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.

Length of Hospital Stay and Oseltamivir in Mild or Moderate Degree COVID-19 Patients in North Sumatra, Indonesia

“…The wide range of length of hospital stay in this patient population was not due to drugs used or comorbidities. It may be due to variation of the genetic of the virus [12], patients [13] and/or interaction with microbiome of the patients [14] which affect the overall speed of clinical response of the patients. Unfortunately, such probabilities could not be tested as there is no sophisticated facilities such as DNA/RNA sequencing for the virus and patients in the studied hospital.…”

Detection of the SARS-CoV-2 Omicron Variant in COVID-19 Patients from South Tangerang Using SNP-Probes S371L and K417N

“…Other, non-conventional PCR techniques may be suitable, such as RT-PCR, quantitative (q) PCR or digital PCR. [23][24][25][26][27][28][29] The principle of these techniques is the same as in conventional PCR; to amplify a DNA fragment. In qPCR, the thermocycler has a sensor to detect a fluorescence signal.…”