Spatiotemporal dynamics of HIV-1 transmission in France (1999–2014) and impact of targeted prevention strategies

Abstract

BackgroundCharacterizing HIV-1 transmission networks can be important in understanding the evolutionary patterns and geospatial spread of the epidemic. We reconstructed the broad molecular epidemiology of HIV from individuals with primary HIV-1 infection (PHI) enrolled in France in the ANRS PRIMO C06 cohort over 15 years.ResultsSociodemographic, geographic, clinical, biological and pol sequence data from 1356 patients were collected between 1999 and 2014. Network analysis was performed to infer genetic relationships, i.e. clusters of transmission, between HIV-1 sequences. Bayesian coalescent-based methods were used to examine the temporal and spatial dynamics of identified clusters from different regions in France. We also evaluated the use of network information to target prevention efforts. Participants were mostly Caucasian (85.9%) and men (86.7%) who reported sex with men (MSM, 71.4%). Overall, 387 individuals (28.5%) were involved in clusters: 156 patients (11.5%) in 78 dyads and 231 participants (17%) in 42 larger clusters (median size: 4, range 3–41). Compared to individuals with single PHI (n = 969), those in clusters were more frequently men (95.9 vs 83%, p < 0.01), MSM (85.8 vs 65.6%, p < 0.01) and infected with CRF02_AG (20.4 vs 13.4%, p < 0.01). Reconstruction of viral migrations across time suggests that Paris area was the major hub of dissemination of both subtype B and CRF02_AG epidemics. By targeting clustering individuals belonging to the identified active transmission network before 2010, 60 of the 143 onward transmissions could have been prevented.ConclusionThese analyses support the hypothesis of a recent and rapid rise of CRF02_AG within the French HIV-1 epidemic among MSM. Combined with a short turnaround time for sample processing, targeting prevention efforts based on phylogenetic monitoring may be an efficient way to deliver prevention interventions but would require near real time targeted interventions on the identified index cases and their partners.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-017-0339-4) contains supplementary material, which is available to authorized users.

Emergence of uncommon HIV‐1 non‐B subtypes and circulating recombinant forms and trends in transmission of antiretroviral drug resistance in patients with primary infection during the 2013‐2015 period in Marseille, Southeastern France

“…A concomitant decrease of the number of PHI cases that involved subtype B strains was observed in 2014 and 2015. The steady increase between 2010 and 2013 of the proportion of non‐B subtypes among patients with PHI in Southeastern France is consistent with recent results from France and other European countries . As stated by Chaix et al, non‐B subtypes were present among patients with PHI diagnosed in all French regions, and their prevalence among PHI cases increased, reaching 28%.…”

“…The emergence of clusters of CRF02_AG strains among MSM experiencing PHI was recently described in Southeastern France and later at the national scale . Overall, in France, the dynamics of the HIV epidemics in the MSM population indicates a recent and rapid dissemination of CRF02_AG strains through connected networks of MSM . In the present work, HIV‐1 variants and atypical recombinants forms were mostly found in the most recent period, in 2013‐2015.…”

“…Most of the CRF02_AG strains (23 of 24) were observed during the 2005‐2014 period and their number peaked in 2012‐2013. The emergence of clusters of CRF02_AG strains among MSM experiencing PHI was recently described in Southeastern France and later at the national scale . Overall, in France, the dynamics of the HIV epidemics in the MSM population indicates a recent and rapid dissemination of CRF02_AG strains through connected networks of MSM .…”

Revealing geographical and population heterogeneity in HIV incidence, undiagnosed HIV prevalence and time to diagnosis to improve prevention and care: estimates for France

“…This offers the opportunity to intensify prevention and testing programmes in this area to eventually impact HIV transmission in this area, and possibly elsewhere in France. Indeed, recent phylogenetic studies concluded that the region Ile‐de‐France was the major hub of dissemination in France , and that among clusters of primary HIV infections involving patients living in not contiguous regions 70% involved one patient living in Paris area . This suggests that reducing HIV transmission in Ile‐de‐France could indirectly reduce HIV transmission in other regions of France.…”

Sensitivity to Broadly Neutralizing Antibodies of Recently Transmitted HIV-1 Clade CRF02_AG Viruses with a Focus on Evolution over Time

“…However, one branch of the tree was overrepresented with 13 sequences from our panel. It has recently been shown that some of the subjects included in this study were part of an ongoing cluster of transmission, based on pol gene analysis (37), which was not known at the time of the panel generation. All individuals infected by these viruses were Caucasian MSM.…”