Investigation of the genome size effects of in vivo and in vitro serial passages of local SARS-CoV-2 isolate

The world is still grappling with the SARS-CoV-2 pandemic, which 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 next-generation sequencing (NGS) platform and the Paragon CleanPlex® SARS-CoV-2 panel. The raw sequence data were then analyzed using various bioinformatics tools such as Genome Detective, Unipro UGENE and Geneious Prime workflows to investigate the genome size effects in the genetic material of the isolates. 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 nonsynonymous 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.