SARS-CoV-2 against Streptococcus pneumoniae Genome by Blast Analysis

Introduction: The study was performed by blastn analysis with SARS-Cov-2 against Streptococcus pneumoniae H17 genomic sequences. Considering there is no hitting when blast analysis with whole length of SARS-Cov-2, we spliced the SARS-Cov-2 virus genome sequence into segments of 1,000bp with sliding windows of 50bp, and then conducted blast analysis on these segments against sequences of Streptococcus pneumoniae. Methods: The genome sequence of SARS-Cov-2 virus were spliced into segments of 1,000bp length, with starting positions shifting from 1 to 950 at interval of 50bp. In total 20 sets of segments were created. The 20 sets of SARS-Cov-2 genome segments were compared against sequences of Streptococcus pneumoniae downloaded from NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/076/835/GCF_002076835.1_ASM207683v1/GCF_002076835.1_ASM207683v1_gen omic.fna.gz) with blastn tools (2.13.0+) on a linux server, respectively. Results: The hits/alignments on genome of Streptococcus pneumoniae reported by the blast analysis were retrieved with customized python scripts. Common hits across different sets of SARS- Cov-2 genome segments were merged. There are 590 hits reported by blast analysis between 576 SARS-Cov-2 segments and 576 Streptococcus pneumoniae sequences, after merging all the blast results from 20 sets of SARS-Cov-2 genome segments.