Abstract
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002–2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2–5 members) declined by 70% from 2006–2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.
Highlights
The HIV/AIDS pandemic remains a global health challenge with an estimated 38 million persons living with HIV and 1.7–2 million new cases added annually over the last decade [1]
Our studies have found no evidence to support a correlation between large cluster size and individuallevel sexual risk behaviour [15,38]
Determining the drivers of individual epidemics is critical in tailoring prevention measures to key vulnerable populations in a timely and effective manner
Summary
The HIV/AIDS pandemic remains a global health challenge with an estimated 38 million persons living with HIV and 1.7–2 million new cases added annually over the last decade [1]. In Western world settings, concentrated HIV-1 subtype B epidemics circulate in key vulnerable populations, including Men having Sex with Men (MSM), People Who. Inject Drugs (PWID), and marginalized Heterosexual groups [2,3,4]. In Africa and Asia, generalized Heterosexual (HET) epidemics have diversified to include 10 HIV-1 subtypes and over 40 circulating recombinant forms [5]. Unprecedented advances in antiretroviral therapy has transformed HIV-1 from a deadly disease to a treatable and potentially eradicable pandemic [8]. The goal of treatment has shifted from addressing individual health benefits to population-level control of HIV epidemics. In 2014, the World Health Organization and UNAIDS launched the “90-90-90”
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