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.
Keywords: ACE2, angiotensin-converting enzyme-2; COVID-19, Coronavirus disease; CT, cycle threshold; D614G mutation; Different geographic origins; E, envelope; M, membrane; Mutational hotspots; N, nucleocapsid; NGS, next-generation sequencing; Nsp3, nonstructural protein; Orf, open reading frame; RDB, receptor-binding domain; RT-qPCR, reverse transcriptase-quantitative polymerase chain reaction; RdRp, RNA-dependent RNA polymerase; S, Spike; SARS-CoV-2; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; Spike gene; Spike protein; TMPRSS2, transmembrane serine protease2.
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