Investigation of spike gene (S) mutations and SNPs in the novelcoronavirus (SARS-CoV-۲) using sequencing method

Background and Purpose:Coronavirus disease ۲۰۱۹ (COVID-۱۹), a contagious viralillness, caused by severe acute respiratory syndrome coronavirus ۲ (SARS-CoV-۲), hasaffected the world’s demographics resulting in more than ۴ million deaths worldwide,emerging as the most consequential global health crisis since the influenza pandemic era in۱۹۱۸. After the first cases of this predominantly respiratory viral illness were first reported inWuhan, China, in December ۲۰۱۹, SARS-CoV-۲ rapidly disseminated across the world,convincing the World Health Organization (WHO) to declare it as a global pandemic onMarch ۱۱, ۲۰۲۰. While adapting to their new human hosts, SARS-CoV-۲, is prone to geneticevolution with the development of mutations over time, resulting in mutant variants that mayhave different characteristics than its ancestral strains. Several variants of SARS-CoV-۲ havebeen described during the course of this pandemic, among which a few are consideredvariants of concern (VOCs) by the WHO, given their effect on global public health. Based onthe recent epidemiological update, as of December ۱۱, ۲۰۲۱, five SARS-CoV-۲ VOCs havebeen identified: Alpha (B.۱.۱.۷), Beta (B.۱.۳۵۱), Gamma(P.۱), Delta (B.۱.۶۱۷.۲),Omicron (B.۱.۱.۵۲۹). In spite of unprecedented rate of vaccine development and robustglobal mass vaccination efforts including vaccine boosters, the emergence of these newSARS-CoV-۲ variants threatens to overturn the significant progress made so far in limitingthe spread of this viral illness. Current study aims to find potential mutations in Spike Geneof SARS-CoV-۲Material & Methods: The human samples included ۸۵ samples collected from patients withCOVID-۱۹. RNAs extracted and cDNAs synthesised. PCR reaction set up and high qualitysamples sequenced. The results of sequencing analysed by appropriate software.Results:Seven alteration in the Spike (S) gene sequence of the SARS-CoV-۲ virus weredetected. ۲۳,۴۰۳ A> G (۱۰۰% of samples), ۲۳,۶۲۵ C> T is the second one in terms ofscattering among reported changes (۱۶.۶%), ۲۴,۲۳۶ G > T(۱۴.۲۸%) and ۲۱,۶۴۲ G> C, ۲۲,۲۴۵G> T, ۲۳,۷۵۰ A> G and ۲۴,۷۷۰ G> T were reported with a frequency of ۲.۳۸%.Conclusion:Mutations in the severe acute respiratory syndrome coronavirus ۲ (SARS-CoV-۲) occur spontaneously during its replication. Numbers of mutations have accumulated andcontinue to since the emergence of the virus. As novel mutations continue, new variants areincreasingly observed. Since the first incidence of the SARS-CoV-۲ infection, a wide varietyof drug compounds affecting the binding sites of the virus have begun to be studied. As thedrug and vaccine trials are continuing, it is of most importance to take into consideration theSARS-CoV-۲ mutations and their respective frequencies since these data could direct the wayto multi-drug combinations. The lack of effective therapeutic and preventive strategiesagainst human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications. The reason why the mutations in glycoprotein S lead to vaccine escape is relatedto the location of the mutation and the affinity of the protein.The workflow described in this article, viral RNA isolation, viral load quantification,sequencing and bioinformatics analysis, and data visualization, can be accomplished in lessthan a week using instruments available at our laboratory. Tracking viral mutations isessential for effective vaccine design, and sequencing may also identify super-spreadingtransmission events. Examining how novel SARS-CoV-۲ mutations impact on patient diseaseoutcomes is key to enhancing our understanding of COVID-۱۹. Inclusion of patient clinicalinformation in future studies will strengthen the sequencing and bioinformatics workflowpresented here by enabling clinicians to link disease symptomology to genomic data.Ultimately, this work will enable public health and infectious disease officials to utilizesecure, password-protected, phylogenetic, and protein modeling data for rapid assessment ofa variety of questions with respect to SARS-CoV-۲.

کلیدواژه ها:

(SARS-CoV-۲) ، spike gene ، mutations ، SNPs ، sequencing