Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985
Date
2019-04-17
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
Abstract
ENGLISH ABSTRACT: HIV-1 subtype C is the most prevalent subtype in South Africa. Although subtype B was previously detected in South Africa, there is limited sequence information available. We characterized near full-length HIV-1 subtype B sequences from samples collected at the start of the South African HIV-1 epidemic, in the 1980s. Five samples were analysed by PCR amplification, Sanger DNA sequencing and phylogenetic analyses. The viral genomes were amplified in two overlapping fragments of 5.5 kb and 3.7 kb. The sequences were subtyped using REGA version 3.0, RIP version 3.0 and jpHMM. Maximum Likelihood phylogenetic trees were inferred with MEGA version 6. Four HIV-1 patient sequences were subtyped as pure HIV-1 subtype B. One sequence was characterized as a novel HIV-1 subtype B and D recombinant. The sequences clustered phylogenetically with other HIV-1 subtype B sequences from South Africa, Europe and the USA. We report the presence of an HIV-1 subtype B and D recombinant strain detected in the beginning of the epidemic. This indicates that viral recombination events were already happening in 1985, but could have been missed as sequence analyses were often limited to small genomic regions of HIV-1.
Description
CITATION: Obasa, A. E., Engelbrecht, S. & Jacobs, G. B. 2019. Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985. Scientific Reports 9. doi:10.1038/s41598-019-42417-1
The original publication is available at https://www.nature.com/srep/
The original publication is available at https://www.nature.com/srep/
Keywords
HIV-1 subtype B, Nucleotide sequence, Viral genomes, Pathology, Cellular
Citation
Obasa, A. E., Engelbrecht, S. & Jacobs, G. B. 2019. Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985. Scientific Reports 9. doi:10.1038/s41598-019-42417-1