PT  - JOURNAL ARTICLE
AU  - R. Shyama Prasad Rao
AU  - Nagib Ahsan
AU  - Chunhui Xu
AU  - Lingtao Su
AU  - Jacob Verburgt
AU  - Luca Fornelli
AU  - Daisuke Kihara
AU  - Dong Xu
TI  - Evolutionary dynamics of indels in SARS-CoV-2 spike glycoprotein
AID  - 10.1101/2021.07.30.454557
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.07.30.454557
4099  - http://biorxiv.org/content/early/2021/08/01/2021.07.30.454557.short
4100  - http://biorxiv.org/content/early/2021/08/01/2021.07.30.454557.full
AB  - SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 4.2 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2 that are currently posing a serious challenge to the global vaccination effort and COVID-19 management. The evolutionary dynamics of this virus are only beginning to be explored. In this work, we have analysed 1.79 million spike glycoprotein sequences of SARS-CoV-2 and found that the virus is fine-tuning the spike with numerous amino acid insertions and deletions (indels). Indels seem to have a selective advantage as the proportions of sequences with indels were steadily increasing over time, currently at over 89%, with similar trends across countries/variants. There were as many as 420 unique indel positions and 447 unique combinations of indels. Despite their high frequency, indels resulted in only minimal alteration, including both gain and loss, of N-glycosylation sites. As indels and point mutations are positively correlated and sequences with indels have significantly more point mutations, they have implications in the context of evolutionary dynamics of the SARS-CoV-2 spike glycoprotein.Competing Interest StatementThe authors have declared no competing interest.