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

Abstract

Co-infection with two SARS-CoV-2 variants is rarely detected, but may have clinical implications and is hypothesized to be a precursor to SARS-CoV-2 variant recombination. It is therefore important to rapidly identify co-infection cases. Here, we report two cases of co-infection detected during routine genomic surveillance. Both samples were initially suspected to have been cross-contaminated due to the unusual number of private mutations identified by Nextclade and positions flagged for nucleotide mixtures by Bammix. To rule out cross-contamination, we decontaminated the workspaces and resequenced the samples. However, the anomalies remained and the samples were therefore investigated for co-infection. To validate this hypothesis, we created a bioinformatics pipeline to determine the lineages present in the samples, performedde novoassembly, and investigated the alternative allele fraction of mutations mapping to both variants. Freyja was used and showed an estimated lineage abundance of 49.81% and 48.09% for Delta and Omicron, respectively, in the first sample. For the second sample, Delta had 82.76% abundance and Omicron had 4.99% abundance, with the presence of 12.24% abundance for other variants. Our findings support that the first sample is a case of co-infection of Delta and Omicron variants while the second sample is a cryptic co-infection of both variants, potentially undergoing recombination events. This study highlights the importance of developing a more stringent bioinformatics workflow to identify co-infection cases in genomic surveillance.