 1c (0.2%), 3b (20.7%), 3i (2.0%), 4a (0.2%), 4d (1.0%), 6 (1.8%), 6n (4.8%), 6 v (0.2%) and one unclassifiable recombinant specimen (0.2%) also identified. The majority of the HIV specimens were subtype C (96.7%), although subtype A (0.4%), CRF01_AE (0.4%) and unique recombinant forms (URFs, 2.5%) were also detected. Notably, the geographical restriction of HIV subtype A and CRF01_AE, and HCV genotypes 4 and 6 to specific sites suggests distinct novel introductions of HIV and HCV into PWID populations, potentially via drug trafficking routes from neighboring countries where these strains are common.
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Affiliation(s)
- Mary A Rodgers
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, USA.
| | | | - Ana Vallari
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, USA
| | | | | | - Shruti Mehta
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Sunil S Solomon
- YR Gaitonde Centre for AIDS Research and Education, Chennai, India
- Johns Hopkins University School of Medicine, Baltimore, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Gavin A Cloherty
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, USA
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2
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Désiré N, Cerutti L, Le Hingrat Q, Perrier M, Emler S, Calvez V, Descamps D, Marcelin AG, Hué S, Visseaux B. Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification. Retrovirology 2018; 15:80. [PMID: 30577842 PMCID: PMC6303845 DOI: 10.1186/s12977-018-0461-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes. RESULTS All HIV full-length genomes available in public databases were analysed (n = 2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes. CONCLUSIONS With this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts.
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Affiliation(s)
- Nathalie Désiré
- INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université, 75013, Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Virologie, 75013, Paris, France
| | - Lorenzo Cerutti
- SmartGene Services, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Quentin Le Hingrat
- IAME, UMR 1137, Université Paris Diderot, INSERM, Paris, France.,AP-HP, Hôpital Bichat, Virologie, 75018, Paris, France
| | - Marine Perrier
- IAME, UMR 1137, Université Paris Diderot, INSERM, Paris, France.,AP-HP, Hôpital Bichat, Virologie, 75018, Paris, France
| | - Stefan Emler
- SmartGene Services, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Vincent Calvez
- INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université, 75013, Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Virologie, 75013, Paris, France
| | - Diane Descamps
- IAME, UMR 1137, Université Paris Diderot, INSERM, Paris, France.,AP-HP, Hôpital Bichat, Virologie, 75018, Paris, France
| | - Anne-Geneviève Marcelin
- INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université, 75013, Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Virologie, 75013, Paris, France
| | - Stéphane Hué
- Department of Epidemiology & Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Benoit Visseaux
- IAME, UMR 1137, Université Paris Diderot, INSERM, Paris, France. .,AP-HP, Hôpital Bichat, Virologie, 75018, Paris, France.
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3
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Sinha S, Gupta K, Khan NH, Mandal D, Kohli M, Das BK, Pandey RM. Higher Frequency of HIV-1 Drug Resistance and Increased Nucleoside Reverse Transcriptase Inhibitor Mutations among the HIV-1 Positive Antiretroviral Therapy-Naïve patients Coinfected With Mycobacterium tuberculosis Compared With Only HIV Infection in India. Infect Dis (Lond) 2018; 11:1178633718788870. [PMID: 30046244 PMCID: PMC6056791 DOI: 10.1177/1178633718788870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/24/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Emergence of human immunodeficiency virus (HIV) drug resistance mutations
prior to highly active antiretroviral therapy is a serious problem in
clinical management of HIV/AIDS. Risk factors for appearance of drug
resistance mutations are not known. We hypothesize that
Mycobacterium tuberculosis infection may contribute to
rapid emergence of such mutations in antiretroviral therapy–naïve
patients. Methods: A total of 115 patients were recruited in this study of which 75 were HIV+TB+
coinfected (group 1) and 40 were HIV+TB− (group 2). Blood samples from all
the patients were collected and CD4+ cell counts; HIV-1 plasma viral load
and sequencing of protease and two-third region of reverse transcriptase of
HIV-1 was performed and analyzed for drug resistance pattern. Results: For patients with HIV+TB+, 10.6% (8/75) had mutations to non-nucleoside
reverse transcriptase inhibitors (NNRTIs), 4% (3/75) to nucleoside reverse
transcriptase inhibitors, and only 2.6% (2/75) patients had mutations to
protease inhibitors. Interestingly, for group 2 (HIV+TB−), there were only
NNRTI mutations found among these patients, and only 3 patients (7.5%) had
these drug-resistant mutations. Clade typing and phylogenetic tree analysis
showed HIV-1 subtype C predominance in these patients. Conclusions: Our study showed that higher percentage of HIV drug resistance mutations was
found among HIV+TB+ individuals compared with tuberculosis-uninfected
patients. Tuberculosis coinfection may be a risk factor for emergence of
high frequency of drug resistance mutations. Studies with a larger sample
size will help to confirm these findings from the Indian population.
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Affiliation(s)
- Sanjeev Sinha
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Kartik Gupta
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Nawaid Hussain Khan
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Dibyakanti Mandal
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Mikashmi Kohli
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - B K Das
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - R M Pandey
- Department of Biostatistics, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
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4
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Phanuphak N, Lo YR, Shao Y, Solomon SS, O'Connell RJ, Tovanabutra S, Chang D, Kim JH, Excler JL. HIV Epidemic in Asia: Implications for HIV Vaccine and Other Prevention Trials. AIDS Res Hum Retroviruses 2015; 31:1060-76. [PMID: 26107771 DOI: 10.1089/aid.2015.0049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An overall decrease of HIV prevalence is now observed in several key Asian countries due to effective prevention programs. The decrease in HIV prevalence and incidence may further improve with the scale-up of combination prevention interventions. The implementation of future prevention trials then faces important challenges. The opportunity to identify heterosexual populations at high risk such as female sex workers may rapidly wane. With unabating HIV epidemics among men who have sex with men (MSM) and transgender (TG) populations, an effective vaccine would likely be the only option to turn the epidemic. It is more likely that efficacy trials will occur among MSM and TG because their higher HIV incidence permits smaller and less costly trials. The constantly evolving patterns of HIV-1 diversity in the region suggest close monitoring of the molecular HIV epidemic in potential target populations for HIV vaccine efficacy trials. CRF01_AE remains predominant in southeast Asian countries and MSM populations in China. This relatively steady pattern is conducive to regional efficacy trials, and as efficacy warrants, to regional licensure. While vaccines inducing nonneutralizing antibodies have promise against HIV acquisition, vaccines designed to induce broadly neutralizing antibodies and cell-mediated immune responses of greater breadth and depth in the mucosal compartments should be considered for testing in MSM and TG. The rationale and design of efficacy trials of combination prevention modalities such as HIV vaccine and preexposure prophylaxis (PrEP) remain hypothetical, require high adherence to PrEP, are more costly, and present new regulatory challenges. The prioritization of prevention interventions should be driven by the HIV epidemic and decided by the country-specific health and regulatory authorities. Modeling the impact and cost-benefit may help this decision process.
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Affiliation(s)
| | - Ying-Ru Lo
- HIV, Hepatitis, and STI Unit, WHO Regional Office for the Western Pacific, Manila, Philippines
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sunil Suhas Solomon
- Johns Hopkins University School of Medicine, Baltimore, Maryland
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Robert J. O'Connell
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - David Chang
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jean Louis Excler
- U.S. Military HIV Research Program, Bethesda, Maryland
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
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5
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Hussain SI, Panneerselvam N, Solomon S, Solomon SS, Adam K, Chandrasekaran E, Montefiori DC, Pachamuthu B. Broadly Neutralizing Antibody Responses in a Subset of HIV-1-Infected Individuals in Chennai, India. J Int Assoc Provid AIDS Care 2013; 16:201-208. [PMID: 23422744 DOI: 10.1177/1545109712467695] [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: 11/16/2022] Open
Abstract
Identification of broadly neutralizing antibodies (NAbs) generated during the course of HIV-1 infection is essential for effective HIV-1 vaccine design. The magnitude and breadth of neutralizing activity in the sera from 46 antiretroviral treatment-naive HIV-1 clade C-infected individuals was measured in a single round infection assay using TZM-bl cells and multisubtype panel of env-pseudotyped viruses. Higher levels of NAb response (NAb titer 500 to >40 000) were measured in these patients against tier 1 and tier 2 viruses. The average magnitude of the NAb responses of chronically infected individuals against heterologous viruses was consistently higher than the response observed from individuals with long-term nonprogressor ( P = .086). To conclude, high titers of HIV-1 cross-neutralizing activity were observed in the sera from a subset of HIV-1-infected individuals in Chennai, India. Additional studies of the epitopes recognized by these antibodies may facilitate the discovery of an effective vaccine immunogen.
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Affiliation(s)
- Syed Iqbal Hussain
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | - Nandagopal Panneerselvam
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | - Suniti Solomon
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | - Sunil S Solomon
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India.,2 Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Ezhilarasi Chandrasekaran
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | | | - Balakrishnan Pachamuthu
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
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Nitayaphan S, Ngauy V, O'Connell R, Excler JL. HIV epidemic in Asia: optimizing and expanding vaccine development. Expert Rev Vaccines 2012; 11:805-19. [PMID: 22913258 DOI: 10.1586/erv.12.49] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent evidence in Thailand for protection from acquisition of HIV through vaccination in a mostly heterosexual population has generated considerable hope. Building upon these results and the analysis of the correlates of risk remains among the highest priorities. Improved vaccine concepts including heterologous prime-boost regimens, improved proteins with potent adjuvants and new vectors expressing mosaic antigens may soon enter clinical development to assess vaccine efficacy in men who have sex with men. Identifying heterosexual populations with sufficient HIV incidence for the conduct of efficacy trials represents perhaps the main challenge in Asia. Fostering translational research efforts in Asian countries may benefit from the development of master strategic plans and program management processes.
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Affiliation(s)
- Sorachai Nitayaphan
- Royal Thai Army Component, Armed Forces Research Institute of Medical Sciences, 315/6 Rajvithi Road, Bangkok 10400, Thailand
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7
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Prevalence of HIV Drug Resistance Mutations in HIV Type 1 Isolates in Antiretroviral Therapy Naïve Population from Northern India. AIDS Res Treat 2012; 2012:905823. [PMID: 22496972 PMCID: PMC3312221 DOI: 10.1155/2012/905823] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/04/2012] [Indexed: 11/17/2022] Open
Abstract
Objective. The increased use of antiretroviral therapy (ART) has reduced the morbidity and mortality associated with HIV, adversely leading to the emergence of HIV drug resistance (HIVDR). In this study we aim to evaluate the prevalence of HIVDR mutations in ART-naive HIV-1 infected patients from northern India. Design. Analysis was performed using Viroseq genotyping system based on sequencing of entire protease and two-thirds of the Reverse Transcriptase (RT) region of pol gene. Results. Seventy three chronic HIV-1 infected ART naïve patients eligible for first line ART were enrolled from April 2006 to August 2008. In 68 patients DNA was successfully amplified and sequencing was done. 97% of HIV-1 strains belonged to subtype C, and one each to subtype A1 and subtype B. The overall prevalence of primary DRMs was 2.9% [2/68, 95% confidence interval (CI), 0.3%–10.2%]. One patient had a major RT mutation M184V, known to confer resistance to lamivudine, and another had a major protease inhibitor (PI) mutation D30N that imparts resistance to nelfinavir. Conclusion. Our study shows that primary HIVDR mutations have a prevalence of 2.9% among ART-naive chronic HIV-1 infected individuals.
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8
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Ringe R, Thakar M, Bhattacharya J. Variations in autologous neutralization and CD4 dependence of b12 resistant HIV-1 clade C env clones obtained at different time points from antiretroviral naïve Indian patients with recent infection. Retrovirology 2010; 7:76. [PMID: 20860805 PMCID: PMC2955667 DOI: 10.1186/1742-4690-7-76] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/22/2010] [Indexed: 12/03/2022] Open
Abstract
Background Limited information is available on HIV-1 Indian clade C sensitivities to autologous antibodies during the course of natural infection. In the present study, a total of 37 complete envelope clones (Env) were amplified at different time points predominantly from the plasma of five Indian patients with recent HIV-1 infection and envelope-pseudotyped viruses were examined for their magnitude of sensitivity to autologous plasma antibodies during natural course of infection. Results Variable low levels of neutralization were consistently detected with contemporaneous autologous plasma. In contrast to clade B and African clade C HIV-1 envelopes, Env clones obtained from four patients were found to be resistant to IgG1b12. The majority of the Env clones were resistant to 2G12 and 2F5 due to the absence of the minimal motifs required for antibody recognition, but were sensitive to 4E10. Nonetheless, Env clones from one patient were found to be sensitive to 2G12, atypical for clade C, and one Env clone exhibited unusual sensitivity to 17b, suggesting spontaneous exposure of CD4i epitopes. Phylogenetic analysis revealed that Env clones were closely clustered within patients. Variation in the potential N-linked glycosylation pattern also appeared to be different in patients over the course of infection. Interestingly, we found that the sensitivity of Envs to contemporaneous autologous NAbs correlated positively with increased sensitivity to soluble CD4 and inversely with anti-CD4 antibody and Envs with increased NAb sensitivity were able to efficiently infect HeLa cells expressing low CD4. Conclusion Our data showed considerable variations in autologous neutralization of these early HIV-1 clade C Envs in each of these patients and indicate greater exposure to CD4 of Envs that showed increased autologous neutralization. Interestingly, Env clones obtained from a single patient at different time points were found to retain sensitivity to b12 antibody that binds to CD4 binding site in Env in contrast to Envs obtained from other patients. However, we did not find any association between increased b12 sensitivity of Envs obtained from this particular patient with their degree of exposure to CD4.
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Affiliation(s)
- Rajesh Ringe
- Department of Molecular Virology, National AIDS Research Institute, Indian Council of Medical Research, G-73 MIDC, Bhosari, Pune, India
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9
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Evolution of HIV-1 in India. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2010; 21:3-7. [PMID: 23637473 DOI: 10.1007/s13337-010-0001-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 05/23/2010] [Indexed: 10/19/2022]
Abstract
Nearly 25 years after the discovery of the human immunodeficiency virus type 1 (HIV-1) effective control of the AIDS pandemic remains elusive. At the root of this challenge is the evolution of this virus to elude immune control. Error-prone nature of replication and retro-transcription is the hallmark of this virus. This fidelity of replication in HIV-1 is due to the absence of proof-reading/repair and post-replicative error correction mechanisms that normally operate during replication of DNA viruses. Advances in sequencing technology and expanded disease surveillance have allowed researchers to characterize the variation in HIV-1 around the world and within individual patient overtime. Although HIV-1 has been classified into distinct subtypes, the classification does not reflect dynamic genetic evolution of HIV-1 through which new strains are constantly emerging. The resultant viral diversity has implications for differential rates of disease progression in different geographical areas, differential responses to antiretroviral therapy (including the development of resistance), and vaccine development. In this review evolution of HIV-1 in India is discussed.
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Ramanathan VD, Kumar M, Mahalingam J, Sathyamoorthy P, Narayanan PR, Solomon S, Panicali D, Chakrabarty S, Cox J, Sayeed E, Ackland J, Verlinde C, Vooijs D, Loughran K, Barin B, Lombardo A, Gilmour J, Stevens G, Smith MS, Tarragona-Fiol T, Hayes P, Kochhar S, Excler JL, Fast P. A Phase 1 study to evaluate the safety and immunogenicity of a recombinant HIV type 1 subtype C-modified vaccinia Ankara virus vaccine candidate in Indian volunteers. AIDS Res Hum Retroviruses 2009; 25:1107-16. [PMID: 19943789 DOI: 10.1089/aid.2009.0096] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A recombinant modified vaccinia Ankara virus vaccine candidate (TBC-M4) expressing HIV-1 subtype C env, gag, tat-rev, and nef-RT genes was tested in a randomized, double-blind, dose escalation Phase I trial in 32 HIV-uninfected healthy volunteers who received three intramuscular injections of TBC-M4 at 0, 1, and 6 months of 5 x 10(7) plaque-forming units (pfu) (low dosage, LD) (n = 12) or 2.5 x 10(8) pfu (high dosage, HD) (n = 12) or placebo (n = 8). Local and systemic reactogenicity was experienced by approximately 67% and 83% of vaccine recipients, respectively. The reactogenicity events were mostly mild in severity. Severe but transient systemic reactogenicity was seen in one volunteer of the HD group. No vaccine-related serious adverse events or events suggesting perimyocarditis were seen. A higher frequency of local reactogenicity events was observed in the HD group. Cumulative HIV-specific IFN-gamma ELISPOT responses were detected in frozen PBMCs from 9/11 (82%), 12/12 (100%), and 1/8 (13%) volunteers after the third injection of the LD, HD, and placebo groups, respectively. Most of the responses were to gag and env proteins (maximum of 430 SFU/10(6) PBMCs) persisting across multiple time points. HIV-specific ELISA antibody responses were detected in 10/11, 12/12, and 0/8 volunteers post-third vaccination, in the LD, HD, and placebo groups, respectively. No neutralizing activity against HIV-1 subtype C isolates was detected. TBC-M4 appears to be generally safe and well-tolerated. The immune response detected was dose dependent, modest in magnitude, and directed mostly to env and gag proteins, suggesting further evaluation of this vaccine in a prime-boost regimen.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Josephine Cox
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Eddy Sayeed
- International AIDS Vaccine Initiative, New York, New York 10038
| | - James Ackland
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Carl Verlinde
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Dani Vooijs
- International AIDS Vaccine Initiative, New York, New York 10038
| | | | - Burc Barin
- EMMES Corporation, Rockville Maryland 20850
| | - Angela Lombardo
- International AIDS Vaccine Initiative, New York, New York 10038
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, UK
| | | | | | | | | | | | | | - Patricia Fast
- International AIDS Vaccine Initiative, New York, New York 10038
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11
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Jones LR, Dilernia DA, Manrique JM, Moretti F, Salomón H, Gomez-Carrillo M. In-depth analysis of the origins of HIV type 1 subtype C in South America. AIDS Res Hum Retroviruses 2009; 25:951-9. [PMID: 19842791 DOI: 10.1089/aid.2008.0293] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The South American HIV-1 epidemic is characterized by the co-circulation of subtype B and BF recombinant variants. Together with the B and BF genotypes, HIV-1 subtype C (HIV-1C), F1, and several other recombinants have been reported. The epidemiological significance and immune correlates of these "non-B-non-BF" strains circulating in South America are still uncertain and therefore are increasingly attracting the interest of the scientific community. In this study, the South American HIV-1C epidemic was studied using new technologies for the phylogenetic analysis of large datasets. Our results indicate that there is a major clade encompassing most of the South American HIV-1C strains. These analyses also agreed that some strains do not group inside this major clade, suggesting that there could be HIV-1C sequences of different origins circulating in South America. Others have proposed different hypotheses about the origins of HIV-1C strains from South America. This study shows that an exact single origin cannot be determined, a fact that could be attributed to sampling problems, phylogenetic uncertainty, and the shortage of historical and epidemiological data. Currently, the reported data indicate that HIV-1C strains were introduced in Brazil and afterward spread to other regions of South America. By using character optimization on the obtained phylogenetic trees, we observed that Argentina could also be a point in which the HIV-1C epidemic entered South America.
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Affiliation(s)
- Leandro R. Jones
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Estación de Fotobiología Playa Unión-CONICET, Playa Unión, Chubut, Argentina
| | - Darío A. Dilernia
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Julieta M. Manrique
- Cátedra de Química Analítica Instrumental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Franco Moretti
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Horacio Salomón
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Manuel Gomez-Carrillo
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
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12
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Ma L, Guo Y, Yuan L, Huang Y, Sun J, Qu S, Yu X, Meng Z, He X, Jiang S, Shao Y. Phenotypic and genotypic characterization of human immunodeficiency virus type 1 CRF07_BC strains circulating in the Xinjiang Province of China. Retrovirology 2009; 6:45. [PMID: 19442296 PMCID: PMC2693499 DOI: 10.1186/1742-4690-6-45] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 05/14/2009] [Indexed: 12/01/2022] Open
Abstract
Background HIV-1 CRF07_BC recombinant previously circulated mainly among the intravenous drug users (IDUs) in Xinjiang province of China and is currently spreading in the entire country. The aim of this study is to characterize the genotypic and phenotypic properties of HIV-1 CRF07_BC isolates in comparison with those of the subtype B' (Thailand B) which is prevalent in the former plasma donors (FPDs) in China. Results Twelve HIV-1 CRF07_BC variants were isolated from the blood of the HIV-1-infected IDUs in Xinjiang province, and 20 subtype B' isolates were obtained from the FPDs in Anhui and Shanxi provinces of China. All the CRF07_BC viruses utilized CCR5 co-receptor, whereas 12 subtype B' viruses were R5-tropic, and the remaining B' isolates were dual (R5X4) tropic. CRF07_BC viruses had lower net charge value in the V3 loop and exhibited slower replication kinetics than subtype B' viruses. The number and location of the potential N-linked glycosylation sites in V1/V2 and the C2 region of the CRF07_BC viruses were significantly different from those of the subtype B' viruses. Conclusion The HIV-1 CRF07_BC recombinant strains with relatively lower net charges in the V3 loop exclusively utilize CCR5 co-receptor for infection and exhibit slow replication kinetics in the primary target cells, suggesting that CRF07_BC may be superior over B' and other HIV-1 subtypes in initiating infection in high-risk population. These findings have molecular implications for the adaptive evolution of HIV-1 circulating in China and the design of tailored therapeutic strategy for treatment of HIV-1 CRF07_BC infection.
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Affiliation(s)
- Liying Ma
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.
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Kulkarni SS, Lapedes A, Tang H, Gnanakaran S, Daniels MG, Zhang M, Bhattacharya T, Li M, Polonis VR, McCutchan FE, Morris L, Ellenberger D, Butera ST, Bollinger RC, Korber BT, Paranjape RS, Montefiori DC. Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India. Virology 2009; 385:505-20. [PMID: 19167740 PMCID: PMC2677301 DOI: 10.1016/j.virol.2008.12.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 12/01/2008] [Accepted: 12/16/2008] [Indexed: 10/21/2022]
Abstract
Little is known about the neutralization properties of HIV-1 in India to optimally design and test vaccines. For this reason, a functional Env clone was obtained from each of ten newly acquired, heterosexually transmitted HIV-1 infections in Pune, Maharashtra. These clones formed a phylogenetically distinct genetic lineage within subtype C. As Env-pseudotyped viruses the clones were mostly resistant to IgG1b12, 2G12 and 2F5 but all were sensitive to 4E10. When compared to a large multi-subtype panel of Env-pseudotyped viruses (subtypes B, C and CRF02_AG) in neutralization assays with a multi-subtype panel of HIV-1-positive plasma samples, the Indian Envs were remarkably complex. With the exception of the Indian Envs, results of a hierarchical clustering analysis showed a strong subtype association with the patterns of neutralization susceptibility. From these patterns we were able to identify 19 neutralization cluster-associated amino acid signatures in gp120 and 14 signatures in the ectodomain and cytoplasmic tail of gp41. We conclude that newly transmitted Indian Envs are antigenically complex in spite of close genetic similarity. Delineation of neutralization-associated amino acid signatures provides a deeper understanding of the antigenic structure of HIV-1 Env.
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Affiliation(s)
| | - Alan Lapedes
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Haili Tang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710
| | - S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Marcus G. Daniels
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ming Zhang
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ming Li
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710
| | - Victoria R. Polonis
- Walter Reed Army Institute of Research and the Henry M. Jackson Foundation, Rockville, Maryland 20850
| | - Francine E. McCutchan
- Walter Reed Army Institute of Research and the Henry M. Jackson Foundation, Rockville, Maryland 20850
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | | | - Robert C. Bollinger
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Bette T. Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | | | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710
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Abstract
OBJECTIVE Our aim was to investigate the monophyletic status of the HIV-1C that circulates in South America and its phylogenetic relationships with other HIV-1C populations around the world in order to shed light on its the geographic origins as well as the place of introduction in the continent. METHODS Fifty-one sequences from South America and 46 from non-South American countries, including samples from Africa and Asia, were obtained from the Los Alamos National Laboratory. The data analyzed corresponded to the entire protease and two-thirds of the polymerase domain from the reverse transcriptase. Phylogenetic analyses using maximum likelihood and Bayesian inference were performed in Phylogenetic Analysis Using Parsymony, PHYlogenetic inferences using Maximum Likelihood, and MrBayes. RESULTS Samples from South America formed a monophyletic group independent of the method used. The bootstrap support of South American HIV-1C was higher than 60% in maximum likelihood trees and its posterior probability was 99% in the Bayesian analysis. These results indicate the monophyletic nature of the South American HIV-1C. Moreover, in all trees estimated, a sequence from Kenya was the most closely related to the South American clade, followed by two from Ethiopia. All South American sequences from countries other than Brazil showed closer phylogenetic relatedness to Brazilian samples, indicating that HIV-1C was introduced in South America in Brazil. CONCLUSION Our results indicate that the entry of HIV-1C in South America occurred in a single episode or in multiples episodes of genetically related viruses, possibly from an eastern African country. HIV-1C was then disseminated to the remaining South American countries from Brazil.
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Michler K, Connell BJ, Venter WD, Stevens WS, Capovilla A, Papathanasopoulos MA. Genotypic characterization and comparison of full-length envelope glycoproteins from South African HIV type 1 subtype C primary isolates that utilize CCR5 and/or CXCR4. AIDS Res Hum Retroviruses 2008; 24:743-51. [PMID: 18507530 DOI: 10.1089/aid.2007.0304] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CCR5 has preferentially been used by all circulating HIV-1 subtype C viruses for cell entry. Recently, we reported the highest proportion of CXCR4-utilizing primary isolates among a cohort of 20 South African AIDS patients. This study describes and compares the Env genotypic characteristics from these 20 HIV-1 subtype C (and unique CD recombinant) primary isolates. Fourteen primary isolates utilized CCR5, four (including the CD recombinant) used CXCR4, and two were dual tropic. Extensive analysis and comparison of important structural motifs such as the N-linked glycosylation sites, signal sequences, CD4-binding sites, variable loops, cleavage sites, known neutralizing antibody and small molecule inhibitor binding sites confirmed that other than the expected differences in the V3 loop, no sequence motifs distinguished between R5 and X4 tropism. Further correlation of the env genotype to functionally relevant motifs is necessary to elucidate the relationship between biologically and immunologically relevant sites and aid vaccine and novel drug design.
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Affiliation(s)
- Katherine Michler
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Bridgette J. Connell
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Willem D.F. Venter
- Reproductive Health and HIV Research Unit, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Wendy S. Stevens
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Alexio Capovilla
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
| | - Maria A. Papathanasopoulos
- HIV Pathogenesis Research Laboratory, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, Johannesburg, 2193, South Africa
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