The whole genome sequence of SARS-CoV-2 was sequenced using the BTSeqTM SARS-CoV-2 WGS Service (Celemics Inc., Seoul, Korea). Reverse transcriptase was used to synthesize complementary DNA (cDNA). The viral cDNA library was amplified with primers designed based on a published SARS-CoV-2 sequence database (data not shown). Using the amplified DNA, a DNA library was constructed through DNA fragmentation, end repair, adaptor ligation, and PCR amplification for next-generation sequencing (NGS). The DNA library was purified with CeleMag DNA Clean-up Beads (Celemics Inc.). Quantification was conducted using an Agilent 2200 TapeStation (Agilent Technologies, Sta. Clara, CA, United States). After quantification, NGS was performed using a MiSeq next-generation sequencer with 150PE (Illumina, San Diego, CA, United States). Sequence data were imported as fastq files and edited using the CLC Genomics Workbench 11.0.1. All low quality (<0.05), ambiguous (0), short (under 64 nucleotides), and adapter sequences were removed in the trimming procedure. Trimmed reads were mapped to a reference strain (GenBank number MN908947.3). Intrahost variant analysis of SARS-CoV-2 was performed against the genome of seed virus using the basic variant analysis in the CLC Genomics Workbench 11.0.1. Minor alleles were identified based on criteria of >50 read depth, >5% minor allele frequency, and >5 minor allele count. The frequency difference of the major and minor alleles was statistically verified using Fisher’s exact test, with a p ≤ 0.05 considered statistically significant.

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