Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination
Description
We hypothesized that some individuals may be co-infected by Delta and Omicron, or that some individuals may be infected by a virus resulting from the recombination of Delta and Omicron during a period when the two SARS-CoV-2 variants were co-circulating. To identify co-infection and recombinant samples, we looked at the sequencing results of SARS-CoV-2 genomes. We specifically looked and visualized the alternate allele fraction for mutations specific to Delta and mutations specific to Omicron. For co-infection samples, we expect that all of the mutations specific to Delta and all of the mutations specific to Omicron be present with complementary alternate allele fractions. While the sequencing of viruses resulting from a recombination will show all of the mutations specific to one variant on the 5'-end and all of the mutations specific to the other variant on the 3'-end. Importantly the alternate allele fraction at each site should be either 0 or 1 for sequences of a virus resulting from a clonal recombination. In this repository, we have the python code used to visualize the alternate allele fractions. This code was used to create the figures of our manuscript. In this repository, we also have the supplemental tables of the paper, which have all of the raw data that were used to create the figures of the paper.