Tıbbi Mikrobiyoloji Laboratuvarı Açısından SARS-CoV-2

Coronaviridae ailesinde yer alan koronaviruslar (CoV), vahşi ve evcil hayvanlarda farklı şiddette gastrointestinal, respiratuvarve sistemik hastalıklara neden olurken, insanlarda bağışıklık durumuna göre soğuk algınlığından pnömoniye kadar farklıklinik tablolara yol açabilir. Günümüze dek insanlarda enfeksiyon etkeni olarak yedi koronavirus türü tanımlanmıştır;bunlardan HCoV 229E, HCoV NL63, HCoV HKU1 ve HCoV OC43, tipik olarak immünokompetan bireylerde soğukalgınlığı semptomlarına neden olurken, SARS-CoV (Ciddi Akut Solunum Sendromu Koronavirus), MERS-CoV (OrtaDoğu Solunum Sendromu Koronavirus) zoonotiktir ve ciddi solunum yolu hastalıklarına ve ölümlere neden olur. Çin’inHubei Eyaleti, Wuhan kentinde Aralık 2019’da başlayan ve kısa sürede pandemi olarak tanımlanan COVID -19’un etkeniSARS-CoV-2 insanlarda enfeksiyon etkeni olarak tanımlanan yedinci koronavirustur. Dünya Sağlık Örgütü(DSÖ)’nünSARS-CoV-2 kaynaklı COVID-19’u pandemi olarak tanımlaması ve dünya üzerinde her geçen gün vaka ve ölümsayılarının artmasından dolayı, aşı çalışmaları için virusun yapısı ve salgını kontrol etmede en önemli basamak olan viraltanı yöntemlerinin kullanılması daha da önem kazanmıştır.

SARS-CoV-2 in Terms of Medical Microbiology Laboratory

Coronaviruses (CoV), which are in the Coronaviridae family, cause different severity of gastrointestinal, respiratory and systemic diseases in wild and domestic animals, and can lead to different clinical manifestations, ranging from colds to pneumonia, depending on immunity. To date, seven types of coronavirus have been identified as infectious agents in humans; of these, HCoV 229E, HCoV NL63, HCoV HKU1 and HCoV OC43 typically cause cold symptoms in immunocompetent individuals, while SARS-CoV (Severe Acute Respiratory Syndrome Coronavirus) and MERS-CoV (Middle East Respiratory Syndrome Coronavirus) is zoonotic and cause severe respiratory diseases and deaths. SARSCoV-2, the causative agent of COVID-19, is the seventh coronavirus identified as an infection agent in humans, which started in December 2019 in Wuhan, Hubei Province of China and was identified as a pandemic in a short time. Since the World Health Organization (WHO) defines SARS-CoV-2-sourced COVID-19 as a pandemic, and because of the increasing number of cases and deaths worldwide, structure of the novel virus and viral diagnosis methods gained importance respectively for vaccine studies and for controlling the outbreak caused by the virus.

PDF

___

1. Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.Nature Microbiology 2020;5:536–44.
2. https://www.who.int/emergencies/diseases/novel-coronavirus-2019
3. Cui J, Li F, Daszak P. Origin and evolution of pathogenic coronaviruses. Nat Rev Genet 2018; 17: 181–92.
4. Su S, Wong G, Shi W, Liu J, Lai A C K, Zhou J et al. Epidemiology, genetic recombination, and Pathogenesis of coronaviruses.Trends Microbiol 2016; 24:490–502.
5. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, et al. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 2003; 348: 1953–66.
6. Peiris JS, Lai ST, Poon LL, Guan Y, Yam LY, Lim W et al. Coronavirus as a possible cause of severe acute respiratory syndrome.Lancet 2003; 361:1319–25.
7. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 2012; 367:1814–20.
8. Assiri A, Al-Tawfiq JA, Al-Rabeeah AA, Al-Rabiah FA, Al-Hajjar S, Al-Barrak A, et al. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study. Lancet Infect Dis 2013;13:752–61.
9. Park SE. Epidemiology, virology, and clinical features of severe acute respiratory syndrome - coronavirus-2 (SARS-CoV-2; Coronavirus Disease-19). Clin Exp Pediatr 2020;63:119-24.
10. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. A Pneumonia Outbreak Associated with a New Coronavirus of Probable Bat Origin. Nature 2020; 579:270-3.
11. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 2020;382:727−33.
12. Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, et al. Commentary Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China. Cell Host Microbe 2020;27:325- 8.
13. Ren LL, Wang YM, Wu ZQ, Xiang ZC, Guo L, Xu T, et al. Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study. Chin Med J (Engl) 2020;133:1015-24.
14. Chan JF, Yuan S, Kok KH, To KK, Chu H, Yang J, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating personto-person transmission: a study of a family cluster. Lancet 2020;395:514-23.
15. Song Z, Xu Y, Bao L, Zhang L, Yu P, Qu Y, et al. From SARS to MERS, thrusting coronaviruses into the spotlight. Viruses 2019;11:59.
16. Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 2019;17:181–92.
17. Chen Y, Liu Q, Guo D. Emerging coronaviruses: Genome structure, replication, and pathogenesis. J Med Virol 2020; 92: 418-23.
18. Hasoksuz M, Sreevatson S, Cho KO, Hoet AE, Saif LJ. Molecular analysis of the S1 subunit of the spike glycoprotein of respiratory and enteric bovine coronavirus isolates. Virus Res 2002; 84: 101-9.
19. Hasoksuz M, Lathrop S, Al-dubaib MA, Lewis P, Saif LJ. Antigenic variation among bovine enteric coronaviruses (BECV) and bovine respiratory coronaviruses (BRCV) detected using monoclonal antibodies. Arch Virol 1999;144: 2441-7.
20. Bosch BJ, Van Der Zee R, De Haan CAM, Rottier PJM. The Coronavirus Spike Protein Is a Class I Virus Fusion Protein: Structural and Functional Characterization of the Fusion Core Complex. J Virol 2003;77:8801-11.
21. Hamming I, Timens W, Bulthuis MLC, Lely AT, Navis GJ, van Goor H. Tissue Distribution of ACE2 Protein, the Functional Receptor for SARS Coronavirus. A First Step in Understanding SARS Pathogenesis. J Pathol 2004;203:631-7.
22. Neuman B, Kiss G, Kunding A, Bhella D, Baksh MF, Connelly S, et al. A structural analysis of M protein in coronavirus assembly and morphology. J Struct Boil 2010;174:11–22.
23. DeDiego ML, Álvarez E, Almazán F, Rejas MT, Lamirande E, Roberts A, et al. A severe acute respiratory syndrome coronavirus that lacks the E Gene is attenuated in vitro and in vivo. J Virol 2006; 81:1701–13.
24. Fehr AR, Perlman S. Coronaviruses: An overview of their replication and pathogenesis. In Therapeutic Antibodies; Springer: Berlin/ Heidelberg, Germany 2015;1282:1–23.
25. Cui L, Wang H, Ji Y, Yang J, Xu S, Huang X, et al. The nucleocapsid protein of coronaviruses acts as a viral suppressor of RNA silencing in mammalian cells. J Virol 2015; 89: 9029–43.
26. Liu YC, Kuo RL, Shih SR. COVID-19: the First Documented Coronavirus Pandemic in History. Biomed J 2020:S2319- 4170(20)30044-5.
27. World Health Organization.Laboratory testing for coronavirus disease (COVID-19) in suspected human cases.19 March 2020.
28. Loeffelholz MJ, Tang YW. Laboratory diagnosis of emerging human coronavirus infections-the state of the art. Emerg Microbes Infect 2020; 9:747-56.
29. Kaye M, Druce J, Tran T, Kostecki R, Chibo D, Morris J, et al. SARS associated coronavirus replication in cell lines. Emerg Infect Dis 2006;12:128-33.
30. www.cdc.gov May 5, 2020. SARS CoV-2 viral culture at CDC.
31. Patel R, Babady E, Theel ES, Storch GA, Pinsky BA, George K, et al. Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of diagnostic testing for SARS-CoV-2/COVID-19. American Society for Microbiology 2020;11: e00722-20.
32. Khailany RA, Safdar M, Ozaslan M. Genomic characterization of a novel SARS CoV-2. Gene Reports 2020;19:100682.
33. Udugama B, Kadhiresan P, Kozlowski HN, Malekjahani A, Osborne M, Li VYC, et al. Diagnosing COVID-19: The disease and tools for detection. ACS Nano 2020;14:3822-35.
34. Sheridan C. Coronavirus and the race to distribute reliable diagnostics. Nat Biotechnol 2020;38:382-4.
35. Miller S, Chiu C, Rodino KG, Miller MB. Point-counterpoint should we be performing metagenomic next-generation sequencing for infectious disease diagnosis in the clinical laboratory? J Clin Microbiol 2020; 58:e01739-19.
36. Freeman WM, Walker SJ, Vrana KE. Quantitative RT-PCR. Pitfalls and potential. BioTechniques 1999; 26:112-22.
37. Corman V, Bleicker T, Brünink S, Zambon M. Diagnostics detection of Wuhan Coronavirus 2019 by real-time RT-PCR. WHO: Geneva 2020.
38. CDC-2019-Novel Coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel, Division of Viral Disease, U.S. Centers for Disease Control and Prevention: Atlanta GA, 2020.
39. Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases: Interim guidance, World Health Organization 2 March 2020.
40. Cheng MP, Papenburg J, Desjardins M, Kanjilal S, Quach C, Libman M, et al. Diagnostic testing for severe acute respiratory syndromerelated Coronavirus-2. Ann Intern Med 2020;172:726-34.
41. Lan L, Xu D, Ye G, Xia C, Wang S, Li Y, et al. Positive RTPCR test results in patients recovered from COVID-19. JAMA 2020;323:1502-3.
42. Zou L, Ruan F, Huang M, Liang L, Huang H, Hang Z, et al. SARS CoV-2 viral load in upper respiratory specimens of infected patients. N Eng J Med 2020;382:1177-9.
43. Pan Y, Zhang D, Yang P, Poon LLM, Wang Q. Viral load of SARSCoV-2 in clinical samples. Lancet Infect Dis 2020; 20:411-12.
44. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019-nCoV) by realtime RT-PCR. Euro Surveill 2020; 25:2000045.
45. Chu DK, Pan Y, Cheng SM, Hui KP, Krishnan P, Liu Y, et al. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clin Chem 2020;66:549-55.
46. XpertÒXpress SARS-CoV-2. https://www.cepheid.com/coronavirus.
47. Abbott launches molecular point-of-care test to detect novel coronavirus in as little as five minutes. https://abbott.mediaroom. com/2020-03-27.
48. Xiang J, Yan M, Hongze L, Ting L, Chenyao L, Shueng H, et al. Evaluation of enzyme-linked immunoassay and colloidal gold- immunochromatographic assay kit for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19). medRxiv doi.org/10.1101/2020.02.27.20028787
49. Bruning AHL, Aatola H, Toivola H, Ikonen N, Savolainen-Kopra C, Blomquist S, et al. Rapid detection and monitoring of human coronavirus infections. New Microbes New Infect 2018; 24:52-5.
50. Sheridan C. Fast portable tests come online to curb coronavirus pandemic. Nat Biotechnol 2020; 38:515-8.
51. Chan CM, Tse H, Wong SS, Woo PCY, Lau SKP, Chen L, et al. Examination of seroprevalence of coronavirus HKU1 infection with S protein-based ELISA and neutralization assay against viral spike pseudotyped virus. J Clin Virol 2009; 45:54-60.
52. Shao X, Guo X, Esper F, Weibel C, Kahn JS. Seroepidemiology of group I human coronaviruses in children. J Clin Virol 2007; 40:207- 13.
53. Infantino M, Damiani A, Gobbi FL, Grossi V, Lari B, Macchia D, et al. Serological assays for SARS-CoV2 ınfectious disease:Benefits, limitations and perspectives.IMAJ 2020; 22:203-10.
54. Che XY, Qiu LW, Liao ZY, Wang YD, Wen K, Pan YX, et al. Antigenic cross-reactivity between severe acute respiratory syndromeassociated coronavirus and human coronaviruses 229E and OC43. J Infect Dis 2005;191:2033-7.
55. Carattoli A, Di Bonito P, Grasso F, Giorgi C, Blasi F, Niedrig M, et al. Recombinant protein‐based ELISA and immuno‐cytochemical assay for the diagnosis of SARS. J Med Virol 2005; 76:137-42.
56. Walls AC, Park YJ, Tortorici MA, Wall A, MacGuire AT, Veesler D. Structure, function, and antigenicity of the SARS CoV-2 spike glycoprotein. Cell 2020 Apr 16;181:281-92.e6.
57. Okba NMA, Müller MA, Li W, Wang C, GeurtsvanKessel CH, Corman VM, Lamers MM, et al. SARS-CoV-2 specific antibody responses in COVID-19 patients. Emerg Infect Dis 2020;26. doi: 10.3201/eid2607.200841.
58. Zhao J, Yuan Q, Wang H, Liu W, Liao X, Su Y, et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. Clin Infect Dis 2020;ciaa344. doi: 10.1093/cid/ciaa344.
59. Guo L, Ren L, Yang S, Xiao M, Chang D , Yang F, et al. Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19). Clin Infect Dis 2020;pii: ciaa310. doi: 10.1093/cid/ ciaa310.
60. Lou B, Li T, Zheng S, Su Y, Li Z, Liu W, et al. Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset. Eur Respir J 2020;2000763. doi: 10.1183/13993003.00763- 2020.
61. Jin Y, Wang M, Zuo Z, Fan C, Ye F, Cai Z, et al. Diagnostic value and dynamic variance of serum antibody in coronavirus disease 2019. Int J Infect Dis 2020; 94:49-52.
62. Yang T, Wang YC, Shen CF, Cheng CM. Point of care RNA based diagnostic device for COVID-19. Diagnostics 2020;10:165.