Research articles
ScienceAsia 49 (2023):ID 77-84 |doi:
10.2306/scienceasia1513-1874.2023.138
Computational analysis of the novel Thailand-specific
mutations in SARS-CoV-2 spike glycoprotein sequences
Pongpat Chaisawasd, Sirawit Ittisoponpisan*
ABSTRACT: 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.
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Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of
Songkhla University, Songkhla 90110 Thailand |
* Corresponding author, E-mail: sirawit.i@psu.ac.th
Received 19 May 2022, Accepted 4 Sep 2022
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