RT Journal Article
SR Electronic
T1 Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.22.440932
DO 10.1101/2021.04.22.440932
A1 Sarah Cherian
A1 Varsha Potdar
A1 Santosh Jadhav
A1 Pragya Yadav
A1 Nivedita Gupta
A1 Mousmi Das
A1 Soumitra Das
A1 Anurag Agarwal
A1 Sujeet Singh
A1 Priya Abraham
A1 Samiran Panda
A1 Shekhar Mande
A1 Renu Swarup
A1 Balram Bhargava
A1 Rajesh Bhushan
A1 NIC team
A1 INSACOG Consortium
YR 2021
UL http://biorxiv.org/content/early/2021/04/24/2021.04.22.440932.abstract
AB As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being constantly used to investigate its transmissions and evolution. In the backdrop of the global emergence of “variants of concern” (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches was undertaken to identify possible new variants and gauge the fitness of current circulating strains.Phylogenetic analysis revealed that the predominant clade in circulation was a distinct newly identified lineage B.1.617 possessing common signature mutations D111D, G142D, L452R, E484Q, D614G and P681R, in the spike protein including within the receptor binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R and E484Q along with P681R in the furin cleavage site, may possibly result in increased ACE2 binding and rate of S1-S2 cleavage resulting in better transmissibility. The same two RBD mutations indicated decreased binding to selected monoclonal antibodies (mAbs) and may affect their neutralization potential. Experimental validation is warranted for accessing both ACE2 binding and the effectiveness of commonly elicited neutralizing mAbs for the strains of lineage B.1.617.The emergence of such local variants through the accumulation of convergent mutations during the COVID-19 second wave needs to be further investigated for their public health impact in the rest of the country and its possibility of becoming a VOC.Competing Interest StatementThe authors have declared no competing interest.