Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

Abstract

Tracking the evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through genomic surveillance programs is undoubtedly one of the key priorities in the current pandemic situation. Although the genome of SARS-CoV-2 acquires mutations at a slower rate compared with other RNA viruses, evolutionary pressures derived from the widespread circulation of SARS-CoV-2 in the human population have progressively favored the global emergence, though natural selection, of several variants of concern that carry multiple non-synonymous mutations in the spike glycoprotein. These are often placed in key sites within major antibody epitopes and may therefore confer resistance to neutralizing antibodies, leading to partial immune escape, or otherwise compensate infectivity deficits associated with other non-synonymous substitutions. As previously shown by other authors, several emerging variants carry recurrent deletion regions (RDRs) that display a partial overlap with antibody epitopes located in the spike N-terminal domain (NTD). Comparatively, very little attention had been directed towards spike insertion mutations prior to the emergence of the B.1.1.529 (omicron) lineage. This manuscript describes a single recurrent insertion region (RIR1) in the N-terminal domain of SARS-CoV-2 spike protein, characterized by at least 49 independent acquisitions of 1-8 additional codons between Val213 and Leu216 in different viral lineages. Even though RIR1 is unlikely to confer antibody escape, its association with two distinct formerly widespread lineages (A.2.5 and B.1.214.2), with the quickly spreading omicron and with other VOCs and VOIs warrants further investigation concerning its effects on spike structure and viral infectivity.

Update on SARS-CoV-2 Omicron Variant of Concern and Its Peculiar Mutational Profile

“…Notably, a recent study has shown that this insertion is present also in seasonal coronaviruses HCoV-229E, thus leading to the hypothesis that it could have been acquired by template switching involving the genomes of HCoV-229E and SARS-CoV-2 in coinfected patients ( 5 ). Notably, a recent structure-based study has speculated that this insertion was not related to immune escape due to lack of overlap with known immune epitopes ( 43 ). No information on the functional role of this insertion is known so far.…”

Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein

“…The recurrent emergence of insertions (between R214 and D215) in the NTD, and their progressive increase in multiple lineages, including VOC have been recently documented. 54 It is important to note that many indel positions are highly variable due to independent/multiple origins of indels 27,53 and/or nearby substitutions that affect alignment. Indels have special relevance as they can fine-tune the 3D structure beyond point mutations and are known to occur in surface-exposed loops.…”

Independent acquisition of short insertions at the RIR1 site in the spike N-terminal domain of the SARS-CoV-2 BA.2 lineage

“…All resulting genomes were grouped based on the inserted nucleotide sequence, whose exact position and phase of insertion were defined based on the alignment with the reference SARS-CoV-2 genome sequence (Wuhan-Hu-1, NCBI accession ID: NC_045512.2) and a reference BA.2 genome (EPI_ISL_8128502). Following the nomenclature scheme proposed in our previous work (Gerdol et al, 2022), each of these groups was labeled with progressive Roman numerals, following their chronological order of identification, starting from insertion L.…”