Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities

Abstract

To improve insight in the drivers of local HIV-1 transmission in Belgium, phylogenetic, demographic, epidemiological and laboratory data from patients newly diagnosed between 2013 and 2015 were combined and analyzed. Characteristics of clustered patients, paired patients and patients on isolated branches in the phylogenetic tree were compared. The results revealed an overall high level of clustering despite the short time frame of sampling, with 47.6% of all patients having at least one close genetic counterpart and 36.6% belonging to a cluster of 3 or more individuals. Compared to patients on isolated branches, patients in clusters more frequently reported being infected in Belgium (95.1% vs. 47.6%; p < 0.001), were more frequently men having sex with men (MSM) (77.9% vs. 42.8%; p < 0.001), of Belgian origin (68.2% vs. 32.9%; p < 0.001), male gender (92.6% vs. 65.8%; p < 0.001), infected with subtype B or F (87.8% vs. 43.4%; p < 0.001) and diagnosed early after infection (55.4% vs. 29.0%; p < 0.001). Strikingly, Sub-Saharan Africans (SSA), overall representing 27.1% of the population were significantly less frequently found in clusters than on individual branches (6.0% vs. 41.8%; p < 0.001). Of the SSA that participated in clustered transmission, 66.7% were MSM and this contrasts sharply with the overall 12.0% of SSA reporting MSM. Transmission clusters with SSA were more frequently non-B clusters than transmission clusters without SSA (44.4% versus 18.2%). MSM-driven clusters with patients of mixed origin may account, at least in part, for the increasing spread of non-B subtypes to the native MSM population, a cross-over that has been particularly successful for subtype F and CRF02_AG. The main conclusions from this study are that clustered transmission in Belgium remains almost exclusively MSM-driven with very limited contribution of SSA. There were no indications for local ongoing clustered transmission of HIV-1 among SSA.

Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing

“…Only a limited number of Africans were diagnosed early. These early diagnosed individuals showed high involvement in pairs and clusters, supporting local transmission and participation in existing sexual networks as reported before [13].…”

“…The phylogenetic analysis however covered the years 2013 to 2017 to ensure that potential sources diagnosed the same year or the year before or after diagnosis of the study patients could be traced. Based on previous experience, we used stringent criteria to define phylogenetic clustering in order to maximize the chance that linkages identified resulted from recent transmission events [13,28,29]. For nearly half (48.3%) of the study population a close genetic link was found in the phylogenetic tree.…”

“…Branch support was obtained by the approximate likelihood-ratio test (LRT) [24]. Identification of clustering was performed as described before [13]. Sequences linked with at least one other sequence with an LRT of ≥0.97 and a mean pairwise distance of ≤0.015 were considered as genetically linked and classified as either paired (2 members) or clustered (≥3 members).…”

“…Previous phylogenetic analyses of the Belgian HIV epidemic showed that local HIV acquisition is almost exclusively driven by MSM and is concentrated in transmission clusters [13]. However, knowledge on the specific characteristics of those individuals that contribute most to the transmission in these clusters is lacking.…”

Daily and event‐driven pre‐exposure prophylaxis for men who have sex with men in Belgium: results of a prospective cohort measuring adherence, sexual behaviour and STI incidence

“…Belgium is among the countries in the European Union reporting a high HIV incidence, with 7.9 new HIV infections per 100,000 inhabitants in 2017 . A recent study suggests that ongoing clustered transmission in Belgium is almost exclusively MSM driven . At the time of this study PrEP was not yet approved or reimbursed.…”