Fig. 1

Framework for identifying population-level SARS-CoV-2 strains and lower frequency quasispecies through pangenome analysis. a GISAID currently has thousands of SARS-CoV-2 genomic sequences banked. By analyzing large numbers of viral genomes together (blue lines), one can pinpoint sequences that are present only once in a given genome but also occur consistently across all genomes (red, green, yellow, and purple bars). These unique and conserved sequences can be used for a number of research and clinical sequencing applications. b This knowledge can fuel epidemiological studies and allow scientists to characterize major SARS-CoV-2 strains. The green, orange, and pink figures represent contagious individuals who contribute to the transmission of a virus within a population. c The targeted sequencing enables the detection of low-frequency quasispecies that are created through de novo mutations within an individual. The mutation profile from pangenome analysis allow us to examine whether these mutations create a unique genetic profile that can be traced to and across individuals