Journey

SARS-CoV-2 Spike Protein and MSH3

Source: 21 Feb 2022: MSH3 Homology and Potential Recombination Link to SARS-CoV-2 Furin Cleavage Site

A peculiar feature of the nucleotide sequence encoding the PRRA furin cleavage site in the SARS-CoV-2 S protein is its two consecutive CGG codons. This arginine codon is rare in coronaviruses: relative synonymous codon usage (RSCU) of CGG in pangolin CoV is 0, in bat CoV 0.08, in SARS-CoV 0.19, in MERS-CoV 0.25, and in SARS-CoV-2 0.299.

A BLAST search for the 12-nucleotide insertion led us to a 100% reverse match in a proprietary sequence (SEQ ID11652, nt 2751-2733) found in the US patent 9,587,003 filed on Feb. 4, 2016 (Figure 1).

• U.S. patent number 9,587,003 [Application Number 15/015,684] was granted by the patent office on 2017-03-07 for modified polynucleotides for the production of oncology-related proteins and peptides. This patent grant is currently assigned to ModernaTX, Inc.. The grantee listed for this patent is Moderna Therapeutics, Inc.. Invention is credited to Stephane Bancel, Tirtha Chakraborty, Antonin de Fougerolles, Kenechi Ejebe, Sayda M. Elbashir, Jeff Lynn Ellsworth, Justin Guild, Paul Hatala, Matthias John, Atanu Roy, Jason P. Schrum, Susan Whoriskey, Kristy M. Wood.
  • US10501513B2 Modified polynucleotides for the production of oncology-related proteins and peptides
  • US9587003B2 Modified polynucleotides for the production of oncology-related proteins and peptides

Figure 1

Figure 1. The origin of the furin sequence in SARS-CoV-2. Comparison of the protein sequences at the S1/S2 junction in SARS-CoV, RaTG13, and SARS-CoV-2 demonstrating the presence of the furin cleavage site (FCS) PRRA only in SARS-CoV-2. Based on a BLAST search of the 12-nucleotide stretch coding for the FCS PRRA, a 19-nucleotide long identical sequence was identified in the patented (US 958 7003) sequence Seq ID11652. SEQ ID11652 is transcribed to a MSH3 mRNA that appears to be codon optimized for humans. This 19-nucleotide sequence including 12 nucleotides coding for the FCS PRRA, present in the human MSH3 gene might have been introduced into the SARS-CoV-2 genome by the illustrated copy choice recombination mechanism in SARS-CoV-2 infected human cells overexpressing the MSH3 gene.

• Examination of SEQ ID11652 revealed that the match extends beyond the 12-nucleotide insertion to a 19-nucleotide sequence: 5′-CTACGTGCCCGCCGAGGAG-3′ (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.
• MSH3 replacement with a codon-optimized mRNA sequence for human expression likely has applications in cancers with mismatch repair deficiencies. While a portion of a reverse complement sequence being present in SARS-CoV-2 could be a random coincidence, other possibilities merit consideration.
• Overexpression of MSH3 is known to interfere with mismatch repair (MSH2 sequestration from the MutS alpha complex comprising MSH2 and MSH6 results in MSH6 degradation and MutS alpha depletion), which holds virologic importance.
• Induction of DNA mismatch repair deficiency results in permissiveness of influenza A virus (IAV) infection of human respiratory cells and increased pathogenicity.
• Mismatch repair deficiency may extend shedding of SARS-CoV-2
• The presence in SARS-CoV-2 of a 19-nucleotide RNA sequence encoding an FCS at amino acid 681 of its spike protein with 100% identity to the reverse complement of a proprietary MSH3 mRNA sequence is highly unusual. Potential explanations for this correlation should be further investigated.