Recombinant And Mix-Infection Finder for SARS-CoV-2 sample
The scientific and public health communities responded to the COVID-19 pandemic with sample acquisition and genome sequencing on a scale that eclipsed all prior sequencing efforts. While this can only be characterized as a resounding success story that has cemented the use of genomics for epidemiological investigations for any future infectious disease outbreak, several retrospective studies are cataloging an array of lessons learned and issues that have yet to be addressed in order to realize the full potential of genomics as a routine biosurveillance tool. We have been both developing methods to accurately assess SARS-CoV-2 genomes from complex samples, and analyzing the large volumes of international data, both at the consensus level and the raw sequencing data. During the course of our investigations and similar to other groups, we have examined COVID-19 samples with signatures from multiple lineages of SARS-CoV-2 and will describe some of our findings during the development of a novel workflow that incorporates detection and reporting of potential co-infection within samples and also highlights any evidence of within-host recombination.