The Molecular Diagnosis Protocols of New Coronavirus (COVID-19); Specificity and Sensitivity an Overview

Abstract = 931 times | PDF = 185 times

Main Article Content

Abdullah Ahmed Hama Othman Abdulrahman Mohammed Fatima Mahmud Ali Osama Hamid Shareef Sardar Muhammad Wli Sabiha Sharif Syamand Ahmed Qadir

Abstract

Acute respiratory tract infection is a common public health concern worldwide a new emerging contagious virus (COVID-2019) or SARSC- 2 causing a pandemic pneumonia outbreak, The main transmission route of this virus is through droplets from respiratory made during sneezing or coughing of infected people like the recent viral infection of severe acute respiratory syndrome (SARS-CoV1) and the Middle East respiratory syndrome (MERS). Many epidemiological factors have a crucial role in promoting the transmission of the COVID-2019 that makes the disease as an emerging and global alarming against this new coronavirus. Early diagnosis of the etiological agents is critical for appropriate management, controlling plan, protection, and treatment. The new outbreak of COVID-19 can be detected by different molecular protocols. Quantitative polymerase chain reaction (qPCR) is the recommended technique used with varied sensitivity due to primers variation and specimen type. The reliable, high specific and sensitive diagnosis protocols are necessary for an emerging control plan. This study will review and explore the most available methods of molecular identification and primers for the diagnosis of the new coronavirus (COVID-19). This review will also open the new clues to develop and select appropriate diagnosis panel and specific primers for new coronavirus. In conclusion of this review, the RNA dependent RNA polymerase (RdRp) and RdRp/Hel protocols will be valuable to distinguish the  COVID-19 from the SARS-CoV and the other respiratory viral pathogens.

Keywords

COVID-19, new coronavirus, diagnostic methods, DNA marker, respiratory viral infection.

Downloads

Download data is not yet available.

Article Details

References

[1] M.Shen, Z. Peng, Y. Xiao, L. Zhang, "Modelling the epidemic trend of the 2019 novel coronavirus outbreak in China", bioRxiv.,.916726. 2020. https://doi.org/10.1101/2020.01.23.916726
[2] D.D. Richman, R.J. Whitley, F.G. Hayden, "Clinical virology", 4th edn. Washington, DC: ASM Press,2016.
[3] Z.Y. Zu, D.J. Meng, P.X. Peng , C.Wen , Q.N.Qian , M.L.Guang , J.Z. Long, " Coronavirus Disease 2019 (COVID-19): A Perspective from China", Radiology, vol. 2019, p. 200490, 2020. https://doi.org/10.1148/radiol.2020200490
[4] N.Zhu, D. Zhang , W.Wang , L. Xingwang ,Y. Bo, S. Jingdong, Zh. Xiang, H. Baoying, S. Weifeng, L. Roujian, N. Peihua, Zh. Faxian, et al, " A novel coronavirus from patients with pneumonia in China, 2019 ", N. Engl. J. Med., vol.382,pp.727-733, 2020. DOI: 10.1056/NEJMoa2001017.
[5] R.Lu, X. Zhao,J. Li,N. Peihua, Y.Bo, W. Honglong, et al. "Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding", Lanc,J, vol.395,pp. 565-574, 2020. DOI: 10.1016/S0140-6736(20)30251-8.
[6] T.G. Ksiazek ,D. Erdman ,C.S. Goldsmith,S.R. Zaki, T.Peret, S.Emery, S.Tong ,C. Urbani , J.A. Comer , W. Lim , P.E. Rollin , S.F. Dowell , A.E. Ling , C.D. ,W.J. , et al. "A novel coronavirus associated with severe acute respiratory syndrome" N. Eng.l J. Med.,vol.348, pp.1953-1966, 2003.
[7] T.G. Kuiken, R.A.M. Fouchier, M. Schutten , R.F. Guus, R.Debby, et al, "Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome", Lanc, J,vol. 362, pp.263-270, 2003. DOI: 10.1016/S0140-6736(03)13967-0.
[8] R.J. de Groot,S.C. Baker, R.S. Baric, S.B. Caroline,D. Christian, E.Luis, et al, "Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group", J. Virol, vol.87, pp,7790-7792, 2013. DOI: 10.1128/JVI.01244-13.
[9] A.M. Zaki , S. van Boheemen, T.M.Bestebroer , A.D.M.E. Osterhaus , R.A.M. Fouchier, " Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia", N. Engl. J. Med,vol.367, pp.1814-1820, 2012.
[10] World Health Organization, "Summary of Probable SARS Cases with Onset of Illness from 1 November 2002 to January 2003.3003. http://www.who.int/csr/sars/country/table2004_04_21/en/index.html
[11] World Health Organization, "Middle East respiratory syndrome coronavirus (MERS-CoV)" Repoet of WHO.2020 http://www.who.int/emergencies/mers-cov/en/
[12] World Health Organization, " Director –Generals remarks at the media briefing on 2019-nCov". 2020. https://www.who.int/dg/speeches/detail/who-director-general-s-remarks-at-the-media-briefing-on-2019-ncov-on-11-february-2020
[13] A.E.Gorbalenya, C. B. Susan, S.B. Ralph,J. de.G. Raoul , D. Christian, A. G. Anastasia, et al., " Severe acute respiratory syndrome-related coronavirus: the species and its viruses - a statement of the Coronavirus Study Group", bioRxiv preprint, 2020. DOI: 10.1101/2020.02.07.
[14] J.F.Chan , S.Yuan , K.H. Kok, K.T.Kelvin, C. Hin, Y.Jin et al, "A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster", Lanc.J, vol.395,pp.514-523, 2020. DOI: 10.1016/S0140-6736(20)30154-9.
[15] S.Hoehl, A. Berger, M.Kortenbusch, et al, " Evidence of SARS-CoV-2 Infection in Returning Travelers from Wuhan, China", N. Engl. J. Med., vol. 382, pp.1278-1280 2020. DOI: 10.1056/NEJMc2001899.
[16] L. Zou , F. Ruan, M. Huang, L.Liang, H. Huang, Z. Hong, et al, " SARS-CoV-2 Viral. Load in Upper Respiratory Specimens of Infected Patients", N. Engl. J.Med., vol. 382, pp.1177-1179, 2020.
DOI: 10.1056/NEJMc2001737.
[17] H. Chen, J. Guo, C. Wang,L. Fan, Y.Xuechen, et al, " Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records", Lanc.J.,vol.395,pp.809-815, 2020. DOI:10.1016/S0140-6736(20)30360-3.
[18] H. Zhu, L.Wang, C.Fang,P.Sicong, Zh.Lianhong, Ch. Guiping, X.Shiwen, Zh. Wenhao, " Clinical analysis of 10 neonates born to mothers with 2019-nCoV pneumonia", Transl. Pediatr., vol. 9,pp. 51-60, 2020.
DOI: 10.21037/tp.2020.02.06.
[19] World Health Organization, " Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases", 17 January 2020. https://apps.who.int/iris/handle/10665/330676.
[20] Z. Li, Y. Yi, X. Luo, N.Xiong, Y.Liu, S.Li, R.Sun,Y. Wang, B.Hu, et al, " Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis", J. Med. Virol., 2020 Feb 27. DOI: 10.1002/jmv.25727.
[21] World Health Organization, "Coronavirus disease (COVID-2019) situation reports", 2020.
[22] Z. M. Chen, J.F. Fu, Q.Shu,Y.H. Chen, C.Z. Hua, F.B. Li, R. Lin, L.F. Tang, et al, " Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus", World. J. Pediatr. 2020. DOi: 10.1007/s12519-020-00345-5.
[23] K.L. Shen, Y.H.Yang, " Diagnosis and treatment of 2019 novel coronavirus infection in children: a pressing issue", World. J. Pediatr. 2020. DOI: 10.1007/s12519-020-00344-6
[24] C.Huang, Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, L. Zhang, G. Fan, J. Xu, X. Gu et al. "Clinical features of patients infected with 2019 novel" Lanc. J., vol.395pp.497-506, 2020. DOI: 10.1016/S0140-6736(20)30183-5.
[25] J. Ying-Hui, C.Lin,Ch. Zhen-Shun, Ch.Hong, D.Tong,F. Yi-Pin,F. Cheng, H. et al., "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version) ", M. Med.Rech.,vol. 7, No. 4-4.2020. DOI: 10.1186/s40779-020-0233-6.
[26] J. She, J. Jiang, L. Ye, L. Hu, C. Bai, and Y. Song, "2019 novel coronavirus of pneumonia in Wuhan, China: emerging attack and management strategies", Clin. Trans.l Med.,( 9) 19, 2020. DOI: 10.1186/s40169-020-00271-z.
[27] L.Xiaoqi,G. Zhenyu, X. Zuke,X. Jingliang,F. Bing, and L. Jiaqi, Liu, " Novel Coronavirus Pneumonia Outbreak in 2019: Computed Tomographic Findings in Two Cases", Korean journal of radiology, (21) ,pp. 365-68, 2020. DOI: 10.3348/kjr.2020.0078.
[28] T. Ai, Z. Yang, H. Hou,C. Zhan,C. Chen, W. Lv, Q. Tao, Z. Sun and L. Xia, "Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases", Radiology, (80), 2, pp. 1–8, 2020. DOI : 10.1148/radiol.2020200642.
[29] P. Zhou, X. L. Yang, X. G. Wang, B. Hu, L. Zhang, W. Zhang, et al, "A pneumonia outbreak associated with a new coronavirus of probable bat origin",2020, Nature, vol. 579, No.7798, pp. 270-273, 2020. DOI: 10.1038/s41586-020-2012-7.
[30 ] M. L. Holshue, C. DeBolt, S. Lindquist, K. H. Lofy, J. Wiesman, H. Bruce, C. Spitters, et al., "First Case of 2019 Novel Coronavirus in the United States", N. Engl. J. Med.,vol. 382, pp. 929-936, 2020. DOI : 10.1056/NEJMoa2001191.
[31] D.S. Hui, I.E. Azhar, T. A. Madani, F. Ntoumi, R. Kock, O. Dar, G. Ippolito, T. D. McHugh, Z. A. Memish, C. Drosten, A. Zumla, and E. Petersen, " The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health - The latest 2019 novel coronavirus outbreak in Wuhan, China", Int.J. Infect. Dis.,vol. 91,pp. 264-66, 2020.
[32] V.M. Corman, O. Landt, M. Kaiser, R. Molenkamp, A. Meijer, D. K. W. Chu, T. Bleicker, etal., " Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR", Euro. Surveill., vol.25, No.3, 2020. DOI: 10.2807/1560-7917.ES.2020.25.3.2000045.
[33] L.L. Poon, K. H. Chan, O. K. Wong, W. C. Yam, K. Y. Yuen, Y. Guan, Y. M. Lo, and J. S. Peiris, " Early diagnosis of SARS coronavirus infection by real time RT-PCR", J. Clin. Virol.,vol. 28, pp. 233-8. 2003.
[34 ] I. F. N. Hung, V. C. C. Cheng, A. K. L. Wu, B. S. F. Tang, K. H. Chan, C. M. Chu, M. M. L. et al., " Viral loads in clinical specimens and SARS manifestations", Emerging infectious diseases, vol. 10, pp. 1550-1557, 2004.
[35] CDC, " CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel ", Centers for Diseade Control and Prevention. Division of Viral Diseases. 2020 https://www.fda.gov/media/134922/download
[36] J. Pang, M. X. Wang, I. Y. H. Ang, S. H. X. Tan, R. F. Lewis, J. I. Chen, R. A., et al. " Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review", J. Clin. Med.,vol. 9. 2020. DOI: 10.3390/jcm9030623.
[37] B. S. Sibylle, R. Patrick, S.Yassoungo, M. Alexandra, C. Christine,S. Anne, M.Matthieu, M. Laure, N. Mathieu, B. Clément, Y.Estelle, B.Sylvie, I. Sophie, N. Duc, M. Denis, X. François, C. Scarlett Georges, Clément Lazarus, Anouk Tabaï, Morgane Stempfelet, Vincent Enouf, Bruno, L.B. Daniel, and Team Investigation, " First cases of coronavirus disease 2019 (COVID-19) in France: surveillance, investigations and control measures, January 2020", Euro. Surveill., vol. 25, 2020.

[38 ] J.F. Chan, C.C. Yip, K.K. To, T.H. Tang, S.C. Wong, K.H. Leung, A.Y. Fung, A.C. Ng, et al, "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", [published online ahead of print, 2020 Mar 4]. J. Clin. Microbiol,. JCM. 00310-20, 2020. DOI:10.1128/JCM.00310-20
[39] L. Jaegyun, J. Seunghyun, Y.S. Hyun, J.K. Moon, M.S. Yu, L. J. Wang, W. C. Kang, M. k. Yu, L. Baeckseung, and J.P. Sang, " Case of the Index Patient Who Caused Tertiary Transmission of COVID-19 Infection in Korea: the Application of Lopinavir/Ritonavir for the Treatment of COVID-19 Infected Pneumonia Monitored by Quantitative RT-PCR"', J. K. M.S., vol. 35, pp. e79-e79, 2020. DOI: 10.3346/jkms.2020.35.e79.
[40] D. K. W.Chu, Y. Pan, S. M. S. Cheng, K. P. Y. Hui, P. Krishnan, Y. Liu, D. Y. M. Ng, C. K. C. Wan, P. Yang, Q. Wang, M. Peiris, and L. L. M. Poon, " Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia", Clin. Chem., vol 1;66 , No.4, pp.549-555, 2020. DOI: 10.1093/clinchem/hvaa029.
[41] K.Kai-qian F.Y. Chee,C. Lin, T.P.L. Raymond, M.M. Tze, M. Matthias, L.Jiahui, Y.C. Chia, N. Nadua, et al., "A Well Infant With Coronavirus Disease 2019 With High Viral Load ", Clin. Infect. Dis., no. February, pp. 2019–2021, 2020. DOI: 10.1093/cid/ciaa201
[42] N. Zhang, L. Wang, X. Deng, R. Liang, M. Su,C. He, L. Hu, Y. Su, J. Ren, F. Yu, L. Du, and S. Jiang, " Recent advances in the detection of respiratory virus infection in humans", j. M. V. , vol.92, No. 4, pp. 408–417, 2020. DOI: 10.1002/jmv.25674.
[43] Z. Hu, C. Song, C. Xu, G. Jin, Y. Chen, X, Xu, H. Ma, W. Chen, Y. Lin, Y.Zheng, J. Wang , Z. Hu, Y. Yi, H. Shen, " Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China", Sci. China Life Sci., 2020. DOI: 10.1007/s11427-020-1661-4.
[44] J. F. W. Chan, S. Sridha, C.C. Yip, S. K. Lau,and P.C. Woo, " The role of laboratory diagnostics in emerging viral infections: the example of the Middle East respiratory syndrome epidemic", J. Microbio., vol. 55, No.3, pp. 172–182, 2017. DOI: 10.1007/s12275-017-7026-y.
[45] Y. Yin and R. G. Wunderink, " MERS, SARS and other coronaviruses as causes of pneumonia", Respirology, 23(2), 130–137, 2018. doi: 10.1111/resp.13196.
[46] C. Kelly-Cirino,L.T. Mazzola, A. Chua,C. J. Oxenford,and M.D. Van Kerkhove, "An updated roadmap for MERS-CoV research and product development: focus on diagnostics", BMJ Global Health, vol. 4(Suppl 2), e001105.2019. DOI: 10.1136/bmjgh-2018-001105. eCollection 2019.
[47] World Health Organization (WHO), " Novel Coronavirus. (2019-nCoV) technical guidance: laboratory guidance. Geneva: WHO", [Accessed 08 March 2020]. Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance
[48] HKU, " Detection of 2019 novel coronavirus (2019-nCoV) in suspected human cases by RT-PCR", LKS Faculty of Medicine School of Public Health, 2020. https://www.who.int/docs/default-source/coronaviruse/peiris-protocol-16-1-20.pdf?sfvrsn=af1aac73_4
[49] S. Al Johani, and A.H. Hajeer, " MERS-CoV diagnosis: An update", J. Infec. and Public Heal.,vol. 9, No.3,pp. 216 –219, 2016. DOI: 10.1016/j.jiph.2016.04.005
[50] J.H. Ko, M.A.Müller,H. Seok,G.E. Park, J.Y.Lee, S.Y.Cho,Y.E., et al. " Serologic responses of 42 MERS-coronavirus-infected patients according to the disease severity", . Diagn. Microbiol. and Infecti. Dis.,vol 89, No.2, pp.106–111, 2017. doi: 10.1016/j.diagmicrobio.2017.07.006.
[51] World Health Organization(WHO), " Laboratory Testing for Middle East Respiratory Syndrome Coronavirus", Who, September 2013, 1–9, 2014. DOI: 0.1016/j.lwt.2018.09.079
[52] H.X. Bai, B. Hsieh, Z. Xiog, K. Halsey, J.W. Choi, T.M.L.Tran, et al. “Performance of radiologists in differentiating COVID-19 from viral pneumonia on chest CT,” Radiology, p. 200823, 2020. DOI: 10.1148/radiol.2020200823.