HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.

摘要: In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoe-leather' epidemiology infers by tracing chains partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying analog such clusters: HIV-TRACE (TRAnsmission Cluster Engine). implements an approach inspired traditional whose viral relatedness imply direct or indirect connections. Molecular constructed using codon-aware pairwise alignment reference followed distance estimation among all sequences. This is computationally tractable and capable HIV-1 large surveillance databases comprising tens hundreds thousands sequences near real time, that is, on the order minutes hours. available at www.hivtrace.org from www.github.com/veg/hivtrace, along with accompanying result visualization module www.github.com/veg/hivtrace-viz. Importantly, underlying not limited study can be applied outbreaks epidemics other pathogens.