High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants

Conclusions Genomic surveillance promises to shed light on outbreak dynamics; however, when the rate of outbreak expansion exceeds the evolutionary rate, there may be insufficient resolution in consensus analysis to adequately track phylogenetic relationships. Advances in sequencing technologies now allow discovering very rare variants present in 1 out of 1,000 viral particles in each patient.6 The study of viral evolutionary dynamics will benefit from treating patients as populations of viruses rather than a collection of single genomes. Our application of Nei’s standard genetic distance in reconstruction phylogenetic relationships incorporates population genetics methodologies. Tracking shared subclonal variants provides further information when tracking disease transmission and enhances resolution of evolutionary relationships to scales in the order of transmission time. In addition, the information from SSV helps elucidate transmission processes beyond traditional consensus-based approaches, informing on the number of viral particles involved and potential sources of coinfections. A caveat of our method is that it does not incorporate temporal information. Time in the case of 2014 ebolavirus outbreak can be a confounder, as the reported sampling time will not reflect where in the course of the infection a patient currently resides. This is of particularly important concern when the time scale of data collection is very short, on the same order as the infection perio...
Source: PLOS Currents Outbreaks - Category: Epidemiology Authors: Source Type: research