Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence

Shay Leary; Silvana Gaudieri; Abha Chopra; Suman Pakala; Eric Alves; Mina John; Suman Das; Simon Mallal; Phillips Jane Phillips

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.029454 doi: bioRxiv preprint polymorphisms L84S in ORF8, D614G in surface glycoprotein (S) and G251V in NS3 (ORF3a) that mark the major worldwide clades S, G and V, respectively. Two newly identified adjacent polymorphisms (R203K and G204R) in the nucleocapsid protein occur in approximately 13.4% of deposited strains and form one of the main strains emerging from Europe ( Figure 1A ). Other common polymorphisms include Q57H in NS3, T85I in NSP2, L37F in NSP6, P323L in the RNA-dependent RNA polymerase, T175M in the membrane glycoprotein and P504L and Y541C in the helicase. Current low frequency polymorphisms at <5% of deposited SARS-CoV-2 sequences include S193I in the nucleocapsid, H93Y in NS3, and the following polymorphisms V378I, G392D, I739V, P765S, A876T, F3071Y, G3278S and K3353R in ORF1ab (Supplementary Table 1 ).