A phylogenetic analysis of the Brighton HIV cohort
Research type
Research Study
Full title
A combined clinical, epidemiological and phylogenetic analysis of the Brighton HIV cohort to assess the current pattern of transmission networking, identify factors associated with transmission and determine the proportion who have acquired infection from an outside or undiagnosed source.
IRAS ID
195958
Contact name
Larissa Mulka
Contact email
Sponsor organisation
Brighton & Sussex University Hospitals NHS Trust
Duration of Study in the UK
0 years, 5 months, 0 days
Research summary
107,800 people were living with HIV in the UK in 2013, approximately one quarter of whom remain unaware of their infection and are at higher risk of passing it on to others. Phylogenetic analysis is a method of analysing small differences in HIV genes (the 'instructions' for building the virus) to determine whether infections may have been recently linked. When combined with additional data, we can identify groups and factors which may be associated with a higher risk of transmission, which provides information to inform HIV prevention strategies. Phylogenetic analysis is performed using sequences from HIV genes which are routinely analysed for all patients at diagnosis to identify any baseline drug resistance and stored at the UK HIV Drug Resistance Database. A previous phylogenetic analysis of 859 men who have sex with men (MSM) in Brighton from 2000-2006 showed factors including recent HIV and other sexually transmitted infections were associated with transmission, though no links were found for 3/4 of those with recent infection. Since then, the HIV cohort has expanded considerably and phylogenetic methods have developed, allowing more accurate reconstruction of large transmission networks and identification of more transmission pairs. With these methods, we aim to analyse the entire cohort, providing greater insight into current transmission patterns, to more accurately determine how many patients' viruses cluster together and which factors are associated with transmission. By comparing unclustered sequences (those who are not linked to any other viruses in the cohort) to those available in the UK HIV Drug Resistance Database and the global Los Alamos HIV sequence database, a more accurate estimation of the proportion of patients who acquired their HIV from an undiagnosed source, rather than from a source outside of Brighton can be made, providing valuable insight for HIV prevention strategies.
REC name
London - Queen Square Research Ethics Committee
REC reference
16/LO/0539
Date of REC Opinion
16 Mar 2016
REC opinion
Favourable Opinion