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.