Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom

PLoS Pathogens

Andrew Rambaut¹  Andrew J. Leigh Brown¹  Samantha J. Lycett¹  Gareth J. Hughes¹  Esther Fearnhill²  David Dunn² 

[1] Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom;Medical Research Council Clinical Trials Unit, London, United Kingdom

关键词: Sequence databases;    HIV epidemiology;    Heterosexuals;    Phylogenetic analysis;    Sequence analysis;    Phylogenetics;    HIV;    HIV infections;   

DOI  :  10.1371/journal.ppat.1000590

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

The heterosexual risk group has become the largest HIV infected group in the United Kingdom during the last 10 years, but little is known of the network structure and dynamics of viral transmission in this group. The overwhelming majority of UK heterosexual infections are of non-B HIV subtypes, indicating viruses originating among immigrants from sub-Saharan Africa. The high rate of HIV evolution, combined with the availability of a very high density sample of viral sequences from routine clinical care has allowed the phylodynamics of the epidemic to be investigated for the first time. Sequences of the viral protease and partial reverse transcriptase coding regions from 11,071 patients infected with HIV of non-B subtypes were studied. Of these, 2774 were closely linked to at least one other sequence by nucleotide distance. Including the closest sequences from the global HIV database identified 296 individuals that were in UK-based groups of 3 or more individuals. There were a total of 8 UK-based clusters of 10 or more, comprising 143/2774 (5%) individuals, much lower than the figure of 25% obtained earlier for men who have sex with men (MSM). Sample dates were incorporated into relaxed clock phylogenetic analyses to estimate the dates of internal nodes. From the resulting time-resolved phylogenies, the internode lengths, used as estimates of maximum transmission intervals, had a median of 27 months overall, over twice as long as obtained for MSM (14 months), with only 2% of transmissions occurring in the first 6 months after infection. This phylodynamic analysis of non-B subtype HIV sequences representing over 40% of the estimated UK HIV-infected heterosexual population has revealed heterosexual HIV transmission in the UK is clustered, but on average in smaller groups and is transmitted with slower dynamics than among MSM. More effective intervention to restrict the epidemic may therefore be feasible, given effective diagnosis programmes.

【 授权许可】

CC BY