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European Journal of Clinical Microbiology & Infectious Diseases

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01-09-2020 | Coronavirus | Review

The genetic sequence, origin, and diagnosis of SARS-CoV-2

Authors: Huihui Wang, Xuemei Li, Tao Li, Shubing Zhang, Lianzi Wang, Xian Wu, Jiaqing Liu

Published in: European Journal of Clinical Microbiology & Infectious Diseases | Issue 9/2020

Abstract

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new infectious disease that first emerged in Hubei province, China, in December 2019, which was found to be associated with a large seafood and animal market in Wuhan. Airway epithelial cells from infected patients were used to isolate a novel coronavirus, named the SARS-CoV-2, on January 12, 2020, which is the seventh member of the coronavirus family to infect humans. Phylogenetic analysis of full-length genome sequences obtained from infected patients showed that SARS-CoV-2 is similar to severe acute respiratory syndrome coronavirus (SARS-CoV) and uses the same cell entry receptor, angiotensin-converting enzyme 2 (ACE2), as SARS-CoV. The possible person-to-person disease rapidly spread to many provinces in China as well as other countries. Without a therapeutic vaccine or specific antiviral drugs, early detection and isolation become essential against novel Coronavirus. In this review, we introduced current diagnostic methods and criteria for the SARS-CoV-2 in China and discuss the advantages and limitations of the current diagnostic methods, including chest imaging and laboratory detection.

Weiss SR, Leibowitz JL (2011) Coronavirus pathogenesis. Adv Virus Res 81:85–164CrossRefPubMedPubMedCentral

Li F (2016) Structure, function, and evolution of coronavirus spike proteins. Annu Rev Virol 3:237–261. https://doi.org/10.1146/annurev-virology-110615-042301CrossRefPubMedPubMedCentral

Tang Q, Song Y, Shi M, Cheng Y, Zhang W, Xia XQ (2015) Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition. Sci Rep 5:17155. https://doi.org/10.1038/srep17155CrossRefPubMedPubMedCentral

Su S, Wong G, Shi W et al (2016) Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol 24:490–502. https://doi.org/10.1016/j.tim.2016.03.003CrossRefPubMedPubMedCentral

Zhu N, Zhang D, Wang W et al (2020) A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 382:727–733. https://doi.org/10.1056/NEJMoa2001017CrossRefPubMedPubMedCentral

Wuhan Municipal Health Commission. Report of clustering pneumonia of unknown etiology in Wuhan City. http://wjw.wuhan.gov.cn/front/web/showDetail/2019123108989. Accessed 31 Dec 2019

Guan WJ, Ni ZY, Hu Y et al (2020) Clinical characteristics of 2019 novel coronavirus infection in China. Medrxiv [Preprint]. [cited 2020 Feb 29]. https://www.medrxiv.org/content/10.1101/2020.02.06.20020974v1

WHO. Novel coronavirus (2019-nCoV) situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/. Accessed 20 Jan 2020

Coronavirus Study Group (2020) Severe acute respiratory syndrome-related coronavirus: the species and its viruses – a statement of the Coronavirus Study Group. Biorxiv [Preprint]. [cited 2020 Fab 29]. https://www.biorxiv.org/content/10.1101/2020.02.07.937862v1.full

10.

National Health Commission Update on February 27, 2020. http://www.nhc.gov.cn/xcs/yqtb/202002/d5e15557ee534fcbb5aaa9301ea5235f.shtml. Accessed 27 Feb 2020

11.

Xu X, Chen P, Wang J et al (2020) Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci 63:457–460. https://doi.org/10.1007/s11427-020-1637-5CrossRefPubMedPubMedCentral

12.

National Health Commission of the People’s Republic of China. New coronavirus pneumonia prevention and control program (trial version 7th ed). http://www.nhc.gov.cn/yzygj/s7653p/202003/46c9294a7dfe4cef80dc7f5912eb1989.shtml Accessed 4 Apr 2020

13.

Song Z, Xu Y, Bao L et al (2019) From SARS to MERS, thrusting coronaviruses into the spotlight. Viruses 11. https://doi.org/10.3390/v11010059

14.

Wu A, Peng Y, Huang B et al (2020) Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe. https://doi.org/10.1016/j.chom.2020.02.001

15.

Zhu Z, Zhang Z, Chen W et al (2018) Predicting the receptor-binding domain usage of the coronavirus based on kmer frequency on spike protein. Infect Genet Evol 61:183–184. https://doi.org/10.1016/j.meegid.2018.03.028CrossRefPubMedPubMedCentral

16.

He Y, Zhou Y, Liu S et al (2004) Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine. Biochem Biophys Res Commun 324:773–781. https://doi.org/10.1016/j.bbrc.2004.09.106CrossRefPubMedPubMedCentral

17.

Lu R, Zhao X, Li J et al (2020) Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 395:565–574. https://doi.org/10.1016/S0140-6736(20)30251-8CrossRefPubMedPubMedCentral

18.

Huang C, Wang Y, Li X et al (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395:497–506. https://doi.org/10.1016/S0140-6736(20)30183-5CrossRefPubMedPubMedCentral

19.

Cui J, Li F, Shi ZL (2019) Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 17:181–192. https://doi.org/10.1038/s41579-018-0118-9CrossRefPubMed

20.

Guan Y, Zheng BJ, He YQ et al (2003) Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 302:276–278. https://doi.org/10.1126/science.1087139CrossRefPubMed

21.

Drosten C, Kellam P, Memish ZA (2014) Evidence for camel-to-human transmission of MERS coronavirus. N Engl J Med 371:1359–1360. https://doi.org/10.1126/science.1087139CrossRefPubMed

22.

Lam TT, Shum MH, Zhu HC et al (2020) Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature. https://doi.org/10.1038/s41586-020-2169-0

23.

Chen G, Wu D, Guo W et al (2020) Clinical and immunologic features in severe and moderate coronavirus disease 2019. J Clin Invest. https://doi.org/10.1172/JCI137244

24.

Qiu H, Wu J, Hong L et al (2020) Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study. Lancet Infect Dis. https://doi.org/10.1016/S1473-3099(20)30198-5

25.

Tian S, Hu N, Lou J et al (2020) Characteristics of COVID-19 infection in Beijing. J Inf Secur 80:401–406. https://doi.org/10.1016/j.jinf.2020.02.018CrossRef

26.

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. Lancet. 395:507–513. https://doi.org/10.1016/S0140-6736(20)30211-7CrossRefPubMedPubMedCentral

27.

Chan JF, Yuan S, Kok KH et al (2020) A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 395:514–523. https://doi.org/10.1016/S0140-6736(20)30154-9CrossRefPubMedPubMedCentral

28.

Wong HYF, Lam HYS, Fong AH et al (2019) Frequency and distribution of chest radiographic findings in COVID-19 positive patients. Radiology 201160. https://doi.org/10.1148/radiol.2020201160

29.

Shi H, Han X, Jiang N et al (2020) Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study. Lancet Infect Dis 20:425–434. https://doi.org/10.1016/S1473-3099(20)30086-4CrossRefPubMedPubMedCentral

30.

Cheng Z, Lu Y, Cao Q et al Clinical Features and Chest CT Manifestations of Coronavirus Disease 2019 (COVID-19) in a single-center study in Shanghai, China. AJR Am J Roentgenol 2020:1–6. https://doi.org/10.2214/AJR.20.22959

31.

Xiong Y, Sun D, Liu Y et al (2020) Clinical and high-resolution CT Features of the COVID-19 infection: comparison of the initial and follow-up changes. Investig Radiol. https://doi.org/10.1097/RLI.0000000000000674

32.

Corman VM, Landt O, Kaiser M et al (2020) Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 25. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045

33.

Konrad R, Eberle U, Dangel A et al (2020) Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020. Euro Surveill 25. https://doi.org/10.2807/1560-7917

34.

Chan JF, Yip CC, To KK et al (2020) Improved molecular diagnosis of COVID-19 by the novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain reaction assay validated in vitro and with clinical specimens. J Clin Microbiol. https://doi.org/10.1128/JCM.00310-20

35.

Reusken CBEM, Broberg EK, Haagmans B et al (2020) Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020. Euro Surveill 25. https://doi.org/10.2807/1560-7917.ES.2020.25.6.2000082

36.

Pan Y, Zhang D, Yang P et al (2020) Viral load of SARS-CoV-2 in clinical samples. Lancet Infect Dis 20:411–412. https://doi.org/10.1016/S1473-3099(20)30113-4CrossRefPubMedPubMedCentral

37.

Chen W, Lan Y, Yuan X et al (2020) Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity. Emerg Microbes Infect 9:469–473. https://doi.org/10.1080/22221751.2020.1732837CrossRefPubMedPubMedCentral

38.

Yu N, Li W, Kang Q et al (2020) Clinical features and obstetric and neonatal outcomes of pregnant patients with COVID-19 in Wuhan, China: a retrospective, single-centre, descriptive study. Lancet Infect Dis. https://doi.org/10.1016/S1473-3099(20)30176-6

39.

Xie X, Zhong Z, Zhao W, Zheng C, Wang F, Liu J (2020) Chest CT for typical 2019-nCoV pneumonia: relationship to negative RT-PCR testing. Radiology. https://doi.org/10.1148/radiol.2020200343

40.

To KK, Tsang OT, Leung WS et al (2020) Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis. https://doi.org/10.1016/S1473-3099(20)30196-1

41.

Liu R, Han H, Liu F et al (2020) Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan, China, from Jan to Feb 2020. Clin Chim Acta 505:172–175. https://doi.org/10.1016/j.cca.2020.03.009CrossRefPubMedPubMedCentral

42.

Yang Y, Yang MH, Shen CG et al Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoVinfections. https://www.medrxiv.org/content/10.1101/2020.02.11.20021493v2. Accessed 17 Feb 2020

43.

Yu F, Yan L, Wang N et al (2020) Quantitative detection and viral load analysis of SARS-CoV-2 in infected patients. Clin Infect Dis. https://doi.org/10.1093/cid/ciaa345

44.

Li Y, Yao L, Li J et al (2020) Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19. J Med Virol. https://doi.org/10.1002/jmv.25786

45.

Zhang T, Cui X, Zhao X et al (2020) Detectable SARS-CoV-2 viral RNA in feces of three children during recovery period of COVID-19 pneumonia. J Med Virol. https://doi.org/10.1002/jmv.25795

46.

Lippi G, Simundic AM, Plebani M (2020) Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med. https://doi.org/10.1515/cclm-2020-0285

47.

Ai T, Yang Z, Hou H et al (2020) Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases. Radiology. 200642. https://doi.org/10.1148/radiol.2020200642

48.

Xie C, Jiang L, Huang G et al (2020) Comparison of different samples for 2019 novel coronavirus detection by nucleic acid amplification tests. Int J Infect Dis 93:264–267. https://doi.org/10.1016/j.ijid.2020.02.050CrossRefPubMedPubMedCentral

49.

Dong X, Cao YY, Lu XX et al (2020) Eleven faces of coronavirus disease 2019. Allergy. https://doi.org/10.1111/all.14289

50.

Damman K, Gori M, Claggett B et al (2018) Renal effects and associated outcomes during angiotensin-Neprilysin inhibition in heart failure. JACC Heart Fail 6:489–498. https://doi.org/10.1016/j.jchf.2018.02.004CrossRefPubMed

51.

Fröhlich H, Nelges C, Täger T et al (2016) Long-term changes of renal function in relation to ace inhibitor/angiotensin receptor blocker dosing in patients with heart failure and chronic kidney disease. Am Heart J 178:28–36. https://doi.org/10.1016/j.ahj.2016.03.024CrossRefPubMed

52.

Liu Y, Yang Y, Zhang C et al (2020) Clinical and biochemical biomarkerses from SARS-CoV-2 infected patients linked to viral loads and lung injury. Sci China Life Sci. https://doi.org/10.1007/s11427-020-1643-8

53.

Imai Y, Kuba K, Penninger JM (2008) Lessons from SARS: a new potential therapy for acute respiratory distress syndrome (ARDS) with angiotensin converting enzyme 2 (ACE2). Masui. 57:302–310PubMed

54.

Huang F, Guo J, Zou Z et al (2014) Angiotensin II plasma levels are linked to disease severity and predict fatal outcomes in H7N9-infected patients. Nat Commun 5:3595CrossRefPubMed

55.

Jing-Wen Ai, Hao-Cheng Zhang, Teng Xu et al (2020) Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China. Medrxiv [Preprint]. [cited 2020 Mar 29]. https://www.medrxiv.org/content/10.1101/2020.02.13.20022673v1

56.

Gong YN, Yang SL, Chen GW et al (2017) A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach. Arch Virol 162:2003–2012. https://doi.org/10.1007/s00705-017-3367-4CrossRefPubMedPubMedCentral

Title: The genetic sequence, origin, and diagnosis of SARS-CoV-2
Authors: Huihui Wang
Xuemei Li
Tao Li
Shubing Zhang
Lianzi Wang
Xian Wu
Jiaqing Liu
Publication date: 01-09-2020
Publisher: Springer Berlin Heidelberg
Keywords: Coronavirus
Severe Acute Respiratory Syndrome Coronavirus
SARS-CoV-2
Middle Eastern Respiratory Syndrome
COVID-19
Published in: European Journal of Clinical Microbiology & Infectious Diseases / Issue 9/2020
Print ISSN: 0934-9723
Electronic ISSN: 1435-4373
DOI: https://doi.org/10.1007/s10096-020-03899-4

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