MSH3 Homology and Potential Recombination Link to SARS-CoV-2 Furin Cleavage Site

Balamurali K Ambati,Bruce D Uhal,Vladimir N Uversky,Giorgio Palú,Akhil Varshney,Kenneth Lundstrom,Adam M Brufsky

doi:10.3389/fviro.2022.834808

Abstract

Among numerous point mutation differences between the SARS-CoV-2 and the bat RaTG13 coronavirus, only the 12-nucleotide furin cleavage site (FCS) exceeds 3 nucleotides. A BLAST search revealed that a 19 nucleotide portion of the SARS-CoV-2 genome encompassing the furin cleavage site is a 100% complementary match to a codon-optimized proprietary sequence that is the reverse complement of the human mutS homolog (MSH3). The reverse complement sequence present in SARS-CoV-2 may occur randomly but other possibilities must be considered. Recombination in an intermediate host is an unlikely explanation. Single stranded RNA viruses such as SARS-CoV-2 utilize negative strand RNA templates in infected cells, which might lead through copy choice recombination with a negative sense SARS-CoV-2 RNA to the integration of the MSH3 negative strand, including the FCS, into the viral genome. In any case, the presence of the 19-nucleotide long RNA sequence including the FCS with 100% identity to the reverse complement of the MSH3 mRNA is highly unusual and requires further investigations.

Highlights

Based on a recent publication describing insertion variants of SARS-CoV-2 [1] we would like to bring the attention to our recent findings related to the sequence of the furin cleavage site (FCS) in SARS-CoV-2 Spike (S) protein
Examination of SEQ ID11652 revealed that the match extends beyond the 12-nucleotide insertion to a 19-nucleotide sequence: 5′-CTACGTGCCCGCCGAGGAG3′, such that the resulting mRNA would have 3′- GAUGCACGGGCGGCUCCUC-5′, or equivalently 5′- CU CCU CGG CGG GCA CGU AG-3′
While a portion of a reverse complement sequence being present in SARS-CoV-2 could be a random coincidence, other possibilities merit consideration

Summary

INTRODUCTION

Based on a recent publication describing insertion variants of SARS-CoV-2 [1] we would like to bring the attention to our recent findings related to the sequence of the furin cleavage site (FCS) in SARS-CoV-2 Spike (S) protein. Examination of SEQ ID11652 revealed that the match extends beyond the 12-nucleotide insertion to a 19-nucleotide sequence: 5′-CTACGTGCCCGCCGAGGAG3′ (nt 2733-2751 of SEQ ID11652), such that the resulting mRNA would have 3′- GAUGCACGGGCGGCUCCUC-5′, or equivalently 5′- CU CCU CGG CGG GCA CGU AG-3′ (nucleotides 23547-23565 in the SARS-CoV-2 genome, in which the four bold codons yield PRRA, amino acids 681–684 of its spike protein). This is very rare in the NCBI BLAST database. We did not find the 19-nucleotide sequence CTCCTCGGCGGGCACGTAG in any eukaryotic or viral genomes except SARS-CoV-2 with 100% coverage and identity in the BLAST database (Supplementary Tables 1–3)

DISCUSSION

DATA AVAILABILITY STATEMENT