My research interests concentrates on viral evolution under selection pressure created in the transmission, acquisition and drug escape processes. A particular point of interest is on the study of virus' origins and the effect of network of transmissions in the spread of epidemics in Africa and other continents. I also enjoy developing bioinformatics software applications and running, KRISP, a next generation sequencing (NGS) and bioinformatics laboratory. Prof. Tulio de Oliveira is a bioinformatician that has been working with HIV research since 1997. He has received his PhD at the Nelson R Mandela School of Medicine, UKZN, South Africa. He was a Marie Curie research fellow at the University of Oxford, U.K. He is current a Research Fellow of the U.K. Royal Society, the President: South African Society for Bioinformatics (SASBi) and the director of the newly stablished, KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), UKZN, Durban, South Africa.
KRISP – DNA Sequencing and Bioinformatics to Answer some of the key Global Health Questions: Pathogen transmission and effective interventions design.
The incidence and prevalence of HIV infection in young women in Africa is extremely high. We did a large-scale community-wide DNA sequencing and 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. 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 1,589 individuals. 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 five (8.3%) were aged 41-49 years: mean age difference 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 difference 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. 78.5% of the men 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. 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. DNA sequencing and phylogenetic analysis identify the source of 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. This results were published in the Lancet HIV (2017) and received major coverage from Science and Nature and became the building block of UNAIDS 2016 report. More info: http://www.krisp.org.za