Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina

Dynamics of HIV-1 Molecular Networks Reveal Effective Control of Large Transmission Clusters in an Area Affected by an Epidemic of Multiple HIV Subtypes

“…Clusters with ≥ 10 cases and between two and nine cases were defined as large and small/medium clusters, respectively. The definition of a large cluster is similar to that used in previous studies (Hughes et al, 2009;Leigh Brown et al, 2011;Lorenzin et al, 2019;Rhee et al, 2019;Dennis et al, 2020). We evaluated demographic features of the study population including the time of diagnosis, sex, risk group, age, ethnic group, resident city, marital status, education, and occupation.…”

“…HIV molecular networks can be used not only to guide targeted intervention in key subpopulations (Aldous et al, 2012;Lubelchek et al, 2015;Castley et al, 2017;Chaillon et al, 2017;Zhang et al, 2017;Stecher et al, 2018;Volz et al, 2018;Ragonnet-Cronin et al, 2019;Board et al, 2020), but also to reconstruct the history of HIV spread between populations (Kouyos et al, 2010;Brenner et al, 2017;Pineda-Pena et al, 2018;Delgado et al, 2019;Fabeni et al, 2019). Several local and national studies conducted in recent years have monitored the dynamics of HIV molecular clusters and evaluated their expansion speed (Chan et al, 2015;Mehta et al, 2018;Ragonnet-Cronin et al, 2018;Wertheim et al, 2018;Jovanovic et al, 2019;Dennis et al, 2020). However, most of these studies focused on areas with only subtype B or C HIV-1 epidemics, and few local studies have reconstructed HIV transmission history in an area with multiple HIV subtypes, which may be more complicated because of the variable transmission dynamics and evolution rates of different HIV-1 strains in the population.…”

Molecular network-based intervention brings us closer to ending the HIV pandemic

“…Software packages (BEAST 1 and BEAST 2) are widely used for phylodynamic and phylogeographic inference [19,20]. Several recent studies also used viral sequences with spatiotemporal characteristics to infer the origin and spread of transmission cluster or network through phylodynamic and phylogeographic approaches [21,22]. The basic idea of molecular network is to classify viral sequences according to genetic similarities.…”

“…Dennis et al revealed the transmission cluster expansion in North Carolina using densely sampled data and characterized active transmission clusters with phylodynamic analysis. They used effective reproductive number (Re) to monitor active clusters, which demonstrated the propensity of steady onward propagations [21]. Another phylodynamic analysis study in Serbia revealed that the Re remained over one during the complete period of the investigation; an MSM transmission group of subtype B was determined to have a recent tMRCA and steep growth curve until 2030, whereas heterosexuals with both subtypes B and C displayed minor growth and stagnation [34].…”

“…The estimated Re of the active clusters was remarkably higher than that of the historical clusters. Determining actively growing clusters is crucial to optimize the approaches for public health responses, and an effective intervention would be expected to reduce the Re [21,84].…”