In order to further screen and identify SARS-CoV-2 accurately and to look for mutation sites which may be related to the ability of transmission and the intensity of symptoms, we have conducted metatranscriptome sequencing and hybrid capture-based sequencing for 12 imported cases confirmed COVID-19 back from Europe to Zhejiang province and 7 domestic SARS-CoV-2 infected cases from China. The result indicated that the capture sequencing samples have accurate mutation detection results, whereas the required data is only～1/10 or less of metatranscriptomic sequencing, which is a more suitable detection method for low viral load samples. Mutation analysis with reference genome (EPI_ISL_402119) showed that most of the domestic virus samples are ORF8:L84S mutation, foreign virus samples are mainly S:D614G mutation, and the rest of the samples were found 2 mutations in the virus gene ORF1a, namely ORF1a:C409S and ORF1a:P1207H. Variation analysis indicated that there are different mutation groups of the SARS-CoV-2 virus genomes in patients with SARS-CoV-2 between China and Italy. The detection of different single nucleotide variations (SNVs) between samples indicated the variation polymorphism of SARS-CoV-2 genomes. Analysis of intra-individual single nucleotide variations (iSNVs) of virus sequencing data in the same host indicated that the iSNVs in gene region of F06 and F11 were unexpectedly the same as the mutation of the other 5 samples from the same Italian restaurant, which indicated they might had co-infection in the same patient.