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Title: Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola

Abstract

Angola has an extremely diverse HIV-1 epidemic fueled in part by the frequent interchange of people with the Democratic Republic of Congo (DRC) and Republic of Congo (RC). Characterization of HIV-1 strains circulating in Angola should help to better understand the origin of HIV-1 subtypes and recombinant forms and their transmission dynamics. In this work we characterize the first near full-length HIV-1 genomic sequences from HIV-1 infected individuals from Angola. Samples were obtained in 1993 from three HIV-1 infected patients living in Cabinda, Angola. Near full-length genomic sequences were obtained from virus isolates. Maximum likelihood phylogenetic tree inference and analyses of potential recombination patterns were performed to evaluate the sequence classifications and origins. Phylogenetic and recombination analyses revealed that one virus was a pure subtype J, another mostly subtype J with a small uncertain region, and the final virus was classified as a H/U/CRF02_AG recombinant. Consistent with their epidemiological data, the subtype J sequences were more closely related to each other than to other J sequences previously published. Based on the env gene, taxa from Angola occur throughout the global subtype J phylogeny. HIV-1 subtypes J and H are present in Angola at low levels since at least 1993. Lowmore » transmission efficiency and/or high recombination potential may explain their limited epidemic success in Angola and worldwide. The high diversity of rare subtypes in Angola suggests that Angola was part of the early establishment of the HIV-1 pandemic.« less

Authors:
 [1];  [1];  [1]; ORCiD logo [2];  [3]
  1. Univ. of Lisbon (Portugal). Research Inst. for Medicines (iMed.Ulisboa) and Faculty of Pharmacy
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Univ. of Lisbon (Portugal). Research Inst. for Medicines (iMed.Ulisboa) and Faculty of Pharmacy; Higher Inst. of Health Sciences Egas Moniz, Almada (Portugal). Center for Interdisciplinary Research Egas Moniz (CiiEM)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE; Foundation for Science and Technology (FCT) (Portugal); European Union (EU); National Institutes of Health (NIH)
OSTI Identifier:
1459811
Report Number(s):
LA-UR-16-27497
Journal ID: ISSN 0889-2229
Grant/Contract Number:  
AC52-06NA25396; PTDC/SAU-EPI/122400/2010; SFRH/BD/70715/2010; SFRH/BPD/76225/2011; R01AI087520
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
AIDS Research and Human Retroviruses
Additional Journal Information:
Journal Volume: 32; Journal Issue: 8; Journal ID: ISSN 0889-2229
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Bartolo, Ines, Calado, Rita, Borrego, Pedro, Leitner, Thomas, and Taveira, Nuno. Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola. United States: N. p., 2016. Web. doi:10.1089/aid.2016.0084.
Bartolo, Ines, Calado, Rita, Borrego, Pedro, Leitner, Thomas, & Taveira, Nuno. Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola. United States. doi:10.1089/aid.2016.0084.
Bartolo, Ines, Calado, Rita, Borrego, Pedro, Leitner, Thomas, and Taveira, Nuno. Mon . "Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola". United States. doi:10.1089/aid.2016.0084. https://www.osti.gov/servlets/purl/1459811.
@article{osti_1459811,
title = {Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola},
author = {Bartolo, Ines and Calado, Rita and Borrego, Pedro and Leitner, Thomas and Taveira, Nuno},
abstractNote = {Angola has an extremely diverse HIV-1 epidemic fueled in part by the frequent interchange of people with the Democratic Republic of Congo (DRC) and Republic of Congo (RC). Characterization of HIV-1 strains circulating in Angola should help to better understand the origin of HIV-1 subtypes and recombinant forms and their transmission dynamics. In this work we characterize the first near full-length HIV-1 genomic sequences from HIV-1 infected individuals from Angola. Samples were obtained in 1993 from three HIV-1 infected patients living in Cabinda, Angola. Near full-length genomic sequences were obtained from virus isolates. Maximum likelihood phylogenetic tree inference and analyses of potential recombination patterns were performed to evaluate the sequence classifications and origins. Phylogenetic and recombination analyses revealed that one virus was a pure subtype J, another mostly subtype J with a small uncertain region, and the final virus was classified as a H/U/CRF02_AG recombinant. Consistent with their epidemiological data, the subtype J sequences were more closely related to each other than to other J sequences previously published. Based on the env gene, taxa from Angola occur throughout the global subtype J phylogeny. HIV-1 subtypes J and H are present in Angola at low levels since at least 1993. Low transmission efficiency and/or high recombination potential may explain their limited epidemic success in Angola and worldwide. The high diversity of rare subtypes in Angola suggests that Angola was part of the early establishment of the HIV-1 pandemic.},
doi = {10.1089/aid.2016.0084},
journal = {AIDS Research and Human Retroviruses},
issn = {0889-2229},
number = 8,
volume = 32,
place = {United States},
year = {2016},
month = {8}
}

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