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Hutchinson JM, Mesa KA, Alexander DL, Yu B, O'Rourke SM, Limoli KL, Wrin T, Deeks SG, Berman PW. Unusual Cysteine Content in V1 Region of gp120 From an Elite Suppressor That Produces Broadly Neutralizing Antibodies. Front Immunol 2019; 10:1021. [PMID: 31156622 PMCID: PMC6530427 DOI: 10.3389/fimmu.2019.01021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/23/2019] [Indexed: 01/21/2023] Open
Abstract
Although it is now possible to produce recombinant HIV envelope glycoproteins (Envs) with epitopes recognized by the 5–6 major classes of broadly neutralizing antibodies (bNAbs), these have failed to consistently stimulate the formation of bNAbs in immunized animals or humans. In an effort to identify new immunogens better able to elicit bNAbs, we are studying Envs derived from rare individuals who possess bNAbs and are able to control their infection without the need for anti-retroviral drugs (elite supressors or ES), hypothesizing that in at least some people the antibodies may mediate durable virus control. Because virus evolution in people with the ES only phenotype was reported to be limited, we reasoned the Env proteins recovered from these individuals may more closely resemble the Envs that gave rise to bNAbs compared to the highly diverse viruses isolated from normal progressors. Using a phenotypic assay, we screened 25 controllers and identified two for more detailed investigation. In this study, we examined 20 clade B proviral sequences isolated from an African American woman, who had the rare bNAb/ES phenotype. Phylogenetic analysis of proviral envelope sequences demonstrated low genetic diversity. Envelope proteins were unusual in that most possessed two extra cysteines within an elongated V1 region. In this report, we examine the impact of the extra cysteines on the binding to bNAbs, virus infectivity, and sensitivity to neutralization. These data suggest structural motifs in V1 can affect infectivity, and that rare viruses may be prevented from developing escape.
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Affiliation(s)
- Jennie M Hutchinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kathryn A Mesa
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - David L Alexander
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Bin Yu
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Sara M O'Rourke
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kay L Limoli
- Monogram Biosciences, South San Francisco, CA, United States
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA, United States
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Phillip W Berman
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
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Subtle differences in selective pressures applied on the envelope gene of HIV-1 in pregnant versus non-pregnant women. INFECTION GENETICS AND EVOLUTION 2018; 62:141-150. [PMID: 29678797 DOI: 10.1016/j.meegid.2018.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 04/09/2018] [Accepted: 04/15/2018] [Indexed: 10/17/2022]
Abstract
Pregnancy is associated with modulations of maternal immunity that contribute to foeto-maternal tolerance. To understand whether and how these alterations impact antiviral immunity, a detailed cross-sectional analysis of selective pressures exerted on HIV-1 envelope amino-acid sequences was performed in a group of pregnant (n = 32) and non-pregnant (n = 44) HIV-infected women in absence of treatment with antiretroviral therapy (ART). Independent of HIV-1 subtype, p-distance, dN and dS were all strongly correlated with one another but were not significantly different in pregnant as compared to non-pregnant patients. Differential levels of selective pressure applied on different Env subdomains displayed similar yet non-identical patterns between the two groups, with pressure applied on C1 being significantly lower in constant regions C1 and C2 than in V1, V2, V3 and C3. To draw a general picture of the selection applied on the envelope and compensate for inter-individual variations, we performed a binomial test on selection frequency data pooled from pregnant and non-pregnant women. This analysis uncovered 42 positions, present in both groups, exhibiting statistically-significant frequency of selection that invariably mapped to the surface of the Env protein, with the great majority located within epitopes recognized by Env-specific antibodies or sites associated with the development of cross-reactive neutralizing activity. The median frequency of occurrence of positive selection per site was significantly lower in pregnant versus non-pregnant women. Furthermore, examination of the distribution of positively selected sites using a hypergeometric test revealed that only 2 positions (D137 and S142) significantly differed between the 2 groups. Taken together, these result indicate that pregnancy is associated with subtle yet distinctive changes in selective pressures exerted on the HIV-1 Env protein that are compatible with transient modulations of maternal immunity.
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CHEN Y, WANG Z, HUANG A, YUAN J, WEI D, YE H. A trend towards increasing viral load in newly diagnosed HIV-infected inpatients in southeast China. Epidemiol Infect 2016; 144:1679-82. [PMID: 26732896 PMCID: PMC9150606 DOI: 10.1017/s0950268815003155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 11/17/2015] [Accepted: 11/24/2015] [Indexed: 01/23/2023] Open
Abstract
Peripheral blood viral load is an important indicator of viral production and clearance. Previous studies have suggested that viral load might predict the rate of decrease in CD4+ cell count and progression to AIDS and death. Here, we conducted a retrospective analysis of the trends in HIV-1 viral load in southeast China. Among inpatients newly diagnosed with HIV infection, we found that viral load has increased over the past decade from 4·20 log10 copies/ml in 2002 to 6·61 log10 copies/ml in 2014, with a mean increase of 0·19 log10 copies/ml each year. However, the CD4+ cell count was stable and insensitive to changes in viral load. Thus, increasing viral load appears to be an emerging trend in newly diagnosed HIV-infected inpatients.
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Affiliation(s)
- Y. CHEN
- Fuzhou Infectious Disease Hospital of Fujian Medical University, Fuzhou, P.R. China
| | - Z. WANG
- Fuzhou Infectious Disease Hospital of Fujian Medical University, Fuzhou, P.R. China
| | - A. HUANG
- Fuzhou Infectious Disease Hospital of Fujian Medical University, Fuzhou, P.R. China
| | - J. YUAN
- Fuzhou Infectious Disease Hospital of Fujian Medical University, Fuzhou, P.R. China
| | - D. WEI
- Fuzhou Infectious Disease Hospital of Fujian Medical University, Fuzhou, P.R. China
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P.R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P.R. China
| | - H. YE
- Fuzhou Infectious Disease Hospital of Fujian Medical University, Fuzhou, P.R. China
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HIV populations are large and accumulate high genetic diversity in a nonlinear fashion. J Virol 2013; 87:10313-23. [PMID: 23678164 DOI: 10.1128/jvi.01225-12] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.
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Rossenkhan R, Novitsky V, Sebunya TK, Musonda R, Gashe BA, Essex M. Viral diversity and diversification of major non-structural genes vif, vpr, vpu, tat exon 1 and rev exon 1 during primary HIV-1 subtype C infection. PLoS One 2012; 7:e35491. [PMID: 22590503 PMCID: PMC3348911 DOI: 10.1371/journal.pone.0035491] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/16/2012] [Indexed: 01/12/2023] Open
Abstract
To assess the level of intra-patient diversity and evolution of HIV-1C non-structural genes in primary infection, viral quasispecies obtained by single genome amplification (SGA) at multiple sampling timepoints up to 500 days post-seroconversion (p/s) were analyzed. The mean intra-patient diversity was 0.11% (95% CI; 0.02 to 0.20) for vif, 0.23% (95% CI; 0.08 to 0.38) for vpr, 0.35% (95% CI; −0.05 to 0.75) for vpu, 0.18% (95% CI; 0.01 to 0.35) for tat exon 1 and 0.30% (95% CI; 0.02 to 0.58) for rev exon 1 during the time period 0 to 90 days p/s. The intra-patient diversity increased gradually in all non-structural genes over the first year of HIV-1 infection, which was evident from the vif mean intra-patient diversity of 0.46% (95% CI; 0.28 to 0.64), vpr 0.44% (95% CI; 0.24 to 0.64), vpu 0.84% (95% CI; 0.55 to 1.13), tat exon 1 0.35% (95% CI; 0.14 to 0.56 ) and rev exon 1 0.42% (95% CI; 0.18 to 0.66) during the time period of 181 to 500 days p/s. There was a statistically significant increase in viral diversity for vif (p = 0.013) and vpu (p = 0.002). No associations between levels of viral diversity within the non-structural genes and HIV-1 RNA load during primary infection were found. The study details the dynamics of the non-structural viral genes during the early stages of HIV-1C infection.
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Affiliation(s)
- Raabya Rossenkhan
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Vladimir Novitsky
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Theresa K. Sebunya
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Rosemary Musonda
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Berhanu A. Gashe
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - M. Essex
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Chamberland A, Sylla M, Boulassel MR, Baril JG, Côté P, Thomas R, Trottier B, Rouleau D, Routy JP, Tremblay C. Effect of antiretroviral therapy on HIV-1 genetic evolution during acute infection. Int J STD AIDS 2011; 22:146-50. [DOI: 10.1258/ijsa.2010.010292] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The rapid evolution of HIV-1 is a major obstacle to viral eradication. Early antiretroviral therapy (ART) during primary HIV-1 infection could limit viral diversity. Eighteen patients recently infected with HIV-1 were selected. Nine initiated ART soon after enrolment and nine remained untreated. Replication-competent (RC) viruses were quantified at baseline and after one year of follow-up. Viral diversity in the C2V5 envelope region was evaluated from plasma, peripheral blood mononuclear cells (PBMCs), and cell culture at both time points. The amount of RC virus in the treated group declined (median −5.42 infectious units per million [IUPM]) while it remained stable or increased in the untreated group (median +0.87 IUPM). At one year post infection, we observed a significant increase in diversity for the C2V5 (+0.150%) region, specifically in the hypervariable loops V4 (+0.73%) and V5 (+0.77%), in the untreated group. More importantly, viral diversity did not significantly increase in treated individuals during the first year post infection. Genetic diversity during primary infection remains low through the first year of infection. Early treatment could contribute to a decrease in RC viruses from PBMCs and to limitation of viral diversification in the viral reservoir. These findings may have relevance for the rational design of specific immunotherapeutic strategies.
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Affiliation(s)
- A Chamberland
- Centre de Recherche du CHUM (CRCHUM)
- Université de Montréal, Montréal, Canada
| | - M Sylla
- Centre de Recherche du CHUM (CRCHUM)
- Université de Montréal, Montréal, Canada
| | | | | | - P Côté
- Centre de Recherche du CHUM (CRCHUM)
- Clinique Médicale du Quartier Latin
| | | | - B Trottier
- Centre de Recherche du CHUM (CRCHUM)
- Clinique Médicale l'Actuel
| | - D Rouleau
- Centre de Recherche du CHUM (CRCHUM)
- Université de Montréal, Montréal, Canada
| | | | - C Tremblay
- Centre de Recherche du CHUM (CRCHUM)
- Université de Montréal, Montréal, Canada
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Casado C, Colombo S, Rauch A, Martínez R, Günthard HF, Garcia S, Rodríguez C, del Romero J, Telenti A, López-Galíndez C. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. PLoS One 2010; 5:e11079. [PMID: 20552027 PMCID: PMC2884031 DOI: 10.1371/journal.pone.0011079] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 05/21/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Various patterns of HIV-1 disease progression are described in clinical practice and in research. There is a need to assess the specificity of commonly used definitions of long term non-progressor (LTNP) elite controllers (LTNP-EC), viremic controllers (LTNP-VC), and viremic non controllers (LTNP-NC), as well as of chronic progressors (P) and rapid progressors (RP). METHODOLOGY AND PRINCIPAL FINDINGS We re-evaluated the HIV-1 clinical definitions, summarized in Table 1, using the information provided by a selected number of host genetic markers and viral factors. There is a continuous decrease of protective factors and an accumulation of risk factors from LTNP-EC to RP. Statistical differences in frequency of protective HLA-B alleles (p-0.01), HLA-C rs9264942 (p-0.06), and protective CCR5/CCR2 haplotypes (p-0.02) across groups, and the presence of viruses with an ancestral genotype in the "viral dating" (i.e., nucleotide sequences with low viral divergence from the most recent common ancestor) support the differences among principal clinical groups of HIV-1 infected individuals. CONCLUSIONS A combination of host genetic and viral factors supports current clinical definitions that discriminate among patterns of HIV-1 progression. The study also emphasizes the need to apply a standardized and accepted set of clinical definitions for the purpose of disease stratification and research.
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Affiliation(s)
- Concepción Casado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Colombo
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Andri Rauch
- University Clinic of Infectious Diseases, University Hospital Bern and University of Bern, Bern, Switzerland
| | - Raquel Martínez
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland
| | - Soledad Garcia
- Centro Sanitario Sandoval, IMSALUD Comunidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Rodríguez
- Centro Sanitario Sandoval, IMSALUD Comunidad Autónoma de Madrid, Madrid, Spain
| | - Jorge del Romero
- Centro Sanitario Sandoval, IMSALUD Comunidad Autónoma de Madrid, Madrid, Spain
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
- * E-mail: (AT); (CLG)
| | - Cecilio López-Galíndez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- * E-mail: (AT); (CLG)
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Bello G, Casado C, Sandonis V, Alvaro-Cifuentes T, dos Santos CAR, García S, Rodríguez C, del Romero J, Pilotto JH, Grinsztejn B, Veloso VG, Morgado MG, López-Galíndez C. Plasma viral load threshold for sustaining intrahost HIV type 1 evolution. AIDS Res Hum Retroviruses 2007; 23:1242-50. [PMID: 17961111 DOI: 10.1089/aid.2007.0074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The objective of the present study was to determine if natural suppression of plasma viremia below the detection limit of commercial assays (50-80 copies HIV-1 RNA/ml) can contain the HIV-1 evolution. HIV-1 quasispecies complexity in PBMC DNA was assessed in the env gene at two time points in 14 long-term nonprogressors (LTNPs). Sequence changes consistent with viral evolution was found in all patients with a median plasma RNA viral load >100 copies/ml. Evidence of low-level viral evolution was detected in two of four patients with intermittent viremia and a median plasma HIV-1 RNA load of >80 copies/ml. No significant evolution was observed in the three LTNPs with persistent viral suppression below the detection limit. Overall, a significant positive correlation (p < 0.001) was observed between viral evolution and plasma RNA viral load in the LTNPs analyzed. These results suggest that the detection limit of ultrasensitive viremia assays could represent an important threshold below which intrahost HIV-1 evolution does not occur.
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Affiliation(s)
- Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Concepción Casado
- Servicio de Virologia Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Virginia Sandonis
- Servicio de Virologia Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Tamara Alvaro-Cifuentes
- Servicio de Virologia Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Soledad García
- Centro Sanitario Sandoval, IMSALUD, Comunidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Rodríguez
- Centro Sanitario Sandoval, IMSALUD, Comunidad Autónoma de Madrid, Madrid, Spain
| | - Jorge del Romero
- Centro Sanitario Sandoval, IMSALUD, Comunidad Autónoma de Madrid, Madrid, Spain
| | - José H. Pilotto
- Instituto de Pesquisa Clinica Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Instituto de Pesquisa Clinica Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Valdilea G. Veloso
- Instituto de Pesquisa Clinica Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza G. Morgado
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Cecilio López-Galíndez
- Servicio de Virologia Molecular, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Shriner D, Liu Y, Nickle DC, Mullins JI. EVOLUTION OF INTRAHOST HIV - 1 GENETIC DIVERSITY DURING CHRONIC INFECTION. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb01195.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Shriner D, Liu Y, Nickle DC, Mullins JI. EVOLUTION OF INTRAHOST HIV-1 GENETIC DIVERSITY DURING CHRONIC INFECTION. Evolution 2006. [DOI: 10.1554/05-473.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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