The SARS-CoV-2 infections in Thailand: Analysis of spike mutations complemented by protein structure insights

Thailand was the first country outside China to officially report COVID-19 cases. With a large number of SARS-CoV-2 sequences collected from patients, the effects of many genetic variations, especially those unique to Thai strains, are yet to be elucidated. In this study, we analyzed 439,197 sequences of the SARS-CoV-2 spike protein collected from NCBI and GISAID databases. 595 sequences were from Thailand and contained 52 amino acid mutations, of which 6 had not been observed outside Thailand (p.T51N, p.P57T, p.I68R, p.S205T, p.K278T, p.G832C). These mutations were not predicted to be of concern. We demonstrate that p.D614G became the prevalent strain during the second outbreak, and the most common spike mutations detected in Thailand (p.A829T, p.S459F and p.S939F) do not appear to cause any major structural change to the spike trimer or the spike-ACE2 interaction. Among the spike mutations identified in Thailand was p.N501T. This mutation was not predicted to increase SARS-CoV-2 binding, in contrast to the spike mutation of interest p.N501Y. In conclusion, Thailand-specific mutations are unlikely to increase the fitness of SARS-CoV-2. The insights obtained from this study could aid in prioritizing SARS-CoV-2 variants and in strain surveillance