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1. Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting: the RV217 acute infection cohort study

Author

Marichannegowda, Manukumar Honnayakanahalli, Zemil, Michelle, Wieczorek, Lindsay, Sanders-Buell, Eric, Bose, Meera, O'Sullivan, Anne Marie, King, David, Francisco, Leilani, Diaz-Mendez, Felisa, Setua, Saini, Chomont, Nicolas, Phanuphak, Nittaya, Ananworanich, Jintanat, Hsu, Denise, Vasan, Sandhya, Michael, Nelson L., Eller, Leigh Anne, Tovanabutra, Sodsai, Tagaya, Yutaka, Robb, Merlin L., Polonis, Victoria R., and Song, Hongshuo

Published
2023
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2. Evolution of HIV-1 envelope towards reduced neutralization sensitivity, as demonstrated by contemporary HIV-1 subtype B from the United States

Author

Wieczorek, Lindsay, primary, Sanders-Buell, Eric, additional, Zemil, Michelle, additional, Lewitus, Eric, additional, Kavusak, Erin, additional, Heller, Jonah, additional, Molnar, Sebastian, additional, Rao, Mekhala, additional, Smith, Gabriel, additional, Bose, Meera, additional, Nguyen, Amy, additional, Dhungana, Adwitiya, additional, Okada, Katherine, additional, Parisi, Kelly, additional, Silas, Daniel, additional, Slike, Bonnie, additional, Ganesan, Anuradha, additional, Okulicz, Jason, additional, Lalani, Tahaniyat, additional, Agan, Brian K., additional, Crowell, Trevor A., additional, Darden, Janice, additional, Rolland, Morgane, additional, Vasan, Sandhya, additional, Ake, Julie, additional, Krebs, Shelly J., additional, Peel, Sheila, additional, Tovanabutra, Sodsai, additional, and Polonis, Victoria R., additional

Published
2023
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3. Neutralizing antibody VRC01 failed to select for HIV-1 mutations upon viral rebound

Author

Cale, Evan M., Bai, Hongjun, Bose, Meera, Messina, Michael A., Colby, Donn J., Sanders-Buell, Eric, Dearlove, Bethany, Li, Yifan, Engeman, Emily, Silas, Daniel, O'Sullivan, Anne Marie, Mann, Brendan, Pinyakorn, Suteeraporn, Intasan, Jintana, Benjapornpong, Khunthalee, Sacdalan, Carlo, Kroon, Eugene, Phanuphak, Nittaya, Gramzinski, Robert, Vasan, Sandhya, Robb, Merlin L., Michael, Nelson L., Lynch, Rebecca M., Bailer, Robert T., Pagliuzza, Amelie, Chomont, Nicolas, Pegu, Amarendra, Doria-Rose, Nicole A., Trautmann, Lydie, Crowell, Trevor A., Mascola, John R., Ananworanich, Jintanat, Tovanabutra, Sodsai, and Rolland, Morgane

Subjects
Highly active antiretroviral therapy -- Health aspects, HIV -- Genetic aspects -- Prevention, Antiretroviral agents -- Health aspects, Antibodies -- Genetic aspects -- Health aspects, Antigenic determinants -- Genetic aspects -- Health aspects, Health care industry
Abstract

Infusion of the broadly neutralizing antibody VRC01 has been evaluated in individuals chronically infected with HIV-1. Here, we studied how VRC01 infusions affected viral rebound after cessation of antiretroviral therapy (ART) in 18 acutely treated and durably suppressed individuals. Viral rebound occurred in all individuals, yet VRC01 infusions modestly delayed rebound and participants who showed a faster decay of VRC01 in serum rebounded more rapidly. Participants with strains most sensitive to VRC01 or with VRC01 epitope motifs similar to known VRC01- susceptible strains rebounded later. Upon rebound, HIV-1 sequences were indistinguishable from those sampled at diagnosis. Across the cohort, participant-derived Env showed different sensitivity to VRC01 neutralization (including 2 resistant viruses), yet neutralization sensitivity was similar at diagnosis and after rebound, indicating the lack of selection for VRC01 resistance during treatment interruption. Our results showed that viremia rebounded despite the absence of HIV-1 adaptation to VRC01 and an average VRC01 trough of 221 micro]g/mL. Although VRC01 levels were insufficient to prevent a resurgent infection, knowledge that they did not mediate Env mutations in acute-like viruses is relevant for antibody-based strategies in acute infection., Introduction Analytic treatment interruption (ATI) studies can help evaluate strategies to mediate long-term remission in HIV-1-infected persons. An ATI study tested the impact of the administration of the broadly neutralizing [...]

Published
2020
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4. Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.

Author

Edlefsen, Paul T, Rolland, Morgane, Hertz, Tomer, Tovanabutra, Sodsai, Gartland, Andrew J, deCamp, Allan C, Magaret, Craig A, Ahmed, Hasan, Gottardo, Raphael, Juraska, Michal, McCoy, Connor, Larsen, Brendan B, Sanders-Buell, Eric, Carrico, Chris, Menis, Sergey, Kijak, Gustavo H, Bose, Meera, RV144 Sequencing Team, Arroyo, Miguel A, O'Connell, Robert J, Nitayaphan, Sorachai, Pitisuttithum, Punnee, Kaewkungwal, Jaranit, Rerks-Ngarm, Supachai, Robb, Merlin L, Kirys, Tatsiana, Georgiev, Ivelin S, Kwong, Peter D, Scheffler, Konrad, Pond, Sergei L Kosakovsky, Carlson, Jonathan M, Michael, Nelson L, Schief, William R, Mullins, James I, Kim, Jerome H, and Gilbert, Peter B

Subjects
RV144 Sequencing Team, Humans, HIV-1, HIV Infections, AIDS Vaccines, Sequence Alignment, Sequence Analysis, Protein, Binding Sites, Genome, Viral, Models, Molecular, Molecular Sequence Data, Human Immunodeficiency Virus Proteins, Sequence Analysis, Protein, Genome, Viral, Models, Molecular, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or "signatures" and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.

Published
2015

5. Safety and efficacy of VRC01 broadly neutralising antibodies in adults with acutely treated HIV (RV397): a phase 2, randomised, double-blind, placebo-controlled trial

Author

Ake, Julie A., Akapirat, Siriwat, Bose, Meera, Cale, Evan, Chan, Phillip, Chanthaburanun, Sararut, Churikanont, Nampueng, Dawson, Peter, Dumrongpisutikul, Netsiri, Getchalarat, Saowanit, Jongrakthaitae, Surat, Jongsakul, Krisada, Lerdlum, Sukalaya, Manasnayakorn, Sopark, McCullough, Corinne, Milazzo, Mark, Nuntapinit, Bessara, On, Kier, Ouellette, Madelaine, Phanuphak, Praphan, Sanders-Buell, Eric, Sangnoi, Nongluck, Shangguan, Shida, Sirivichayakul, Sunee, Tragonlugsana, Nipattra, Trichavaroj, Rapee, Ubolyam, Sasiwimol, Vasan, Sandhya, Wattanaboonyongcharoen, Phandee, Yamchuenpong, Thipvadee, Crowell, Trevor A, Colby, Donn J, Pinyakorn, Suteeraporn, Sacdalan, Carlo, Pagliuzza, Amélie, Intasan, Jintana, Benjapornpong, Khunthalee, Tangnaree, Kamonkan, Chomchey, Nitiya, Kroon, Eugène, de Souza, Mark S, Tovanabutra, Sodsai, Rolland, Morgane, Eller, Michael A, Paquin-Proulx, Dominic, Bolton, Diane L, Tokarev, Andrey, Thomas, Rasmi, Takata, Hiroshi, Trautmann, Lydie, Krebs, Shelly J, Modjarrad, Kayvon, McDermott, Adrian B, Bailer, Robert T, Doria-Rose, Nicole, Patel, Bijal, Gorelick, Robert J, Fullmer, Brandie A, Schuetz, Alexandra, Grandin, Pornsuk V, O'Connell, Robert J, Ledgerwood, Julie E, Graham, Barney S, Tressler, Randall, Mascola, John R, Chomont, Nicolas, Michael, Nelson L, Robb, Merlin L, Phanuphak, Nittaya, and Ananworanich, Jintanat

Published
2019
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6. Next-generation sequencing of HIV-1 single genome amplicons

Author

Kijak, Gustavo H., Sanders-Buell, Eric, Pham, Phuc, Harbolick, Elizabeth A., Oropeza, Celina, O’Sullivan, Anne Marie, Bose, Meera, Beckett, Charmagne G., Milazzo, Mark, Robb, Merlin L., Peel, Sheila A., Scott, Paul T., Michael, Nelson L., Armstrong, Adam W., Kim, Jerome H., Brett-Major, David M., and Tovanabutra, Sodsai

Published
2019
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7. Transmission of highly virulent CXCR4 tropic HIV-1 through the mucosal route in an individual with a wild-type CCR5 genotype

Author

Song, Hongshuo, primary, Marichannegowda, Manukumar, additional, Setua, Saini, additional, Bose, Meera, additional, Sanders-Buell, Eric, additional, King, David, additional, Zemil, Michelle, additional, Wieczorek, Lindsay, additional, Diaz-Mendez, Felisa, additional, Chomont, Nicolas, additional, Thomas, Rasmi, additional, Francisco, Leilani, additional, Eller, Leigh Anne, additional, Polonis, Victoria, additional, Tovanabutra, Sodsai, additional, Tagaya, Yutaka, additional, Michael, Nelson, additional, and Robb, Merlin, additional

Published
2023
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8. Transmission of highly virulent CXCR4 tropic HIV-1 through the mucosal route in an individual with a wild-type CCR5 genotype

Author

Marichannegowda, Manukumar Honnayakanahalli, primary, Setua, Saini, additional, Bose, Meera, additional, Sanders-Buell, Eric, additional, King, David, additional, Zemil, Michelle, additional, Wieczorek, Lindsay, additional, Diaz-Mendez, Felisa, additional, Chomont, Nicolas, additional, Thomas, Rasmi, additional, Francisco, Leilani, additional, Eller, Leigh Anne, additional, Polonis, Victoria R., additional, Tovanabutra, Sodsai, additional, Tagaya, Yutaka, additional, Michael, Nelson L., additional, Robb, Merlin L., additional, and Song, Hongshuo, additional

Published
2023
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9. Molecular epidemiology of a primarily MSM acute HIV-1 cohort in Bangkok, Thailand and connections within networks of transmission in Asia

Author

Chang, David, Sanders-Buell, Eric, Bose, Meera, O'Sullivan, Anne Marie, Pham, Phuc, Kroon, Eugene, Colby, Donn J., Sirijatuphat, Rujipas, Billings, Erik, Pinyakorn, Suteeraporn, Chomchey, Nitiya, Rutvisuttinunt, Wiriya, Kijak, Gustavo, Souza, Mark de, Excler, Jean-Louis, Phanuphak, Praphan, Phanuphak, Nittaya, O'Connell, Robert J., Kim, Jerome H., Robb, Merlin L., Michael, Nelson L., Ananworanich, Jintanat, and Tovanabutra, Sodsai

Subjects
AIDS vaccines -- Usage -- Research, HIV infections -- Prevention -- Care and treatment -- Research, Disease transmission -- Development and progression -- Analysis -- Health aspects -- Research, MSM (Men who have sex with men) -- Health aspects, Epidemiology -- Analysis, Health
Abstract

Introduction: Thailand plays a substantial role in global HIV-1 transmission of CRF01_AE. Worldwide, men who have sex with men (MSM) are at elevated risk for HIV-1 infection. Hence, understanding HIV-1 diversity in a primarily Thai MSM cohort with acute infection, and its connections to the broader HIV-1 transmission network in Asia is crucial for research and development of HIV-1 vaccines, treatment and cure. Methods: Subtypes and diversity of infecting viruses from individuals sampled from 2009 to 2015 within the RV254/SEARCH 010 cohort were assessed by multiregion hybridization assay (MHAbce), multiregion subtype-specific PCR assay (MSSPbce) and full-length single-genome sequencing (SGS). Phylogenetic analysis was performed by maximum likelihood. Pairwise genetic distances of envelope gp160 sequences obtained from the cohort and from Asia (Los Alamos National Laboratory HIV Database) were calculated to identify potential transmission networks. Results: MHAbce/MSSPbce results identified 81.6% CRF01AE infecting strains in RV254. CRF01AE/B recombinants and sub-type B were found at 7.3% and 2.8% respectively. Western subtype B strains outnumbered Thai B' strains. Phylogenetic analysis revealed one C, one CRF01_AE/CRF02_AG recombinant and one CRF01_AE/B/C recombinant. Asian network analysis identified one hundred and twenty-three clusters, including five clusters of RV254 participants. None of the RV254 sequences clustered with non-RV254 sequences. The largest international cluster involved 15 CRF01AE strains from China and Vietnam. The remaining clusters were mostly intracountry connections, of which 31.7% included Thai nodes and 43.1% included Chinese nodes. Conclusion: While the majority of strains in Thailand are CRF01AE and subtype B, emergence of unique recombinant forms (URFs) are found in a moderate fraction of new HIV-1 infections. Approaches to vaccine design and immunotherapeutics will need to monitor and consider the expanding proportion of recombinants and the increasing genetic diversity in the region. Identified HIV-1 transmission networks indicate ongoing spread of HIV-1 among MSM. As HIV-1 epidemics continue to expand in other Asian countries, transmission network analyses can inform strategies for prevention, intervention, treatment and cure. Keywords: HIV-1 molecular epidemiology; Thailand; Asia transmission network; MSM; acute infection; recombinants; vaccine; intervention, Additional Supporting Information may be found online in the Supporting information tab for this article. 1 INTRODUCTION Over 30 years have passed since the first case of HIV-1 was reported [...]

Published
2018
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10. Evolution of Antibody Responses in HIV-1 CRF01_AE Acute Infection: Founder Envelope V1V2 Impacts the Timing and Magnitude of Autologous Neutralizing Antibodies

Author

Kuriakose Gift, Syna, primary, Wieczorek, Lindsay, additional, Sanders-Buell, Eric, additional, Zemil, Michelle, additional, Molnar, Sebastian, additional, Donofrio, Gina, additional, Townsley, Samantha, additional, Chenine, Agnes L., additional, Bose, Meera, additional, Trinh, Hung V., additional, Barrows, Brittani M., additional, Sriplienchan, Somchai, additional, Kitsiripornchai, Suchai, additional, Nitayapan, Sorachai, additional, Eller, Leigh-Anne, additional, Rao, Mangala, additional, Ferrari, Guido, additional, Michael, Nelson L., additional, Ake, Julie A., additional, Krebs, Shelly J., additional, Robb, Merlin L., additional, Tovanabutra, Sodsai, additional, and Polonis, Victoria R., additional

Published
2023
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11. Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting

Author

Marichannegowda, Manukumar Honnayakanahalli, primary, Zemil, Michelle, additional, Wieczorek, Lindsay, additional, Sanders-Buell, Eric, additional, Bose, Meera, additional, O’Sullivan, Anne Marie, additional, King, David, additional, Francisco, Leilani, additional, Diaz-Mendez, Felisa, additional, Setua, Saini, additional, Chomont, Nicolas, additional, Phanuphak, Nittaya, additional, Ananworanich, Jintanat, additional, Hsu, Denise, additional, Vasan, Sandhya, additional, Michael, Nelson L., additional, Eller, Leigh Anne, additional, Tovanabutra, Sodsai, additional, Tagaya, Yutaka, additional, Robb, Merlin L., additional, Polonis, Victoria R., additional, and Song, Hongshuo, additional

Published
2023
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12. Tracking Coreceptor Switch of the Transmitted/Founder HIV-1 Identifies Co-Evolution of HIV-1 Antigenicity, Coreceptor Usage and CD4 Subset Targeting: The RV217 Acute Infection Cohort Study

Author

Marichannegowda, Manukumar Honnayakanahalli, primary, Zemil, Michelle, additional, Wieczorek, Lindsay, additional, Sanders-Buell, Eric, additional, Bose, Meera, additional, O&apos;Sullivan, Anne Marie, additional, King, David, additional, Francisco, Leilani, additional, Diaz-Mendez, Felisa, additional, Setua, Saini, additional, Chomont, Nicolas, additional, Phanuphak, Nittaya, additional, Ananworanich, Jintanat, additional, Hsu, Denise, additional, Vasan, Sandhya, additional, Michael, Nelson L., additional, Eller, Leigh Anne, additional, Tovanabutra, Sodsai, additional, Tagaya, Yutaka, additional, Robb, Merlin L., additional, Polonis, Victoria R., additional, and Song, Hongshuo, additional

Published
2023
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13. Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting

Author

Marichannegowda, Manukumar Honnayakanahalli, Zemil, Michelle, Wieczorek, Lindsay, Sanders-Buell, Eric, Bose, Meera, O’Sullivan, Anne Marie, King, David, Francisco, Leilani, Diaz-Mendez, Felisa, Setua, Saini, Chomont, Nicolas, Phanuphak, Nittaya, Ananworanich, Jintanat, Hsu, Denise, Vasan, Sandhya, Michael, Nelson L., Eller, Leigh Anne, Tovanabutra, Sodsai, Tagaya, Yutaka, Robb, Merlin L., Polonis, Victoria R., and Song, Hongshuo

Subjects
Article
Abstract

The CCR5 (R5) to CXCR4 (X4) coreceptor switch in natural HIV-1 infection is associated with faster progression to AIDS, but the underlying mechanisms remain unclear. The difficulty in capturing the earliest moment of coreceptor switchin vivolimits our understanding of this phenomenon. Here, by tracking the evolution of the transmitted/founder (T/F) HIV-1 in a prospective cohort of individuals at risk for HIV-1 infection identified very early in acute infection, we investigated this process with high resolution. The earliest X4 variants evolved from the R5 tropic T/F strains. Strong X4 usage can be conferred by a single mutation. The mutations responsible for coreceptor switch can confer escape to neutralization and drive X4 variants to replicate mainly in the central memory and naïve CD4+ T cells. We propose a novel concept to explain the co-evolution of virus antigenicity and entry tropism termed “escape by shifting”. This concept posits that for viruses with receptor or coreceptor flexibility, entry tropism alteration represents a mechanism of immune evasionin vivo.

Published
2023

14. HIV-1 infections with multiple founders associate with the development of neutralization breadth

Author

Lewitus, Eric, primary, Townsley, Samantha M., additional, Li, Yifan, additional, Donofrio, Gina C., additional, Dearlove, Bethany L., additional, Bai, Hongjun, additional, Sanders-Buell, Eric, additional, O’Sullivan, Anne Marie, additional, Bose, Meera, additional, Kibuuka, Hannah, additional, Maganga, Lucas, additional, Nitayaphan, Sorachai, additional, Sawe, Fredrick K., additional, Eller, Leigh Anne, additional, Michael, Nelson L., additional, Polonis, Victoria R., additional, Ake, Julie A., additional, Vasan, Sandhya, additional, Robb, Merlin L., additional, Tovanabutra, Sodsai, additional, Krebs, Shelly J., additional, and Rolland, Morgane, additional

Published
2022
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15. Limited Evidence for a Relationship between HIV-1 Glycan Shield Features in Early Infection and the Development of Neutralization Breadth

Author

Li, Yifan, primary, Bai, Hongjun, additional, Sanders-Buell, Eric, additional, Dussupt, Vincent, additional, Townsley, Samantha, additional, Donofrio, Gina, additional, Bose, Meera, additional, O’Sullivan, Anne Marie, additional, Kibuuka, Hannah, additional, Maganga, Lucas, additional, Nitayaphan, Sorachai, additional, Kosgei, Josphat, additional, Pitisuttithum, Punnee, additional, Rerks-Ngarm, Supachai, additional, Eller, Leigh Anne, additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Ake, Julie, additional, Vasan, Sandhya, additional, Tovanabutra, Sodsai, additional, Krebs, Shelly J., additional, and Rolland, Morgane, additional

Published
2021
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16. RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection

Author

Lewitus, Eric, primary, Sanders-Buell, Eric, additional, Bose, Meera, additional, O’Sullivan, Anne Marie, additional, Poltavee, Kultida, additional, Li, Yifan, additional, Bai, Hongjun, additional, Mdluli, Thembi, additional, Donofrio, Gina, additional, Slike, Bonnie, additional, Zhao, Hong, additional, Wong, Kim, additional, Chen, Lennie, additional, Miller, Shana, additional, Lee, Jenica, additional, Ahani, Bahar, additional, Lepore, Steven, additional, Muhammad, Sevan, additional, Grande, Rebecca, additional, Tran, Ursula, additional, Dussupt, Vincent, additional, Mendez-Rivera, Letzibeth, additional, Nitayaphan, Sorachai, additional, Kaewkungwal, Jaranit, additional, Pitisuttithum, Punnee, additional, Rerks-Ngarm, Supachai, additional, O’Connell, Robert J, additional, Janes, Holly, additional, Gilbert, Peter B, additional, Gramzinski, Robert, additional, Vasan, Sandhya, additional, Robb, Merlin L, additional, Michael, Nelson L, additional, Krebs, Shelly J, additional, Herbeck, Joshua T, additional, Edlefsen, Paul T, additional, Mullins, James I, additional, Kim, Jerome H, additional, Tovanabutra, Sodsai, additional, and Rolland, Morgane, additional

Published
2021
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18. Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2

Author

Rolland, Morgane, Edlefsen, Paul T., Larsen, Brendan B., Tovanabutra, Sodsai, Sanders-Buell, Eric, Hertz, Tomer, deCamp, Allan C., Carrico, Chris, Menis, Sergey, Magaret, Craig A., Ahmed, Hasan, Juraska, Michal, Chen, Lennie, Konopa, Philip, Nariya, Snehal, Stoddard, Julia N., Wong, Kim, Zhao, Hong, Deng, Wenjie, Maust, Brandon S., Bose, Meera, Howell, Shana, Bates, Adam, Lazzaro, Michelle, O’Sullivan, Annemarie, Lei, Esther, Bradfield, Andrea, Ibitamuno, Grace, Assawadarachai, Vatcharain, O’Connell, Robert J., deSouza, Mark S., Nitayaphan, Sorachai, Rerks-Ngarm, Supachai, Robb, Merlin L., McLellan, Jason S., Georgiev, Ivelin, Kwong, Peter D., Carlson, Jonathan M., Michael, Nelson L., Schief, William R., Gilbert, Peter B., Mullins, James I., and Kim, Jerome H.

Published
2012
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19. Dynamics of Human Immunodeficiency Virus-1 Genetic Diversification During Acute Infection

Author

Song, Hongshuo, primary, Bose, Meera, additional, Pinyakorn, Suteeraporn, additional, Sanders-Buell, Eric, additional, O’Sullivan, Anne Marie, additional, Silas, Daniel, additional, Trichavaroj, Rapee, additional, Nuntapinit, Bessara, additional, Pham, Phuc T, additional, Akapirat, Siriwat, additional, Kroon, Eugène, additional, de Souza, Mark, additional, Gramzinski, Robert, additional, Michael, Nelson L, additional, Robb, Merlin L, additional, Vasan, Sandhya, additional, Tovanabutra, Sodsai, additional, and Ananworanich, Jintanat, additional

Published
2020
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20. Correction: Trinh, H.V., et al. Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort. Cells 2019, 8, 365

Author

Trinh, Hung V., primary, Gohain, Neelakshi, additional, Pham, Peter T., additional, Hamlin, Christopher, additional, Song, Hongshuo, additional, Sanders-Buell, Eric, additional, Bose, Meera, additional, Eller, Leigh A., additional, Jain, Swati, additional, Uritskiy, Gherman, additional, Rao, Venigalla B., additional, Tovanabutra, Sodsai, additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Joyce, M. Gordon, additional, and Rao, Mangala, additional

Published
2019
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21. HIV-1 genetic diversity and demographic characteristics in Bulgaria

Author

Billings, Erik, primary, Heipertz, Richard A., additional, Varleva, Tonka, additional, Sanders-Buell, Eric, additional, O'Sullivan, Anne Marie, additional, Bose, Meera, additional, Howell, Shana, additional, Kijak, Gustavo H., additional, Taskov, Hristo, additional, Elenkov, Ivailo, additional, Nenova, Marina, additional, Popivanova, Nedialka, additional, Valenzuela, Aimee Bolen, additional, Myles, Otha, additional, Bautista, Christian T., additional, Robb, Merlin L., additional, Michael, Nelson L., additional, Kim, Jerome H., additional, Scott, Paul T., additional, Tovanabutra, Sodsai, additional, and Ake, Julie A., additional

Published
2019
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22. Safety and efficacy of VRC01 broadly neutralising antibodies in adults with acutely treated HIV (RV397): a phase 2, randomised, double-blind, placebo-controlled trial

Author

Crowell, Trevor A, primary, Colby, Donn J, additional, Pinyakorn, Suteeraporn, additional, Sacdalan, Carlo, additional, Pagliuzza, Amélie, additional, Intasan, Jintana, additional, Benjapornpong, Khunthalee, additional, Tangnaree, Kamonkan, additional, Chomchey, Nitiya, additional, Kroon, Eugène, additional, de Souza, Mark S, additional, Tovanabutra, Sodsai, additional, Rolland, Morgane, additional, Eller, Michael A, additional, Paquin-Proulx, Dominic, additional, Bolton, Diane L, additional, Tokarev, Andrey, additional, Thomas, Rasmi, additional, Takata, Hiroshi, additional, Trautmann, Lydie, additional, Krebs, Shelly J, additional, Modjarrad, Kayvon, additional, McDermott, Adrian B, additional, Bailer, Robert T, additional, Doria-Rose, Nicole, additional, Patel, Bijal, additional, Gorelick, Robert J, additional, Fullmer, Brandie A, additional, Schuetz, Alexandra, additional, Grandin, Pornsuk V, additional, O'Connell, Robert J, additional, Ledgerwood, Julie E, additional, Graham, Barney S, additional, Tressler, Randall, additional, Mascola, John R, additional, Chomont, Nicolas, additional, Michael, Nelson L, additional, Robb, Merlin L, additional, Phanuphak, Nittaya, additional, Ananworanich, Jintanat, additional, Ake, Julie A., additional, Akapirat, Siriwat, additional, Bose, Meera, additional, Cale, Evan, additional, Chan, Phillip, additional, Chanthaburanun, Sararut, additional, Churikanont, Nampueng, additional, Dawson, Peter, additional, Dumrongpisutikul, Netsiri, additional, Getchalarat, Saowanit, additional, Jongrakthaitae, Surat, additional, Jongsakul, Krisada, additional, Lerdlum, Sukalaya, additional, Manasnayakorn, Sopark, additional, McCullough, Corinne, additional, Milazzo, Mark, additional, Nuntapinit, Bessara, additional, On, Kier, additional, Ouellette, Madelaine, additional, Phanuphak, Praphan, additional, Sanders-Buell, Eric, additional, Sangnoi, Nongluck, additional, Shangguan, Shida, additional, Sirivichayakul, Sunee, additional, Tragonlugsana, Nipattra, additional, Trichavaroj, Rapee, additional, Ubolyam, Sasiwimol, additional, Vasan, Sandhya, additional, Wattanaboonyongcharoen, Phandee, additional, and Yamchuenpong, Thipvadee, additional

Published
2019
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23. Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual

Author

Krebs, Shelly J., primary, Kwon, Young D., additional, Schramm, Chaim A., additional, Law, William H., additional, Donofrio, Gina, additional, Zhou, Kenneth H., additional, Gift, Syna, additional, Dussupt, Vincent, additional, Georgiev, Ivelin S., additional, Schätzle, Sebastian, additional, McDaniel, Jonathan R., additional, Lai, Yen-Ting, additional, Sastry, Mallika, additional, Zhang, Baoshan, additional, Jarosinski, Marissa C., additional, Ransier, Amy, additional, Chenine, Agnes L., additional, Asokan, Mangaiarkarasi, additional, Bailer, Robert T., additional, Bose, Meera, additional, Cagigi, Alberto, additional, Cale, Evan M., additional, Chuang, Gwo-Yu, additional, Darko, Samuel, additional, Driscoll, Jefferson I., additional, Druz, Aliaksandr, additional, Gorman, Jason, additional, Laboune, Farida, additional, Louder, Mark K., additional, McKee, Krisha, additional, Mendez, Letzibeth, additional, Moody, M. Anthony, additional, O’Sullivan, Anne Marie, additional, Owen, Christopher, additional, Peng, Dongjun, additional, Rawi, Reda, additional, Sanders-Buell, Eric, additional, Shen, Chen-Hsiang, additional, Shiakolas, Andrea R., additional, Stephens, Tyler, additional, Tsybovsky, Yaroslav, additional, Tucker, Courtney, additional, Verardi, Raffaello, additional, Wang, Keyun, additional, Zhou, Jing, additional, Zhou, Tongqing, additional, Georgiou, George, additional, Alam, S. Munir, additional, Haynes, Barton F., additional, Rolland, Morgane, additional, Matyas, Gary R., additional, Polonis, Victoria R., additional, McDermott, Adrian B., additional, Douek, Daniel C., additional, Shapiro, Lawrence, additional, Tovanabutra, Sodsai, additional, Michael, Nelson L., additional, Mascola, John R., additional, Robb, Merlin L., additional, Kwong, Peter D., additional, and Doria-Rose, Nicole A., additional

Published
2019
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24. Factors influencing estimates of HIV-1 infection timing using BEAST.

Author

Dearlove, Bethany, Tovanabutra, Sodsai, Owen, Christopher L., Lewitus, Eric, Li, Yifan, Sanders-Buell, Eric, Bose, Meera, O'Sullivan, Anne-Marie, Kijak, Gustavo, Miller, Shana, Poltavee, Kultida, Lee, Jenica, Bonar, Lydia, Harbolick, Elizabeth, Ahani, Bahar, Pham, Phuc, Kibuuka, Hannah, Maganga, Lucas, Nitayaphan, Sorachai, and Sawe, Fred K.

Subjects
HIV, MOLECULAR clock, GENES, BAYESIAN analysis, TIME management, INFECTION
Abstract

While large datasets of HIV-1 sequences are increasingly being generated, many studies rely on a single gene or fragment of the genome and few comparative studies across genes have been done. We performed genome-based and gene-specific Bayesian phylogenetic analyses to investigate how certain factors impact estimates of the infection dates in an acute HIV-1 infection cohort, RV217. In this cohort, HIV-1 diagnosis corresponded to the first RNA positive test and occurred a median of four days after the last negative test, allowing us to compare timing estimates using BEAST to a narrow window of infection. We analyzed HIV-1 sequences sampled one week, one month and six months after HIV-1 diagnosis in 39 individuals. We found that shared diversity and temporal signal was limited in acute infection, and insufficient to allow timing inferences in the shortest HIV-1 genes, thus dated phylogenies were primarily analyzed for env, gag, pol and near full-length genomes. There was no one best fitting model across participants and genes, though relaxed molecular clocks (73% of best fitting models) and the Bayesian skyline (49%) tended to be favored. For infections with single founders, the infection date was estimated to be around one week pre-diagnosis for env (IQR: 3–9 days) and gag (IQR: 5–9 days), whilst the genome placed it at a median of 10 days (IQR: 4–19). Multiply-founded infections proved problematic to date. Our ability to compare timing inferences to precise estimates of HIV-1 infection (within a week) highlights that molecular dating methods can be applied to within-host datasets from early infection. Nonetheless, our results also suggest caution when using uniform clock and population models or short genes with limited information content. Author summary: Molecular dating using phylogenetics allows us to estimate the date of an infection from time-stamped within-host sequences alone. There are large datasets of HIV-1 sequences, but genome and gene analyses are not often performed in parallel and rarely with the possibility to compare results against a known narrow window of infection. We showed that all but the longest genes are near-clonal in acute infection, with little information for dating purposes. For infections with single founders, we estimated the eclipse phase—the time between HIV-1 exposure and the first positive diagnostic test—to last between one and two weeks using env, gag, pol and near full-length genomes. This approach could be used to narrow the date of suspected infection in ongoing clinical trials for the prevention of HIV-1 infection. [ABSTRACT FROM AUTHOR]

Published
2021
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25. Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.

Author

Rolland, Morgane, Tovanabutra, Sodsai, Dearlove, Bethany, Li, Yifan, Owen, Christopher L., Lewitus, Eric, Sanders-Buell, Eric, Bose, Meera, O'Sullivan, AnneMarie, Rossenkhan, Raabya, Labuschagne, Jan Phillipus Lourens, Edlefsen, Paul T., Reeves, Daniel B., Kijak, Gustavo, Miller, Shana, Poltavee, Kultida, Lee, Jenica, Bonar, Lydia, Harbolick, Elizabeth, and Ahani, Bahar

Subjects
HAMMING distance, PEAK load, PATHOLOGY, ADULTS, VIRAL load, ECLIPSES
Abstract

Most HIV-1 infected individuals do not know their infection dates. Precise infection timing is crucial information for studies that document transmission networks or drug levels at infection. To improve infection timing, we used the prospective RV217 cohort where the window when plasma viremia becomes detectable is narrow: the last negative visit occurred a median of four days before the first detectable HIV-1 viremia with an RNA test, referred below as diagnosis. We sequenced 1,280 HIV-1 genomes from 39 participants at a median of 4, 32 and 170 days post-diagnosis. HIV-1 infections were dated by using sequence-based methods and a viral load regression method. Bayesian coalescent and viral load regression estimated that infections occurred a median of 6 days prior to diagnosis (IQR: 9–3 and 11–4 days prior, respectively). Poisson-Fitter, which analyzes the distribution of hamming distances among sequences, estimated a median of 7 days prior to diagnosis (IQR: 15–4 days) based on sequences sampled 4 days post-diagnosis, but it did not yield plausible results using sequences sampled at 32 days. Fourteen participants reported a high-risk exposure event at a median of 8 days prior to diagnosis (IQR: 12 to 6 days prior). These different methods concurred that HIV-1 infection occurred about a week before detectable viremia, corresponding to 20 days (IQR: 34–15 days) before peak viral load. Together, our methods comparison helps define a framework for future dating studies in early HIV-1 infection. Author summary: HIV-1 infected individuals rarely know when they became infected but knowing when an infection occurred provides critical information regarding HIV-1 pathogenesis and epidemiology. Using a unique cohort in which infection was known to have occurred in a narrow interval, we investigated methods to estimate the timing of infections. Several methods suggested that HIV-1 infection typically occurs a median of one week before the infection can be detected by HIV-1 RNA testing. Going forward, we provide a strategy that can be used to elucidate the origin of an acute/early infection. [ABSTRACT FROM AUTHOR]

Published
2020
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26. Neutralization Sensitivity of a Novel HIV-1 CRF01_AE Panel of Infectious Molecular Clones

Author

Chenine, Agnes-Laurence, primary, Merbah, Melanie, additional, Wieczorek, Lindsay, additional, Molnar, Sebastian, additional, Mann, Brendan, additional, Lee, Jenica, additional, O'Sullivan, Anne-Marie, additional, Bose, Meera, additional, Sanders-Buell, Eric, additional, Kijak, Gustavo H., additional, Herrera, Carolina, additional, McLinden, Robert, additional, O'Connell, Robert J., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Kim, Jerome H., additional, Polonis, Victoria R., additional, and Tovanabutra, Sodsai, additional

Published
2018
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27. HIV-1 sequences with more predicted glycans in acute infection were associated with the development of higher neutralization breadth

Author

Merbah, Melanie, primary, Sanders-Buell, Eric, additional, Donofrio, Gina, additional, Li, Yifan, additional, Bose, Meera, additional, O’Sullivan, Anne-Marie, additional, Townsley, Samantha, additional, Slike, Bonnie, additional, Kibuuka, Hannah, additional, Maganga, Lucas, additional, Nitayaphan, Sorachai, additional, Eller, Leigh-Ann, additional, Krebs, Shelly, additional, Tovanabutra, Sodsai, additional, Michael, Nelson, additional, Robb, Merlin, additional, and Rolland, Morgane, additional

Published
2018
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28. Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120

Author

deCamp, Allan C., primary, Rolland, Morgane, additional, Edlefsen, Paul T., additional, Sanders-Buell, Eric, additional, Hall, Breana, additional, Magaret, Craig A., additional, Fiore-Gartland, Andrew J., additional, Juraska, Michal, additional, Carpp, Lindsay N., additional, Karuna, Shelly T., additional, Bose, Meera, additional, LePore, Steven, additional, Miller, Shana, additional, O'Sullivan, Annemarie, additional, Poltavee, Kultida, additional, Bai, Hongjun, additional, Dommaraju, Kalpana, additional, Zhao, Hong, additional, Wong, Kim, additional, Chen, Lennie, additional, Ahmed, Hasan, additional, Goodman, Derrick, additional, Tay, Matthew Z., additional, Gottardo, Raphael, additional, Koup, Richard A., additional, Bailer, Robert, additional, Mascola, John R., additional, Graham, Barney S., additional, Roederer, Mario, additional, O’Connell, Robert J., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Adams, Elizabeth, additional, D’Souza, Patricia, additional, Kublin, James, additional, Corey, Lawrence, additional, Geraghty, Daniel E., additional, Frahm, Nicole, additional, Tomaras, Georgia D., additional, McElrath, M. Juliana, additional, Frenkel, Lisa, additional, Styrchak, Sheila, additional, Tovanabutra, Sodsai, additional, Sobieszczyk, Magdalena E., additional, Hammer, Scott M., additional, Kim, Jerome H., additional, Mullins, James I., additional, and Gilbert, Peter B., additional

Published
2017
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29. Correction: Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection

Author

Kijak, Gustavo H., primary, Sanders-Buell, Eric, additional, Chenine, Agnes-Laurence, additional, Eller, Michael A., additional, Goonetilleke, Nilu, additional, Thomas, Rasmi, additional, Leviyang, Sivan, additional, Harbolick, Elizabeth A., additional, Bose, Meera, additional, Pham, Phuc, additional, Oropeza, Celina, additional, Poltavee, Kultida, additional, O’Sullivan, Anne Marie, additional, Billings, Erik, additional, Merbah, Melanie, additional, Costanzo, Margaret C., additional, Warren, Joanna A., additional, Slike, Bonnie, additional, Li, Hui, additional, Peachman, Kristina K., additional, Fischer, Will, additional, Gao, Feng, additional, Cicala, Claudia, additional, Arthos, James, additional, Eller, Leigh A., additional, O’Connell, Robert J., additional, Sinei, Samuel, additional, Maganga, Lucas, additional, Kibuuka, Hannah, additional, Nitayaphan, Sorachai, additional, Rao, Mangala, additional, Marovich, Mary A., additional, Krebs, Shelly J., additional, Rolland, Morgane, additional, Korber, Bette T., additional, Shaw, George M., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Tovanabutra, Sodsai, additional, and Kim, Jerome H., additional

Published
2017
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30. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection

Author

Kijak, Gustavo H., primary, Sanders-Buell, Eric, additional, Chenine, Agnes-Laurence, additional, Eller, Michael A., additional, Goonetilleke, Nilu, additional, Thomas, Rasmi, additional, Leviyang, Sivan, additional, Harbolick, Elizabeth A., additional, Bose, Meera, additional, Pham, Phuc, additional, Oropeza, Celina, additional, Poltavee, Kultida, additional, O’Sullivan, Anne Marie, additional, Billings, Erik, additional, Merbah, Melanie, additional, Costanzo, Margaret C., additional, Warren, Joanna A., additional, Slike, Bonnie, additional, Li, Hui, additional, Peachman, Kristina K., additional, Fischer, Will, additional, Gao, Feng, additional, Cicala, Claudia, additional, Arthos, James, additional, Eller, Leigh A., additional, O’Connell, Robert J., additional, Sinei, Samuel, additional, Maganga, Lucas, additional, Kibuuka, Hannah, additional, Nitayaphan, Sorachai, additional, Rao, Mangala, additional, Marovich, Mary A., additional, Krebs, Shelly J., additional, Rolland, Morgane, additional, Korber, Bette T., additional, Shaw, George M., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Tovanabutra, Sodsai, additional, and Kim, Jerome H., additional

Published
2017
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31. Antibody responses induced to the C1 region of HIV-1 gp120 in acute HIV-1 infection and after vaccination

Author

Trinh, Hung Viet, primary, Pham, Peter, additional, Hamlin, Christopher, additional, Bose, Meera, additional, Tovanabutra, Sodsai, additional, Kijak, Gustavo, additional, Sanders-Buell, Eric, additional, Eller, Leigh A., additional, Alving, Carl R., additional, Kim, Jerome H., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, and Rao, Mangala, additional

Published
2017
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32. HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania

Author

Billings, Erik, primary, Sanders-Buell, Eric, additional, Bose, Meera, additional, Kijak, Gustavo H., additional, Bradfield, Andrea, additional, Crossler, Jacqueline, additional, Arroyo, Miguel A., additional, Maboko, Leonard, additional, Hoffmann, Oliver, additional, Geis, Steffen, additional, Birx, Deborah L., additional, Kim, Jerome H., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Hoelscher, Michael, additional, and Tovanabutra, Sodsai, additional

Published
2017
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33. HIV DNA Set Point is Rapidly Established in Acute HIV Infection and Dramatically Reduced by Early ART

Author

Ananworanich, Jintanat, primary, Chomont, Nicolas, additional, Eller, Leigh Ann, additional, Kroon, Eugene, additional, Tovanabutra, Sodsai, additional, Bose, Meera, additional, Nau, Martin, additional, Fletcher, James L.K., additional, Tipsuk, Somporn, additional, Vandergeeten, Claire, additional, O'Connell, Robert J., additional, Pinyakorn, Suteeraporn, additional, Michael, Nelson, additional, Phanuphak, Nittaya, additional, and Robb, Merlin L., additional

Published
2016
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34. Significant contribution of subtype G to HIV-1 genetic complexity in Nigeria identified by a newly developed subtyping assay specific for subtype G and CRF02_AG

Author

Heipertz, Richard A., primary, Ayemoba, Ojor, additional, Sanders-Buell, Eric, additional, Poltavee, Kultida, additional, Pham, Phuc, additional, Kijak, Gustavo H., additional, Lei, Esther, additional, Bose, Meera, additional, Howell, Shana, additional, OʼSullivan, Anne Marie, additional, Bates, Adam, additional, Cervenka, Taylor, additional, Kuroiwa, Janelle, additional, Akintunde, Akindiran, additional, Ibezim, Onyekachukwu, additional, Alabi, Abraham, additional, Okoye, Obumneke, additional, Manak, Mark, additional, Malia, Jennifer, additional, Peel, Sheila, additional, Maisaka, Mohammed, additional, Singer, Darrell, additional, O’Connell, Robert J., additional, Robb, Merlin L., additional, Kim, Jerome H., additional, Michael, Nelson L., additional, Njoku, Ogbonnaya, additional, and Tovanabutra, Sodsai, additional

Published
2016
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35. 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

Author

Billings, Erik, primary, Sanders-Buell, Eric, additional, Bose, Meera, additional, Bradfield, Andrea, additional, Lei, Esther, additional, Kijak, Gustavo H., additional, Arroyo, Miguel A., additional, Kibaya, Rukia M., additional, Scott, Paul T., additional, Wasunna, Monique K., additional, Sawe, Frederick K., additional, Shaffer, Douglas N., additional, Birx, Deborah L., additional, McCutchan, Francine E., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Kim, Jerome H., additional, and Tovanabutra, Sodsai, additional

Published
2015
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36. Real Time Fitness Assay of Two CRF01_A/E HIV-1 Transmitted Founder Variants

Author

Merbah, Melanie, primary, Kijak, Gustavo, additional, Eller, Leigh Anne, additional, Sanders-Buell, Eric, additional, Mann, Brendan T., additional, Pillis, Devin M., additional, O'Sullivan, Anne Marie, additional, Bose, Meera, additional, Lee, Jenica L., additional, Poltavee, Kultida, additional, Michael, Nelson, additional, Kim, Jerome, additional, Robb, Merlin, additional, Tovanabutra, Sodsai, additional, and Chenine, Agnes-Laurence, additional

Published
2014
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37. Cryptic Multiple HIV-1 Infection Revealed by Early, Frequent, and Deep Sampling during Acute Infection

Author

Kijak, Gustavo Hernan, primary, Sanders-Buell, Eric, additional, Chenine, Agnes-Laurance, additional, Eller, Michael, additional, Goonetilleke, Nilu, additional, Thomas, Rasmi, additional, Leviyang, Sivan, additional, Harbolick, Elizabeth, additional, Bose, Meera, additional, Pham, Phuc, additional, Oropeza, Celina, additional, Poltavee, Kultida, additional, O'Sullivan, Anne Marie, additional, Merbah, Melanie, additional, Costanzo, Margaret, additional, Li, Hui, additional, Fischer, Will, additional, Gao, Feng, additional, Eller, Leigh Anne, additional, O'Connell, Robert J., additional, Sinei, Samuel, additional, Maganga, Lucas, additional, Kibuuka, Hannah, additional, Nitayaphan, Sorachai, additional, Rolland, Morgane, additional, Korber, Bette, additional, McCutchan, Francine, additional, Shaw, George, additional, Michael, Nelson, additional, Robb, Merlin, additional, Tovanabutra, Sodsai, additional, and Kim, Jerome, additional

Published
2014
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38. No Selection for Env with Shorter Variable Loops in Acute HIV-1 Infection

Author

Rolland, Morgane, primary, Tovanabutra, Sodsai, additional, Sanders-Buell, Eric, additional, Bose, Meera, additional, Sullivan, Anne Marie O, additional, Howell, Shana, additional, Poltavee, Kultida, additional, Lee, Jenica, additional, Ibitamuno, Grace, additional, Muhammad, Sevan, additional, Ahani, Bahar, additional, Lepore, Steven, additional, Harbolick, Elizabeth, additional, Oropeza, Celina, additional, Patterson, Joey, additional, Bates, Adam, additional, Lazzaro, Michelle, additional, Kijak, Gustavo, additional, Dommaraju, Kalpana, additional, Herr, Christopher, additional, Eller, Leigh Anne, additional, Nitayaphan, Sorachai, additional, Rono, Kathleen, additional, Maganga, Lucas, additional, Sekiziyivu, Arthur, additional, Michael, Nelson, additional, Kim, Jerome, additional, and Robb, Merlin, additional

Published
2014
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39. Analysis of HLA A*02 Association with Vaccine Efficacy in the RV144 HIV-1 Vaccine Trial

Author

Gartland, Andrew J., primary, Li, Sue, additional, McNevin, John, additional, Tomaras, Georgia D., additional, Gottardo, Raphael, additional, Janes, Holly, additional, Fong, Youyi, additional, Morris, Daryl, additional, Geraghty, Daniel E., additional, Kijak, Gustavo H., additional, Edlefsen, Paul T., additional, Frahm, Nicole, additional, Larsen, Brendan B., additional, Tovanabutra, Sodsai, additional, Sanders-Buell, Eric, additional, deCamp, Allan C., additional, Magaret, Craig A., additional, Ahmed, Hasan, additional, Goodridge, Jodie P., additional, Chen, Lennie, additional, Konopa, Philip, additional, Nariya, Snehal, additional, Stoddard, Julia N., additional, Wong, Kim, additional, Zhao, Hong, additional, Deng, Wenjie, additional, Maust, Brandon S., additional, Bose, Meera, additional, Howell, Shana, additional, Bates, Adam, additional, Lazzaro, Michelle, additional, O'Sullivan, Annemarie, additional, Lei, Esther, additional, Bradfield, Andrea, additional, Ibitamuno, Grace, additional, Assawadarachai, Vatcharain, additional, O'Connell, Robert J., additional, deSouza, Mark S., additional, Nitayaphan, Sorachai, additional, Rerks-Ngarm, Supachai, additional, Robb, Merlin L., additional, Sidney, John, additional, Sette, Alessandro, additional, Zolla-Pazner, Susan, additional, Montefiori, David, additional, McElrath, M. Juliana, additional, Mullins, James I., additional, Kim, Jerome H., additional, Gilbert, Peter B., additional, and Hertz, Tomer, additional

Published
2014
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40. Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

Author

Kijak, Gustavo H., primary, Tovanabutra, Sodsai, additional, Rerks-Ngarm, Supachai, additional, Nitayaphan, Sorachai, additional, Eamsila, Chirapa, additional, Kunasol, Prayura, additional, Khamboonruang, Chirasak, additional, Thongcharoen, Prasert, additional, Namwat, Chawetsan, additional, Premsri, Nakorn, additional, Benenson, Michael, additional, Morgan, Patricia, additional, Bose, Meera, additional, Sanders-Buell, Eric, additional, Paris, Robert, additional, Robb, Merlin L., additional, Birx, Deborah L., additional, De Souza, Mark S., additional, McCutchan, Francine E., additional, Michael, Nelson L., additional, and Kim, Jerome H., additional

Published
2013
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41. Distinct Circulating Recombinant HIV-1 Strains Among Injecting Drug Users and Sex Workers in Afghanistan

Author

WALTER REED ARMY INST OF RESEARCH ROCKVILLE MD US MILITARY HIV RESEARCH PROGRAM/DIVISION OF RETROVIROLOGY, Sanders-Buell, Eric, Bose, Meera, Nasir, Abdul, Todd, Catherine S., Stanekzai, M. R., Tovanabutra, Sodsai, Scott, Paul T., Strathdee, Steffanie A., Tjaden, Jeffrey, Michael, Nelson L., McCutchan, Francine E., WALTER REED ARMY INST OF RESEARCH ROCKVILLE MD US MILITARY HIV RESEARCH PROGRAM/DIVISION OF RETROVIROLOGY, Sanders-Buell, Eric, Bose, Meera, Nasir, Abdul, Todd, Catherine S., Stanekzai, M. R., Tovanabutra, Sodsai, Scott, Paul T., Strathdee, Steffanie A., Tjaden, Jeffrey, Michael, Nelson L., and McCutchan, Francine E.

Abstract

Little information is available regarding a circulating HIV genotype among high-risk groups in Afghanistan; we describe HIV genotypes among injecting drug users (IDUs) and sex workers (SWs) in four Afghan cities. Participants completed behavioral questionnaires and HIV testing. Western blot-confirmed specimens had peripheral mononuclear blood cells isolated for genotyping. Analysis of recombinants was done by bootscanning and manual sequence alignment. The single SW sample harbored a CRF01_AE strain. Of 10 IDUs available for analysis, all were CRF35_AD and from Hirat. Analyzed subregions (gag p17 and env C1-C5) revealed close homology between the Hirat specimens. Three distinct subclusters comprising two or three strains were identified whereas two other strains were generally equidistant from previously identified Kabul strains. Results suggest that the nascent HIV epidemic among IDUs in Hirat is largely, if not entirely, subtype CRF35_AD, and the close homology suggests recent infection; harm reduction should be supported to avert further transmission., AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 26, Number 5, 2010. The original document contains color images.

Published
2010

42. Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

Author

Rolland, Morgane, primary, Tovanabutra, Sodsai, additional, deCamp, Allan C, additional, Frahm, Nicole, additional, Gilbert, Peter B, additional, Sanders-Buell, Eric, additional, Heath, Laura, additional, Magaret, Craig A, additional, Bose, Meera, additional, Bradfield, Andrea, additional, O'Sullivan, Annemarie, additional, Crossler, Jacqueline, additional, Jones, Teresa, additional, Nau, Marty, additional, Wong, Kim, additional, Zhao, Hong, additional, Raugi, Dana N, additional, Sorensen, Stephanie, additional, Stoddard, Julia N, additional, Maust, Brandon S, additional, Deng, Wenjie, additional, Hural, John, additional, Dubey, Sheri, additional, Michael, Nelson L, additional, Shiver, John, additional, Corey, Lawrence, additional, Li, Fusheng, additional, Self, Steve G, additional, Kim, Jerome, additional, Buchbinder, Susan, additional, Casimiro, Danilo R, additional, Robertson, Michael N, additional, Duerr, Ann, additional, McElrath, M Juliana, additional, McCutchan, Francine E, additional, and Mullins, James I, additional

Published
2011
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43. Distinct Circulating Recombinant HIV-1 Strains Among Injecting Drug Users and Sex Workers in Afghanistan

Author

Sanders-Buell, Eric, primary, Bose, Meera, additional, Nasir, Abdul, additional, Todd, Catherine S., additional, Stanekzai, M. Raza, additional, Tovanabutra, Sodsai, additional, Scott, Paul T., additional, Strathdee, Steffanie A., additional, Tjaden, Jeffrey, additional, Michael, Nelson L., additional, and McCutchan, Francine E., additional

Published
2010
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44. Deep Sequencing Reveals Central Nervous System Compartmentalization in Multiple Transmitted/Founder Virus Acute HIV-1 Infection.

Author

Tovanabutra, Sodsai, Sirijatuphat, Rujipas, Pham, Phuc T., Bonar, Lydia, Harbolick, Elizabeth A., Bose, Meera, Song, Hongshuo, Chang, David, Oropeza, Celina, O'Sullivan, Anne Marie, Balinang, Joyce, Kroon, Eugene, Colby, Donn J., Sacdalan, Carlo, Hellmuth, Joanna, Chan, Phillip, Prueksakaew, Peeriya, Pinyakorn, Suteeraporn, Jagodzinski, Linda L., and Sutthichom, Duanghathai

Subjects
CENTRAL nervous system, CENTRAL nervous system physiology, CEREBROSPINAL fluid, CEREBROSPINAL fluid examination, INFECTION
Abstract

HIV-1 disseminates to a broad range of tissue compartments during acute HIV-1 infection (AHI). The central nervous system (CNS) can serve as an early and persistent site of viral replication, which poses a potential challenge for HIV-1 remission strategies that target the HIV reservoir. CNS compartmentalization is a key feature of HIV-1 neuropathogenesis. Thus far, the timing of how early CNS compartmentalization develops after infection is unknown. We examined whether HIV-1 transmitted/founder (T/F) viruses differ between CNS and blood during AHI using single-genome sequencing of envelope gene and further examined subregions in pol and env using next-generation sequencing in paired plasma and cerebrospinal fluid (CSF) from 18 individuals. Different proportions of mostly minor variants were found in six of the eight multiple T/F-infected individuals, indicating enrichment of some variants in CSF that may lead to significant compartmentalization in the later stages of infection. This study provides evidence for the first time that HIV-1 compartmentalization in the CNS can occur within days of HIV-1 exposure in multiple T/F infections. Further understanding of factors that determine enrichment of T/F variants in the CNS, as well as potential long-term implications of these findings for persistence of HIV-1 reservoirs and neurological impairment in HIV, is needed. [ABSTRACT FROM AUTHOR]

Published
2019
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45. Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort.

Author

Trinh, Hung V., Gohain, Neelakshi, Pham, Peter T., Hamlin, Christopher, Song, Hongshuo, Sanders-Buell, Eric, Bose, Meera, Eller, Leigh A., Tovanabutra, Sodsai, Michael, Nelson L., Robb, Merlin L., Joyce, M. Gordon, and Rao, Mangala

Subjects
VIRAL envelope proteins, SURFACE plasmon resonance, VIRAL variation, ANTIBODY formation, IMMUNE response, INFECTION
Abstract

Reduced risk of HIV-1 infection correlated with antibody responses to the envelope variable 1 and 2 regions in the RV144 vaccine trial. To understand the relationship between antibody responses, V2 sequence, and structure, plasma samples (n = 16) from an early acute HIV-1 infection cohort from Thailand infected with CRF01_AE strain were analyzed for binding to V2 peptides by surface plasmon resonance. Five participants with a range of V2 binding responses at week 24 post-infection were further analyzed against a set of four overlapping V2 peptides that were designed based on envelope single-genome amplification. Antibody responses that were relatively consistent over the four segments of the V2 region or a focused response to the C-strand (residues 165–186) of the V2 region were observed. Viral escape in the V2 region resulted in significantly reduced antibody binding. Structural modeling indicated that the C-strand and the sites of viral variation were highly accessible in the open conformation of the HIV-1 Env trimer. V2 residues, 165–186 are preferentially targeted during acute infection. Residues 169–184 were also preferentially targeted by the protective immune response in the RV144 trial, thus emphasizing the importance of these residues for vaccine design. [ABSTRACT FROM AUTHOR]

Published
2019
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46. Molecular epidemiology of a primarily MSM acute HIV‐1 cohort in Bangkok, Thailand and connections within networks of transmission in Asia.

Author

Michael, Nelson L, Chang, David, Sanders‐Buell, Eric, Bose, Meera, O'Sullivan, Anne Marie, Pham, Phuc, Billings, Erik, Pinyakorn, Suteeraporn, Kijak, Gustavo, Excler, Jean‐Louis, Robb, Merlin L, Tovanabutra, Sodsai, Ananworanich, Jintanat, Sirijatuphat, Rujipas, O'Connell, Robert J, Kim, Jerome H, Souza, Mark, Kroon, Eugene, Colby, Donn J, and Chomchey, Nitiya

Abstract

Introduction: Thailand plays a substantial role in global HIV‐1 transmission of CRF01_AE. Worldwide, men who have sex with men (MSM) are at elevated risk for HIV‐1 infection. Hence, understanding HIV‐1 diversity in a primarily Thai MSM cohort with acute infection, and its connections to the broader HIV‐1 transmission network in Asia is crucial for research and development of HIV‐1 vaccines, treatment and cure. Methods: Subtypes and diversity of infecting viruses from individuals sampled from 2009 to 2015 within the RV254/SEARCH 010 cohort were assessed by multiregion hybridization assay (MHAbce), multiregion subtype‐specific PCR assay (MSSPbce) and full‐length single‐genome sequencing (SGS). Phylogenetic analysis was performed by maximum likelihood. Pairwise genetic distances of envelope gp160 sequences obtained from the cohort and from Asia (Los Alamos National Laboratory HIV Database) were calculated to identify potential transmission networks. Results: MHAbce/MSSPbce results identified 81.6% CRF01_AE infecting strains in RV254. CRF01_AE/B recombinants and subtype B were found at 7.3% and 2.8% respectively. Western subtype B strains outnumbered Thai B′ strains. Phylogenetic analysis revealed one C, one CRF01_AE/CRF02_AG recombinant and one CRF01_AE/B/C recombinant. Asian network analysis identified one hundred and twenty‐three clusters, including five clusters of RV254 participants. None of the RV254 sequences clustered with non‐RV254 sequences. The largest international cluster involved 15 CRF01_AE strains from China and Vietnam. The remaining clusters were mostly intracountry connections, of which 31.7% included Thai nodes and 43.1% included Chinese nodes. Conclusion: While the majority of strains in Thailand are CRF01_AE and subtype B, emergence of unique recombinant forms (URFs) are found in a moderate fraction of new HIV‐1 infections. Approaches to vaccine design and immunotherapeutics will need to monitor and consider the expanding proportion of recombinants and the increasing genetic diversity in the region. Identified HIV‐1 transmission networks indicate ongoing spread of HIV‐1 among MSM. As HIV‐1 epidemics continue to expand in other Asian countries, transmission network analyses can inform strategies for prevention, intervention, treatment and cure. [ABSTRACT FROM AUTHOR]

Published
2018
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47. Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120

Author

DeCamp, Allan C., Rolland, Morgane, Edlefsen, Paul T., Sanders-Buell, Eric, Hall, Breana, Magaret, Craig A., Fiore-Gartland, Andrew J., Juraska, Michal, Carpp, Lindsay N., Karuna, Shelly T., Bose, Meera, LePore, Steven, Miller, Shana, O’Sullivan, Annemarie, Poltavee, Kultida, Bai, Hongjun, Dommaraju, Kalpana, Zhao, Hong, Wong, Kim, Chen, Lennie, Ahmed, Hasan, Goodman, Derrick, Tay, Matthew Z., Gottardo, Raphael, Koup, Richard A., Bailer, Robert, Mascola, John R., Graham, Barney S., Roederer, Mario, O’Connell, Robert J., Michael, Nelson L., Robb, Merlin L., Adams, Elizabeth, D’Souza, Patricia, Kublin, James G., Corey, Lawrence, Geraghty, Daniel E., Frahm, Nicole, Tomaras, Georgia D., McElrath, M. Juliana, Frenke, Lisa, Styrchak, Sheila, Tovanabutra, Sodsai, Sobieszczyk, Magdalena, Hammer, Scott M., Kim, Jerome H., Mullins, James I., and Gilbert, Peter B.

Subjects
Immune response--Molecular aspects, viruses, Vaccines--Research, virus diseases, Medicine, 3. Good health, HIV (Viruses)--Prevention
Abstract

Although the HVTN 505 DNA/recombinant adenovirus type 5 vector HIV-1 vaccine trial showed no overall efficacy, analysis of breakthrough HIV-1 sequences in participants can help determine whether vaccine-induced immune responses impacted viruses that caused infection. We analyzed 480 HIV-1 genomes sampled from 27 vaccine and 20 placebo recipients and found that intra-host HIV-1 diversity was significantly lower in vaccine recipients (P ≤ 0.04, Q-values ≤ 0.09) in Gag, Pol, Vif and envelope glycoprotein gp120 (Env-gp120). Furthermore, Env-gp120 sequences from vaccine recipients were significantly more distant from the subtype B vaccine insert than sequences from placebo recipients (P = 0.01, Q-value = 0.12). These vaccine effects were associated with signatures mapping to CD4 binding site and CD4-induced monoclonal antibody footprints. These results suggest either (i) no vaccine efficacy to block acquisition of any viral genotype but vaccine-accelerated Env evolution post-acquisition; or (ii) vaccine efficacy against HIV-1s with Env sequences closest to the vaccine insert combined with increased acquisition due to other factors, potentially including the vaccine vector.

48. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection

Author

O’Connell, Robert J., Michael, Nelson L., Oropeza, Celina, Arthos, James, Bose, Meera, Nitayaphan, Sorachai, Slike, Bonnie, Thomas, Rasmi, Chenine, Agnes-Laurence, Tovanabutra, Sodsai, Marovich, Mary A., O’Sullivan, Anne Marie, Rolland, Morgane, Maganga, Lucas, Merbah, Melanie, Warren, Joanna A., Shaw, George M., Billings, Erik, Goonetilleke, Nilu, Cicala, Claudia, Eller, Michael A., Poltavee, Kultida, Kibuuka, Hannah, Pham, Phuc, Kim, Jerome H., Sanders-Buell, Eric, Korber, Bette T., Fischer, Will, Li, Hui, Peachman, Kristina K., Leviyang, Sivan, Sinei, Samuel, Harbolick, Elizabeth A., Eller, Leigh A., Krebs, Shelly J., Gao, Feng, Costanzo, Margaret C., Rao, Mangala, Robb, Merlin L., and Kijak, Gustavo H.

Subjects
3. Good health
Abstract

In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.

49. Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.

Author

Rolland, Morgane, Hertz, Tomer, Tovanabutra, Sodsai, Gartland, Andrew J., deCamp, Allan C., Magaret, Craig A., Ahmed, Hasan, Gottardo, Raphael, Juraska, Michal, McCoy, Connor, Larsen, Brendan B., Sanders-Buell, Eric, Carrico, Chris, Menis, Sergey, Bose, Meera, Arroyo, Miguel A., O'Connell, Robert J., deSouza, Mark S., Nitayaphan, Sorachai, and Pitisuttithum, Punnee

Abstract

An abstract of the article "Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial" by Paul T. Edlefsen, Morgane Rolland, Tomer Hertz is presented.

Published
2014
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50. Real Time Fitness Assay of Two CRF01_A/E HIV-1 Transmitted Founder Variants.

Author

Kijak, Gustavo, Eller, Leigh Anne, Sanders-Buell, Eric, Mann, Brendan T., Pillis, Devin M., O'Sullivan, Anne Marie, Bose, Meera, Lee, Jenica L., Poltavee, Kultida, Michael, Nelson, Kim, Jerome, Robb, Merlin, Tovanabutra, Sodsai, and Chenine, Agnes-Laurence

Abstract

An abstract of the article "Real Time Fitness Assay of Two CRF01_A/E HIV-1 Transmitted Founder Variants" by Melanie Merbah, Gustavo Kijak and colleagues is presented.

Published
2014
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