SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

Timokratis Karamitros; Gethsimani Papadopoulou; Maria Bousali; Anastasios Mexias; Sotiris Tsiodras; Andreas Mentis

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.27.009480 doi: bioRxiv preprint HCoV-229E, recombination breakpoints are located near 3'-and 5'-end of the gene [1] [47] . S is a trimeric protein, which is cleaved into two subunits, the globular N-terminal S1 and the Cterminal S2 [48] . The S1 subunit consists of a signal peptide and the NT and receptor binding (RB) domains, with the latter sharing only 40% amino acid identity with other SARS-related CoVs. Our analysis revealed that similarly to other genomic regions, the S1 subunit hosts many low-frequency SNVs, characterized by higher density compared to the rest of the S gene sequence (Figure 1-E) . The S2 subunit is highly conserved, with 99% identity compared to human SARS-CoV and two bat SARS-like CoVs [9] . The S2 subunit consists of two fusion peptides (FP, IFP), followed by two heptad repeats (HR 1 and 2) , the pretransmembrane domain (PTM), the transmembrane and the cytoplasmic domain (TM, CP) [48] . In S gene, the same rearrangement event has taken place in two samples analyzed in this study. This observation highlights a potential recombination hot-spot in S gene. The rearrangement that was common between the two samples of this study is located in nt24,000 of the 2019-nCoV genome, which corresponds to the ~200nt linking region between the fusion peptides FP and IFP (aa 812-813). Examining closely the secondary structure of the RNA genome around the breakpoints, we suggest a model where the palindromes 5'-UGGUUUU-3' and 5'-AAAACCAA-3', have served as donor-acceptor sequences during the recombination event, since they are both exposed in the single-stranded internal loops formed in a highly structured RNA pseudoknot (Figure 3-C) . The RB domain of the S protein has been tested as a potential immunogen as it contains neutralization epitopes which appear to have a role in the induction of neutralizing antibodies [16] , [49] . It should be mentioned though that S protein of SARS-CoV is the most divergent in all strains infecting humans [50], [51] , as in both C and N-terminal domains variations arise rapidly, allowing immunological escape [52] . Our findings support that apart from these variations, the N-terminal region also hosts a recombination hot-spot, which together with the rest of the observed rearrangements, indicates the genomic instability of SARS-CoV-2 over poly-A and poly-U regions. author/funder. All rights reserved. No reuse allowed without permission.