Analysis of RdRp Gene in SARS CoV-2 Variants

Abstract

SARS CoV-2 was discovered in Wuhan, China, in December 2019 and has since mutated into new variants. One of the genes that mutated in SARS CoV-2 is RNA-dependent RNA polymerase (RdRp), a gene playing roles in viral replication and transcription. This study aimed to determine the variation of the RdRp gene in the SARS CoV-2 variant. We used VTM-preserved biological samples from positive nasopharyngeal swabs confirmed by qRT-PCR testing stored at -80°C. We isolated samples using the QIAamp Viral RNA Mini Kit and determined their concentration with Qubit RNA HS Assay reagents. After amplifying the RNA using qRT-PCR, we prepared the samples for sequencing with the Illumina RNA prep kit. Sequencing was carried out with the Miseq system and results were produced in FASTQ format. This study identified 251 samples, and analysis of the RdRp gene showed 69 substitution mutations and one deletion mutation. The highest point mutation was found in the C14408T nucleotide sequence, almost in all study samples of all variants (98.4%). There were 28 missense mutations, including C14408T, which converts the amino acid proline to leucine. Four research samples that did not have mutations in C14408T were samples in the early period of the COVID-19 pandemic before various variants were reported. In summary, our study on the variation of the RdRp gene in the SARS CoV-2 variant demonstrated remarkable C14408T mutations. Utilizing this mutation is a crucial genetic indicator for tracking alterations in the SARS-CoV-2 and comprehending its evolutionary patterns. Keywords: SARS CoV-2, COVID-19, variant, mutation, RdRp gene