Analysis of SARS-CoV-2 sequences reveals transmission path and emergence of S-D (614G) mutation

Li, M. J.; Prasad, N.; Hall, D.; Wu, H. M.

The coronavirus disease 2019 (COVID-19) outbreak caused by SARS-CoV-2 virus began in Wuhan, China, and has spread quickly throughout the world. The development of vaccines for SARS-CoV-2 is difficult due to many obstacles, such as the lack of knowledge of important proteins, genes, and mutations of the viral genome. In this study, we selected and utilized 852 strains of COVID-19 from major countries in the National Center for Biotechnology Information (NCBI) global virus bank. The information of these strains was processed by using Nextstrain software, a program that provided a visual phylogenetic tree, transmission map, and diversity panel that explains entropy and number of mutations for each codon in the genome. The general data about the spread and evolution of COVID-19 supported the current knowledge that it began in China and spread throughout the country in an interrelated manner instead of a clear "patient zero" manner. A recent study reported that codon 614 on COVID-19 spike protein (S614) was an important codon for viral spread, specifically, a mutation from aspartic acid to glycine facilitated the spread of the virus. Therefore, we chose to geographically track this mutation during the spread of COVID-19 to investigate where it emerged and whether it can affect the spread COVID-19. Our results showed that the glycine mutation first emerged in France. Also, the transmission rates in France versus China, where the mutation was not prevalent, did reflect the hypothesized change in viral behavior.