Research Article
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Year 2021, Volume: 68 Issue: 1, 69 - 75, 25.12.2020

Alper Karagöz , Hidayet Tutun , Tutku Arslantaş , Özlem Altıntaş , Nadir Koçak , Levent Altıntaş

https://doi.org/10.33988/auvfd.775884
Cited By: 1

Abstract

References

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  • 2. Bustin SA, Nolan T (2020): RT-qPCR testing of SARS-CoV-2: a primer. Int J Mol Sci, 21, 3004.
  • 3. Cai Q, Yang M, Liu D, et al (2020): Experimental treatment with favipiravir for COVID-19: an open-label control study. Engineering.
  • 4. Chen B, Tian EK., He B, et al (2020): Overview of lethal human coronaviruses. Signal Transduct Tar, 5, 1-16.
  • 5. Chen N, Zhou M, Dong X, et al (2020): Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. The Lancet, 395, 507-513.
  • 6. Corman VM, Landt O, Kaiser M, et al (2020): Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance, 25, 2000045.
  • 7. Emery SL, Erdman DD, Bowen MD, et al (2004): Real-time reverse transcription–polymerase chain reaction assay for SARS-associated coronavirus. Emerg Infect Dis, 10, 311-316.
  • 8. Holshue ML, DeBolt C, Lindquist S, et al (2020): First case of 2019 novel coronavirus in the United States. N Engl J Med, 36, 929-936.
  • 9. Kilic AU, Kara F, Alp E, et al (2020): New threat: 2019 novel Coronavirus infection and infection control perspective in Turkey. North Clin Istanb, 7, 95-98.
  • 10. Kodaz H (2020): Editorial: Successful Treatment Strategy of Turkey against Covid-19 Outbreak. EJMO, 4, 177-178.
  • 11. Kumar S, Nyodu R, Maurya VK, et al (2020): Morphology, Genome Organization, Replication, and Pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). 23-31. In: SK Saxena (Ed) Coronavirus Disease 2019 (COVID-19). Springer, Singapore.
  • 12. Luan J, Lu Y, Jin X, et al (2020): Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem Biophys Res Commun, 526, 165-169.
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  • 18. Singh AK, Singh A, Shaikh A, et al (2020): Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries. Diabetes Metab Syndr, 14, 241-246.
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  • 29. Yoldar ZA, Koç BT, Oğuzoğlu TÇ (2020): Phylogenetic analysis of partial transmembrane protein gene of canine coronaviruses detected in Turkey. Ankara Univ Vet Fak Derg, 67, 265-271.
  • 30. Yousefifard M, Zali A, Ali KM, et al (2020): Antiviral therapy in management of COVID-19: a systematic review on current evidence. Arch Acad Emerg Med, 8, e45.
  • 31. Zhang J, Zhou L, Yang Y, et al (2020): Therapeutic and triage strategies for 2019 novel coronavirus disease in fever clinics. Lancet Respir Med, 8, e11-e12.
  • 32. Zhu H, Wei L, Niu P (2020): The novel coronavirus outbreak in Wuhan, China. Global Health Research and Policy, 5, 1-3.

Detection of SARS-CoV-2 using five primer sets

Year 2021, Volume: 68 Issue: 1, 69 - 75, 25.12.2020

Alper Karagöz , Hidayet Tutun , Tutku Arslantaş , Özlem Altıntaş , Nadir Koçak , Levent Altıntaş

https://doi.org/10.33988/auvfd.775884
Cited By: 1

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.

Keywords

Conventional RT-PCR COVID-19 Diagnosis E gene N gene ORF1ab

References

  • 1. Alsuliman T, Sulaiman R, Ismail S, et al (2020): COVID-19 paraclinical diagnostic tools: Updates and future trends. Curr Res Transl Med. 68, 83-91.
  • 2. Bustin SA, Nolan T (2020): RT-qPCR testing of SARS-CoV-2: a primer. Int J Mol Sci, 21, 3004.
  • 3. Cai Q, Yang M, Liu D, et al (2020): Experimental treatment with favipiravir for COVID-19: an open-label control study. Engineering.
  • 4. Chen B, Tian EK., He B, et al (2020): Overview of lethal human coronaviruses. Signal Transduct Tar, 5, 1-16.
  • 5. Chen N, Zhou M, Dong X, et al (2020): Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. The Lancet, 395, 507-513.
  • 6. Corman VM, Landt O, Kaiser M, et al (2020): Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance, 25, 2000045.
  • 7. Emery SL, Erdman DD, Bowen MD, et al (2004): Real-time reverse transcription–polymerase chain reaction assay for SARS-associated coronavirus. Emerg Infect Dis, 10, 311-316.
  • 8. Holshue ML, DeBolt C, Lindquist S, et al (2020): First case of 2019 novel coronavirus in the United States. N Engl J Med, 36, 929-936.
  • 9. Kilic AU, Kara F, Alp E, et al (2020): New threat: 2019 novel Coronavirus infection and infection control perspective in Turkey. North Clin Istanb, 7, 95-98.
  • 10. Kodaz H (2020): Editorial: Successful Treatment Strategy of Turkey against Covid-19 Outbreak. EJMO, 4, 177-178.
  • 11. Kumar S, Nyodu R, Maurya VK, et al (2020): Morphology, Genome Organization, Replication, and Pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). 23-31. In: SK Saxena (Ed) Coronavirus Disease 2019 (COVID-19). Springer, Singapore.
  • 12. Luan J, Lu Y, Jin X, et al (2020): Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem Biophys Res Commun, 526, 165-169.
  • 13. Mathuria JP, Yadav R (2020): Laboratory diagnosis of SARS-CoV-2- a review of current methods. J Infect Public Heal, 13, 901-905.
  • 14. Mollaei HR, Afshar AA, Kalantar-Neyestanaki D, et al (2020): Comparison five primer sets from different genome region of COVID-19 for detection of virus infection by conventional RT-PCR. Iran J Microbiol, 12, 185-193.
  • 15. Omolo CA, Soni N, Fasiku VO, et al (2020): Update on therapeutic approaches and emerging therapies for SARS-CoV-2 virus. Eur J Pharmacol, 883, 173348.
  • 16. Rodríguez-Morales AJ, Balbin-Ramon GJ, Rabaan AA, et al (2020): Genomic Epidemiology and its importance in the study of the COVID-19 pandemic. InfezMed, 2, 139-142.
  • 17. Sağlık Bakanlığı (2020): Genel Koronavirus Tablosu. Available at https://covid19. saglik.gov.tr/TR-66122/genel-koronavirus-tablosu.html (Accessed September 13, 2020).
  • 18. Singh AK, Singh A, Shaikh A, et al (2020): Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries. Diabetes Metab Syndr, 14, 241-246.
  • 19. Stebbing J, Phelan A, Griffin I, et al (2020): COVID-19: combining antiviral and anti-inflammatory treatments. Lancet Infect Dis, 20, 400-402.
  • 20. Tang YW, Schmitz JE, Persing DH, et al (2020): Laboratory diagnosis of COVID-19: current issues and challenges. J Clin Microbiol, 58, e00512-20.
  • 21. The Republic of Turkey Ministry of Health (2020): COVID-19 (SARS-CoV-2 Infection) Guide. July 17, 2020. Available at https://hsgm.saglik.gov.tr/en/covid-19-i-ngilizce-dokumanlar/rehberler.html. (Accessed July 20, 2020).
  • 22. Udugama B, Kadhiresan P, Kozlowski HN, et al (2020): Diagnosing COVID-19: the disease and tools for detection. ACS Nano, 14, 3822-3835.
  • 23. Wei Q, Wang Y, Ma J, et al (2020): Description of the First Strain of 2019-nCoV, C-Tan-nCoV Wuhan Strain—National Pathogen Resource Center, China, 2020. China CDC Weekly, 2, 81-82.
  • 24. Weiss P, Murdoch DR (2020): Clinical course and mortality risk of severe COVID-19. The Lancet, 395, 1014-1015.
  • 25. Woo PC, Lau SK, Lam CS, et al (2012): Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol, 86, 3995-4008.
  • 26. Woolhouse M, Scott F, Hudson Z, et al (2012): Human viruses: discovery and emergence. Philos T R Soc B, 367, 2864-2871.
  • 27. Wordometers (2020): COVID-19 Coronavirus Pandemic. Available at https://www.worldometers.info/coronavirus/ (Accessed September 13, 2020).
  • 28. Yang D, Leibowitz JL (2015): The structure and functions of coronavirus genomic 3′ and 5′ ends. Virus Res, 206, 120-133.
  • 29. Yoldar ZA, Koç BT, Oğuzoğlu TÇ (2020): Phylogenetic analysis of partial transmembrane protein gene of canine coronaviruses detected in Turkey. Ankara Univ Vet Fak Derg, 67, 265-271.
  • 30. Yousefifard M, Zali A, Ali KM, et al (2020): Antiviral therapy in management of COVID-19: a systematic review on current evidence. Arch Acad Emerg Med, 8, e45.
  • 31. Zhang J, Zhou L, Yang Y, et al (2020): Therapeutic and triage strategies for 2019 novel coronavirus disease in fever clinics. Lancet Respir Med, 8, e11-e12.
  • 32. Zhu H, Wei L, Niu P (2020): The novel coronavirus outbreak in Wuhan, China. Global Health Research and Policy, 5, 1-3.
There are 32 citations in total.

Details

Primary Language English
Subjects Veterinary Surgery
Journal Section Research Article
Authors

Alper Karagöz 0000-0002-8178-223X

Hidayet Tutun 0000-0001-9512-8637

Tutku Arslantaş 0000-0002-4351-6600

Özlem Altıntaş 0000-0001-6467-9647

Nadir Koçak 0000-0002-1727-1582

Levent Altıntaş 0000-0002-5148-723X

Publication Date December 25, 2020
Published in Issue Year 2021Volume: 68 Issue: 1

Cite

APA Karagöz, A., Tutun, H., Arslantaş, T., Altıntaş, Ö., et al. (2020). Detection of SARS-CoV-2 using five primer sets. Ankara Üniversitesi Veteriner Fakültesi Dergisi, 68(1), 69-75. https://doi.org/10.33988/auvfd.775884
AMA Karagöz A, Tutun H, Arslantaş T, Altıntaş Ö, Koçak N, Altıntaş L. Detection of SARS-CoV-2 using five primer sets. Ankara Univ Vet Fak Derg. December 2020;68(1):69-75. doi:10.33988/auvfd.775884
Chicago Karagöz, Alper, Hidayet Tutun, Tutku Arslantaş, Özlem Altıntaş, Nadir Koçak, and Levent Altıntaş. “Detection of SARS-CoV-2 Using Five Primer Sets”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 68, no. 1 (December 2020): 69-75. https://doi.org/10.33988/auvfd.775884.
EndNote Karagöz A, Tutun H, Arslantaş T, Altıntaş Ö, Koçak N, Altıntaş L (December 1, 2020) Detection of SARS-CoV-2 using five primer sets. Ankara Üniversitesi Veteriner Fakültesi Dergisi 68 1 69–75.
IEEE A. Karagöz, H. Tutun, T. Arslantaş, Ö. Altıntaş, N. Koçak, and L. Altıntaş, “Detection of SARS-CoV-2 using five primer sets”, Ankara Univ Vet Fak Derg, vol. 68, no. 1, pp. 69–75, 2020, doi: 10.33988/auvfd.775884.
ISNAD Karagöz, Alper et al. “Detection of SARS-CoV-2 Using Five Primer Sets”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 68/1 (December 2020), 69-75. https://doi.org/10.33988/auvfd.775884.
JAMA Karagöz A, Tutun H, Arslantaş T, Altıntaş Ö, Koçak N, Altıntaş L. Detection of SARS-CoV-2 using five primer sets. Ankara Univ Vet Fak Derg. 2020;68:69–75.
MLA Karagöz, Alper et al. “Detection of SARS-CoV-2 Using Five Primer Sets”. Ankara Üniversitesi Veteriner Fakültesi Dergisi, vol. 68, no. 1, 2020, pp. 69-75, doi:10.33988/auvfd.775884.
Vancouver Karagöz A, Tutun H, Arslantaş T, Altıntaş Ö, Koçak N, Altıntaş L. Detection of SARS-CoV-2 using five primer sets. Ankara Univ Vet Fak Derg. 2020;68(1):69-75.

Cited By

Comparison of analytical sensitivity and efficiency for SARS-CoV-2 primer sets by TaqMan-based and SYBR Green-based RT-qPCR
Applied Microbiology and Biotechnology
https://doi.org/10.1007/s00253-022-11822-4
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