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Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) needs human samples, which inevitably contain trace human DNA and RNA. Sequence similarity may cause invalid detection results; however, there is still a lack of gene similarity analysis of SARS-CoV-2 and humans. All publicly reported complete genome assemblies in the Entrez genome database were collected for multiple sequence alignment, similarity and phylogenetic analysis. The complete genomes showed high similarity (>99.88% sequence identity). Phylogenetic analysis divided these viruses into three major clades with significant geographic group effects. Viruses from the United States showed considerable variability. Sequence similarity analysis revealed that SARS-CoV-2 has 612 similar sequences with the human genome and 100 similar sequences with the human transcriptome. The sequence characteristics and genome distribution of these similar sequences were confirmed. The sequence similarity and evolutionary mutations provide indispensable references for dynamic updates of SARS-CoV-2 detection primers and methods.