Fig. 3: Population and phylogenetic analysis of two cases of SARS-CoV-2 co-infection with Delta and Omicron VOCs.
From: Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance
A Population analysis of key lineage-defining mutations in the SARS-CoV-2 spike gene for each specimen. Nucleotide frequency and relative coverage of genomic regions specific for either Omicron or Delta. The X-axis represents genomic positions and Y-axis indicates their relative frequencies derived from RVOP data. B Unrooted maximum likelihood phylogeny representing the sequences obtained from Cases A, B and C in the context of global diversity of SARS-CoV-2. Genomes generated as part of this study are labelled individually. The predominant Delta lineage in Australia, AY.39.1, is highlighted. The Delta strains from cases A and B are from separate clades of AY.39.1 circulating in Australia, whereas the two Omicron strains are both in the same sub-lineage of Omicron (BA.1) which dominated in Australia in December 2021–January 2022. Note that the Omicron samples from patients A and C are identical and hence overlap. Branch lengths are scaled according to the number of nucleotide substitutions per site.
