The Identification of the SARS-CoV-2 Whole Genome: Nine Cases Among Patients in Banten Province, Indonesia

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the current pandemic. Viral genome sequencing has been widely applied during outbreaks to study the relatedness of this virus to other viruses, its transmission mode, pace, evolution and geographical spread, and also its adaptation to human hosts. To date, more than 90,000 SARS-CoV-2 genome sequences have been uploaded to the GISAID database. The availability of sequencing data along with clinical and geographical data may be useful for epidemiological investigations. In this study, we aimed to analyse the genetic background of SARS-CoV-2 from patients in Indonesia by whole genome sequencing. We examined nine samples from COVID-19 patients with RT-PCR cycle threshold (Ct) of less than 25 using ARTIC Network protocols for Oxford Nanopore’s Gridi On sequencer. The analytical methods were based on the ARTIC multiplex PCR sequencing protocol for COVID-19. In this study, we found that several genetic variants within the nine COVID-19 patient samples. We identified a mutation at position 614 P323L mutation in the ORF1ab gene often found in our severe patient samples. The number of SNPs and their location within the SARS-CoV-2 genome seems to vary. This diversity might be responsible for the virulence of the virus and its clinical manifestation.

Keywords

• sars-cov-19
• covid-19
• rna
• whole genome
• snp
• banten
• indonesia