de Oliveira, Tulio

Engelbrecht, Susan

Wilkinson, Eduan

Retrovirology

English

PubMed

Susan Engelbrecht

Eduan Wilkinson

Tulio de Oliveira

Crossref

Diversity and molecular epidemiology of HIV-1 in Cape Town; 1984 to 2010

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POSTER PRESENTATION Open Access
Diversity and molecular epidemiology of HIV-1 in
Cape Town; 1984 to 2010
Susan Engelbrecht1*, Eduan Wilkinson1, Tulio de Oliveira2
From Frontiers of Retrovirology 2011
Amsterdam, The Netherlands. 3-5 October 2011
Background
HIV-1 is a major health problem in South Africa with
more than 6 million people infected. One of the features
of the virus is the extreme genetic diversity, resulting in
an uneven distribution of the different viral subtypes.
This diversity may also impact on diagnostic assays,
antiretroviral treatment, prevention and vaccine devel-
opment. We investigated the diversity and molecular
epidemiology of HIV-1 in the CapeTown area between
1984 and 2010.
Materials and methods
Patient samples were collected from the Cape Town
area between 1984 and 2010. HIV-1 RNA was extracted,
amplified by RT-PCR and sequenced. High resolution
phylogenetic analysis was used to investigate the mole-
cular epidemiology and introduction of HIV-1 into
South Africa. Maximum Likelihood trees were inferred
in PhyMLv3.0 with the best nucleotide substitution
model for each dataset. Bayesian genealogies were
inferred in BEAST v1.6.1 using different substitution
models, a relaxed molecular clock and different coales-
cent priors. A Markov chain Monte Carlo (MCMC)
chain was run for 10,000,000 generations with sampling
every 10,000th generation using super computer clusters.
Results were visualized in Tracer v1 .5.
Results
Phylogenetic analysis indicated two different epidemics
in Cape Town: HIV-1 subtypes B and D in homosexual
men and subtype C in the heterosexual population.
Molecular clock and likelihood mapping analysis indi-
cated that HIV-1 subtype C was introduced in South
Africa, dating back to the 1960-1970s, much earlier than
previously thought. More recent samples also indicated
that the epidemic is evolving with the frequent detection
of unique recombinant forms (URFs) which may be the
precursors of emerging CRFs in the future.
Conclusion
The detection of URFs may indicate a change in the
dynamics of the predominant subtype C epidemic in
South Africa. It is essential to study HIV-1 in order to
improve our knowledge of these viruses and to obtain a
better understanding of the viruses in circulation in
South Africa.
Author details
1Division of Medical Virology, Stellenbosch University, Tygerberg, 7505, South
Africa. 2Africa Centre for Health and Population Studies, Nelson R Mandela
School of Medicine, University of KwaZulu-Natal, South Africa.
Published: 3 October 2011
doi:10.1186/1742-4690-8-S2-P21
Cite this article as: Engelbrecht et al.: Diversity and molecular
epidemiology of HIV-1 in Cape Town; 1984 to 2010. Retrovirology 2011 8
(Suppl 2):P21.
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1Division of Medical Virology, Stellenbosch University, Tygerberg, 7505, South
Africa
Full list of author information is available at the end of the article
Engelbrecht et al. Retrovirology 2011, 8(Suppl 2):P21
http://www.retrovirology.com/content/8/S2/P21
© 2011 Engelbrecht et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.


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Diversity and molecular epidemiology of HIV-1 in Cape Town; 1984 to 2010

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