SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

Timokratis Karamitros; Gethsimani Papadopoulou; Maria Bousali; Anastasios Mexias; Sotiris Tsiodras; Andreas Mentis

In all cases we isolated the same 5 SNVs with 98-100% read concordance, thus in total divergence with the reference strain (MN975262.1), which were excluded from the downstream analysis. For sample SRR10903401 we isolated 34 lower frequency SNVs in total. Off these, 33 were present with frequencies ranking between 2 and 15%, while only one was present in 40% of the intra-host viral population. The sequencing depth, which is also evaluated during the SNV calling by the LoFreq algorithm, ranked between 39x and 290x at the corresponding SNV positions. The sequencing depth of sample SRR10903402 at the polymorphic positions was substantially higher (103x -1137x), allowing the isolation of 55 SNVs with frequencies distributed between 0.9% and 14%. The depth over the polymorphic positions of sample SRR10971381 was between 159x -1872x, allowing the isolation of 10 intra-host SNVs, with frequencies 1.1% -6.8% (Figure 1 .A, Suppl. Table 2 ).