Elsevier

Gene Reports

Volume 23, June 2021, 101100
Gene Reports

Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins

https://doi.org/10.1016/j.genrep.2021.101100Get rights and content

Highlights

  • D614G mutation in SARS-CoV-2 spike protein increases the viral infectivity.

  • Our sequencing method can efficiently detect six mutational hotspots including D614G.

  • D614G is a predominant variant in clinical isolates from different geographical regions.

  • Analysis of publicly available 113,381 sequences shows the highest predominance of D614G globally.

  • Virus carrying D614G is more likely to infect and spread in North America and Europe than in East Asia.

Abstract

The spike (S) protein mutations of SARS-CoV-2 are of major concern in terms of viral transmission and pathogenesis. Hence, we developed a PCR-based method to rapidly detect the 6 mutational hotspots (H49Y, G476S, V483A, H519Q, A520S, and D614G) in the S protein and applied this method to analyze the hotspots in the viral isolates from different geographical origins. Here, we identified that there was only the D614G mutation in the viral isolates. As of September 30, 2020, the analysis of 113,381 sequences available from the public repositories revealed that the SARS-CoV-2 variant carrying G614 has become the most prevalent form globally. Our results support recent epidemiological and genomic data demonstrating that the viral infectivity and transmission are enhanced by the S protein D614G mutation.

Abbreviations

COVID-19
Coronavirus disease
SARS-CoV-2
severe acute respiratory syndrome coronavirus 2
S
Spike
E
envelope
M
membrane
N
nucleocapsid
RdRp
RNA-dependent RNA polymerase
RT-qPCR
reverse transcriptase-quantitative polymerase chain reaction
CT
cycle threshold
ACE2
angiotensin-converting enzyme-2
TMPRSS2
transmembrane serine protease2
Nsp3
nonstructural protein
Orf
open reading frame
RDB
receptor-binding domain
NGS
next-generation sequencing

Keywords

SARS-CoV-2
Spike protein
Spike gene
Mutational hotspots
D614G mutation
Different geographic origins

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