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Ebbert MTW, Mallory MA, Wilson AR, Dooley SK, Hillyard DR. Application of a new informatics tool for contamination screening in the HIV sequencing laboratory. J Clin Virol 2013; 57:249-53. [PMID: 23583427 DOI: 10.1016/j.jcv.2013.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/14/2013] [Accepted: 03/16/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND Current HIV-1 sequencing-based methods for detecting drug resistance-associated mutations are open and susceptible to contamination. Informatic identification of clinical sequences that are nearly identical to one another may indicate specimen-to-specimen contamination or another laboratory-associated issue. OBJECTIVES To design an informatic tool to rapidly identify potential contamination in the clinical laboratory using sequence analysis and to establish reference ranges for sequence variation in the HIV-1 protease and reverse transcriptase regions among a U.S. patient population. STUDY DESIGN We developed an open-source tool named HIV Contamination Detection (HIVCD). HIVCD was utilized to make pairwise comparisons of nearly 8000 partial HIV-1 pol gene sequences from patients across the United States and to calculate percent identities (PIDs) for each pair. ROC analysis and standard deviations of PID data were used to determine reference ranges for between-patient and within-patient comparisons and to guide selection of a threshold for identifying abnormally high PID between two unrelated sequences. RESULTS The PID reference range for between-patient comparisons ranged from 83.8 to 95.7% while within-patient comparisons ranged from 96 to 100%. Interestingly, 48% of between-patient sequence pairs with a PID>96.5 were geographically related. The selected threshold for abnormally high PIDs was 96 (AUC=0.993, sensitivity=0.980, specificity=0.999). During routine use, HIVCD identified a specimen mix-up and the source of contamination of a negative control. CONCLUSIONS In our experience, HIVCD is easily incorporated into laboratory workflow, useful for identifying potential laboratory errors, and contributes to quality testing. This type of analysis should be incorporated into routine laboratory practice.
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Affiliation(s)
- Mark T W Ebbert
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA.
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2
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Heath L, Frenkel LM, Foley BT, Mullins JI. Comment on "The origins of sexually transmitted HIV among men who have sex with men". Sci Transl Med 2011; 2:50le1; author reply 50lr1. [PMID: 20861507 DOI: 10.1126/scitranslmed.3001416] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Whether HIV from seminal cells or free HIV in semen is the origin of transmitted virus has important implications for the design of transmission prevention strategies. We found that a recent claim that HIV originates from seminal plasma and not from seminal cells was erroneous, because it was based on biological specimens that had been mislabeled, mixed-up, or contaminated. The origin of transmitted virus from semen therefore remains an open question.
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3
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Shapshak P, Kangueane P, Fujimura RK, Commins D, Chiappelli F, Singer E, Levine AJ, Minagar A, Novembre FJ, Somboonwit C, Nath A, Sinnott JT. Editorial neuroAIDS review. AIDS 2011; 25:123-41. [PMID: 21076277 PMCID: PMC4464840 DOI: 10.1097/qad.0b013e328340fd42] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Paul Shapshak
- Division of Infectious Disease, Department of Internal Medicine, Tampa General Hospital, Tampa, Florida, USA
- Department of Psychiatry and Behavioral Medicine, University of South Florida, College of Medicine, Tampa, Florida, USA
| | - Pandjassarame Kangueane
- Biomedical Informatics, 17A lrulan Sundai Annex, Pondicherry, India
- AIMST University, Kedha, Malaysia
| | - Robert K. Fujimura
- Geriatric Research Education and Clinical Centers, Veterans Administration, Puget Sound Healthcare System, Seattle, Washington
| | - Deborah Commins
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles
| | | | - Elyse Singer
- Department of Neurology and National Neurological AIDS Bank, UCLA School of Medicine, Westwood, California
| | - Andrew J. Levine
- Department of Neurology and National Neurological AIDS Bank, UCLA School of Medicine, Westwood, California
| | - Alireza Minagar
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, Louisiana
| | | | - Charurut Somboonwit
- Division of Infectious Disease, Department of Internal Medicine, Tampa General Hospital, Tampa, Florida, USA
- Clinical Research Unit, Hillsborough Health Department, Tampa, Florida
| | - Avindra Nath
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - John T. Sinnott
- Division of Infectious Disease, Department of Internal Medicine, Tampa General Hospital, Tampa, Florida, USA
- Clinical Research Unit, Hillsborough Health Department, Tampa, Florida
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4
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Li L, Liang S, Chen L, Liu W, Li H, Liu Y, Bao Z, Wang Z, Zhuang D, Liu S, Li J. Genetic characterization of 13 subtype CRF01_AE near full-length genomes in Guangxi, China. AIDS Res Hum Retroviruses 2010; 26:699-704. [PMID: 20528151 DOI: 10.1089/aid.2010.0026] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Guangxi is an important transit area for HIV transmission in South China. Characterization of the full-length genome of HIV-1 prevalent in the area is important for phylogenetic analysis and vaccine development. CRF01_AE is one of the most rapidly spreading subtypes in Guangxi. In this study, we reported thirteen near full-length CRF01_AE genomes from Guangxi, China. The nearly full-length genome was reverse transcripted and amplified in two halves with the 1-kb overlap regions. The PCR products were sequenced directly. The sequence analysis showed that all of 13 strains were CRF01_AE recombinant subtypes. Two clusters were set up with all of the sequences that grouped separately with sequences from Vietnam and Fujian, China, which strongly suggested multiple introductions of CRF01_AE strains into Guangxi province. The results will improve our understanding on the phylogenetic relationship of CRF01_AE strains in South China and also help in the development of a successful HIV vaccine.
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Affiliation(s)
- Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shujia Liang
- GuangXi Center for Disease Prevention and Control, Nanning, China
| | - Lili Chen
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Blood Transfusion, Urumqi General Hospital of Lanzhou Military Region, PLA, Urumqi, China
| | - Wei Liu
- GuangXi Center for Disease Prevention and Control, Nanning, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zheng Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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5
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Li L, Chen L, Yang S, Liu Y, Li H, Bao Z, Wang Z, Zhuang D, Liu S, Li J. Near full-length genomic characterization of a novel HIV type 1 subtype B/C recombinant strain from Yunnan, China. AIDS Res Hum Retroviruses 2010; 26:711-6. [PMID: 20528150 DOI: 10.1089/aid.2010.0001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombination contributes substantially to the genetic diversity of HIV-1, and mosaic strains arise frequently, especially in populations in which multiple subtypes circulate. Yunnan, which borders the "Golden triangle" region of Southeast Asia in the south, was considered as the epicenter of China. B, CRF01_AE, CRF07_BC, and CRF08_BC are all currently involved in the HIV-1 epidemiology in the area, which suggested the possible emergence of a new recombination. This study presented a near full-length genomic analysis of a novel HIV-1 recombination involving B and C. Different from the reported CRF07_BC and CRF08_BC, the new recombination revealed more breakpoints. This is the first report of a novel recombination involving subtype B and C in Yunnan, China. More work is needed to determine the epidemiologic significance of the new recombination.
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Affiliation(s)
- Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lili Chen
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Blood Transfusion, Urumqi General Hospital of Lanzhou Military Region, PLA, Urumqi 830000, China
| | | | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zheng Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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6
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Genetic linkage of hepatitis B virus in peripheral blood leukocytes provides evidence for contamination. J Virol 2010; 84:2184-6. [PMID: 20097886 DOI: 10.1128/jvi.02263-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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7
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Moreau I, Levis J, Crosbie O, Kenny-Walsh E, Fanning LJ. Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a. Virol J 2008; 5:78. [PMID: 18613968 PMCID: PMC2483966 DOI: 10.1186/1743-422x-5-78] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/09/2008] [Indexed: 12/25/2022] Open
Abstract
Pre-treatment HCV quasispecies complexity and diversity may predict response to interferon based anti-viral therapy. The objective of this study was to retrospectively (1) examine temporal changes in quasispecies prior to the start of therapy and (2) investigate extensively quasispecies evolution in a group of 10 chronically infected patients with genotype 3a, treated with pegylated α2a-Interferon and ribavirin. The degree of sequence heterogeneity within the hypervariable region 1 was assessed by analyzing 20–30 individual clones in serial serum samples. Genetic parameters, including amino acid Shannon entropy, Hamming distance and genetic distance were calculated for each sample. Treatment outcome was divided into (1) sustained virological responders (SVR) and (2) treatment failure (TF). Our results indicate, (1) quasispecies complexity and diversity are lower in the SVR group, (2) quasispecies vary temporally and (3) genetic heterogeneity at baseline can be use to predict treatment outcome. We discuss the results from the perspective of replicative homeostasis.
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Affiliation(s)
- Isabelle Moreau
- Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, Clinical Sciences Building, Cork University Hospital, Cork, Ireland.
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8
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Diem K, Nickle DC, Motoshige A, Fox A, Ross S, Mullins JI, Corey L, Coombs RW, Krieger JN. Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). AIDS Res Hum Retroviruses 2008; 24:561-71. [PMID: 18426336 DOI: 10.1089/aid.2007.0115] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We present phylogenetic evidence supporting viral compartmentalization between the blood (peripheral blood mononuclear cells or plasma) and multiple genitourinary sites in HIV-infected men. Four of the five subjects evaluated demonstrated compartmentalization of viral sequences between urogenital tract specimens (tissue or fluid) and at least one blood category. HIV sequence migration from blood to urogenital tract was detected in four of five men, with migration from urogenital tract to blood in the fifth, and cross migration between both compartments noted in one man. These observations add 5 additional cases to the 27 total reported cases in which male urogenital tract compartmentalization has been studied, investigate surgical samples/specimens that have not been evaluated previously, and provide further evidence for restricted flow of HIV between the blood and the genital tract. As such, our study findings are important for understanding the long-term response to antiretroviral therapy, the design of vaccines, and the sexual transmission of HIV.
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Affiliation(s)
- Kurt Diem
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | - David C. Nickle
- Department of Microbiology, University of Washington, Seattle, Washington 98195
| | - Alexis Motoshige
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | - Alan Fox
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | - Susan Ross
- Department of Urology, University of Washington, Seattle, Washington 98195
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington 98195
| | - Lawrence Corey
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | - Robert W. Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | - John N. Krieger
- Department of Urology, University of Washington, Seattle, Washington 98195
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9
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Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Kaslow RA, Shepherd JC, Margolick JB, Mullins JI. HIV Type 1 Superinfection with a Dual-Tropic Virus and Rapid Progression to AIDS: A Case Report. Clin Infect Dis 2007; 45:501-9. [PMID: 17638203 DOI: 10.1086/520024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 04/20/2007] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The occurrence of human immunodeficiency virus type 1 (HIV-1) superinfection has implications for vaccine development and our understanding of HIV pathogenesis and transmission. METHODS AND RESULTS We describe a subject from the Multicenter AIDS Cohort Study who was superinfected with a dual-tropic (CXCR4/CCR5-utilizing) HIV-1 subtype B strain between 0.8 and 1.3 years after seroconversion who had rapid progression to AIDS; the subject developed Pneumocystis pneumonia 3.4 years after seroconversion, as well as multiple other opportunistic infections. The superinfecting strain rapidly became the predominant population virus, suggesting that the initial and superinfecting viruses in this individual differed in virulence. However, we found no molecular epidemiological evidence in the HIV database to suggest that this strain had been found in other individuals. In addition, this subject's HIV-1 viral load and pattern of human leukocyte antigen and coreceptor polymorphisms only partially explained his rapid disease progression. CONCLUSIONS Additional studies are needed to determine whether superinfection itself and/or infection with a dual-tropic virus causes rapid disease progression, or whether certain individuals who are innately more susceptible to rapid disease progression also lack the ability to resist the challenge of a second infection. This case appears to support the latter hypothesis.
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Affiliation(s)
- Geoffrey S Gottlieb
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA 98195, USA.
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10
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Jobes DV, Daoust M, Nguyen VT, Padua A, Sinangil F, Pérez-Losada M, Crandall KA, Oliphant T, Posada D, Rambaut A, Fuchs J, Berman PW. Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial. AIDS Res Hum Retroviruses 2006; 22:968-78. [PMID: 17067266 PMCID: PMC1982842 DOI: 10.1089/aid.2006.22.968] [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: 11/12/2022] Open
Abstract
This study documents a case of coinfection (simultaneous infection of an individual with two or more strains) of two HIV-1 subtype B strains in an individual from a Phase 3 HIV-1 vaccine efficacy trial, conducted in North American and the Netherlands. We examined 86 full-length gp120 (env) gene sequences from this individual collected from nine different time points over a 20-month period. We estimated evolutionary relationships using maximum likelihood and Bayesian methods and inferred recombination breakpoints and recombinant sequences using phylogenetic and substitutional methods. These analyses identified two strongly supported monophyletic clades (clades A and B) of 14 and 69 sequences each and a small paraphyletic recombinant clade of three sequences. We then studied the genetic characteristics of these lineages by comparing estimates of genetic diversity generated by mutation and recombination and adaptive selection within a coalescent and maximum likelihood framework. Our results suggest significant differences on the evolutionary dynamics of these strains. We then discuss the implications of these results for vaccine development.
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Affiliation(s)
- David V Jobes
- VaxGen, Inc., South San Francisco, California 94080, USA.
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11
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Sanabani S, Kleine Neto W, Kalmar EMN, Diaz RS, Janini LM, Sabino EC. Analysis of the near full length genomes of HIV-1 subtypes B, F and BF recombinant from a cohort of 14 patients in São Paulo, Brazil. INFECTION GENETICS AND EVOLUTION 2006; 6:368-77. [PMID: 16522378 DOI: 10.1016/j.meegid.2006.01.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 01/04/2006] [Accepted: 01/06/2006] [Indexed: 11/20/2022]
Abstract
The human immune deficiency virus (HIV) exhibits strikingly tremendous amount of genetic variability. Such feature is critically important for the virus to adapt to environmental changes by escaping the host immune system and by escaping candidate vaccine. Therefore, understanding of such diversity is fundamental for the design of successful drugs or vaccine, which is urgently needed to bring the HIV/AIDS epidemic under control. In this study, we investigated the magnitude of diversity of the HIV-1 near full-length genomes from patients previously assigned as infected with non-recombinant HIV-1 subtypes B and F1 variants based on small portion of viral genome. HIV-1 proviral DNA was extracted from 14 samples previously classified in our laboratory as six subtypes B and eight subtypes F on the basis of small amplicon sequencing. Reamplifications of DNA from these samples were carried out by an overlapping PCR followed by direct sequencing. The data were phylogenetically inferred. Sequence analysis revealed that two out of six partially identified subtype B and six out of eight partially identified subtype F were in fact BF recombinants throughout their full genomes. Two pairs BF recombinants had identical genomic recombination structure and distinct from the Argentinean CRF 12_BF strains, probably represents a novel circulating recombinant forms in Brazil. Our data provided new genetic material of some of the HIV-1 subtypes currently circulating in the country and points to the widespread of BF recombinants which are expected to change the epidemic nature by approaching the level of subtype B in Brazil.
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12
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Sanabani S, Neto WK, de Sa Filho DJ, Diaz RS, Munerato P, Janini LM, Sabino EC. Full-length genome analysis of human immunodeficiency virus type 1 subtype C in Brazil. AIDS Res Hum Retroviruses 2006; 22:171-6. [PMID: 16478399 DOI: 10.1089/aid.2006.22.171] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The most prevalent HIV-1 clade in the global epidemics is C, and this clade is also becoming important in the Brazilian epidemics. In this study, we characterized HIV-1 subtype C variants by sequencing their near full-length genomes. DNA was extracted from six samples previously classified in our laboratory as subtype C on the basis of partial genome sequencing. Amplification was carried out by overlapping PCR followed by direct sequencing. Phylogenetic analysis of full length genomes confirmed that all isolates belonged to subtype C, which formed a highly supported monophyletic cluster and showed a nucleotide distance of 5.4%. The core promoter of all isolates contained three NF-kappaB binding motifs. Our results suggest that subtype C viruses circulating in Brazil were likely introduced recently from a unique point source. The independent clustering of Brazilian subtype C on the phylogenetic tree suggests the profile of an ideal local candidate for the development of a single subtype vaccine.
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Affiliation(s)
- Sabri Sanabani
- Molecular Biology Laboratory, Fundação Pro-Sangue, Hemocentro de São Paulo Brazil, Av. Dr. Eneas de Carvalho Aguiar, 155 1o andar, São Paulo, Brazil
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13
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Sundaravaradan V, Hahn T, Ahmad N. Conservation of functional domains and limited heterogeneity of HIV-1 reverse transcriptase gene following vertical transmission. Retrovirology 2005; 2:36. [PMID: 15918905 PMCID: PMC1166575 DOI: 10.1186/1742-4690-2-36] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Accepted: 05/26/2005] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The reverse transcriptase (RT) enzyme of human immunodeficiency virus type 1 (HIV-1) plays a crucial role in the life cycle of the virus by converting the single stranded RNA genome into double stranded DNA that integrates into the host chromosome. In addition, RT is also responsible for the generation of mutations throughout the viral genome, including in its own sequences and is thus responsible for the generation of quasi-species in HIV-1-infected individuals. We therefore characterized the molecular properties of RT, including the conservation of functional motifs, degree of genetic diversity, and evolutionary dynamics from five mother-infant pairs following vertical transmission. RESULTS The RT open reading frame was maintained with a frequency of 87.2% in five mother-infant pairs' sequences following vertical transmission. There was a low degree of viral heterogeneity and estimates of genetic diversity in mother-infant pairs' sequences. Both mothers and infants RT sequences were under positive selection pressure, as determined by the ratios of non-synonymous to synonymous substitutions. Phylogenetic analysis of 132 mother-infant RT sequences revealed distinct clusters for each mother-infant pair, suggesting that the epidemiologically linked mother-infant pairs were evolutionarily closer to each other as compared with epidemiologically unlinked mother-infant pairs. The functional domains of RT which are responsible for reverse transcription, DNA polymerization and RNase H activity were mostly conserved in the RT sequences analyzed in this study. Specifically, the active sites and domains required for primer binding, template binding, primer and template positioning and nucleotide recruitment were conserved in all mother-infant pairs' sequences. CONCLUSION The maintenance of an intact RT open reading frame, conservation of functional domains for RT activity, preservation of several amino acid motifs in epidemiologically linked mother-infant pairs, and a low degree of genetic variability following vertical transmission is consistent with an indispensable role of RT in HIV-1 replication in infected mother-infant pairs.
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Affiliation(s)
- Vasudha Sundaravaradan
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
| | - Tobias Hahn
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
| | - Nafees Ahmad
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
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14
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Jaafar A, Massip P, Sandres-Sauné K, Souyris C, Pasquier C, Aquilina C, Izopet J. HIV therapy after treatment interruption in patients with multiple failure and more than 200 CD4+T lymphocyte count. J Med Virol 2004; 74:8-15. [PMID: 15258962 DOI: 10.1002/jmv.20139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The aim of the study was to investigate the safety and efficacy of a salvage therapy initiated after interrupting treatment in patients with virological failure and more than 200 CD4(+) T lymphocyte count. In this prospective study, 77 patients who received failing regimens had stopped completely all medication for 3 months before starting an optimised regimen consisting of 3-5 drugs. Patients were tested for HIV resistance before and after treatment interruption. Discontinuation of therapy for 3 months was associated with a median increase in HIV RNA of 1.1 log(10), a median decrease in CD4(+) T cell count of 136 x 10(6)/L and five clinical events related to HIV, but no AIDS-defining event. Eighty-seven percent of patients showed a shift from a drug resistant genotype to a wild-type genotype based on the major resistance mutations. Forty-seven percent of patients with a genotype shift reached fewer than 200 HIV RNA copies/ml of plasma 6 and 12 months after treatment resumption whereas none of those without a genotype shift did so (P = 0.03). However, the genotypic shift was not associated with a sustained virological response by multivariate analysis. The use of a new therapeutic class of compound in the salvage regimen was the only predictor of the sustained virological response. Salvage therapy with 3-5 drugs after interrupting treatment for 3 months can be a safe and effective strategy provided the HIV disease is not too advanced. Randomised trials in this population are needed to assess the clinical benefit of this strategy.
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Affiliation(s)
- Acil Jaafar
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse Cédex, France
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15
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Soares EAJM, Santos RP, Pellegrini JA, Sprinz E, Tanuri A, Soares MA. Epidemiologic and molecular characterization of human immunodeficiency virus type 1 in southern Brazil. J Acquir Immune Defic Syndr 2004; 34:520-6. [PMID: 14657764 DOI: 10.1097/00126334-200312150-00012] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HIV subtype C is the most prevalent subtype in the world. Despite its recent expansion in Brazil, HIV-1C already prevails in the southernmost state of Brazil, Rio Grande do Sul. This unique HIV epidemiology has prompted us to characterize that population. Seventy-seven HIV-1-infected subjects attending the largest HIV/AIDS clinic of the state had the protease and reverse transcriptase (RT) genes of their virus subtyped and genotyped. When subtype-specific infections were plotted according to year of diagnosis, the prevalence of subtype C was shown to increase over the last 18 years of the epidemic, along with a concomitant decrease of subtype B. Comparison of subtype C-infected treated and untreated subjects revealed amino acid differences in protease and RT, especially in the RT mutation D/G123S. The overall analysis of drug resistance mutations in viruses from treated subjects has highlighted some associations between subtypes and particular mutations, such as V82A/F/T/S in protease and subtype F1 and M41L and L210W in RT and subtype B. The characterization of this important population, which is one of a few in the developing world where a large number of HIV-1C-infected subjects are under antiretroviral treatment, underscores its potential usefulness in clinical, treatment, and vaccine trials in Brazil.
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Affiliation(s)
- Esmeralda A J M Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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16
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Gottlieb GS, Sow PS, Hawes SE, Ndoye I, Coll-Seck AM, Curlin ME, Critchlow CW, Kiviat NB, Mullins JI. Molecular epidemiology of dual HIV-1/HIV-2 seropositive adults from Senegal, West Africa. AIDS Res Hum Retroviruses 2003; 19:575-84. [PMID: 12908935 DOI: 10.1089/088922203322230941] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dual infection with HIV-1 and HIV-2 can occur in locales where these viruses co-circulate, most commonly in West Africa. Although dual seropositivity is common in this region, the true rate of dual infection remains unclear. In addition, whether unique HIV-1 subtypes are circulating in dually infected individuals is unknown. A cohort of 47 HIV-1 and HIV-2 dually seropositive individuals from Senegal, West Africa was screened for the presence of HIV-1 and HIV-2 gag and env PBMC viral DNA sequences using PCR. Of the 47 dual HIV-1/HIV-2 seropositive individuals tested, 19 (40.4%) had infection with both HIV-1 and HIV-2 confirmed by genetic sequence analysis, whereas only HIV-1 or HIV-2 was confirmed in 17 (36.2%) or 9 (19.1%), respectively. The majority of HIV-1 subtypes found were CRF-02 and A, although subtypes D, C, G, J and B were also found, reflecting the subtypes known to be circulating in Senegal. There was no significant difference in HIV-1 subtype distribution between individuals with confirmed dual infection and patients in this study with dual seropositivity but lacking HIV-2, or with HIV-1 infected patients within the general population in Senegal, although the study was underpowered to detect anything but large differences. The prevalence of HIV-1/HIV-2 dual infection appears to be significantly less than that of dually seropositive individuals and this likely reflects cross-reactive serology. The common HIV-1 subtypes prevalent in West Africa (CRF-02 and subtype A) have a similar distribution to those found in our cohort of dually infected and dually seropositive subjects.
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Affiliation(s)
- Geoffrey S Gottlieb
- Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.
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17
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Altfeld M, Addo MM, Shankarappa R, Lee PK, Allen TM, Yu XG, Rathod A, Harlow J, O'Sullivan K, Johnston MN, Goulder PJR, Mullins JI, Rosenberg ES, Brander C, Korber B, Walker BD. Enhanced detection of human immunodeficiency virus type 1-specific T-cell responses to highly variable regions by using peptides based on autologous virus sequences. J Virol 2003; 77:7330-40. [PMID: 12805431 PMCID: PMC164796 DOI: 10.1128/jvi.77.13.7330-7340.2003] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The antigenic diversity of human immunodeficiency virus type 1 (HIV-1) represents a significant challenge for vaccine design as well as the comprehensive assessment of HIV-1-specific immune responses in infected persons. In this study we assessed the impact of antigen variability on the characterization of HIV-1-specific T-cell responses by using an HIV-1 database to determine the sequence variability at each position in all expressed HIV-1 proteins and a comprehensive data set of CD8 T-cell responses to a reference strain of HIV-1 in infected persons. Gamma interferon Elispot analysis of HIV-1 clade B-specific T-cell responses to 504 overlapping peptides spanning the entire expressed HIV-1 genome derived from 57 infected subjects demonstrated that the average amino acid variability within a peptide (entropy) was inversely correlated to the measured frequency at which the peptide was recognized (P = 6 x 10(-7)). Subsequent studies in six persons to assess T-cell responses against p24 Gag, Tat, and Vpr peptides based on autologous virus sequences demonstrated that 29% (12 of 42) of targeted peptides were only detected with peptides representing the autologous virus strain compared to the HIV-1 clade B consensus sequence. The use of autologous peptides also allowed the detection of significantly stronger HIV-1-specific T-cell responses in the more variable regulatory and accessory HIV-1 proteins Tat and Vpr (P = 0.007). Taken together, these data indicate that accurate assessment of T-cell responses directed against the more variable regulatory and accessory HIV-1 proteins requires reagents based on autologous virus sequences. They also demonstrate that CD8 T-cell responses to the variable HIV-1 proteins are more common than previously reported.
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Affiliation(s)
- Marcus Altfeld
- Partners AIDS Research Center and Infectious Disease Unit, Massachusetts General Hospital, and Division of AIDS, Harvard Medical School, Boston, Massachusetts, USA
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18
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Soares MA, De Oliveira T, Brindeiro RM, Diaz RS, Sabino EC, Brigido L, Pires IL, Morgado MG, Dantas MC, Barreira D, Teixeira PR, Cassol S, Tanuri A. A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS 2003; 17:11-21. [PMID: 12478065 DOI: 10.1097/00002030-200301030-00004] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To characterize the subtype C strains of HIV type 1 that circulate in Brazil, especially those originated from the southern part of the country. DESIGN AND METHODS One hundred and twelve HIV-1-positive subjects had their plasma viral RNA extracted. Protease (PR) and reverse transcriptase (RT) genomic regions were polymerase chain reaction-amplified and sequenced for subtype determination. Subtype C strains were selected and compared to other strains of this subtype from the database, and specific amino acid signature patterns were searched. RESULTS Brazilian subtype C viruses form a very strong monophyletic group when compared to subtype C viruses from other countries and presented specific signature amino acids. Recombinants between subtype C and B viruses have been documented in areas of co-circulation. The incidence of primary PR and RT inhibitor resistance mutations in drug-naïve subjects was observed. An increasing number of secondary resistance mutations was also seen, some of which are characteristic of subtype C-related sequences. CONCLUSIONS Introduction of subtype C of HIV-1 in Brazil was likely a single event of one or a mixture of similarly related strains. Recombination between subtype C and B viruses is an ongoing process in the country. Primary and secondary drug resistance mutations were observed, although some of the secondary mutations could be associated with subtype C molecular signatures. Subtype-specific polymorphisms of PR and RT sequences found in this subtype C Brazilian variant might influence this emergence and have an impact on HIV treatment and on vaccine development in the country.
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Affiliation(s)
- Marcelo A Soares
- Laboratório de Virologia Molecular, Departamento de Genética, Universidade Federal do Rio de Janeiro, CCS - Bloco A - Cidade Universitária - Ilha do Fundão, 21944-970 Rio de Janeiro, RJ, Brazil
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19
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Izopet J, Souyris C, Sandres-Sauné K, Puissant B, Obadia M, Pasquier C, Puel J, Blancher A, Massip P. Virological and immunological effects of salvage therapy following treatment interruption and a shift in HIV-1 resistance genotype. J Med Virol 2002; 68:305-10. [PMID: 12226815 DOI: 10.1002/jmv.10204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The circulating human immunodeficiency virus type 1 (HIV-1) population of patients in whom many prior therapy regimens have failed often undergo a shift from a drug-resistant virus to a wild-type virus following interruption of treatment. This study analyses the virological and immunological effects of salvage therapy following treatment interruption and a shift from a drug-resistance genotype. Twenty-one HIV-1 infected patients who had genotype reversion by population-based sequencing after 3 months of treatment interruption were given a new salvage regimen consisting of 3-5 drugs selected according to their treatment history. Seven (33%) of 21 patients who had fewer than 200 HIV-1 RNA copies/ml until month 12 were defined as virological responders. Four patients were transient responders and 10 were nonresponders. The virological responders were more frequently CDC group A and had higher CD4 + T lymphocyte counts at the time of treatment resumption. The peripheral blood T CD4 + and T CD8 + lymphocyte populations of the patients declined significantly during treatment interruption. Only virological responders showed significant increases in their CD4 + T lymphocyte count 12 months after treatment resumption and these counts rapidly returned to pre-interruption baseline values in most of these patients. Treatment interruption could be useful for optimising salvage therapy for patients previously given many failing regimens. However, controlled trials are needed to assess the clinical benefit of this strategy.
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Affiliation(s)
- Jacques Izopet
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Place du Dr Baylac, Toulouse, France.
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20
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Metzker ML, Mindell DP, Liu XM, Ptak RG, Gibbs RA, Hillis DM. Molecular evidence of HIV-1 transmission in a criminal case. Proc Natl Acad Sci U S A 2002; 99:14292-7. [PMID: 12388776 PMCID: PMC137877 DOI: 10.1073/pnas.222522599] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gastroenterologist was convicted of attempted second-degree murder by injecting his former girlfriend with blood or blood-products obtained from an HIV type 1 (HIV-1)-infected patient under his care. Phylogenetic analyses of HIV-1 sequences were admitted and used as evidence in this case, representing the first use of phylogenetic analyses in a criminal court case in the United States. Phylogenetic analyses of HIV-1 reverse transcriptase and env DNA sequences isolated from the victim, the patient, and a local population sample of HIV-1-positive individuals showed the victim's HIV-1 sequences to be most closely related to and nested within a lineage comprised of the patient's HIV-1 sequences. This finding of paraphyly for the patient's sequences was consistent with the direction of transmission from the patient to the victim. Analysis of the victim's viral reverse transcriptase sequences revealed genotypes consistent with known mutations that confer resistance to AZT, similar to those genotypes found in the patient. A priori establishment of the patient and victim as a suspected transmission pair provided a clear hypothesis for phylogenetic testing. All phylogenetic models and both genes examined strongly supported the close relationship between the HIV-1 sequences of the patient and the victim. Resampling of blood from the suspected transmission pair and independent sequencing by different laboratories provided precaution against laboratory error.
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Affiliation(s)
- Michael L Metzker
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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21
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Peleg O, Brunak S, Trifonov EN, Nevo E, Bolshoy A. RNA secondary structure and squence conservation in C1 region of human immunodeficiency virus type 1 env gene. AIDS Res Hum Retroviruses 2002; 18:867-78. [PMID: 12201910 DOI: 10.1089/08892220260190353] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
We have analyzed amino acid, nucleotide sequence, and RNA secondary structure variability in the env gene of human immunodeficiency virus type (HIV-1). In applying algorithms for computing optimal RNA-folding patterns to a nonredundant data set of 178 env nucleotide sequences, we found a conserved RNA stem-loop structure in the first conserved (C1) region of the env gene. This detailed examination also revealed the known secondary structure conservation of the Rev-responsive element (RRE). This finding is also supported by a higher third position conservation of the translatable reading frame along these subregions. The typical folding of the C1 region consists of two isolated stem-loop structures. These highly conserved structures are likely to have a biological function. This assumption is supported by the conservation of the third position along the coding region of these structures. The third position retains a conservation level above what would be statistically expected.
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Affiliation(s)
- Ofer Peleg
- Genome Diversity Center, Institute of Evolution, Haifa University, Mt. Carmel, Haifa 31905, Israel
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22
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Quigg M, Frost SDW, McDonagh S, Burns SM, Clutterbuck D, McMillan A, Leen CS, Brown AJL. Association of Antiretroviral Resistance Genotypes with Response to Therapy – Comparison of Three Models. Antivir Ther 2002. [DOI: 10.1177/135965350200700303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Genotype-based resistance assays are commonly used to aid treatment in HIV-infected individuals failing anti-retroviral therapy. The relationship between genotype and antiretroviral therapy comes mostly from in vitro assays of the response to a single drugs although there is a need for a prediction of clinical response to combination therapy. We have compared three different methods of analysing genotype data as a predictor of clinical response in a small clinical cohort of highly antiretro-viral-experienced individuals failing therapy. No method performed well beyond 8 weeks into a new therapeutic regimen. A model based on the number of ‘primary’ mutations was statistically significant, but a multiple regression model, which identified specific mutations explained threefold more variation in response. Optimal prediction in this dataset was given by a model obtained from a classification tree analysis, in which genotype at amino acid sites 135 and 202 were combined with amino acid site 184, which explained over 50% of the deviance in the data and had a classification success of 86%.
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Affiliation(s)
- Marlynne Quigg
- Centre for HIV Research, Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
| | - Simon DW Frost
- Centre for HIV Research, Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | - Clifford S Leen
- Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
| | - Andrew J Leigh Brown
- Centre for HIV Research, Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
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23
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Shankarappa R, Chatterjee R, Learn GH, Neogi D, Ding M, Roy P, Ghosh A, Kingsley L, Harrison L, Mullins JI, Gupta P. Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: identification of features that distinguish subtype C sequences in India from other subtype C sequences. J Virol 2001; 75:10479-87. [PMID: 11581417 PMCID: PMC114623 DOI: 10.1128/jvi.75.21.10479-10487.2001] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2001] [Accepted: 08/02/2001] [Indexed: 11/20/2022] Open
Abstract
India is experiencing a rapid spread of human immunodeficiency virus type 1 (HIV-1), primarily through heterosexual transmission of subtype C viruses. To delineate the molecular features of HIV-1 circulating in India, we sequenced the V3-V4 region of viral env from 21 individuals attending an HIV clinic in Calcutta, the most populous city in the eastern part of the country, and analyzed these and the other Indian sequences in the HIV database. Twenty individuals were infected with viruses having a subtype C env, and one had viruses with a subtype A env. Analyses of 192 subtype C sequences that included one sequence for each subject from this study and from the HIV database revealed that almost all sequences from India, along with a small number from other countries, form a phylogenetically distinct lineage within subtype C, which we designate C(IN). Overall, C(IN) lineage sequences were more closely related to each other (level of diversity, 10.2%) than to subtype C sequences from Botswana, Burundi, South Africa, Tanzania, and Zimbabwe (range, 15.3 to 20.7%). Of the three positions identified as signature amino acid substitution sites for C(IN) sequences (K340E, K350A, and G429E), 56% of the C(IN) sequences contained all three amino acids while 87% of the sequences contained at least two of these substitutions. Among the non-C(IN) sequences, all three amino acids were present in 2%, while 22% contained two or more of these amino acids. These results suggest that much of the current Indian epidemic is descended from a single introduction into the country. Identification of conserved signature amino acid positions could assist epidemiologic tracking and has implications for the development of a vaccine against subtype C HIV-1 in India.
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Affiliation(s)
- R Shankarappa
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
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24
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Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17:911-23. [PMID: 11461677 DOI: 10.1089/088922201750290032] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) vif and vpr sequences were analyzed from four nontransmitting mothers (infected mothers who failed to transmit HIV-1 to their infants mainly in the absence of anti-retroviral therapy), including a mother with multiple deliveries, and compared with the vif and vpr sequences of five and six previously analyzed transmitting mothers, respectively. In contrast to a high functional conservation of vif and vpr genes in transmitting mother isolates, we found that there was a low degree of conservation of functional domains of these genes in nontransmitting (NT) mother isolates. For vif sequences, NT-2 contained stop codons and no initiation codons, whereas NT-1 sequences carried a substitution of a highly conserved tyrosine to histidine at position 30. In addition, NT-3 and NT-4 sequences contained additional substitutions, including asparagine at position 22, lysine at position 77 and histidine at position 110, that were absent in transmitting mother and consensus subtype B sequences. Similarly, the vpr sequences of NT-2 contained stop codons and no initiation codons, NT-4 contained a substitution of serine in place of alanine at position 30, some NT-1 sequences substituted arginine in place of glycine at position 75, and NT-3 sequences presented a deletion in the C terminus that was absent in transmitting mother and consensus subtype B sequences and is essential for Vpr function. Furthermore, vif and vpr sequences of nontransmitting mothers were less heterogeneous compared with transmitting mother sequences. In conclusion, a low degree of conservation of functional domains and heterogeneity of HIV-1 vif and vpr genes in these infected mothers correlates with lack of vertical transmission.
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Affiliation(s)
- V R Yedavalli
- Department of Microbiology and Immunology, College of Medicine, University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
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25
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Husain M, Hahn T, Yedavalli VR, Ahmad N. Characterization of HIV type 1 tat sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 2001; 17:765-73. [PMID: 11429117 DOI: 10.1089/088922201750237040] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) tat exon I sequences were analyzed from six mother-infant pairs after perinatal transmission. The tat open reading frame was maintained in 140 of the 154 clones analyzed, with a 90.9% frequency of intact tat open reading frames. In addition, a low degree of heterogeneity was observed in tat sequences within mothers, within infants, and between epidemiologically linked mother-infant pairs. However, the distances of tat sequences between epidemiologically unlinked individuals were greater than in epidemiologically linked mother-infant pairs. The infant sequences showed amino acid sequence patterns similar to those present in their respective mothers. The functional domains required for Tat function, including amino-terminal, cysteine-rich, core and basic regions, which constitute domains for activation and RNA binding, were highly conserved in most of the sequences. Phylogenetic analysis of 154 mother-infant tat sequences showed that they formed distinct clusters for each mother-infant pair and grouped with subtype B sequence. These findings suggest that an intact and functional tat gene is conserved in HIV-1 mother-infant isolates that are involved in perinatal transmission.
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Affiliation(s)
- M Husain
- Department of Microbiology and Immunology, College of Medicine, University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
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26
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Abstract
Erythropoietin is an obligatory growth factor for red blood cell production. The receptor for erythropoietin contains a single membrane-spanning domain with no intrinsic tyrosine kinase motifs. On binding to erythropoietin, the receptor dimerizes and activates multiple intracellular signaling molecules, including but not limited to JAK2, STAT5, PI 3-kinase, IRS-2, RAS, and Ca2+ channels. This review focuses on cytoplasmic signaling cascades involved in erythropoietin action.
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Affiliation(s)
- J Y Cheung
- Department of Medicine, Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, PA 17033-0850, USA.
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27
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Izopet J, Massip P, Souyris C, Sandres K, Puissant B, Obadia M, Pasquier C, Bonnet E, Marchou B, Puel J. Shift in HIV resistance genotype after treatment interruption and short-term antiviral effect following a new salvage regimen. AIDS 2000; 14:2247-55. [PMID: 11089612 DOI: 10.1097/00002030-200010200-00005] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To investigate the changes in genotypic drug-resistance pattern, plasma HIV RNA and CD4 cell count after treatment interruption and assess the short-term antiviral effect of a new salvage regimen. DESIGN Prospective study of 38 patients with multiple failing regimens who had completely stopped all medication for 3 months before a three to five-drug regimen was reintroduced according to clinical guidelines. METHODS Patients were tested for HIV resistance before and after treatment interruption by population-based sequencing and clonal analysis of selected patients. RESULTS Discontinuation of therapy for 3 months was associated with a median increase in HIV RNA of 0.4 log10 and a median decrease in CD4 cell count of 43 x 10(6)/l. Sixty-one per cent of patients had a shift from the drug-resistant genotype to a predominantly wild-type genotype. The patients significantly likely to show genotype reversion were those in Centers for Disease Control groups A or B, who had been exposed to few drugs, had a low plasma HIV RNA, or a high CD4 cell count. The only independent factor predicting genotype reversion was the clinical stage. The median change in plasma HIV RNA at month 3 after treatment reintroduction was -2.3 log10 copies/ml in patients who had genotype reversion compared with -0.6 log10 copies/ml in patients without genotype reversion (P = 0.004). CONCLUSION Suspending treatment for 3 months after multiple failures could be a suitable strategy for optimizing salvage therapy provided it is instituted early, before the HIV disease becomes too advanced.
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Affiliation(s)
- J Izopet
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, France.
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28
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Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16:1481-9. [PMID: 11054261 DOI: 10.1089/088922200750006001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) envelope V3 region sequences of peripheral blood mononuclear cell DNA were analyzed from three nontransmitting mothers (infected mothers who failed to transmit HIV-1 to their infants in the absence of antiretroviral therapy), including one mother with two deliveries, and compared with the sequences of seven previously analyzed transmitting mothers. The coding potential of the envelope open reading frame, including several patient-specific amino acid motifs and previously described molecular features across the V3 region, were highly conserved. There was a low degree of heterogeneity within the sequences of each nontransmitting mother compared with the sequences of transmitting mothers. In addition, the estimates of genetic diversity of nontransmitting mother sequences were significantly lower compared with transmitting mother sequences. Phylogenetic analysis showed that the sequences of each nontransmitting mother formed distinct clusters that were well discriminated from each other and the sequences of seven transmitting mothers. In conclusion, a low degree of HIV-1 genetic heterogeneity in these infected mothers correlates with lack of vertical transmission; this finding may be useful in developing strategies for further prevention of maternal-fetal transmission.
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Affiliation(s)
- E Matala
- Department of Microbiology and Immunology, College of Medicine, University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
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29
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Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15:875-88. [PMID: 10408724 DOI: 10.1089/088922299310584] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The gag p17 matrix sequences of human immunodeficiency virus type 1 (HIV-1) from seven infected mother-infant pairs were analyzed after perinatal transmission. The p17 matrix open reading frame was maintained in 143 of the 166 clones analyzed (86.2% frequency of intact p17 open reading frames). The functional domains essential for p17 matrix function in HIV-1 replication, including targeting of Gag to the plasma membrane, virus assembly and release, envelope glycoprotein incorporation into virus particle, virus entry, and localization of the virus preintegration complex to the nucleus of nondividing cells, were highly conserved in most of the sequences. In addition, examination of the three-dimensional structure of the p17 matrix protein in mother-infant isolates showed a high degree of conservation of amino acids required for correct folding and biological activity. Several amino acid motifs common to most of the mother-infant pairs sequences, including pair-specific signature sequences, were observed. There was a low degree of heterogeneity of gag p17 sequences within mothers, within infants, and between mother-infant pairs, but the distances were greater between epidemiologically unlinked individuals. Phylogenetic analyses of 166 mother-infant pairs and 181 other p17 sequences available from HIV-1 databases revealed distinct clusters for each mother-infant pair and for other p17 sequences. In conclusion, these findings indicate that an intact and functional gag p17 matrix is maintained during maternal-fetal transmission and that several motifs in p17 may be associated with perinatal transmission.
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Affiliation(s)
- T Hahn
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson 85724, USA
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30
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Martínez MA, Cabana M, Ibáñez A, Clotet B, Arnó A, Ruiz L. Human immunodeficiency virus type 1 genetic evolution in patients with prolonged suppression of plasma viremia. Virology 1999; 256:180-7. [PMID: 10191182 DOI: 10.1006/viro.1999.9601] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Treatment of human immunodeficiency virus type 1 (HIV-1)-infected patients with combination drug regimens results in a reduction of plasma viral load to levels below the limit of detection. To investigate the genomic fluctuations in HIV-1 populations from long-term responders to antiviral therapies we analyzed the viral sequence evolution of env and pol genes from sequential peripheral blood mononuclear cell (PBMC) DNA samples of three infected patients. Analyses of sequences covering the V3 and flanking env regions obtained from blood samples at the beginning of the therapy and at 14 or 24 months from baseline revealed that HIV-1 quasispecies continue to evolve in the three patients following combination antiretroviral therapy. Minor drug-resistant mutant subpopulations were also searched for and found in one patient. Interestingly, no minor resistant subpopulations were found in the other two patients despite the fact that they showed evidence of ongoing viral replication. Finally, the genetic analysis of the env gene shows a reduction in PBMC env viral population diversity after long-term response to the therapy in all the patients analyzed.
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Affiliation(s)
- M A Martínez
- Laboratori de Retrovirologia, Hospital Universitari Germans Trias i Pujol, Badalona, 08916, Spain.
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31
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Yedavalli VR, Chappey C, Ahmad N. Maintenance of an intact human immunodeficiency virus type 1 vpr gene following mother-to-infant transmission. J Virol 1998; 72:6937-43. [PMID: 9658150 PMCID: PMC109910 DOI: 10.1128/jvi.72.8.6937-6943.1998] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/1998] [Accepted: 05/05/1998] [Indexed: 02/08/2023] Open
Abstract
The vpr sequences from six human immunodeficiency virus type 1 (HIV-1)-infected mother-infant pairs following perinatal transmission were analyzed. We found that 153 of the 166 clones analyzed from uncultured peripheral blood mononuclear cell DNA samples showed a 92.17% frequency of intact vpr open reading frames. There was a low degree of heterogeneity of vpr genes within mothers, within infants, and between epidemiologically linked mother-infant pairs. The distances between vpr sequences were greater in epidemiologically unlinked individuals than in epidemiologically linked mother-infant pairs. Moreover, the infants' sequences displayed patterns similar to those seen in their mothers. The functional domains essential for Vpr activity, including virion incorporation, nuclear import, and cell cycle arrest and differentiation were highly conserved in most of the sequences. Phylogenetic analyses of 166 mother-infant pairs and 195 other available vpr sequences from HIV databases formed distinct clusters for each mother-infant pair and for other vpr sequences and grouped the six mother-infant pairs' sequences with subtype B sequences. A high degree of conservation of intact and functional vpr supports the notion that vpr plays an important role in HIV-1 infection and replication in mother-infant isolates that are involved in perinatal transmission.
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Affiliation(s)
- V R Yedavalli
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
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Connor RI, Korber BT, Graham BS, Hahn BH, Ho DD, Walker BD, Neumann AU, Vermund SH, Mestecky J, Jackson S, Fenamore E, Cao Y, Gao F, Kalams S, Kunstman KJ, McDonald D, McWilliams N, Trkola A, Moore JP, Wolinsky SM. Immunological and virological analyses of persons infected by human immunodeficiency virus type 1 while participating in trials of recombinant gp120 subunit vaccines. J Virol 1998; 72:1552-76. [PMID: 9445059 PMCID: PMC124637 DOI: 10.1128/jvi.72.2.1552-1576.1998] [Citation(s) in RCA: 167] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/1997] [Accepted: 11/04/1997] [Indexed: 02/05/2023] Open
Abstract
We have studied 18 participants in phase I/II clinical trials of recombinant gp120 (rgp120) subunit vaccines (MN and SF-2) who became infected with human immunodeficiency virus type 1 (HIV-1) during the course of the trials. Of the 18 individuals, 2 had received a placebo vaccine, 9 had been immunized with MN rgp120, and seven had been immunized with SF-2 rgp120. Thirteen of the 18 infected vaccinees had received three or four immunizations prior to becoming infected. Of these, two were placebo recipients, six had received MN rgp120, and five had received SF-2 rgp120. Only 1 of the 11 rgp120 recipients who had multiple immunizations failed to develop a strong immunoglobulin G antibody response to the immunogen. However, the antibody response to rgp120 was transient, typically having a half-life of 40 to 60 days. No significant neutralizing activity against the infecting strain was detected in any of the infected individuals at any time prior to infection. Antibody titers in subjects infected despite vaccination and in noninfected subjects were not significantly different. Envelope-specific cytotoxic T-lymphocyte responses measured after infection were infrequent and weak in the nine vaccinees who were tested. HIV-1 was isolated successfully from all 18 individuals. Sixteen of these strains had a non-syncytium-inducing (NSI) phenotype, while two had a syncytium-inducing (SI) phenotype. NSI strains used the CCR5 coreceptor to enter CD4+ cells, while an SI strain from one of the vaccinees also used CXCR4. Viruses isolated from the blood of rgp120 vaccinees were indistinguishable from viruses isolated from control individuals in terms of their inherent sensitivity to neutralization by specific monoclonal antibodies and their replication rates in vitro. Furthermore, genetic sequencing of the env genes of strains infecting the vaccinees did not reveal any features that clearly distinguished these viruses from contemporary clade B viruses circulating in the United States. Thus, despite rigorous genetic analyses, using various breakdowns of the data sets, we could find no evidence that rgp120 vaccination exerted selection pressure on the infecting HIV-1 strains. The viral burdens in the infected rgp120 vaccine recipients were also determined, and they were found to be not significantly different from those in cohorts of placebo-vaccinated and nonvaccinated individuals. In summary, we conclude that vaccination with rgp120 has had,to date, no obvious beneficial or adverse effects on the individuals we have studied.
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Affiliation(s)
- R I Connor
- The Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10016, USA
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33
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Yedavalli VR, Chappey C, Matala E, Ahmad N. Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998; 72:1092-102. [PMID: 9445004 PMCID: PMC124582 DOI: 10.1128/jvi.72.2.1092-1102.1998] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/1997] [Accepted: 10/20/1997] [Indexed: 02/05/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) vif gene is conserved among most lentiviruses, suggesting that vif is important for natural infection. To determine whether an intact vif gene is positively selected during mother-to-infant transmission, we analyzed vif sequences from five infected mother-infant pairs following perinatal transmission. The coding potential of the vif open reading frame directly derived from uncultured peripheral blood mononuclear cell DNA was maintained in most of the 78,912 bp sequenced. We found that 123 of the 137 clones analyzed showed an 89.8% frequency of intact vif open reading frames. There was a low degree of heterogeneity of vif genes within mothers, within infants, and between epidemiologically linked mother-infant pairs. The distances between vif sequences were greater in epidemiologically unlinked individuals than in epidemiologically linked mother-infant pairs. Furthermore, the epidemiologically linked mother-infant pair vif sequences displayed similar patterns that were not seen in vif sequences from epidemiologically unlinked individuals. The functional domains, including the two cysteines at positions 114 and 133, a serine phosphorylation site at position 144, and the C-terminal basic amino acids essential for vif protein function, were highly conserved in most of the sequences. Phylogenetic analyses of 137 mother-infant pair vif sequences and 187 other available vif sequences from HIV-1 databases revealed distinct clusters for vif sequences from each mother-infant pair and for other vif sequences. Taken together, these findings suggest that vif plays an important role in HIV-1 infection and replication in mothers and their perinatally infected infants.
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Affiliation(s)
- V R Yedavalli
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson 85724, USA
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34
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Segal DM, Shapshak P, Zhang BT, Crandall KA, Page B, Fujimura R, Goodkin K, Douyon R, McCoy CB. Novel tetrameric tip motifs (APGK and VPGK) in the V3 loop of HIV type 1 envelope sequences in blood and brain from two injection drug users in Miami, Florida. AIDS Res Hum Retroviruses 1997; 13:1643-6. [PMID: 9430257 DOI: 10.1089/aid.1997.13.1643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- D M Segal
- Department of Psychiatry and Behavioral Sciences, University of Miami School of Medicine, Florida 33136, USA
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35
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Liu SL, Schacker T, Musey L, Shriner D, McElrath MJ, Corey L, Mullins JI. Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. J Virol 1997; 71:4284-95. [PMID: 9151816 PMCID: PMC191644 DOI: 10.1128/jvi.71.6.4284-4295.1997] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The rate of progression to AIDS in human immunodeficiency virus type 1 (HIV-1)-infected individuals is determined by a complex series of interactions between the host and virus. Here we evaluate virologic properties and host responses in two men near-simultaneously infected with HIV-1 from the same sexual partner--one individual progressed to AIDS in less than 2 years, and the other remains asymptomatic 3 years postinfection. Distinct neutralizing antibody and cellular immune responses were evident, with the slower progressor exhibiting generally stronger and broader responses, except for cytotoxic T-lymphocyte responses early in infection. Virtually identical, homogeneous virus populations were found in both patients in the first sample obtained; however, a second unrelated HIV-1 virus population was also found in the fast progressor. Whether the second population emanated from an additional source of infection or the two were transmitted from the original source could not be determined. The virus population in the slower progressor turned over and diversified rapidly, whereas both virus populations in the rapid progressor evolved at a much slower rate. In addition, the character of mutational changes underlying these diversities appeared to be distinct, with a bias for diversifying selection developing in the slower progressor and a reciprocal bias towards purifying selection maintained in both populations in the fast progressor. Thus, the rapid evolution that is a hallmark of HIV replication may be a reflection of strong host resistance against emerging virus variants and a longer period of asymptomatic infection. Furthermore, rapid progression was not linked to a collapse of any appreciable immune response following attainment of some threshold of antigenic diversity but rather to a failure to drive this diversification and a condition of relatively unimpeded expansion of variants with optimized replicative capacity within the host.
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Affiliation(s)
- S L Liu
- Department of Microbiology, University of Washington, Seattle 98105-7740, USA
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36
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Contag CH, Ehrnst A, Duda J, Bohlin AB, Lindgren S, Learn GH, Mullins JI. Mother-to-infant transmission of human immunodeficiency virus type 1 involving five envelope sequence subtypes. J Virol 1997; 71:1292-300. [PMID: 8995653 PMCID: PMC191184 DOI: 10.1128/jvi.71.2.1292-1300.1997] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Genetic analysis of human immunodeficiency virus type 1 (HIV-1) from cases of mother-to-infant transmission were analyzed in an effort to provide insights into the viral selection that may occur during transmission, as well as the timing and source of transmitted viruses. HIV-1 env genes obtained from seven mothers and their perinatally infected infants in Sweden were studied. Five envelope sequence clades (A to E) were found to be represented. We used a heteroduplex tracking assay (HTA) to assess the genetic relatedness between early viral isolates from the infants and serial maternal virus populations taken during pregnancy and at delivery. HTA findings were used to select for DNA sequence analysis maternal virus populations that were either closely or more distantly related to the infant virus. In each case, nucleotide sequence analysis confirmed the genetic relationships inferred by the HTA. Only maternal peripheral blood was sampled, and large sets of maternal specimens throughout pregnancy were generally not available. However, no consistent correlation was found to support the hypothesis that infant viruses should match blood-derived maternal virus genotypes found early in pregnancy if infants were found to be infected at birth or, conversely, that infant viruses should match blood-derived maternal virus genotypes found at delivery if infants were found to be infected only some time later.
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Affiliation(s)
- C H Contag
- Department of Pediatrics, Stanford University School of Medicine, California, USA
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37
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Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM. Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J Virol 1997; 71:663-77. [PMID: 8985398 PMCID: PMC191099 DOI: 10.1128/jvi.71.1.663-677.1997] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The rate of development of disease varies considerably among human immunodeficiency virus type 1 (HIV-1)-infected children. The reasons for these observed differences are not clearly understood but most probably depend on the dynamic interplay between the HIV-1 quasispecies virus population and the immune constraints imposed by the host. To study the relationship between disease progression and genetic diversity, we analyzed the evolution of viral sequences within six perinatally infected children by examining proviral sequences spanning the C2 through V5 regions of the viral envelope gene by PCR of blood samples obtained at sequential visits. PCR product DNAs from four sample time points per child were cloned, and 10 to 13 clones from each sample were sequenced. Greater genetic distances relative to the time of infection were found for children with low virion-associated RNA burdens and slow progression to disease relative to those found for children with high virion-associated RNA burdens and rapid progression to disease. The greater branch lengths observed in the phylogenetic reconstructions correlated with a higher accumulation rate of nonsynonymous base substitutions per potential nonsynonymous site, consistent with positive selection for change rather than a difference in replication kinetics. Viral sequences from children with slow progression to disease also showed a tendency to form clusters that associated with different sampling times. These progressive shifts in the viral population were not found in viral sequences from children with rapid progression to disease. Therefore, despite the HIV-1 quasispecies being a diverse, rapidly evolving, and competing population of genetic variants, different rates of genetic evolution could be found under different selective constraints. These data suggest that the evolutionary dynamics exhibited by the HIV-1 quasispecies virus populations are compatible with a Darwinian system evolving under the constraints of natural selection.
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Affiliation(s)
- S Ganeshan
- Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611, USA
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38
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Paxton WA, Koup RA. Mechanisms of resistance to HIV infection. SPRINGER SEMINARS IN IMMUNOPATHOLOGY 1997; 18:323-40. [PMID: 9089952 DOI: 10.1007/bf00813501] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- W A Paxton
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA
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39
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Fujimura RK, Bockstahler LE, Goodkin K, Werner T, Brack-Werner R, Shapshak P. Neuropathology and Virology of HIV Associated Dementia. Rev Med Virol 1996; 6:141-150. [PMID: 10398454 DOI: 10.1002/(sici)1099-1654(199609)6:3<141::aid-rmv141>3.0.co;2-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- RK Fujimura
- Department of Psychiatry, University of Miami School of Medicine, Miami FL 33136, USA
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40
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Learn GH, Korber BT, Foley B, Hahn BH, Wolinsky SM, Mullins JI. Maintaining the integrity of human immunodeficiency virus sequence databases. J Virol 1996; 70:5720-30. [PMID: 8764096 PMCID: PMC190542 DOI: 10.1128/jvi.70.8.5720-5730.1996] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) sequences are accumulating in the literature at a rapid pace. For this ever-expanding resource to be maximally useful, it is critical that researchers strive to maintain a high level of quality assurance, both in experimental design and conduct and in analyses. Here we present detailed analyses of problematic sets of HIV-1 sequences in the database that include sequence anomalies suggestive of mislabeling or sample contamination problems. These data are examined in the context of currently available HIV-1 sequence information to provide an example of how to identify potentially flawed data. Indicators of potential problems with sequences are (i) sequences that are nearly identical that are supposed to be derived from unlinked individuals and that are markedly distinct from other sequences from the putative source or (ii) sequences that are nearly identical to those of laboratory strains. We provide an outline of methods that researchers can use to perform preliminary laboratory and computational analyses that could help identify problematic data and thus help ensure the integrity of sequence databases.
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Affiliation(s)
- G H Learn
- Department of Microbiology, University of Washington, Seattle 98195-7740, USA
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41
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Hutto C, Zhou Y, He J, Geffin R, Hill M, Scott W, Wood C. Longitudinal studies of viral sequence, viral phenotype, and immunologic parameters of human immunodeficiency virus type 1 infection in perinatally infected twins with discordant disease courses. J Virol 1996; 70:3589-98. [PMID: 8648693 PMCID: PMC190234 DOI: 10.1128/jvi.70.6.3589-3598.1996] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Perinatal human immunodeficiency virus type 1 (HIV-1) infections cause a broad spectrum of clinical disease and are variable in both the age of the patient at onset of serious disease and the progression of the clinical course. Heterozygotic perinatally infected twins with a marked difference in their clinical courses were monitored during the first 2 years of life. Twin B, the second-born twin, developed AIDS by 6 months of age and died at 22 months of age, while twin A remained minimally symptomatic through the first 2 years. Sequential blood specimens were obtained from the twins in order to characterize the immunologic properties of the children and the phenotypes and genotypes of the HIV-1 isolates at various times. Twin A developed neutralizing antibodies and a high-level antibody-mediated cellular cytotoxicity (ADCC) response, while twin B had no neutralizing antibody and a much lower ADCC response. The virus isolates obtained from the two children at various time points proliferated equally well in peripheral blood mononuclear cells, were nonsyncytium inducing, and could not infect established T-cell lines. They differed in their ability to infect primary macrophages. In parallel to the biological studies, the HIV-1 tat and part of the env gene sequences of the longitudinal isolates at four time points were determined. Sequences of virus from both twins at different time points were highly conserved; the viruses evolved at a similar rate until the last analyzed time point, at which there was a dramatic increase in sequence diversity for the sicker child, especially in the tat gene. Our results show that the viruses isolated at different times do not have significant changes in growth properties. The absence or low levels of neutralizing antibodies may correlate with disease progression in the twins.
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Affiliation(s)
- C Hutto
- Department of Pediatrics, University of Miami School of Medicine, Florida 33136, USA
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42
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Wolinsky SM, Korber BT, Neumann AU, Daniels M, Kunstman KJ, Whetsell AJ, Furtado MR, Cao Y, Ho DD, Safrit JT. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 1996; 272:537-42. [PMID: 8614801 DOI: 10.1126/science.272.5261.537] [Citation(s) in RCA: 468] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The rate of progression to disease varies considerably among individuals infected with human immunodeficiency virus-type 1 (HIV-1). Analyses of semiannual blood samples obtained from six infected men showed that a rapid rate of CD4 T cell loss was associated with relative evolutionary stasis of the HIV-1 quasispecies virus population. More moderate rates of CD4 T cell loss correlated with genetic evolution within three of four subjects. Consistent with selection by the immune constraints of these subjects, amino acid changes were apparent within the appropriate epitopes of human leukocyte antigen class I-restricted cytotoxic T lymphocytes. Thus, the evolutionary dynamics exhibited by the HIV-1 quasispecies virus populations under natural selection are compatible with adaptive evolution.
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Affiliation(s)
- S M Wolinsky
- Department of Medicine, Northwestern University Medical School, Chicago, IL 60611, USA
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43
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44
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Gao F, Morrison SG, Robertson DL, Thornton CL, Craig S, Karlsson G, Sodroski J, Morgado M, Galvao-Castro B, von Briesen H, Beddows S, Weber J, Sharp PM, Shaw GM, Hahn BH. Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization. J Virol 1996; 70:1651-67. [PMID: 8627686 PMCID: PMC189989 DOI: 10.1128/jvi.70.3.1651-1667.1996] [Citation(s) in RCA: 240] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Present knowledge of human immunodeficiency virus type 1 (HIV-1) envelope immunobiology has been derived almost exclusively from analyses of subtype B viruses, yet such viruses represent only a minority of strains currently spreading worldwide. To generate a more representative panel of genetically diverse envelope genes, we PCR amplified, cloned, and sequenced complete gp160 coding regions of 35 primary (peripheral blood mononuclear cell-propagated) HIV-1 isolates collected at major epicenters of the current AIDS pandemic. Analysis of their deduced amino acid sequences revealed several important differences from prototypic subtype B strains, including changes in the number and distribution of cysteine residues, substantial length differences in hypervariable regions, and premature truncations in the gp41 domain. Moreover, transiently expressed glycoprotein precursor molecules varied considerably in both size and carbohydrate content. Phylogenetic analyses of full-length env sequences indicated that the panel included members of all major sequence subtypes of HIV-1 group M (clades A to G), as well as an intersubtype recombinant (F/B) from an infected individual in Brazil. In addition, all subtype E and three subtype G viruses initially classified on the basis of partial env sequences were found to cluster in subtype A in the 3' half of their gp41 coding region, suggesting that they are also recombinant. The biological activity of PCR-derived env genes was examined in a single-round virus infectivity assay. This analysis identified 20 clones, including 1 from each subtype (or recombinant), which expressed fully functional envelope glycoproteins. One of these, derived from a patient with rapid CD4 cell decline, contained an amino acid substitution in a highly conserved endocytosis signal (Y721C), as mediated virus entry with very poor efficiency, although they did not contain sequence changes predicted to alter protein function. These results indicate that the env genes of primary HIV-1 isolates collected worldwide can vary considerably in their genetic, phylogenetic, and biological properties. The panel of env constructs described here should prove valuable for future structure-function studies of naturally occurring envelope glycoproteins as well as AIDS vaccine development efforts targeted against a broader spectrum of viruses.
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Affiliation(s)
- F Gao
- Department of Medicine, University of Alabama at Birmingham 35294, USA
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45
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Shapshak P, Crandall KA, Xin KQ, Goodkin K, Fujimura RK, Bradley W, McCoy CB, Nagano I, Yoshioka M, Petito C, Sun NC, Srivastava AK, Weatherby N, Stewart R, Delgado S, Matthews A, Douyon R, Okuda K, Yang J, Zhangl BT, Cao XR, Shatkovsky S, Fernandez JB, Shah SM, Perper J. HIV-1 neuropathogenesis and abused drugs: current reviews, problems, and solutions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1996; 402:171-86. [PMID: 8787658 DOI: 10.1007/978-1-4613-0407-4_23] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- P Shapshak
- Department of Psychiatry, University of Miami Medical School, Florida, USA
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