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

SNVs and quasispecies that are observed at low frequency could represent viral variations of low impact on the functionality of the genome. However, their abundance is largely affected by the population size and the epidemic characteristics. For example, a neutral substitution in a region that represents a primer target for a molecular diagnostic assay can drift to fixation rather quickly in a rapidly spreading virus, jeopardizing the sensitivity of the assay [38], [39] . Here, we highlight three intra-host but also two fixed variants that colocalized with primers or probes of real-time PCR diagnostics assays that are currently in use ( Figure 2 ). Since the alignment of these oligos with their genomic targets is directly linked to the performance of the corresponding diagnostic assays, the community should pay extra attention in the evaluation of these potentially emerging variations and be alerted, in case redesigning of these oligos is needed.