Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study. Lancet HIV, (2016).

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Title: Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study
Authors: de Oliveira T, Kharsany ABM, Graf T, Cawood C, Khanyile D, Grobler A, Puren A, Madurai S, Baxter C, Karim QA, Karim SSA.
Journal: Lancet HIV, (2016)

Journal Impact Factor (I.F.): 11
Number of citations (Google Scholar): 5


Background The incidence of HIV infection in young women in Africa is very high. We did a large-scale community-wide phylogenetic study to examine the underlying HIV transmission dynamics and the source and consequences of high rates of HIV infection in young women in South Africa.

Methods We did a cross-sectional household survey of randomly selected individuals aged 15-49 years in two neighbouring subdistricts (one urban and one rural) with a high burden of HIV infection in KwaZulu-Natal, South Africa. Participants completed structured questionnaires that captured general demographic, socioeconomic, psychosocial, and behavioural data. Peripheral blood samples were obtained for HIV antibody testing. Samples with HIV RNA viral load greater than 1000 copies per mL were selected for genotyping. We constructed a phylogenetic tree to identify clusters of linked infections (defi ned as two or more sequences with bootstrap or posterior support >90% and genetic distance <4.5%).

Findings From June 11, 2014, to June 22, 2015, we enrolled 9812 participants, 3969 of whom tested HIV positive. HIV prevalence (weighted) was 59.8% in 2835 women aged 25-40 years, 40.3% in 1548 men aged 25-40 years, 22.3% in 2224 women younger than 25 years, and 7.6% in 1472 men younger than 25 years. HIV genotyping was done in 1589 individuals with a viral load of more than 1000 copies per mL. In 90 transmission clusters, 123 women were linked to 103 men. Of 60 possible phylogenetically linked pairings with the 43 women younger than 25 years, 18 (30.0%) probable male partners were younger than 25 years, 37 (61.7%) were aged 25-40 years, and fi ve (8.3%) were aged 41-49 years: mean age diff erence 8.7 years (95% CI 6.8-10.6; p<0.0001). For the 92 possible phylogenetically linked pairings with the 56 women aged 25-40 years, the age diff erence dropped to 1.1 years (95% CI -0.6 to 2.8; p=0.111). 16 (39.0%) of 41 probable male partners linked to women younger than 25 years were also linked to women aged 25-40 years. Of 79 men (mean age 31.5 years) linked to women younger than 40 years, 62 (78.5%) were unaware of their HIV-positive status, 76 (96.2%) were not on antiretroviral therapy, and 29 (36.7%) had viral loads of more than 50 000 copies per mL.

Interpretation Sexual partnering between young women and older men, who might have acquired HIV from women of similar age, is a key feature of the sexual networks driving transmission. Expansion of treatment and combination prevention strategies that include interventions to address age-disparate sexual partnering is crucial to reducing HIV incidence and enabling Africa to reach the goal of ending AIDS as a public health threat.

Funding President's Emergency Program for AIDS Relief, US Centers for Disease Control and Prevention, South African Medical Research Council, and MAC AIDS Fund.

Download: Full text paper

Citation: de Oliveira T, Kharsany ABM, Graf T, Cawood C, Khanyile D, Grobler A, Puren A, Madurai S, Baxter C, Karim QA, Karim SSA. Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study Lancet HIV, (2016).


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This is a short video of our keynote presentation at the AIDS 2016 conference in Durban.

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Printed and Online Media Coverage


South Africa's bid to end AIDS

Science - 2016-06-29

Science magazine (Vol. 353, Issue 6294, pp. 18-21, 2016). This issue was published before the AIDS conference in Durban 2016 and highlights some of our research, including our treatment as prevention trial (TasP) as well our phylogenetic analysis (de Oliveira et al. Lancet HIV 2016).


Social cycle aids HIV spread

Nature - 2016-07-21

Nature (Vol. 535, pp. 335, 2016) report our recent results on the use of genetic sequences to uncover HIV-1 transmission patterns in young woman in South Africa (de Oliveira et al. Lancet HIV 2016). The paper was presented as a Keynote at AIDS 2016 conference.


UNAIDS Report 2016 - Get on the Fast-Track - The life-cycle approach to HIV

UNAIDS - 2016-11-22

In this report, UNAIDS is announcing that 18.2 million people now have access to HIV treatment. The Fast-Track response is working. Increasing treatment coverage is reducing AIDS-related deaths among adults and children. But the life-cycle approach, which highlight our phylogenetics manuscript (de Oliveira et al. Lancet HIV 2016), has to include more than just treatment.


More than 18 million on HIV treatment, a million more than 2015: UNAIDS 2016 Report

Reuters - 2016-11-22

More than 18 million people now have access to life-saving AIDS treatment, 1.2 million more than at the end of last year, the United Nations said on Monday. With detailed data showing some of the many complexities of the HIV epidemic, the report found that people are particularly vulnerable to HIV at certain points in their lives (de Oliveira et al. Lancet HIV 2016). It called for 'life-cycle; approach to offer help and prevention measures for everyone at every stage of life.

Wall Street Journal

Studies Offer Fresh Hope in Fight Against HIV/AIDS in South Africa.

Wall Street Journal - 2016-07-18

Researchers with the Centre for the AIDS Programme of Research in South Africa, or CAPRISA, a consortium of South African and North American scientists, analyzed genetic codes (de Oliveira et al. Lancet HIV 2016) from study subjects in South Africa to try to pinpoint biological factors that may contribute, along with behavioral factors, to the large number of infections.


Unrelenting spread of HIV amongst Adolescent girls and young women in rural and urban KwaZulu-Natal

Mercury - 2016-12-01

By Professor Ayesha Kharsany, December 1, 2016, Durban - Globally, over 1.6 billion people are in the age group 12-24 years, the largest generation of adolescents and young people. However, almost 42% of new HIV infections occur in this age group, nearly 80% of these live in sub-Saharan Africa and more than 70% of these infections occur in adolescent girls and young women. Not only do these adolescent girls and young women have higher rates of HIV, they also acquire infection 5-7 years earlier than their male peers.

The Lancet

Two manuscripts featured in the Lancet website front webpage on AIDS day.

The Lancet - 2016-12-01

Two of our recently published manuscripts (de Oliveira et al. Lancet HIV 2016 & Gregson et al Lancet Infectious Diseases 2016) are highlighed in the Lancet website front webpage...

BioAfrica & SATuRN

Newsletter, Dec 2016: Ethics & phylogenetics, HIV transmission cycle, UNAIDS Report, Drug resistance increases in Africa

BioAfrica & SATuRN - 2016-12-15

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about our research work. In this December 2016 issue of our newsletter, we have included interesting news, blogs, reports, tweets, publications and training information produced by our group.

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration
Journal: EBioMedicine (2017)

High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients
Journal: Clinical Infectious Diseases (2017)

Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis
Journal: Clinical Infectious Diseases (2017)
All publications...

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN

Contact: Prof. Tulio de Oliveira, Tel: +27 31 260 4898, Email: &

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