Spike Protein Mutations in SARS-CoV-2 at Rajasthan, India in December 2020

Abstract

Introduction: Many mutations have been reported in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) since its first identification. Some are variants of concern (VOC) as they have higher transmission rates. Mutations in the spike protein region are of main concern as they affect transmission rates and can affect efficacy of the vaccines. The objective of present study was to look for spike protein mutations in SARS-CoV-2 using Next Generation Sequencing (NGS) in representative samples received in December 2020 at Rajasthan. Methodology: Ten nasopharyngeal/throat swab specimens from known COVID-19 positive patients were processed for RNA extraction, library preparation, and sequencing was done using specific SARS-CoV-2 Ion-Ampliseq panel by Ion torrent S5 system. Results: Only seven samples gave high quality data. All the isolates belonged to clade GH. We found 11 different mutations in the spike protein region most common were Q1201K, Q677R, D614G, L18F. Some novel mutations were found like S689I, Q23R, D1146E, andM153K. D614G mutation was present in all the samples which are known to promote transmissibility oftheSARS-CoV-2 virus. Conclusion: We did not find any VOC but one sample had N440K mutation which is reported to escape immune response, was found to be prevalent in some other parts of India also, and was considered epidemiologically important at the beginning of second wave. There is a need to carry out sequencing on regular basis to check for emerging mutants and monitor their effect on vaccine efficacy.

Keywords

• Introduction: Many mutations have been reported in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) since its first identification. Some are variants of concern (VOC) as they have higher transmission rates. Mutations in the spike protein region are of main concern as they affect transmission rates and can affect efficacy of the vaccines. The objective of present study was to look for spike protein mutations in SARS-CoV-2 using Next Generation Sequencing (NGS) in representative samples received in December 2020 at Rajasthan. Methodology: Ten nasopharyngeal/throat swab specimens from known COVID-19 positive patients were processed for RNA extraction, library preparation, and sequencing was done using specific SARS-CoV-2 Ion-Ampliseq panel by Ion torrent S5 system. Results: Only seven samples gave high quality data. All the isolates belonged to clade GH. We found 11 different mutations in the spike protein region most common were Q1201K, Q677R, D614G, L18F. Some novel mutations were found like S689I, Q23R, D1146E, andM153K. D614G mutation was present in all the samples which are known to promote transmissibility oftheSARS-CoV-2 virus. Conclusion: We did not find any VOC but one sample had N440K mutation which is reported to escape immune response, was found to be prevalent in some other parts of India also, and was considered epidemiologically important at the beginning of second wave. There is a need to carry out sequencing on regular basis to check for emerging mutants and monitor their effect on vaccine efficacy.