Cilt:68 Sayı:01 (2021)

Permanent URI for this collection

https://dspace.ankara.edu.tr/handle/20.500.12575/75360

Browse

Browsing Cilt:68 Sayı:01 (2021) by Subject "Conventional RT-PCR"

Now showing 1 - 1 of 1
  • No Thumbnail Available
    Item
    Detection of SARS-CoV-2 using five primer sets
    (Ankara Üniversitesi, 2020-12-25) Karagöz, Alper; Tutun, Hidayet; Arslantaş, Tutku; Altıntaş, Özlem; Koçak, Nadir; Altıntaş, Nadir; Veteriner Fakültesi
    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.