Investigation of the Genome Size Effects of In Vivo and In Vitro Serial
Passages of the Local SARS-CoV-2 Isolate
Abstract
The SARS-CoV-2 pandemic has affected many aspects of our lives. The
scientific community is in awe of the SARS-CoV-2 virus’s ability to
evolve through mutations that affect its transmission bottlenecks and
ability to evade the host immune system. In this study, we aimed to gain
a better understanding of the genomic changes that might occur during
serial passaging of the local SARS-CoV-2 Ank1 isolate. The local
SARS-CoV-2 isolate was serially passaged ten times in vitro and
in vivo (Vero E6 cells and type 1 interferon knockout transgenic
mice (IFNAR-/-), respectively). Whole genome sequencing of the isolates
was performed using the Illumina NextSeq 550 platform and the Paragon
CleanPlex® SARS-CoV-2 panel. The Genome Detective tool was used to
analyze the raw sequence data. According to our results, in vitro
passaging, at passage number 10, four non-synonymous substitutions and
two synonymous substitutions were detected compared to the original
isolate. Interestingly, in vivo passaging, at passages 9 and 10,
two additional non-synonymous substitutions were observed. Our obtained
result indicated that the SARS-CoV-2 passaging processes in vitro
and in vivo affect its genome, we speculated that the host
environments obtained in the laboratory selectively pressed on the
isolate.