δ1 variant of SARS-COV-2 acquires spike V1176F and yields a highly mutated subvariant in Europe

Abstract

Genomic surveillance of SARS-COV-2 has revealed that in addition to many variants of interests, this virus has yielded four variants of concern, , {beta}, {gamma} and {delta}, as designated by the World Health Organization. {delta} variant has recently become the predominant pandemic driver around the world and yielded four different subvariants ({delta}1, {delta}2, {delta}3 and {delta}4). Among them, {delta}1 has emerged as the key subvariant that drives the pandemic in India, Europe and the USA. A relevant question is whether {delta}1 subvariant continues to evolve and acquires additional mutations. Related to this, this subvariant has acquired spike V1176F, a signature substitution of {gamma} variant, and yielded a new sublineage, {delta}1F. The substitution alters heptad repeat 2 of spike protein and is expected to improve interaction with heptad repeat 1 and enhance virus entry. Moreover, there are {delta}1F sublineages encoding spike N501Y, A783S, Q836E and V1264L. While N501Y is a signature substitution shared by , {beta} and {gamma} variants, V1264L is a key substitution in a {delta}1 sublineage that is a major pandemic driver in Southeast Asia. The Q836E-encoding lineage carries an average of 50 mutations per genome, making it the most mutated variant identified so far. Similar to {delta}1 subvariant, {delta}2 subvariant has also acquired spike V1176F and yielded new sublineages. Together, these results suggest that V1176F is a recurrent spike substitution that is frequently acquired by SARS-COV-2 variants to improve viral fitness. It is thus important to track the evolutionary trajectory of related variants for considering and instituting the most effective public health measures.