Computational analysis of the novel Thailand-specific mutations in SARS-CoV-2 spike glycoprotein sequences

As of 14 January 2022, 2.3 million people in Thailand had been reportedly infected with SARS-CoV-2, and 21,883 people had died. Spike glycoprotein, on the SARS-CoV-2 membrane, is a key factor for viral infection. Some scientists have demonstrated that some amino acid mutations in the protein increase infectivity and transmissibility of the virus. However, many studies concerning mutations in the spike glycoprotein, particularly in Thailand, were not comprehensive enough to illustrate the impacts of the mutations on the spike glycoprotein. To narrow this gap, we examined approximately 8.3 million spike glycoprotein sequences retrieved from GISAID Initiative and NCBI Virus databases to identify novel mutations. Limiting our scope to the Thai samples, we demonstrated how local SARS-CoV-2 strains changed over 2021. In addition, we found that T95I had emerged and become one of the main characteristics of delta strains in Thailand. We further detected 28 Thailand-specific novel mutations, which were then analyzed with amino acid-based analysis tools to gain insights into their impacts on the spike glycoprotein. Upon closer examination, we found that 2 novel mutations, L249E and R457W, were likely to diminish the interactions between the spike glycoprotein and neutralizing antibodies in silico. This finding suggests that both mutations may hinder the neutralization, allowing the virus to escape the antibodies. Additionally, our study highlights the significant effects of some novel mutations on the stability and functionality of the spike glycoprotein, which may be useful for COVID-19 diagnosis and vaccine development.