Detection of sars-cov-2 using five primer sets Sars-cov-2’nin beş primer seti kullanılarak belirlenmesi


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KARAGÖZ A., Tutun H., Arslantaş T., Altintaş Ö., Koçak N., ALTINTAŞ L.

Ankara Universitesi Veteriner Fakultesi Dergisi, vol.68, no.1, pp.69-75, 2021 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 68 Issue: 1
  • Publication Date: 2021
  • Doi Number: 10.33988/auvfd.775884
  • Journal Name: Ankara Universitesi Veteriner Fakultesi Dergisi
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, CAB Abstracts, EMBASE, Veterinary Science Database, TR DİZİN (ULAKBİM)
  • Page Numbers: pp.69-75
  • Keywords: Conventional RT-PCR, COVID-19, Diagnosis, E gene, N gene, ORF1ab
  • Uşak University Affiliated: No

Abstract

A novel coronavirus (SARS-CoV-2) outbreak, responsible for a pneumonia-associated respiratory disorder (COVID-19), has started in early December 2019 in Wuhan, China, and has rapidly spread around the world. Rapid and accurate diagnostic testing plays a crucial role in tackling the COVID-19 pandemic. In this study, it was aimed to compare 5 primer sets designed to amplify different regions for the detection of SARS-CoV-2 and to perform sequence analysis. Conventional RT-PCR was carried out using primers targeting different regions of the virus genome including ORF1ab, Envelope (E), RNA-dependent RNA polymerase (RdRp), Spike (S) and Nucleocapsid (N) genes for the diagnosis of COVID-19. DNA sequence of ORF1ab gene from each sample were compared with the DNA sequence data of SARS-CoV-2 stored in the GenBank and ORF1ab phylogenetic tree was constructed. The amplicon sizes of ORF1ab, S, E, N and RdRp genes were 588 bp, 440 bp, 145 bp, 323 bp and 196 bp, respectively. The SARS-CoV-2 RNA was detected from 74% of total samples from RdRp gene, 87% for N gene, 74% for S gene, 61% for E gene and 82% for ORF1ab region. The ORF1ab sequences of SARS-CoV-2 from 82 patients were had 100% identity to the sequence of Wuhan isolate and among themselves. The phylogenetic analysis revealed that all isolates formed a cluster. The results of this study suggest that the N region is the best for SARS-CoV-2 identification.