The categorization of HIV-1 into genetic subtypes based on viral sequencing is a powerful epidemiological tool with which to evaluate the HIV-1 epidemic. HIV-1 subtypes have historically broadly reflected geographical region and risk group . Clade C infection represents approximately 50% of all infections worldwide  originating from sub-Saharan Africa ; it is the most prevalent clade amongst heterosexuals in the UK . Amongst men having sex with men (MSM), clade B predominates throughout Europe  and the majority of MSM infected in the UK, are infected with subtype B irrespective of country of birth . However, it cannot be assumed that these genetic subtypes will continue to maintain a strict geographical or risk group restriction.
The distribution and evolution of HIV subtypes within heterosexuals in the UK is well established  but less is known about the MSM population. Small studies have reported the presence of non-B clade HIV-1 infection in MSM in the UK and Europe [7–11] but the extent of and the risk factors for this have not been explored extensively.
The aim of our study was to describe the frequency of non-B HIV-1 infection in HIV-positive MSM in the UK diagnosed from pre1996 to 2007 and to investigate time trends, regional variation and demographic risk factors associated with the acquisition of a non-B virus.
The UK HIV Drug Resistance Database is a central repository of genotypic resistance tests carried out as part of routine clinical care in the United Kingdom . Demographic and clinical data were obtained via linkage to the UK Collaborative HIV Cohort study (UK CHIC) , as well as local hospital databases. Eight thousand and fifty-eight MSM diagnosed with HIV-1 between 1980 and 2007 with a resistance test in the UK HIV Drug Resistance Database were identified. HIV subtype was defined using the REGA genotyping tool  and was classified as B or non-B for the purpose of this analysis; in-depth analysis of individual non-B subtypes was not possible due to small numbers. The associations between demographic variables and subtype were analysed using logistic regression. Patients diagnosed before 1996 were grouped together as there were very few patients with non-B subtype previous to 1996. All analysis used Stata statistical software, version 10.0 (StataCorp LP, College Station, Texas, USA).
Overall 437 out of 8058 (5.4%) MSM testing HIV positive in the UK with a resistance test in the UK HIV Drug Resistance Database were infected with non-B clade HIV-1 virus; clades C (n = 102) and A (n = 53) were the most common non-B subtypes. Recombinant viruses accounted for 245 cases; AE (n = 49), AG (n = 35), rare but recognized CRF viruses (n = 30), unrecognized recombinants (n = 131). Of the 437 MSM individuals diagnosed with non-B virus, 302 (69%) were white and 185 (42%) were born in the UK. The distribution of subtype was similar in white MSM born in the UK with non-B virus compared with other patients with non-B virus; of 163 white MSM born in the UK with non-B virus, 41 (25%) were clade C, 17 (10%) clade A and 94 (58%) recombinant forms, compared with 61 (22%), 36 (13%) and 151 (55%), respectively, of the remaining patients.
Risk factors for the acquisition of non-B virus
The prevalence of non-B subtype HIV infection increased with year of diagnosis from pre1996 to 2002, and has subsequently remained relatively stable at around 7–9% after 2002, with a recent increase in 2007 to 13% (Table 1). The increase occurred in both white and nonwhite MSM, from pre1996 (1% (28/2091) white; 3% (6/234) nonwhite) to 2002 (8% (30/367) white; 16% (7/45) nonwhite).
Thirteen percent (48/358) of Black MSM and 11% (26/246) Asian MSM were infected with non-B clade HIV-1 infection; 12 of the 48 (25%), and none of the 26 were born in the UK. The majority (7756/8058; 96%) of individuals were accessing care in the South-East UK.
Univariate analysis showed associations between subtype and the year of diagnosis, age, ethnicity and country of birth, but not geographical location within the UK (P = 0.7) (Table 1). Multivariate analysis showed that acquisition of non-B HIV was independently associated with later year of HIV diagnosis (P < 0.001), black African ethnicity (P < 0.001) and non-European country of birth (P = 0.01). Age was also associated with subtype with individuals aged 25–39 years being statistically significantly less likely to have non-B virus than those aged less than 25 years (P = 0.01) (Table 1). Repeating the analysis including only patients diagnosed from 2004 onwards, when resistance testing (and therefore subtype obtained) for all ART-naive patients was recommended in the UK, showed similar results (data not shown).
The independent association between subtype and year of diagnosis occurred even after adjustment for ethnicity and country of birth. Restricting analysis to white men born in the UK (Table 1), the association remained statistically significant (P < 0.001) and those diagnosed in 2002 were 8.5 times more likely to have non-B subtype than those diagnosed pre1996 (95% CI OR 4.0–18.2). Age was also associated with subtype in these patients (P < 0.001) (Table 1), as for the whole group.
This large multicentre study is the first to describe the changing HIV-1 epidemic among gay men in the UK. We report an increase over 10 years in non-B clade HIV-1 infection across the MSM population, in both UK and non-UK born individuals and irrespective of ethnicity. The strength of this study is in the duration of recruitment and the UK-wide coverage, making this the largest epidemiological study of MSM in Europe. Limitations include the use of standard consensus sequencing of the pol gene, which only detects minority quasi-species to a level of 20%, and the inability to validate the accuracy of demographic information.
Overall 5.4% of MSM were infected with a non-B clade HIV-1 infection and of these 42% were born in the UK; the most common non-B clade viruses amongst UK MSM were C and A. Just over half of infections with Clade A and Clade C HIV-1 infection occurred in individuals born outside of the UK. The increasing prevalence of non-B HIV-1 within MSM (both overall and within UK-born MSM) is suggestive that HIV acquisition amongst this population may be occurring within the UK. This study, therefore, suggests that sexual mixing between individuals originally from countries where these viral subtypes are more prevalent and UK born individuals has occurred and that local transmission of non-B HIV-1 may be occurring also; although with lack of data on foreign travel we cannot verify this. A phylogenetic analysis of transmission dynamics in the UK identified three transmission chains involving MSM patients with non-B subtype (two clusters composed of sequences belonging to the Kenyan strain of subtype A, and one cluster of Spanish subtype G origin), suggesting that non-B subtypes are spreading among men who have sex with men in the UK . In agreement with non-UK epidemiological studies an increasing proportion of non-B subtypes were recombinant viral subtypes [pre2002: 60/132 (45%), 2002–2007: 185/305 (61%)] [16–18].
This study provides evidence that in the UK there has been an increase in non-B clade HIV-infections in MSM since the start of the epidemic, and with time the traditional geographical and risk-group segregation of clades of HIV are becoming less distinct. The impact of introducing non-B HIV-1 infection to a formerly B clade restricted population on clinical outcome or vaccine efforts is unclear. The former is controversial [19–23] and the latter highlights the need for a cross-clade prophylactic vaccine.
UK Collaborative Group on HIV Drug Resistance.
Steering Committee: Jane Anderson, Homerton University Hospital, London; David Asboe and Anton Pozniak, Chelsea & Westminster Hospital, London; Sheila Burns, Royal Infirmary of Edinburgh; Sheila Cameron, Gartnavel General Hospital, Glasgow; Patricia Cane, Health Protection Agency, Porton Down; Ian Chrystie, Guy's and St. Thomas' NHS Foundation Trust, London; Duncan Churchill, Brighton and Sussex University Hospitals NHS Trust; Duncan Clark, St Bartholomew's and The London NHS Trust; Valerie Delpech and Deenan Pillay, Health Protection Agency, Centre for Infections, London; Linda Lazarus, Expert Advisory Group on AIDS Secretariat, Health Protection Agency, London; David Dunn, Esther Fearnhill, Hannah Castro and Kholoud Porter, MRC Clinical Trials Unit, London; Philippa Easterbrook and Mark Zuckerman, King's College Hospital, London; Anna Maria Geretti, Royal Free NHS Trust, London; Paul Kellam, Deenan Pillay, Andrew Phillips and Caroline Sabin, Royal Free and University College Medical School, London; David Goldberg, Health Protection Scotland, Glasgow; Mark Gompels, Southmead Hospital, Bristol; Antony Hale, Leeds Teaching Hospitals NHS Trust; Steve Kaye, Imperial College London; Svilen Konov, Community Advisory Board; Andrew Leigh-Brown, University of Edinburgh; Nicola Mackie, St. Mary's Hospital, London; Chloe Orkin, St. Bartholomew's Hospital, London; Erasmus Smit, Health Protection Agency, Birmingham Heartlands Hospital; Peter Tilston, Manchester Royal Infirmary; Ian Williams, Mortimer Market Centre, London; Hongyi Zhang, Addenbrooke's Hospital, Cambridge.
Participating laboratories: Addenbooke's Hospital, Cambridge (Hongyi Zhang); Department of Virology, St Bartholomew's and The London NHS Trust (Duncan Clark, Ines Ushiro-Lumb, Tony Oliver, David Bibby); Belfast Health and Social Care Trust (Suzanne Mitchell); HPA Birmingham Public Health Laboratory (Erasmus Smit); Chelsea and Westminster Hospital, London (Adrian Wildfire); Dulwich Hospital, London (Melvyn Smith); Royal Infirmary of Edinburgh (Jill Shepherd); West of Scotland Specialist Virology Lab Gartnavel, Glasgow (Alasdair MacLean); Guy's and St. Thomas' NHS Foundation Trust, London (Ian Chrystie); Leeds Teaching Hospitals NHS Trust (Diane Bennett); Specialist Virology Centre, Liverpool (Mark Hopkins) and Manchester (Peter Tilston); Department of Virology at Royal Free Hospital, London (Clare Booth, Ana Garcia-Diaz); Imperial College London (Steve Kaye); University College London Hospitals (Stuart Kirk).
J.F., H.C., S.K., M.M., J.W., S.F. did statistical analysis and manuscript preparation.
The UK HIV Drug Resistance Database is partly funded by the Department of Health; the views expressed in the publication are those of the authors and not necessarily those of the Department of Health. Additional financial support is provided by Boehringer Ingelheim; Bristol-Myers Squibb; Gilead; Roche; Tibotec, a division of Janssen-Cilag Ltd.
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