Detecting Delta and Omicron co-infection cases in the Philippines during SARS-CoV-2 genomic surveillance

Co-infection with two SARS-CoV-2 variants is rarely detected. This may have clinical implications and is hypothesized to be a precursor to SARS-CoV-2 variant recombination, therefore, it is important to rapidly identify these cases during genomic surveillance. We created a pipeline to determine the lineages present in the samples, performed de novo assembly, and investigated the alternative allele fraction of mutations mapping to Omicron and Delta variants. This study highlights the importance of developing a more stringent bioinformatics workflow to identify co-infection cases in genomic surveillance.