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Hani L, Chaillon A, Nere ML, Ruffin N, Alameddine J, Salmona M, Lopez Zaragoza JL, Smith DM, Schwartz O, Lelièvre JD, Delaugerre C, Lévy Y, Seddiki N. Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations. PLoS Pathog 2019; 15:e1007868. [PMID: 31220191 PMCID: PMC6605680 DOI: 10.1371/journal.ppat.1007868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 07/02/2019] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
We previously reported the presence of memory CD4+ T cells that express low levels of SAMHD1 (SAMHD1low) in peripheral blood and lymph nodes from both HIV-1 infected and uninfected individuals. These cells are enriched in Th17 and Tfh subsets, two populations known to be preferentially targeted by HIV-1. Here we investigated whether SAMHD1low CD4+ T-cells harbour replication-competent virus and compartimentalized HIV-1 genomes. We sorted memory CD4+CD45RO+SAMHD1low, CD4+CD45RO+SAMHD1+ and naive CD4+CD45RO-SAMHD1+ cells from HIV-1-infected patients on anti-retroviral therapy (c-ART) and performed HIV-1 DNA quantification, ultra-deep-sequencing of partial env (C2/V3) sequences and phenotypic characterization of the cells. We show that SAMHD1low cells include novel Th17 CCR6+ subsets that lack CXCR3 and CCR4 (CCR6+DN). There is a decrease of the % of Th17 in SAMHD1low compartment in infected compared to uninfected individuals (41% vs 55%, p<0.05), whereas the % of CCR6+DN increases (7.95% vs 3.8%, p<0.05). Moreover, in HIV-1 infected patients, memory SAMHD1low cells harbour high levels of HIV-1 DNA compared to memory SAMHD1+ cells (4.5 vs 3.8 log/106cells, respectively, p<0.001), while naïve SAMHD1+ showed significantly lower levels (3.1 log/106cells, p<0.0001). Importantly, we show that SAMHD1low cells contain p24-producing cells. Moreover, phylogenetic analyses revealed well-segregated HIV-1 DNA populations with compartmentalization between SAMHD1low and SAMHD1+ memory cells, and limited viral exchange. As expected, the % of Ki67+ cells was significantly higher in SAMHD1low compared to SAMHD1+ cells. There was positive association between levels of HIV-1 DNA and Ki67+ in memory SAMHD1low cells, but not in memory and naïve SAMHD1+ CD4+ T-cells. Altogether, these data suggest that proliferative memory SAMHD1low cells contribute to viral persistence. In our previous results we reported that memory CD4+ T cells expressing low levels of SAMHD1 (SAMHD1low) are present in peripheral blood and lymph nodes from HIV-1 infected and uninfected individuals. These cells were enriched in Th17 and Tfh, two populations targeted by HIV-1. Here we used purified memory CD4+CD45RO+SAMHD1low, CD4+CD45RO+SAMHD1+ and naive CD4+CD45RO-SAMHD1+ cells from HIV-1-infected and treated patients to perform cell-associated HIV-1 DNA quantification, p24-producing cells detection, ultra-deep-sequencing of partial env (C2/V3) HIV-1 DNA and further phenotypic characterization. Our results demonstrate that (i) Th17 and CCR6+DN-expressing transcriptional signature of early Th17, two major populations that are susceptible to HIV-1 infection, are present in SAMHD1low cells, and while the former decreased significantly in c-ART HIV-1 infected compared to uninfected individuals, the latter significantly increased; (ii) memory SAMHD1low cells from c-ART patients carry high levels of HIV-1 DNA compared to SAMHD1+ cells, and these levels positively and significantly correlated with Ki67 expression; (iii) memory SAMHD1low cells from patients harbour p24-producing cells; (iv) phylogenetic analyses revealed well-segregated HIV-1 DNA populations with significant compartmentalization between SAMHD1low and SAMHD1+ cells and limited viral exchange. Our data demonstrate that memory SAMHD1low cells contribute to HIV-1 persistence.
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Affiliation(s)
- Lylia Hani
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Antoine Chaillon
- Vaccine Research Institute (VRI), Créteil, France
- Department of Medicine, University of California San Diego, CA, United States of America
| | - Marie-Laure Nere
- Hôpital Saint Louis, INSERM U944, Université de Paris, Paris, France
| | - Nicolas Ruffin
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Joudy Alameddine
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Maud Salmona
- Hôpital Saint Louis, INSERM U944, Université de Paris, Paris, France
| | - José-Luiz Lopez Zaragoza
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- AP-HP, Hôpital H. Mondor—A. Chenevier, Service d'immunologie clinique et maladies infectieuses, Créteil, France
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, CA, United States of America
| | - Olivier Schwartz
- Vaccine Research Institute (VRI), Créteil, France
- Unité Virus et Immunité, Département de Virologie, Institut Pasteur, Paris, France
| | - Jean-Daniel Lelièvre
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- AP-HP, Hôpital H. Mondor—A. Chenevier, Service d'immunologie clinique et maladies infectieuses, Créteil, France
| | - Constance Delaugerre
- Vaccine Research Institute (VRI), Créteil, France
- Hôpital Saint Louis, INSERM U944, Université de Paris, Paris, France
| | - Yves Lévy
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- AP-HP, Hôpital H. Mondor—A. Chenevier, Service d'immunologie clinique et maladies infectieuses, Créteil, France
| | - Nabila Seddiki
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- * E-mail:
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Feder AF, Kline C, Polacino P, Cottrell M, Kashuba ADM, Keele BF, Hu SL, Petrov DA, Pennings PS, Ambrose Z. A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host. PLoS Pathog 2017; 13:e1006358. [PMID: 28542550 PMCID: PMC5444849 DOI: 10.1371/journal.ppat.1006358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/17/2017] [Indexed: 12/25/2022] Open
Abstract
The process by which drug-resistant HIV-1 arises and spreads spatially within an infected individual is poorly understood. Studies have found variable results relating how HIV-1 in the blood differs from virus sampled in tissues, offering conflicting findings about whether HIV-1 throughout the body is homogeneously distributed. However, most of these studies sample only two compartments and few have data from multiple time points. To directly measure how drug resistance spreads within a host and to assess how spatial structure impacts its emergence, we examined serial sequences from four macaques infected with RT-SHIVmne027, a simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT), and treated with RT inhibitors. Both viral DNA and RNA (vDNA and vRNA) were isolated from the blood (including plasma and peripheral blood mononuclear cells), lymph nodes, gut, and vagina at a median of four time points and RT was characterized via single-genome sequencing. The resulting sequences reveal a dynamic system in which vRNA rapidly acquires drug resistance concomitantly across compartments through multiple independent mutations. Fast migration results in the same viral genotypes present across compartments, but not so fast as to equilibrate their frequencies immediately. The blood and lymph nodes were found to be compartmentalized rarely, while both the blood and lymph node were more frequently different from mucosal tissues. This study suggests that even oft-sampled blood does not fully capture the viral dynamics in other parts of the body, especially the gut where vRNA turnover was faster than the plasma and vDNA retained fewer wild-type viruses than other sampled compartments. Our findings of transient compartmentalization across multiple tissues may help explain the varied results of previous compartmentalization studies in HIV-1.
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Affiliation(s)
- Alison F. Feder
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Christopher Kline
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Patricia Polacino
- Washington National Primate Research Center, University of Washington, Seattle, WA, United States
| | - Mackenzie Cottrell
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Angela D. M. Kashuba
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Shiu-Lok Hu
- Washington National Primate Research Center, University of Washington, Seattle, WA, United States
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Zandrea Ambrose
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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3
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Choi JY, Chaillon A, Oh JO, Ahn JY, Ann HW, Jung IY, Ahn MY, Jeon YD, Ku NS, Smith DM, Kim JM. HIV migration between blood plasma and cellular subsets before and after HIV therapy. J Med Virol 2015; 88:606-13. [PMID: 26348372 DOI: 10.1002/jmv.24375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2015] [Indexed: 01/29/2023]
Abstract
The cellular source of HIV RNA circulating in blood plasma remains unclear. Here, we investigated whether sequence analysis of HIV RNA populations circulating before combination antiretroviral therapy (cART) and HIV DNA populations in cellular subsets (CS) after cART could identify the cellular sources of circulating HIV RNA. Blood was collected from five subjects at cART initiation and again 6 months later. Naïve CD4+ T cells, resting central memory and effector memory CD4+ T cells, activated CD4+ T cells, monocytes, and natural killer cells were sorted using a fluorescence-activated cell sorter. HIV-1 env C2V3 sequences from HIV RNA in blood plasma and HIV DNA in CSs were generated using single genome sequencing. Sequences were evaluated for viral compartmentalization (Fst test) and migration events (MEs; Slatkin Maddison and cladistic measures) between blood plasma and each CS. Viral compartmentalization was observed in 88% of all cellular subset comparisons (range: 77-100% for each subject). Most observed MEs were directed from blood plasma to CSs (52 MEs, 85.2%). In particular, there was only viral movement from plasma to NK cells (15 MEs), monocytes (seven MEs), and naïve cells (five ME). We observed a total of nine MEs from activated CD4 cells (2/9 MEs), central memory T cells (3/9 MEs), and effector memory T cells (4/9 MEs) to blood plasma. Our results revealed that the HIV RNA population in blood plasma plays an important role in seeding various cellular reservoirs and that the cellular source of the HIV RNA population is activated central memory and effector memory T cells.
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Affiliation(s)
- Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Antoine Chaillon
- Department of Medicine, University of California San Diego, La Jolla, California.,Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Jin Ok Oh
- AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Jin Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Hae Won Ann
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - In Young Jung
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Mi-Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yong Duk Jeon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Nam Su Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Davey M Smith
- Department of Medicine, University of California San Diego, La Jolla, California.,Veterans Affairs San Diego Healthcare System, San Diego, California
| | - June Myung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
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Pena-Cruz V, Etemad B, Chatziandreou N, Nyein PH, Stock S, Reynolds SJ, Laeyendecker O, Gray RH, Serwadda D, Lee SJ, Quinn TC, Sagar M. HIV-1 envelope replication and α4β7 utilization among newly infected subjects and their corresponding heterosexual partners. Retrovirology 2013; 10:162. [PMID: 24369910 PMCID: PMC3883469 DOI: 10.1186/1742-4690-10-162] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/10/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Previous studies suggest that active selection limits the number of HIV-1 variants acquired by a newly infected individual from the diverse variants circulating in the transmitting partner. We compared HIV-1 envelopes from 9 newly infected subjects and their linked transmitting partner to explore potential mechanisms for selection. RESULTS Recipient virus envelopes had significant genotypic differences compared to those present in the transmitting partner. Recombinant viruses incorporating pools of recipient and transmitter envelopes showed no significant difference in their sensitivity to receptor and fusion inhibitors, suggesting they had relatively similar entry capacity in the presence of low CD4 and CCR5 levels. Aggregate results in primary cells from up to 4 different blood or skin donors showed that viruses with envelopes from the transmitting partner as compared to recipient envelopes replicated more efficiently in CD4+ T cells, monocyte derived dendritic cell (MDDC) - CD4+ T cell co-cultures, Langerhans cells (LCs) - CD4+ T cell co-cultures and CD4+ T cells expressing high levels of the gut homing receptor, α4β7, and demonstrated greater binding to α4β7 high / CD8+ T cells. These transmitter versus recipient envelope virus phenotypic differences, however, were not always consistent among the primary cells from all the different blood or skin donation volunteers. CONCLUSION Although genotypically unique variants are present in newly infected individuals compared to the diverse swarm circulating in the chronically infected transmitting partner, replication in potential early target cells and receptor utilization either do not completely dictate this genetic selection, or these potential transmission phenotypes are lost very soon after HIV-1 acquisition.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Manish Sagar
- Department of Medicine, Division of Infectious Diseases, Boston University, Boston, MA, USA.
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5
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Kent SJ, Reece JC, Petravic J, Martyushev A, Kramski M, De Rose R, Cooper DA, Kelleher AD, Emery S, Cameron PU, Lewin SR, Davenport MP. The search for an HIV cure: tackling latent infection. THE LANCET. INFECTIOUS DISEASES 2013; 13:614-21. [PMID: 23481675 DOI: 10.1016/s1473-3099(13)70043-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Strategies to eliminate infectious HIV that persists despite present treatments and with the potential to cure HIV infection are of great interest. One patient seems to have been cured of HIV infection after receiving a bone marrow transplant with cells resistant to the virus, although this strategy is not viable for large numbers of infected people. Several clinical trials are underway in which drugs are being used to activate cells that harbour latent HIV. In a recent study, investigators showed that activation of latent HIV infection in patients on antiretroviral therapy could be achieved with a single dose of vorinostat, a licensed anticancer drug that inhibits histone deacetylase. Although far from a cure, such studies provide some guidance towards the logical next steps for research. Clinical studies that use a longer duration of drug dosing, alternative agents, combination approaches, gene therapy, and immune-modulation approaches are all underway.
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Affiliation(s)
- Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, VIC, Australia.
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6
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Skar H, Gutenkunst RN, Wilbe Ramsay K, Alaeus A, Albert J, Leitner T. Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality. PLoS One 2011; 6:e21747. [PMID: 21829600 PMCID: PMC3149046 DOI: 10.1371/journal.pone.0021747] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 06/06/2011] [Indexed: 01/29/2023] Open
Abstract
The molecular evolution of HIV-1 is characterized by frequent substitutions, indels and recombination events. In addition, a HIV-1 population may adapt through frequency changes of its variants. To reveal such population dynamics we analyzed HIV-1 subpopulation frequencies in an untreated patient with stable, low plasma HIV-1 RNA levels and close to normal CD4+ T-cell levels. The patient was intensively sampled during a 32-day period as well as approximately 1.5 years before and after this period (days −664, 1, 2, 3, 11, 18, 25, 32 and 522). 77 sequences of HIV-1 env (approximately 3100 nucleotides) were obtained from plasma by limiting dilution with 7–11 sequences per time point, except day −664. Phylogenetic analysis using maximum likelihood methods showed that the sequences clustered in six distinct subpopulations. We devised a method that took into account the relatively coarse sampling of the population. Data from days 1 through 32 were consistent with constant within-patient subpopulation frequencies. However, over longer time periods, i.e. between days 1…32 and 522, there were significant changes in subpopulation frequencies, which were consistent with evolutionarily neutral fluctuations. We found no clear signal of natural selection within the subpopulations over the study period, but positive selection was evident on the long branches that connected the subpopulations, which corresponds to >3 years as the subpopulations already were established when we started the study. Thus, selective forces may have been involved when the subpopulations were established. Genetic drift within subpopulations caused by de novo substitutions could be resolved after approximately one month. Overall, we conclude that subpopulation frequencies within this patient changed significantly over a time period of 1.5 years, but that this does not imply directional or balancing selection. We show that the short-term evolution we study here is likely representative for many patients of slow and normal disease progression.
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Affiliation(s)
- Helena Skar
- Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Karin Wilbe Ramsay
- Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Annette Alaeus
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Jan Albert
- Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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7
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Whitney JB, Hraber PT, Luedemann C, Giorgi EE, Daniels MG, Bhattacharya T, Rao SS, Mascola JR, Nabel GJ, Korber BT, Letvin NL. Genital tract sequestration of SIV following acute infection. PLoS Pathog 2011; 7:e1001293. [PMID: 21379569 PMCID: PMC3040679 DOI: 10.1371/journal.ppat.1001293] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 01/13/2011] [Indexed: 11/18/2022] Open
Abstract
We characterized the evolution of simian immunodeficiency virus (SIV) in the male genital tract by examining blood- and semen-associated virus from experimentally and sham vaccinated rhesus monkeys during primary infection. At the time of peak virus replication, SIV sequences were intermixed between the blood and semen supporting a scenario of high-level virus “spillover” into the male genital tract. However, at the time of virus set point, compartmentalization was apparent in 4 of 7 evaluated monkeys, likely as a consequence of restricted virus gene flow between anatomic compartments after the resolution of primary viremia. These findings suggest that SIV replication in the male genital tract evolves to compartmentalization after peak viremia resolves. Methods to reduce the transmission of HIV-1 are hindered by a lack of information regarding early viral dynamics and evolution in the male genital tract. In the present study, we show that SIV in the blood and genital tract are homogeneous during early infection, indicating facile virus gene flow between these compartments. Importantly, the coincidence of the resolution of primary viremia with the decreased virus levels in genital secretions suggest that the dramatic fall in virus replication during early infection underlies the development of viral compartmentalization. Our demonstration of early virus compartmentalization in the male genital tract has important implications for the understanding of early events leading to infection of the male genital tract and the nature of the transmitted virus during primary retrovirus infection.
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Affiliation(s)
- James B Whitney
- Division of Viral Pathogenesis, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.
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8
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Abstract
DESIGN the origin and evolution of HIV-1 in breast milk is unclear, despite the continuing significance of this tissue as a transmitting compartment. To elucidate the evolutionary trajectory of viral populations in a transient mucosal compartment, longitudinal sequences of the envelope glycoprotein (gp120) region from plasma and breast milk spanning the first year after delivery were analyzed in six women infected by HIV-1 subtype C. METHODS multiple phylogenetic algorithms were used to elucidate the evolutionary history and spatial structure of virus populations between tissues. RESULTS overall persistent mixing of viral sequences between plasma and breast milk indicated that breast milk is not a distinct genetic viral compartment. Unexpectedly, longitudinal phylogenies showed multiple lineages defined by long branches that included virus from both the breast milk and the plasma. Plasma was unlikely the anatomical origin of the most recent common ancestor (MRCA) in at least three of the patients, although in other women, the temporal origin of the MRCA of the viral populations following delivery occurred well before the onset of breast milk production. CONCLUSIONS these findings suggest that during pregnancy/lactation, a viral variant distinct from the plasma virus initially seeds the breast milk, followed by subsequent gene flow between the plasma and breast milk tissues. This study indicates the potential for reactivation or reintroduction of distinct lineages during major immunological disruptions during the course of natural infection.
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9
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Padhi A, Ross H, Terwee J, VandeWoude S, Poss M. Profound differences in virus population genetics correspond to protection from CD4 decline resulting from feline lentivirus coinfection. Viruses 2010; 2:2663-80. [PMID: 21994636 PMCID: PMC3185597 DOI: 10.3390/v2122663] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 11/25/2010] [Accepted: 11/29/2010] [Indexed: 11/25/2022] Open
Abstract
CD4 decline is a hallmark of disease onset in individuals infected with Feline Immunodeficiency Virus (FIV) or Human Immunodeficiency Virus type 1 (HIV-1). Cats that are infected with a poorly replicating, apathogenic FIV (PLV) prior to exposure to a virulent FIV strain (FIVC) maintain CD4 numbers by mechanisms that are not correlated with a measurable adaptive immune response or reduction in circulating viral load. We employed population genetic approaches based on the 3′ portion of the viral genome to estimate the population structure of FIVC from single and dual infected cats. In dual infected cats, FIVC effective population size was decreased during the initial viral expansion phase, and after three weeks of infection, the population declined sharply. The FIVC population recovered to pre-bottleneck levels approximately seven weeks post-FIVC infection. However, the population emerging from the bottleneck in dual infected cats was distinct based on estimates of temporal population structure and substitution profiles. The transition to transversion rate ratio (κ) increased from early to late phases in dual infected cats due primarily to a decrease in transversions whereas in single infected cats, κ declined over time. Although one clone with extensive G to A substitutions, indicative of host cytidine deaminase editing, was recovered from a dual infected cat during the bottleneck, the post bottleneck population had an overall reduction in G to A substitutions. These data are consistent with a model of PLV-induced host restriction, putatively involving host DNA editing, that alters the dynamics of FIVC throughout the course of infection leading to disease attenuation.
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Affiliation(s)
- Abinash Padhi
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; E-Mail:
| | - Howard Ross
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand; E-Mail:
| | - Julie Terwee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft. Collins, CO 80523, USA; E-Mails: (J.T.); (S.V.)
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft. Collins, CO 80523, USA; E-Mails: (J.T.); (S.V.)
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; E-Mail:
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
- 208 Mueller Lab, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-814-867 1213, Fax: +1-814-865 9131
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10
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Saksena NK, Wang B, Zhou L, Soedjono M, Ho YS, Conceicao V. HIV reservoirs in vivo and new strategies for possible eradication of HIV from the reservoir sites. HIV AIDS (Auckl) 2010; 2:103-22. [PMID: 22096389 PMCID: PMC3218690 DOI: 10.2147/hiv.s6882] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Even though the treatment of human immunodeficiency virus (HIV)-infected individuals with highly active antiretroviral therapy (HAART) provides a complete control of plasma viremia to below detectable levels (<40 copies/mL plasma), there is an unequal distribution of all antiretroviral drugs across diverse cellular and anatomic compartments in vivo. The main consequence of this is the acquisition of resistance by HIV to all known classes of currently prescribed antiretroviral drugs and the establishment of HIV reservoirs in vivo. HIV has a distinct advantage of surviving in the host via both pre-and postintegration latency. The postintegration latency is caused by inert and metabolically inactive provirus, which cannot be accessed either by the immune system or the therapeutics. This integrated provirus provides HIV with a safe haven in the host where it is incessantly challenged by its immune selection pressure and also by HAART. Thus, the provirus is one of the strategies for viral concealment in the host and the provirus can be rekindled, through unknown stimuli, to create progeny for productive infection of the host. Thus, the reservoir establishment remains the biggest impediment to HIV eradication from the host. This review provides an overview of HIV reservoir sites and discusses both the virtues and problems associated with therapies/strategies targeting these reservoir sites in vivo.
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Affiliation(s)
- Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, The University of Sydney, Westmead, NSW, Sydney, Australia
| | - Bin Wang
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, The University of Sydney, Westmead, NSW, Sydney, Australia
| | - Li Zhou
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, The University of Sydney, Westmead, NSW, Sydney, Australia
| | - Maly Soedjono
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, The University of Sydney, Westmead, NSW, Sydney, Australia
| | - Yung Shwen Ho
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, The University of Sydney, Westmead, NSW, Sydney, Australia
| | - Viviane Conceicao
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, The University of Sydney, Westmead, NSW, Sydney, Australia
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11
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Abstract
Current antiretroviral therapy regimens can effectively suppress HIV in patients for prolonged periods of time, but do not constitute a cure, since they are incapable of eradicating viral reservoirs. It is, therefore, necessary for us to refocus on the partially understood pathogenesis of HIV, on the issue of viral persistence, and on the development of strategies for a temporally contained therapy capable of purging HIV from the body. Macrophages play a pivotal role in all three of these scenarios. This review summarizes important aspects of macrophage biology as they relate to HIV and discusses conceptual challenges for virus suppression and eradication in this cell type. We highlight a number of significant recent advances in understanding differences in HIV replication and pharmacotherapy between macrophages and CD4 T cells, as well as the role of macrophages in various aspects of the disease process and in different anatomical compartments. Finally, the importance of infected macrophages in the persistence of HIV, regarding both pathogenesis and advancement of eradication strategies, is discussed.
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Affiliation(s)
- Stephanie Venzke
- Department of Virology, University of Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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12
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Shi B, Kitchen C, Weiser B, Mayers D, Foley B, Kemal K, Anastos K, Suchard M, Parker M, Brunner C, Burger H. Evolution and recombination of genes encoding HIV-1 drug resistance and tropism during antiretroviral therapy. Virology 2010; 404:5-20. [PMID: 20451945 DOI: 10.1016/j.virol.2010.04.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 02/15/2010] [Accepted: 04/12/2010] [Indexed: 02/04/2023]
Abstract
Characterization of residual plasma virus during antiretroviral therapy (ART) is a high priority to improve understanding of HIV-1 pathogenesis and therapy. To understand the evolution of HIV-1 pol and env genes in viremic patients under selective pressure of ART, we performed longitudinal analyses of plasma-derived pol and env sequences from single HIV-1 genomes. We tested the hypotheses that drug resistance in pol was unrelated to changes in coreceptor usage (tropism), and that recombination played a role in evolution of viral strains. Recombinants were identified by using Bayesian and other computational methods. High-level genotypic resistance was seen in approximately 70% of X4 and R5 strains during ART. There was no significant association between resistance and tropism. Each patient displayed at least one recombinant encompassing env and representing a change in predicted tropism. These data suggest that, in addition to mutation, recombination can play a significant role in shaping HIV-1 evolution.
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Affiliation(s)
- Binshan Shi
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
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13
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Hayward JJ, Rodrigo AG. The distribution of feline immunodeficiency virus in tissue compartments of feral domestic cats. Arch Virol 2010; 155:411-6. [PMID: 20112119 DOI: 10.1007/s00705-010-0598-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 12/21/2009] [Indexed: 11/28/2022]
Affiliation(s)
- Jessica J Hayward
- Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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14
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Shanmugasundaram U, Solomon S, Shanmugam S, Murugavel KG, Nagalingeswaran K, Solomon SS, Mayer KH, Pachamuthu B. HIV-I reverse transcriptase variation in plasma and genital secretion of antiretroviral-naive females. ACTA ACUST UNITED AC 2009; 8:375-8. [PMID: 19822735 DOI: 10.1177/1545109709347374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The reverse transcriptase (RT) enzyme of HIV type 1 (HIV-1) is largely targeted by the host immune selection pressure and would differ in the anatomical compartments, thereby having a drastic impact on viral quasi-species evolution. The HIV-1 RT region sequenced from plasma and genital secretions of 8 antiretroviral treatment (ART)-naive females was analyzed for the pattern of amino acid mutations and the ratio of synonymous and nonsynonymous substitutions to determine whether it is under different selection pressure in both the compartments. Phylogenetic and mutational analysis of the HIV-1 RT in plasma and genital secretions of HIV-1-infected ART-naive females showed limited variation likely reflecting the absence of differential selection pressure and therefore genetic variation in these compartments.
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15
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Hayward JJ, Rodrigo AG. Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus). Vet Immunol Immunopathol 2009; 134:68-74. [PMID: 19896220 DOI: 10.1016/j.vetimm.2009.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Studying the evolutionary mechanisms of feline immunodeficiency virus in the domestic cat (Felis catus), FIV(Fca), provides a good comparison to other lentiviruses, such as HIV and FIV(Pco) in the cougar (Puma concolor). We review the current epidemiological and evolutionary findings of FIV(Fca). In addition to the five accepted FIV(Fca), subtypes, several recent phylogenetic studies have found strains that form separate clades, indicative of novel subtypes. In New Zealand cats, these strains of unknown subtype have been found to be involved in complex patterns of intergenic recombination, and whole genome sequences are required to resolve these. Evidence of recombination events has been documented with the highest levels in the env gene, the region involved in host cell receptor recognition. Several cases of FIV(Fca) multiple infections, both inter- and intra-subtype, have been reported. The findings of both unknown subtypes and relatively high levels of recombination suggest the need for further testing of the current vaccine. Limited studies on the evolutionary rate of FIV(Fca) document a value twice to three times that of FIV in the cougar, a result suggesting the different levels of co-adaptation between the viruses and their respective hosts. We studied the tissue distribution of FIV(Fca) in feral domestic cats, finding the first case of FIV compartmentalisation, a phenomenon well documented in HIV-1 patients.
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Affiliation(s)
- Jessica J Hayward
- Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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16
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Heeregrave EJ, Geels MJ, Brenchley JM, Baan E, Ambrozak DR, van der Sluis RM, Bennemeer R, Douek DC, Goudsmit J, Pollakis G, Koup RA, Paxton WA. Lack of in vivo compartmentalization among HIV-1 infected naïve and memory CD4+ T cell subsets. Virology 2009; 393:24-32. [PMID: 19698967 PMCID: PMC2753733 DOI: 10.1016/j.virol.2009.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 06/29/2009] [Accepted: 07/13/2009] [Indexed: 11/28/2022]
Abstract
Viral compartmentalization between naïve and memory CD4(+) T cell subsets has been described, but only for individuals who were receiving antiretroviral therapy (ART). We present here an extensive analysis of the viral quasispecies residing in the naïve, central and effector memory CD4(+) T cell subsets in a number of therapy naïve individuals and representing an array of HIV-1 subtypes. We longitudinally analyzed subset-specific infection and evolution in a subtype B infected individual who switches from CCR5 to dual CCR5/CXCR4 coreceptor usage. We show that the central memory subset, the predominantly infected subset, harbors a more diverse viral population compared to the others. Through sequence analysis of the env C2V3 region we demonstrate a lack of viral compartmentalization among all subsets. Upon coreceptor switch we observe a pronounced increase in the infection level of the naïve population. Our findings emphasize the importance of all CD4(+) T cell subsets to viral evolution.
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Affiliation(s)
- Edwin J. Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Mark J. Geels
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - Elly Baan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - David R. Ambrozak
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - Renee M. van der Sluis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Rune Bennemeer
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | | | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | - Richard A. Koup
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, USA
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
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17
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Genetic characterization of hepatitis B virus in peripheral blood leukocytes: evidence for selection and compartmentalization of viral variants with the immune escape G145R mutation. J Virol 2009; 83:9983-92. [PMID: 19420079 DOI: 10.1128/jvi.01905-08] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The compartmentalization of viral variants in distinct host tissues is a frequent event in many viral infections. Although hepatitis B virus (HBV) classically is considered hepatotropic, it has strong lymphotropic properties as well. However, unlike other viruses, molecular evolutionary studies to characterize HBV variants in compartments other than hepatocytes or sera have not been performed. The present work attempted to characterize HBV sequences from the peripheral blood leukocytes (PBL) of a large set of subjects, using advanced molecular biology and computational methods. The results of this study revealed the exclusive compartmentalization of HBV subgenotype Ae/A2-specific sequences with a potent immune escape G145R mutation in the PBL of the majority of the subjects. Interestingly, entirely different HBV genotypes/subgenotypes (C, D, or Aa/A1) were found to predominate in the sera of the same study populations. These results suggest that subgenotype Ae/A2 is selectively archived in the PBL, and the high prevalence of G145R indicates high immune pressure and high evolutionary rates of HBV DNA in the PBL. The results are analogous to available literature on the compartmentalization of other viruses. The present work thus provides evidence in favor of the compartment-specific abundance, evolution, and emergence of the potent immune escape mutant. These findings have important implications in the field of HBV molecular epidemiology, transmission, transfusion medicine, organ transplantation, and vaccination strategies.
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18
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Lawrence P, Berlier W, Delezay O, Palle S, Olivier T, Saoudin H, Mottin S, Lucht F, Pozzetto B, Bourlet T. Construction and tropism characterisation of recombinant viruses exhibiting HIV-1 env gene from seminal strains. Virology 2009; 386:373-9. [PMID: 19232661 DOI: 10.1016/j.virol.2009.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 12/06/2008] [Accepted: 01/21/2009] [Indexed: 11/27/2022]
Abstract
Genetic differences between blood and mucosal-derived HIV-1 strains have been widely reported. As amplification of HIV-1 strains from mucosal samples including semen or saliva by co-culture has low sensitivity, we developed the construction of chimeric viruses expressing wild-type seminal HIV-1 envelope protein. Chimeric viruses were produced by co-transfection of a V1-V3 deleted pNL 43 vector and PCR fragments spanning the deleted region, amplified from HIV-1 RNA positive seminal plasma samples. After an initial testing of co-receptor usage by a tropism recombinant test, replication capacity and amplification of these recombinant viruses were assessed using PBMC. Four chimeric replicative strains, all using CXCR4 as coreceptor, were produced. The interaction between cell-free viral particles and reporter cell lines was assessed by confocal microscopy. These replicative chimeras exhibiting HIV-1 env from seminal strains represent useful tools for the in vitro study of the heterosexual transmission of HIV-1 and testing of microbicide activity.
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Affiliation(s)
- Philip Lawrence
- Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP-EA 3064), Faculté de Médecine J. Lisfranc, Université Jean Monnet, IFRESIS et CHU de Saint-Etienne, 15 rue Ambroise Paré, 42023 Saint-Etienne cedex 02, France
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19
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Pisoni G, Moroni P, Turin L, Bertoni G. Compartmentalization of small ruminant lentivirus between blood and colostrum in infected goats. Virology 2007; 369:119-30. [PMID: 17719071 DOI: 10.1016/j.virol.2007.06.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 05/31/2007] [Accepted: 06/21/2007] [Indexed: 11/15/2022]
Abstract
The compartmentalization of small ruminant lentivirus (SRLV) subtype A (Maedi-Visna virus) and B (caprine arthritis-encephalitis virus) variants was analyzed in colostrum and peripheral blood mononuclear cells of four naturally infected goats. Sequence analysis of DNA and RNA encompassing the V4-V5 env regions showed a differential distribution of SRLV variants between the two compartments. Tissue-specific compartmentalization was demonstrated by phylogenetic analysis in three of the four cases. In these animals colostrum proviral sequences were clustered relative to the blood viral sequences. In one goat, the blood and colostrum-derived provirus sequences were intermingled, suggesting trafficking of virus between the two tissues or mirroring a recent infection. Surprisingly, the pattern of free virus variants in the colostrum of all animals corresponded only partially to that of the proviral form, suggesting that free viruses might not derive from infected colostral cells. The compartmentalization of SRLV between peripheral blood and colostrum indicates that lactogenic transmission may involve specific viruses not present in the proviral populations circulating in the blood.
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Affiliation(s)
- Giuliano Pisoni
- Department of Veterinary Pathology, Hygiene and Public Health, University of Milano, via Celoria 10, 20133 Milano, Italy.
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20
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Chomont N, Hocini H, Grésenguet G, Brochier C, Bouhlal H, Andréoletti L, Becquart P, Charpentier C, de Dieu Longo J, Si-Mohamed A, Kazatchkine MD, Bélec L. Early archives of genetically-restricted proviral DNA in the female genital tract after heterosexual transmission of HIV-1. AIDS 2007; 21:153-62. [PMID: 17197805 DOI: 10.1097/qad.0b013e328011f94b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES AND METHOD In order to characterize human immunodeficiency virus type 1 (HIV-1) variants that are transmitted in women via heterosexual intercourse, the env V1-V3 sequences of HIV-1 provirus (DNA) and free virus (RNA) in paired samples of blood and cervicovaginal secretions of untreated chronically and primary infected African women were compared. RESULTS Env RNA sequences retrieved from plasma and genital compartments formed a single cluster in primary infection. In contrast, env RNA sequences from these two compartments were distinct in chronically infected women. Analysis of proviral DNA of primary infected women showed that most HIV-1 sequences derived from the genital epithelia form independent clusters from HIV-1 sequences of DNA from peripheral blood mononuclear cells and RNA recovered from plasma and genital secretions. Similarly, the analysis of proviral DNA in the genital compartment of chronically infected women showed the persistence of genetically-restricted cluster of HIV-1. CONCLUSIONS These observations indicate that a viral subpopulation is archived as proviral DNA in the female genital tract early in primary infection, and suggest that HIV-1 variants from the male donor are selected in the female mucosal site during male to female transmission of HIV-1.
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Affiliation(s)
- Nicolas Chomont
- Université Paris V, Unité INSERM Internationale d'Immunologie Humaine U743, Equipe Immunité et Biothérapie Muqueuse, Centre de Recherches Biomédicales des Cordeliers, and Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
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21
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Tu YB, Zhou T, Yuan XF, Qiu HJ, Xue F, Sun CQ, Wang L, Wu DL, Peng JM, Kong XG, Tong GZ. Long terminal repeats are not the sole determinants of virulence for equine infectious anemia virus. Arch Virol 2006; 152:209-18. [PMID: 16932982 DOI: 10.1007/s00705-006-0830-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 06/30/2006] [Indexed: 10/24/2022]
Abstract
The long terminal repeats (LTRs) of equine infectious anemia virus donkey leukocyte-attenuated virus (EIAV-DLA) were substituted with those of the wild-type EIAV-L (wt EIAV-L, the parent virus of EIAV-DLA). The resulting chimeric plasmid was designated pOK-LTR DLA/L. Purified pOK-LTR DLA/L was transfected into monocyte-derived macrophage (MDM) cultures prepared from EIAV-negative, heparinized whole blood from a donkey. Eighth-passage cell cultures developed the typical cytopathogenic effects (CPE) of EIAV infection, and virions with typical EIAV profiles were observed with an electron microscope. Horses were inoculated with the chimeric virus or EIAV-DLA and challenged with the wt EIAV-L strain six months later. All of the horses inoculated with either the chimeric virus or EIAV-DLA were protected from disease, whereas the control horses died with typical EIA symptoms.
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Affiliation(s)
- Y-B Tu
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, PR China
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22
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Chen MF, Westmoreland S, Ryzhova EV, Martín-García J, Soldan SS, Lackner A, González-Scarano F. Simian immunodeficiency virus envelope compartmentalizes in brain regions independent of neuropathology. J Neurovirol 2006; 12:73-89. [PMID: 16798669 DOI: 10.1080/13550280600654565] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) gp160s obtained from the brain are often genetically distinct from those isolated from other organs, suggesting the presence of brain-specific selective pressures or founder effects that result in the compartmentalization of viral quasi-species. Whereas HIV has also been found to compartmentalize within different regions of the brain, the extent of brain-regional compartmentalization of SIV in rhesus macaques has not been characterized. Furthermore, much is still unknown about whether phenotypic differences exist in envelopes from different brain regions. To address these questions, env DNA sequences were amplified from four SIVmac239-infected macaques and subjected to phylogenetic and phenetic analysis. The authors demonstrated that sequences from different areas of the brain form distinct clades, and that the long-term progressing macaques demonstrated a greater degree of regional compartmentalization compared to the rapidly progressing macaques. In addition, regional compartmentalization occurred regardless of the presence of giant-cell encephalitis. Nucleotide substitution rates at synonymous and nonsynonymous sites (ds:dn rates) indicated that positive selection varied among envelopes from different brain regions. In one macaque, envelopes from some but not all brain regions acquired changes in a conserved CD4-binding motif GGGDPE at amino acids 382 to 387. Furthermore, gp160s with the mutation G383E were able to mediate cell-to-cell fusion in a CD4-independent manner and were more susceptible to fusion inhibition by pooled plasma from infected macaques. Reversion of this mutation by site-directed mutagenesis resulted in reduction of CD4-independence and resistance to fusion inhibition in cell fusion assays. These studies demonstrate that SIV evolution within the brain results in a heterogeneous viral population with different phenotypes among different regions.
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Affiliation(s)
- Maria F Chen
- Department of Neurology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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23
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Yang CF, Chen HY, Jorba J, Sun HC, Yang SJ, Lee HC, Huang YC, Lin TY, Chen PJ, Shimizu H, Nishimura Y, Utama A, Pallansch M, Miyamura T, Kew O, Yang JY. Intratypic recombination among lineages of type 1 vaccine-derived poliovirus emerging during chronic infection of an immunodeficient patient. J Virol 2005; 79:12623-34. [PMID: 16188964 PMCID: PMC1235840 DOI: 10.1128/jvi.79.20.12623-12634.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 07/20/2005] [Indexed: 11/20/2022] Open
Abstract
We determined the complete genomic sequences of nine type 1 immunodeficient vaccine-derived poliovirus (iVDPV) isolates obtained over a 337-day period from a poliomyelitis patient from Taiwan with common variable immunodeficiency. The iVDPV isolates differed from the Sabin type 1 oral poliovirus vaccine (OPV) strain at 1.84% to 3.15% of total open reading frame positions and had diverged into at least five distinct lineages. Phylogenetic analysis suggested that the chronic infection was initiated by the fifth and last OPV dose, given 567 days before onset of paralysis, and that divergence of major lineages began very early in the chronic infection. Key determinants of attenuation in Sabin 1 had reverted in the iVDPV isolates, and representative isolates of each lineage showed increased neurovirulence for PVR-Tg21 transgenic mice. None of the isolates had retained the temperature-sensitive phenotype of Sabin 1. All isolates were antigenic variants of Sabin 1, having multiple amino acid substitutions within or near neutralizing antigenic sites 1, 2, and 3a. Antigenic divergence of the iVDPV variants from Sabin 1 followed two major independent evolutionary pathways. The emergence of distinct coreplicating lineages suggests that iVDPVs can replicate for many months at separate sites in the gastrointestinal tract. Some isolates had mosaic genome structures indicative of recombination across and within lineages. iVDPV excretion apparently ceased after 30 to 35 months of chronic infection. The appearance of a chronic VDPV excretor in a tropical, developing country has important implications for the strategy to stop OPV immunization after eradication of wild polioviruses.
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Affiliation(s)
- Chen-Fu Yang
- Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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24
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Ewing G, Nicholls G, Rodrigo A. Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations. Genetics 2005; 168:2407-20. [PMID: 15611198 PMCID: PMC1448755 DOI: 10.1534/genetics.104.030411] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a Bayesian statistical inference approach for simultaneously estimating mutation rate, population sizes, and migration rates in an island-structured population, using temporal and spatial sequence data. Markov chain Monte Carlo is used to collect samples from the posterior probability distribution. We demonstrate that this chain implementation successfully reaches equilibrium and recovers truth for simulated data. A real HIV DNA sequence data set with two demes, semen and blood, is used as an example to demonstrate the method by fitting asymmetric migration rates and different population sizes. This data set exhibits a bimodal joint posterior distribution, with modes favoring different preferred migration directions. This full data set was subsequently split temporally for further analysis. Qualitative behavior of one subset was similar to the bimodal distribution observed with the full data set. The temporally split data showed significant differences in the posterior distributions and estimates of parameter values over time.
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Affiliation(s)
- Greg Ewing
- Allan Wilson Centre for Molecular Ecology and Evolution, Bioinformatics Institute, University of Auckland, Auckland, New Zealand 1020
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25
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Iversen AKN, Learn GH, Skinhøj P, Mullins JI, McMichael AJ, Rambaut A. Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected woman. AIDS 2005; 19:990-3. [PMID: 15905685 DOI: 10.1097/01.aids.0000171418.91786.ad] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Pillai SK, Good B, Pond SK, Wong JK, Strain MC, Richman DD, Smith DM. Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. J Virol 2005; 79:1734-42. [PMID: 15650198 PMCID: PMC544119 DOI: 10.1128/jvi.79.3.1734-1742.2005] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) in the male genital tract may comprise virus produced locally in addition to virus transported from the circulation. Virus produced in the male genital tract may be genetically distinct, due to tissue-specific cellular characteristics and immunological pressures. HIV-1 env sequences derived from paired blood and semen samples from the Los Alamos HIV Sequence Database were analyzed to ascertain a male genital tract-specific viral signature. Machine learning algorithms could predict seminal tropism based on env sequences with accuracies exceeding 90%, suggesting that a strong genetic signature does exist for virus replicating in the male genital tract. Additionally, semen-derived viral populations exhibited constrained diversity (P < 0.05), decreased levels of positive selection (P < 0.025), decreased CXCR4 coreceptor utilization, and altered glycosylation patterns. Our analysis suggests that the male genital tract represents a distinct selective environment that contributes to the apparent genetic bottlenecks associated with the sexual transmission of HIV-1.
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Affiliation(s)
- Satish K Pillai
- University of California, San Diego, Division of Biological Sciences, 9500 Gilman Dr., MC 0679, La Jolla, CA 92093, USA.
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27
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Philpott S, Burger H, Tsoukas C, Foley B, Anastos K, Kitchen C, Weiser B. Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination. J Virol 2005; 79:353-63. [PMID: 15596829 PMCID: PMC538688 DOI: 10.1128/jvi.79.1.353-363.2005] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different sites within one individual have rarely been documented. We compared full-length HIV-1 RNA sequences in the plasma and female genital tract, focusing on a woman with high HIV-1 RNA loads in each compartment who had been infected heterosexually and then transmitted HIV-1 by the same route. We cloned and sequenced 10 full-length HIV-1 RNA genomes from her genital tract and 10 from her plasma. We also compared viral genomes from the genital tract and plasma of four additional heterosexually infected women, sequencing 164 env and gag clones obtained from the two sites. Four of five women, including the one whose complete viral sequences were determined, displayed compartmentalized HIV-1 genomes. Analyses of full-length, compartmentalized sequences made it possible to document complex intrapatient HIV-1 recombinants that were composed of alternating viral sequences characteristic of each site. These findings demonstrate that the genital tract and blood harbor genetically distinct populations of replicating HIV-1 and provide evidence that recombination between strains from the two compartments contributes to rapid evolution of viral sequence variation in infected individuals.
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Affiliation(s)
- Sean Philpott
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
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28
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Fulcher JA, Hwangbo Y, Zioni R, Nickle D, Lin X, Heath L, Mullins JI, Corey L, Zhu T. Compartmentalization of human immunodeficiency virus type 1 between blood monocytes and CD4+ T cells during infection. J Virol 2004; 78:7883-93. [PMID: 15254161 PMCID: PMC446117 DOI: 10.1128/jvi.78.15.7883-7893.2004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Distinct sequences of human immunodeficiency virus type 1 (HIV-1) have been found between different tissue compartments or subcompartments within a given tissue. Whether such compartmentalization of HIV-1 occurs between different cell populations is still unknown. Here we address this issue by comparing HIV-1 sequences in the second constant region through the fifth hypervariable region (C2 to V5) of the surface envelope glycoprotein (Env) between viruses in purified blood CD14(+) monocytes and CD4(+) T cells obtained longitudinally from five infected patients over a time period ranging from 117 to 3,409 days postseroconversion. Viral populations in both cell types at early infection time points appeared relatively homogeneous. However, later in infections, all five patients showed heterogeneous populations in both CD14(+) monocytes and CD4(+) T cells. Three of the five patients had CD14(+) monocyte populations with significantly more genetic diversity than the CD4(+) T-cell population, while the other two patients had more genetic diversity in CD4(+) T cells. The cellular compartmentalization of HIV-1 between CD14(+) monocytes and CD4(+) T cells was not seen early during infections but was evident at the later time points for all five patients, indicating an association of viral compartmentalization with the time course of HIV-1 infection. The majority of HIV-1 V3 sequences indicated a macrophage-tropic phenotype, while a V3 sequence-predicted T-cell tropic virus was found in the CD4(+) T cells and CD14(+) monocytes of two patients. These findings suggest that HIV-1 in CD14(+) monocytes could disseminate and evolve independently from that in CD4(+) T cells over the course of HIV-1 infection, which may have implications on the development of new therapeutic strategies.
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Affiliation(s)
- Jennifer A Fulcher
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195-8070, USA
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29
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Tirado G, Jove G, Kumar R, Noel RJ, Reyes E, Sepulveda G, Yamamura Y, Kumar A. Differential virus evolution in blood and genital tract of HIV-infected females: evidence for the involvement of drug and non-drug resistance-associated mutations. Virology 2004; 324:577-86. [PMID: 15207642 DOI: 10.1016/j.virol.2004.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 01/30/2004] [Accepted: 04/09/2004] [Indexed: 11/19/2022]
Abstract
There is increasing evidence that male or female genital tract represent a distinct replication compartment for human immunodeficiency virus type 1 (HIV-1) and that such compartments may serve as a virus reservoir. Forty-four paired plasma and vaginal samples from HIV-infected females undergoing HAART were collected to examine the viral responses to antiretroviral therapy and to assess the possible role of the vaginal tract as a reservoir for drug-resistant variants. Twenty-one females had detectable viral RNA both in plasma and vaginal fluid, whereas 14 females had detectable virus only in plasma. Twelve paired samples were used to analyze HIV-1 pol sequences for the presence of drug resistance-associated mutations. Nine of the twelve paired samples exhibited discordant drug resistance mutation patterns. The other three females showed identical drug resistance-associated mutations. However, further examination of protease and RT showed numerous non-drug-associated mutations that corresponded to predefined CTL epitopes. These non-drug-associated mutations were different between plasma and vaginal viruses, suggesting that evolution of HIV-1 was independent in these two compartments.
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Affiliation(s)
- Grissell Tirado
- Laboratory of Viral Immunology, Ponce School of Medicine, Ponce 00732, Puerto Rico
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30
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Sanjuán R, Codoñer FM, Moya A, Elena SF. Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region. Evolution 2004; 58:1185-94. [PMID: 15266969 DOI: 10.1111/j.0014-3820.2004.tb01699.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The existence of organ-specific HIV-1 populations within infected hosts has been studied for many years; nonetheless results reported by different authors are somewhat discrepant. To tackle this problem, we used a population genetics approach to analyze previously published data from the V3 hypervariable region of the envelope env gene. Our results are compatible with a population subdivision by organs in 95% of individuals analyzed at autopsy. In addition, populations infecting the nervous system and testicles clearly appear as differentiated subsets of the so-called macrophage-tropic variants. Liver and kidney may harbor differentiated populations as well. Although it is widely accepted that organ compartmentalization arises as a consequence of different selective pressures imposed by different organs, a definitive demonstration has not yet been provided. Our analysis of the pattern of synonymous and nonsynonymous nucleotide substitutions provides evidence supporting this hypothesis, without discarding the role of other evolutionary processes. In contrast, positive selection does not seem to be the mechanism responsible for the evolution of patient-specific sequences.
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Affiliation(s)
- Rafael Sanjuán
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, 46071 València, Spain
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31
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Daniels RS, Wilson P, Patel D, Longhurst H, Patterson S. Analysis of full-length HIV type 1 env genes indicates differences between the virus infecting T cells and dendritic cells in peripheral blood of infected patients. AIDS Res Hum Retroviruses 2004; 20:409-13. [PMID: 15157359 DOI: 10.1089/088922204323048159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dendritic cells (DC) are targets for HIV-1 infection and may harbor distinct populations of virus variants. To test this hypothesis full length env genes have been amplified and sequenced from DC and T cells purified from the blood of five symptomatic HIV-1-infected patients. For three of the patients, showing slow and slow/standard disease progression, distinct subsets of HIV variants infected DC and T cells, and the diversity of the DC-derived env genes was less than that observed in T cells. Amino acid substitutions differentiating DC and T cell variants were dispersed throughout the length of the glycoproteins and were patient/HIV-1 strain specific. However, the V1 and V2 domains of T cell-derived clones were generally shorter than those from DC. These findings suggest that there may be distinct populations of HIV-1 variants infecting blood DC and T cells in patients showing slow and slow/standard disease progression.
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Affiliation(s)
- R S Daniels
- Virology Division, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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32
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Tsui R, Herring BL, Barbour JD, Grant RM, Bacchetti P, Kral A, Edlin BR, Delwart EL. Human immunodeficiency virus type 1 superinfection was not detected following 215 years of injection drug user exposure. J Virol 2004; 78:94-103. [PMID: 14671091 PMCID: PMC303392 DOI: 10.1128/jvi.78.1.94-103.2004] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evidence for human immunodeficiency virus type 1 (HIV-1) superinfection was sought among 37 HIV-1-positive street-recruited active injection drug users (IDUs) from the San Francisco Bay area. HIV-1 sequences from pairs of samples collected 1 to 12 years apart, spanning a total of 215 years of exposure, were generated at p17 gag, the V3-V5 region of env, and/or the first exon of tat and phylogenetically analyzed. No evidence of HIV-1 superinfection was detected in which a highly divergent HIV-1 variant emerged at a frequency >20% of the serum viral quasispecies. Based on the reported risk behavior of the IDUs and the HIV-1 incidence in uninfected subjects in the same cohort, a total of 3.4 new infections would have been expected if existing infection conferred no protection from superinfection. Adjusted for risk behaviors, the estimated relative risk of superinfection compared with initial infection was therefore 0.0 (95% confidence interval, 0.00, 0.79; P = 0.02), indicating that existing infection conferred a statistically significant level of protection against superinfection with an HIV-1 strain of the same subtype, which was between 21 and 100%.
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Affiliation(s)
- Rose Tsui
- Blood Systems Research Institute, University of California, San Francisco, San Francisco, California, USA
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33
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Sanjuán R, Codoñer FM, Moya A, Elena SF. NATURAL SELECTION AND THE ORGAN-SPECIFIC DIFFERENTIATION OF HIV-1 V3 HYPERVARIABLE REGION. Evolution 2004. [DOI: 10.1554/03-577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Poumbourios P, Maerz AL, Drummer HE. Functional evolution of the HIV-1 envelope glycoprotein 120 association site of glycoprotein 41. J Biol Chem 2003; 278:42149-60. [PMID: 12923196 DOI: 10.1074/jbc.m305223200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein-protein interaction surfaces can exhibit structural plasticity, a mechanism whereby an interface adapts to mutations as binding partners coevolve. The HIV-1 envelope glycoprotein gp120-gp41 complex, which is responsible for receptor attachment and membrane fusion, represents an extreme example of a coevolving complex as up to 35% amino acid sequence divergence has been observed in these proteins among HIV-1 isolates. In this study, the function of conserved gp120 contact residues, Leu593, Trp596, Gly597, Lys601, and Trp610 within the disulfide-bonded region of gp41, was examined in envelope glycoproteins derived from diverse HIV-1 isolates. We found that the gp120-gp41 association function of the disulfide-bonded region is conserved. However, the contribution of individual residues to gp41 folding and/or stability, gp120-gp41 association, membrane fusion function, and viral entry varied from isolate to isolate. In gp120-gp41 derived from the dual-tropic isolate, HIV-189.6, the importance of Trp596 for fusion function was dependent on the chemokine receptor utilized as a fusion cofactor. Thus, the engagement of alternative chemokine receptors may evoke distinct fusion-activation signals involving the site of gp120-gp41 association. An examination of chimeric glycoproteins revealed that the isolate-specific functional contributions of particular gp120-contact residues are influenced by the sequence of gp120 hypervariable regions 1, 2, and 3. These data indicate that the gp120-gp41 association site is structurally and functionally adaptable, perhaps to maintain a functional glycoprotein complex in a setting of host selective pressures driving the rapid coevolution of gp120 and gp41.
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Affiliation(s)
- Pantelis Poumbourios
- Virology Unit, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia.
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35
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Kemal KS, Foley B, Burger H, Anastos K, Minkoff H, Kitchen C, Philpott SM, Gao W, Robison E, Holman S, Dehner C, Beck S, Meyer WA, Landay A, Kovacs A, Bremer J, Weiser B. HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation. Proc Natl Acad Sci U S A 2003; 100:12972-7. [PMID: 14557540 PMCID: PMC240729 DOI: 10.1073/pnas.2134064100] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Worldwide, 90% of HIV-1 infections are transmitted heterosexually. Because the genital mucosa are the sites of initial contact with HIV-1 for most exposed individuals, study of the virus from the genital tract is critical for the development of vaccines and therapeutics. Previous analyses of HIV-1 in various tissues have documented compartmentalization of viral genomes. Whether compartmentalization was associated with viral phenotypic differences or immune status, however, was not well understood. We compared HIV-1 gp120 env sequences from the genital tract and plasma of 12 women. Eight women displayed compartmentalized HIV-1 RNA genomes, with viral sequences from each site that were clearly discrete, yet phylogenetically related. The remaining four exhibited env sequences that were intermingled between the two sites. Women with compartmentalized HIV-1 genomes had higher CD4+ cell counts than those displaying intermingled strains (P = 0.02). Intrapatient HIV-1 recombinants comprising sequences that were characteristic of both sites were identified. We next compared viral phenotypes in each compartment. HIV-1 coreceptor usage was often compartmentalized (P 0.01). The number of N-linked glycosylation sites, associated with neutralization resistance, also differed between compartments (P < 0.01). Furthermore, disparities between the density of gp120 glycosylations in each compartment correlated with higher CD4+ counts (P = 0.03). These data demonstrate that the genital tract and plasma can harbor populations of replicating HIV-1 with different phenotypes. The association of higher CD4+ cell counts with compartmentalization of viral genomes and density of gp120 glycosylations suggests that the immune response influences the development of viral genotypes in each compartment. These findings are relevant to the prevention and control of HIV-1 infection.
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Affiliation(s)
- Kimdar Sherefa Kemal
- New York State Department of Health, Wadsworth Center, 120 New Scotland Avenue, Albany, NY 12208, USA
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36
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Reis JKP, Craigo JK, Cook SJ, Issel CJ, Montelaro RC. Characterization of EIAV LTR variability and compartmentalization in various reservoir tissues of long-term inapparent carrier ponies. Virology 2003; 311:169-80. [PMID: 12832214 DOI: 10.1016/s0042-6822(03)00168-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Dynamic genomic variation resulting in changes in envelope antigenicity has been established as a fundamental mechanism of persistence by equine infectious anemia virus (EIAV), as observed with other lentiviruses, including HIV-1. In addition to the reported changes in envelope sequences, however, certain studies indicate the viral LTR as a second variable EIAV gene, with the enhancer region being designated as hypervariable. These observations have lead to the suggestion that LTR variation may alter viral replication properties to optimize to the microenvironment of particular tissue reservoirs. To test this hypothesis directly, we examined the population of LTR quasispecies contained in various tissues of two inapparent carrier ponies experimentally infected with a reference EIAV biological clone for 18 months. The results of these studies demonstrated that the EIAV LTR is in fact highly conserved with respect to the infecting LTR species after 1.5 years of persistent infection and regardless of the tissue reservoir. Thus, these comprehensive analyses demonstrate for the first time that the EIAV LTR is highly conserved during long-term persistent infection and that the observed variations in viral LTR are associated more with in vitro adaptation to replication in cultured cells rather than in vivo replication in natural target cells.
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Affiliation(s)
- Jenner K P Reis
- Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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