A Method of Identification of SARS-CoV-2 Variant Using NCBI BLAST-2 100% Homology Search with Specific Oligonucleotides Selected at the Deletion Boundaries of S, N, ORF7a, ORF8 and ORF1ab Proteins

Genomic sequencing of many SARS-CoV-2 variants with higher transmission and immune-escape were reported due to point mutations and deletions. Thus, whether a newly sequenced SARS-CoV-2 belongs to Alpha, Beta, Gamma, Delta, or Omicron (BA.1, BA.2, BA.4 and BA.5) variants must be known. We multi-aligned the different Spike, ORF1ab and Nucleocapsid proteins of those corona virus variants and detected different lineage specific deletions and point mutations. Different COVID-19 sequences were aligned with CLUSTAL Omega software and oligonucleotides from deletion boundary were selected. BLAST search using those oligonucleotides clearly predicted the specific variant type with 100% homology and was very useful for new corona virus sequence characterization. Selection of sub-variants were done by oligonucleotides selected at the specific point mutation boundaries leading to amino acid change. COVID-19 variant status was not reported in most published corona virus sequences and this method would be very useful application to understand the nature of expected prognosis of corona virus infected patients in less technology-equipped countries.