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Published April 29, 2020 | Version v1
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Genomic and Biologic Characteristics of SARS-CoV-2 and Other Coronaviruses

  • 1. Department of Medical Microbiology, Gulhane Medical Faculty, University of Health Sciences, Ankara, Turkey

Description

Özet

Koronaviruslar iyi tanımlanmış insan ve hayvan patojenleri olup, insanlarda başlıca solunum yolu enfeksiyonları ile ilişkilidirler. Sayıları 40’a yakın olan koronavirus türlerinden yedisi insan enfeksiyonları ile ilişkilidir. Bu virüslerden dördü (HCoV-229E, HCoV-NL63, HCoV-OC43 ve HCoV-HKU1) mevsimsel enfeksiyonlara neden olan solunum yolları patojenleri iken, özellikle hastane salgınları ile karşımıza çıkan SARS-CoV ve MERS-CoV ise ciddi solunum yolu enfeksiyonlarına neden olan türler olarak ilk kez 2003 ve 2012 yıllarında tanımlandı. SARS-CoV ile genomik benzerliği nedeniyle Uluslararası Virüs Taksonomi Komitesi tarafından SARS-CoV-2 olarak adlandırılan yeni bir tür 2019 yılı sonlarında Çin’den başlayarak 3 ay içerisinde tüm dünyaya yayıldı. Gelişmiş ülkelerde sağlık sistemlerinin çöküşü ve dünya genelinde neden olduğu yaygın endişe ile dikkatleri üzerine çeken bu salgın ile ilgili hala öngörülemeyen birçok nokta bulunmaktadır. Virüsün genetiği ve biyolojisi, neden olduğu enfeksiyonun klinik seyri ve komplikasyonları, yeni aşı ve ilaç çalışmaları ve salgının boyutları ile ilgili literatüre yoğun bir şekilde her gün yeni bilgiler eklenmektedir. Bununla beraber virüsün koronavirus ailesindeki diğer virüs türleri ile paylaştığı birçok ortak özellik bulunmakta ve bunların bilinmesi SARS-CoV-2 salgınının nereye doğru gideceğini, aşıların olası yararlılıklarını veya mutasyon hızı gibi bilinmeyen ve endişelere neden olan konuların daha kolay anlaşılmasında önem taşımaktadır. Bu makalede koronavirusların genel biyolojik ve genetik özellikleri ele alınarak bunlardan bazılarının SARS-CoV-2 ile karşılaştırmaları yapılmıştır.

Abstract

Coronaviruses are well-defined human and animal pathogens and are primarily associated with respiratory tract infections in humans. The number of coronavirus species is close to 40 and seven of which are associated with human infections. While four of these viruses (HCoV-229E, HCoV-NL63, HCoV-OC43 and HCoV-HKU1) are respiratory pathogens that cause seasonal infections, SARS-CoV and MERS-CoV, which are especially encountered with hospital outbreaks, cause severe acute respiratory infections and discovered in 2003 and 2012, respectively. A new species named SARS-CoV-2 due to its genomic similarity with SARS-CoV by the International Virus Taxonomy Committee spread to all the countries of the world within 3 months starting from China at the end of 2019. There are many unpredictable points regarding this epidemic, which attracted attention due to the collapse of health systems in developed countries and widespread concern in the world. New information is intensively added to the literature on the genetics and biology of the virus, the clinical course and complications of the infection, new vaccine and drug studies, and the extent of the outbreak. However, there are many common features that the virus shares with other types of viruses in the coronavirus family, and knowing them is important for easier understanding of unknown and anxious issues such as where the SARS-CoV-2 outbreak is going, the possible benefits of the vaccines, or the rate of mutation. In this article, general biological and genetic characteristics of coronaviruses are discussed and some of them are compared with SARS-CoV-2.

Notes

SARS-Cov-2 ve Diğer Koronavirusların Genomik ve Biyolojik Özellikleri

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References

  • 1. International Committee on Taxonomy of Viruses, Washington, DC. ICTV reports; Coronaviridae. Available at: https://talk.ictvonline.org/ictv-reports/ictv_9th_report/positive-sense-rna-viruses-2011/w/posrna_viruses/222/coronaviridae [Accessed March 30, 2020].
  • 2. To KK, Hung IF, Chan JF, Yuen KY. From SARS coronavirus to novel animal and human coronaviruses. J Thorac Dis 2013; 5 Suppl 2: S103-8.
  • 3. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med 2020; 26(4): 450-2.
  • 4. Shaw K. The 2003 SARS outbreak and its impact on infection control practices. Public Health 2006; 120(1): 8-14.
  • 5. 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(19): 1814-20.
  • 6. Park JE, Jung S, Kim A, Park JE. MERS transmission and risk factors: a systematic review. BMC Public Health 2018; 18(1): 574.
  • 7. 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. Nat Microbiol 2020; 5(4): 536-44.
  • 8. Zhang L, Liu Y. Potential interventions for novel coronavirus in China: A systematic review. J Med Virol 2020; 92(5): 479-90.
  • 9. International Committee on Taxonomy of Viruses, Washington, DC. Virus Taxonomy: 2018b, July 2018. Available at: https://talk.ictvonline.org/taxonomy/ [Accessed July 26, 2019].
  • 10. Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, et al. 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 2012; 86(7): 3995-4008.
  • 11. Bárcena M, Oostergetel GT, Bartelink W, Faas FG, Verkleij A, Rottier PJ, et al. Cryo-electron tomography of mouse hepatitis virus: Insights into the structure of the coronavirion. Proc Natl Acad Sci U S A 2009; 106(2): 582-7.
  • 12. van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BN, et al. Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1. N Engl J Med 2020; 382(16): 1564-7.
  • 13. Bai Y, Yao L, Wei T, Tian F, Jin DY, Chen L, et al. Presumed asymptomatic carrier transmission of COVID-19. JAMA 2020.
  • 14. Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z, et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med 2020.
  • 15. Chen YC, Huang LM, Chan CC, Su CP, Chang SC, Chang YY, et al. SARS in hospital emergency room. Emerg Infect Dis 2004; 10(5): 782-8.
  • 16. Bar-On YM, Flamholz A, Phillips R, Milo R. SARS-CoV-2 (COVID-19) by the numbers. Elife 2020; 9. pii: e57309.
  • 17. Wang C, Liu Z, Chen Z, Huang X, Xu M, He T, et al. The establishment of reference sequence for SARS-CoV-2 and variation analysis. J Med Virol 2020. [Epub ahead of print]
  • 18. Global Initiative on Sharing All Influenza Data, Munich, Germany. Genomic epidemiology of hCoV-19. Available at: https://www.gisaid.org/ [Accessed April 18, 2020].
  • 19. Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B 2020. [Epub ahead of print]
  • 20. Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol 2020; 30(7): 1346-51.e2.
  • 21. National Center for Biotechnology Information (NCBI), Bethesda, Maryland, U.S. Genbank BLAST. SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences. Available at: https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/ [Accessed April 18, 2020].
  • 22. D'Amico F, Baumgart DC, Danese S, Peyrin-Biroulet L. Diarrhea during COVID-19 infection: pathogenesis, epidemiology, prevention and management. Clin Gastroenterol Hepatol 2020. pii: S1542-3565(20)30481-X.
  • 23. ViralZone, Swiss Institute of Bioinformatics, Switzerland. Coronaviruses. Available at: https://viralzone.expasy.org/30?outline=all_by_species [Accessed April 18, 2020].
  • 24. 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(7798): 270-3.
  • 25. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 2020; 367(6483): 1260-3.
  • 26. Dong L, Hu S, Gao J. Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discov Ther 2020; 14(1): 58-60.
  • 27. Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses. J Adv Res 2020; 24: 91-8.
  • 28. Guo YR, Cao QD, Hong ZS, Tan YY, Chen SD, Jin HJ, et al. The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak - an update on the status. Mil Med Res 2020; 7(1): 11.
  • 29. Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, et al. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell 2020. pii: S0092-8674(20)30338-X.
  • 30. Wan WY, Lim SH, Seng EH. Cross-reaction of sera from COVID-19 patients with SARS-CoV assays. medRxiv 2020.
  • 31. 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(8): 727-33.
  • 32. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 2005; 310(5748): 676-9.
  • 33. Xu RH, He JF, Evans MR, Peng GW, Field HE, Yu DW, et al. Epidemiologic clues to SARS origin in China. Emerg Infect Dis 2004; 10(6): 1030-7.
  • 34. Shi Z, Hu Z. A review of studies on animal reservoirs of the SARS coronavirus. Virus Res 2008; 133(1): 74-87.
  • 35. Menachery VD, Yount BL Jr, Debbink K, Agnihothram S, Gralinski LE, Plante JA, et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med 2015; 21(12): 1508-13.
  • 36. Perlman S. Another Decade, Another Coronavirus. N Engl J Med 2020; 382(8): 760-2.
  • 37. Azhar EI, El-Kafrawy SA, Farraj SA, Hassan AM, Al-Saeed MS, Hashem AM, et al. Evidence for camel-to-human transmission of MERS coronavirus. N Engl J Med 2014; 370(26): 2499-505.
  • 38. Hamming I, Timens W, Bulthuis ML, Lely AT, Navis G, 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(2): 631-7.
  • 39. Wong RS, Wu A, To KF, Lee N, Lam CW, Wong CK, et al. Haematological manifestations in patients with severe acute respiratory syndrome: retrospective analysis. Br Med J 2003; 326(7403): 1358-62.
  • 40. O'Donnell R, Tasker RC, Roe MF. SARS: understanding the coronavirus: apoptosis may explain lymphopenia of SARS. Br Med J 2003; 327(7415): 620.
  • 41. Baig AM, Khaleeq A, Ali U, Syeda H. Evidence of the COVID-19 Virus Targeting the CNS: Tissue Distribution, Host-Virus Interaction, and Proposed Neurotropic Mechanisms. ACS Chem Neurosci 2020; 11(7): 995-8.
  • 42. Li YC, Bai WZ, Hashikawa T. The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients. J Med Virol 2020.
  • 43. Li YC, Bai WZ, Hashikawa T. Response to Commentary on "The neuroinvasive potential of SARS-CoV-2 may play a role in the respiratory failure of COVID-19 patients". J Med Virol 2020.
  • 44. Netland J, Meyerholz DK, Moore S, Cassell M, Perlman S. Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2. J Virol 2008; 82(15): 7264-75.
  • 45. Xu J, Zhong S, Liu J, Li L, Li Y, Wu X, et al. Detection of severe acute respiratory syndrome coronavirus in the brain: potential role of the chemokine mig in pathogenesis. Clin Infect Dis 2005; 41(8): 1089-96.
  • 46. Ding Y, He L, Zhang Q, Huang Z, Che X, Hou J, et al. Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways. J Pathol 2004; 203(2): 622-30.
  • 47. Zhang C, Shi L, Wang FS. Liver injury in COVID-19: management and challenges. Lancet Gastroenterol Hepatol 2020; 5(5): 428-30.
  • 48. Chau TN, Lee KC, Yao H, Yao H, Tsang TY, Chow TC, et al. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases. Hepatology 2004; 39(2): 302-10.
  • 49. Alsaad KO, Hajeer AH, Al Balwi M. Al Moaiqel M, Al Oudah N, Al Ajlan A, et al. Histopathology of Middle East respiratory syndrome coronovirus (MERS-CoV) infection—clinicopathological and ultrastructural study. Histopathology 2018; 72(3): 516-24.