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.

Authors:
Adetayo Emmanuel Obasa
Adetayo Emmanuel Obasa
Stellenbosch University
Susan Engelbrecht
Susan Engelbrecht
University of Stellenbosch
South Africa
Graeme Brendon Jacobs
Graeme Brendon Jacobs
Institute of Organic Chemistry and Biochemistry
Czech Republic

Sci Rep 2019 Apr 17;9(1):6227. Epub 2019 Apr 17.

Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.

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.

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Source
http://www.nature.com/articles/s41598-019-42417-1
Publisher Site
http://dx.doi.org/10.1038/s41598-019-42417-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6470202PMC
April 2019
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