Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study

Abstract

Molecular HIV surveillance is a promising public health strategy for curbing the HIV epidemic. Clustering technologies used by health departments to date are limited in their ability to infer/forecast cluster growth trajectories. Resolution of the spatiotemporal dynamics of clusters, through phylodynamic and phylogeographic modelling, is one potential strategy to develop a forecasting tool; however, the projected utility of this approach needs assessment. Prior to incorporating novel phylodynamic-based molecular surveillance tools, we sought to identify possible issues related to their feasibility, acceptability, interpretation, and utility. Qualitative data were collected via focus groups among field experts (n = 17, 52.9% female) using semi-structured, open-ended questions. Data were coded using an iterative process, first through the development of provisional themes and subthemes, followed by independent line-by-line coding by two coders. Most participants routinely used molecular methods for HIV surveillance. All agreed that linking molecular sequences to epidemiological data is important for improving HIV surveillance. We found that, in addition to methodological challenges, a variety of implementation barriers are expected in relation to the uptake of phylodynamic methods for HIV surveillance. The participants identified several opportunities to enhance current methods, as well as increase the usability and utility of promising works-in-progress.

Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria

“…In this study, we reconstructed and analyzed transmission networks of CRF01_AE, the most prevalent recombinant form of HIV-1 in Bulgaria, by combining traditional epidemiological data with HIV-1 pol sequences collected through 2019 and conducting phylogenetic and network analyses. Our phylodynamic approach has been used successfully before for the subtype B sub-epidemic in Bulgarian [ 30 ] and these methods are becoming standard analyses for cluster and outbreak investigations for HIV prevention [ 31 , 32 , 33 , 34 ]. We found that CRF01_AE infections grew into a large sub-epidemic among PWID, after it was first introduced into Bulgaria, most likely from Vietnam, with some onward transmission to other European countries.…”

The impact of armed conflict on the prevalence and transmission dynamics of HIV Infection in Libya.

“…Furthermore, population displacement may be re ected in the treatment of HIV-infected individuals as patients who had to relocate because of the con ict may be more likely to reduce treatment adherence. Hence then the spread of HIV-1 strains is becoming a serious public health challenge that requires further studies to understand deeply their origin and distribution (29). Different comments should be raised concerning the limitations of this study.…”

Early emergence phase of SARS-CoV-2 Delta variant in Florida

“…Last, we assessed variation in relative transmission dynamics among individual clades as well as local Florida sub-trees within each clade in the context of mutational patterns. For each cluster, we calculated the Oster statistic, which is a function of the size in tips, the sum of the branch lengths, and the length of the longest branch within an individual subtree [45,46]. This method was recently developed to infer transmission rates using human immunodeficiency virus (HIV) sequencing data.…”