Review
BibTex RIS Cite

OVERVIEW OF MOLECULAR DIAGNOSTIC METHODS FOR COVID-19

Year 2020, Volume: 11 Issue: 2, 72 - 79, 28.08.2020
https://doi.org/10.38137/vetfarmatoksbulten.772452

Abstract

This review is prepared to give information about the molecular diagnosis methods of a new coronavirus SARS-CoV-2, which causes pandemic in a short time. In order to prevent the COVID-19 pandemic, which causes serious global destruction, the development of sensitive and specific laboratory diagnostic methods are crucial to identify cases quickly and reliably. Diagnostic tests have played an important role in the COVID-19 pandemic and will continue to play. Rapid sampling and testing of patients meeting the suspected case definition for COVID-19 is a priority for clinical management and outbreak control. The ability to detect SARS-CoV-2 in respiratory secretions is necessary to determine when an individual becomes infected and the potential for infecting other persons. Viral detection is used to identify individual patients, manage pandemics, as well as determine when and how quickly the virus is transmitted to a community. As communities seek to re-open after closure periods, the detection of both SARS-CoV-2 and specific antibodies that recognize the virus will become increasingly important as a tool for assessing infection and immunity in individuals and populations. For this purpose, nucleic acid amplification and serological tests are used to detect the SARS-CoV-2.

References

  • CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel; Division of Viral Diseases, U.S. Centers for Disease Control and Prevention: Atlanta, GA, 2020.
  • Chan J. F., Yuan S., Kok K. H. (2020) A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet (London, England), 395(10223): 514-23.
  • Chan J.F.W, Yip C.C.Y., To K.K.W, Tang T.H.C, Wongh S.C.Y., Leung K.H., Fung A.Y.F, Ng A.C.K, Zou Z., Tsoi H.W., Choi G.K.Y., Tam A.R., Cheng V.C.C., Chan K.H., Tsang O.T.Y., Yuenb K.Y. (2020) Improved molecular diagnosis of 1 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, 58 (5), e00310-20.
  • Chang D, Lin M, Wei L, et al. (2020) Epidemiologic and Clinical Characteristics of Novel Coronavirus Infections Involving 13 Patients Outside Wuhan, China. JAMA, 323(11), 1092-1093.
  • Corman V. M., Landt O., Kaiser M., Molenkamp R. (2020) Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR, Euro Surveill. 25(3), 2000045.
  • Craw P., Balachandran W. (2012) Isothermal Nucleic Acid Amplification Technologies for Point-of-Care Diagnostics: A Critical Review. Lab Chip, 12, 2469.
  • Donoghue M., Hsieh F., Baronas E., Godbout K., Gosselin M., Stagliano N., Donovan M., Woolf B., Robison K., Jeyaseelan R. (2000) A novel angiotensin-converting enzyme-related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1-9. Circ. Res, 87, E1–E9.
  • Guan W. J., Ni Z. Y., Hu Y., Liang W. H., Ou C. Q., He J. X. (2020) Clinical characteristics of coronavirus disease 2019 in China; N. Engl. J. Med, 382(18), 1708-1720.
  • Henry BM, de Oliveira MHS, Benoit S, Plebani M, Lippi G. (2020) Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis. Clin Chem Lab Med, 58(7), 1021-1028.
  • Herold T., Jurinovic V., Arnreich C. (2020) Elevated levels of IL-6 and CRP predict the need for mechanical ventilation in COVID-19. J Allergy Clin Immunol, 146(1), 128-136.e.
  • Huang A.T., Garcia-Carreras B., Hitchings M. D. T., Yang B., Katzelnick L., Rattigan S. M., Borgert B., Moreno C., Solomon B. D., Rodriguez-Barraquer I., Lessler J., Salje H., Burke D. S., Wesolowski A., Cummings D. A. T. (2020) A systematic review of antibody mediated immunity to coronaviruses: Antibody kinetics, correlates of protection, and association of antibody responses with severity of disease. medRxiv, https://doi.org/10.1101/2020.04.14.20065771.
  • Huang C., Wang Y., Li X., Ren L., Zhao J., Hu Y. (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet, 395(10223), 497–506.
  • Interim Guidelines for Collecting (2020) Handling, and Testing Clinical Specimens from Persons Under Investigation (PUIs) for Coronavirus Disease 2019 (COVID-19); Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html.
  • Jin Y., Wang M., Zuo Z. et al. (2020) Diagnostic value and dynamic variance of serum antibody in coronavirus disease 2019. Int J Infect Dis, 94, 49-52.
  • Jin Y., Yang H., Ji W., Wu W., Chen S., Zhang W., Duan G. (2020) Virology, Epidemiology, Pathogenesis, and Control of COVID-19. Viruses, 12, 372.
  • Lai C. C., Shih T. P., Ko W. C., Tang H. J., Hsueh P. R. (2020) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. International journal of antimicrobial agents, 105924.
  • Lamb L. E., Bartolone S. N., Ward E., Chancellor M. B. (2020) Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification. MedRxiv, https://doi.org/10.1101/2020.02.19.20025155.
  • Lassaunière R., Frische A., Harboe Z.B. et al. (2020) Evaluation of nine commercial SARS-CoV-2 immunoassays. medRxiv, https://doi.org/10.1101/2020.04.09.20056325.
  • Long Q. X., Liu B. Z., Deng H.J. et al. (2020) Antibody responses to SARS-CoV-2 in patients with COVID-19. Nat Med, 26, 845–848.
  • Miller S., Chiu C., Rodino K. G., Miller M. B. (2020) Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory J. Clin. Microbiol, 58(3), e01739-19.
  • Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K. (2000) Amino, N.; Hase, T. Loop-Mediated Isothermal Amplification of DNA. Nucleic Acids Res, 28 (12), e63.
  • Okba N. M. A., Müller M. A., Li W. (2020) Severe acute respiratory syndrome coronavirus 2-specific antibody responses in coronavirus disease 2019 Patients. Emerg Infect Dis, 26(7):1478-1488.
  • T.C. Sağlık Bakanlığı (2020). COVID-19 Rehberi. https://covid19bilgi.saglik.gov.tr/depo/rehberler/COVID-19_Rehberi.pdf.
  • Theel E. S., Slev P., Wheeler S., Couturier M. R., Wong S. J., Kadkhoda K (2020) The role of antibody testing for SARS-CoV-2: Is there one?. J Clin Microbiol, 58 (8), e00797-20.
  • Udugama B., Kadhiresan P., Kozlowski H. N.., Malekjahani A., Osborne M., Li V. Y. C., Chen H., Mubareka S., Gubbay J. B., Chan W. C. W. (2020) Diagnosing COVID-19: The Disease and Tools for Detection. ACS Nano 2020, 14, 3822−3835.
  • Wang W., Xu Y., Gao R., Lu R., Han K., Wu G., Tan W. (2020) Detection of SARS-CoV-2 in different types of clinical specimens. JAMA, 323, 1843–1844.
  • Weissleder R., Lee H., Ko J., Pittet M. J. (2020) COVID-19 diagnostics in context, Sci. Transl. Med. 12 (546), eabc1931.
  • Whitman J. D., Hiatt J., Mowery C. T. (2020) Test performance evaluation of SARS-CoV-2 serological assays. medRxiv, https://doi.org/10.1101/2020.04.25.20074856.
  • WHO (2020) Clinical management of severe acute respiratory infection when Novel coronavirus (nCoV) infection is suspected: interim guidance. Jan 11.
  • Winichakoon P., Chaiwarith R., Liwsrisakun C., Salee P., Goonna A., Limsukon A., Kaewpoowat Q. (2020) Negative Nasopharyngeal and Oropharyngeal Swab Does Not Rule Out COVID-19. J. Clin. Microbiol, 00297-20.
  • Wong, M. L.; Medrano, J. F. Real-Time PCR for mRNA Quantitation. BioTechniques, 2005, 39 (1), 75−85.
  • Wu F., Zhao S., Yu B., Chen Y. M., Wang W., Hu Y., Song Z. G., Tao Z. W., Tian J. H., Pei Y. Y. (2020) Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China, bioRxiv, https://doi.org/10.1101/2020.01.24.919183.
  • Yang W., Dang X. et al. (2020) Rapid Detection of SARS-CoV-2 Using Reverse Transcription RT-LAMP Method. medRxiv, https://doi.org/10.1101/2020.03.02.20030130.
  • Yang Y., Yang M., Shen C., Wang F., Yuan J., Li J., Zhang M., Wang Z., Xing L., Wei J. (2020) Laboratory Diagnosis and Monitoring the Viral Shedding of 2019-nCoV Infections. medRxiv, https://doi.org/10.1101/2020.02.11.20021493.
  • Yu L., Wu S. et al (2020) Rapid Colorimetric Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform: iLACO. medRxiv, https://doi.org/10.1093/clinchem/hvaa102.
  • Zhang Y., Odiwuor N. et al. (2020) Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP. medRxiv, https://doi.org/10.1101/2020.02.26.20028373.
  • Zhao R., Li M., Song H. (2020) Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection. Clin Infect Dis, https://doi.org/10.1093/cid/ciaa523.
  • Zhu N, Zhang D, Wang W (2020) A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med, 382(8): 727-33.

COVID-19 İÇİN MOLEKÜLER TANI YÖNTEMLERİNE GENEL BAKIŞ

Year 2020, Volume: 11 Issue: 2, 72 - 79, 28.08.2020
https://doi.org/10.38137/vetfarmatoksbulten.772452

Abstract

Bu derleme, kısa bir süre içinde pandemiye sebep olan, yeni bir koronavirüs SARS-CoV-2’nin moleküler tanı yöntemleri ile ilgili bilgi vermek amacıyla hazırlanmıştır. Global olarak ciddi bir tahribata yol açan COVID-19 pandemisini önleyebilmek adına, hassas ve spesifik laboratuvar teşhis metotlarının geliştirilmesi, vakaların hızlı ve güvenilir şekilde tanımlanabilmesi için oldukça önemlidir. Diyagnostik testler COVID-19 pandemisinde önemli bir rol oynamıştır ve oynamaya devam edecektir. COVID-19 için şüphelenilen vaka tanımını karşılayan hastalardan hızla numune alınması ve test edilmesi klinik yönetim ve salgın kontrolü için bir önceliktir. Solunum sekresyonlarında SARS-CoV-2 saptama yeteneği, bireyin enfekte olma zamanını ve diğer kişilere bulaştırma potansiyelini belirlemek için gereklidir. Viral tespit, bireysel hastaların tanımlanması, pandemi yönetimi ve ayrıca virüsün bir topluluğa ne zaman bulaştığını ve ne kadar hızla yayıldığını belirlemek için kullanılır. Topluluklar, kapanma dönemlerinin ardından yeniden açılmaya çalıştıkça, hem SARS-CoV-2'nin hem de virüsü tanıyan spesifik antikorların saptanması, bireylerde ve topluluklarda enfeksiyon ve bağışıklığın değerlendirilmesi için bir araç olarak giderek daha önemli hale gelecektir. Bu amaçla, SARS-CoV-2 genomunu tespit etmeye yönelik nükleik asit amplifikasyon testleri ve serolojik testler kullanılmaktadır.

References

  • CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel; Division of Viral Diseases, U.S. Centers for Disease Control and Prevention: Atlanta, GA, 2020.
  • Chan J. F., Yuan S., Kok K. H. (2020) A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet (London, England), 395(10223): 514-23.
  • Chan J.F.W, Yip C.C.Y., To K.K.W, Tang T.H.C, Wongh S.C.Y., Leung K.H., Fung A.Y.F, Ng A.C.K, Zou Z., Tsoi H.W., Choi G.K.Y., Tam A.R., Cheng V.C.C., Chan K.H., Tsang O.T.Y., Yuenb K.Y. (2020) Improved molecular diagnosis of 1 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, 58 (5), e00310-20.
  • Chang D, Lin M, Wei L, et al. (2020) Epidemiologic and Clinical Characteristics of Novel Coronavirus Infections Involving 13 Patients Outside Wuhan, China. JAMA, 323(11), 1092-1093.
  • Corman V. M., Landt O., Kaiser M., Molenkamp R. (2020) Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR, Euro Surveill. 25(3), 2000045.
  • Craw P., Balachandran W. (2012) Isothermal Nucleic Acid Amplification Technologies for Point-of-Care Diagnostics: A Critical Review. Lab Chip, 12, 2469.
  • Donoghue M., Hsieh F., Baronas E., Godbout K., Gosselin M., Stagliano N., Donovan M., Woolf B., Robison K., Jeyaseelan R. (2000) A novel angiotensin-converting enzyme-related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1-9. Circ. Res, 87, E1–E9.
  • Guan W. J., Ni Z. Y., Hu Y., Liang W. H., Ou C. Q., He J. X. (2020) Clinical characteristics of coronavirus disease 2019 in China; N. Engl. J. Med, 382(18), 1708-1720.
  • Henry BM, de Oliveira MHS, Benoit S, Plebani M, Lippi G. (2020) Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis. Clin Chem Lab Med, 58(7), 1021-1028.
  • Herold T., Jurinovic V., Arnreich C. (2020) Elevated levels of IL-6 and CRP predict the need for mechanical ventilation in COVID-19. J Allergy Clin Immunol, 146(1), 128-136.e.
  • Huang A.T., Garcia-Carreras B., Hitchings M. D. T., Yang B., Katzelnick L., Rattigan S. M., Borgert B., Moreno C., Solomon B. D., Rodriguez-Barraquer I., Lessler J., Salje H., Burke D. S., Wesolowski A., Cummings D. A. T. (2020) A systematic review of antibody mediated immunity to coronaviruses: Antibody kinetics, correlates of protection, and association of antibody responses with severity of disease. medRxiv, https://doi.org/10.1101/2020.04.14.20065771.
  • Huang C., Wang Y., Li X., Ren L., Zhao J., Hu Y. (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet, 395(10223), 497–506.
  • Interim Guidelines for Collecting (2020) Handling, and Testing Clinical Specimens from Persons Under Investigation (PUIs) for Coronavirus Disease 2019 (COVID-19); Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html.
  • Jin Y., Wang M., Zuo Z. et al. (2020) Diagnostic value and dynamic variance of serum antibody in coronavirus disease 2019. Int J Infect Dis, 94, 49-52.
  • Jin Y., Yang H., Ji W., Wu W., Chen S., Zhang W., Duan G. (2020) Virology, Epidemiology, Pathogenesis, and Control of COVID-19. Viruses, 12, 372.
  • Lai C. C., Shih T. P., Ko W. C., Tang H. J., Hsueh P. R. (2020) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. International journal of antimicrobial agents, 105924.
  • Lamb L. E., Bartolone S. N., Ward E., Chancellor M. B. (2020) Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification. MedRxiv, https://doi.org/10.1101/2020.02.19.20025155.
  • Lassaunière R., Frische A., Harboe Z.B. et al. (2020) Evaluation of nine commercial SARS-CoV-2 immunoassays. medRxiv, https://doi.org/10.1101/2020.04.09.20056325.
  • Long Q. X., Liu B. Z., Deng H.J. et al. (2020) Antibody responses to SARS-CoV-2 in patients with COVID-19. Nat Med, 26, 845–848.
  • Miller S., Chiu C., Rodino K. G., Miller M. B. (2020) Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory J. Clin. Microbiol, 58(3), e01739-19.
  • Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K. (2000) Amino, N.; Hase, T. Loop-Mediated Isothermal Amplification of DNA. Nucleic Acids Res, 28 (12), e63.
  • Okba N. M. A., Müller M. A., Li W. (2020) Severe acute respiratory syndrome coronavirus 2-specific antibody responses in coronavirus disease 2019 Patients. Emerg Infect Dis, 26(7):1478-1488.
  • T.C. Sağlık Bakanlığı (2020). COVID-19 Rehberi. https://covid19bilgi.saglik.gov.tr/depo/rehberler/COVID-19_Rehberi.pdf.
  • Theel E. S., Slev P., Wheeler S., Couturier M. R., Wong S. J., Kadkhoda K (2020) The role of antibody testing for SARS-CoV-2: Is there one?. J Clin Microbiol, 58 (8), e00797-20.
  • Udugama B., Kadhiresan P., Kozlowski H. N.., Malekjahani A., Osborne M., Li V. Y. C., Chen H., Mubareka S., Gubbay J. B., Chan W. C. W. (2020) Diagnosing COVID-19: The Disease and Tools for Detection. ACS Nano 2020, 14, 3822−3835.
  • Wang W., Xu Y., Gao R., Lu R., Han K., Wu G., Tan W. (2020) Detection of SARS-CoV-2 in different types of clinical specimens. JAMA, 323, 1843–1844.
  • Weissleder R., Lee H., Ko J., Pittet M. J. (2020) COVID-19 diagnostics in context, Sci. Transl. Med. 12 (546), eabc1931.
  • Whitman J. D., Hiatt J., Mowery C. T. (2020) Test performance evaluation of SARS-CoV-2 serological assays. medRxiv, https://doi.org/10.1101/2020.04.25.20074856.
  • WHO (2020) Clinical management of severe acute respiratory infection when Novel coronavirus (nCoV) infection is suspected: interim guidance. Jan 11.
  • Winichakoon P., Chaiwarith R., Liwsrisakun C., Salee P., Goonna A., Limsukon A., Kaewpoowat Q. (2020) Negative Nasopharyngeal and Oropharyngeal Swab Does Not Rule Out COVID-19. J. Clin. Microbiol, 00297-20.
  • Wong, M. L.; Medrano, J. F. Real-Time PCR for mRNA Quantitation. BioTechniques, 2005, 39 (1), 75−85.
  • Wu F., Zhao S., Yu B., Chen Y. M., Wang W., Hu Y., Song Z. G., Tao Z. W., Tian J. H., Pei Y. Y. (2020) Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China, bioRxiv, https://doi.org/10.1101/2020.01.24.919183.
  • Yang W., Dang X. et al. (2020) Rapid Detection of SARS-CoV-2 Using Reverse Transcription RT-LAMP Method. medRxiv, https://doi.org/10.1101/2020.03.02.20030130.
  • Yang Y., Yang M., Shen C., Wang F., Yuan J., Li J., Zhang M., Wang Z., Xing L., Wei J. (2020) Laboratory Diagnosis and Monitoring the Viral Shedding of 2019-nCoV Infections. medRxiv, https://doi.org/10.1101/2020.02.11.20021493.
  • Yu L., Wu S. et al (2020) Rapid Colorimetric Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform: iLACO. medRxiv, https://doi.org/10.1093/clinchem/hvaa102.
  • Zhang Y., Odiwuor N. et al. (2020) Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP. medRxiv, https://doi.org/10.1101/2020.02.26.20028373.
  • Zhao R., Li M., Song H. (2020) Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection. Clin Infect Dis, https://doi.org/10.1093/cid/ciaa523.
  • Zhu N, Zhang D, Wang W (2020) A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med, 382(8): 727-33.
There are 38 citations in total.

Details

Primary Language Turkish
Subjects Veterinary Sciences
Journal Section Review
Authors

Zeynep Semen 0000-0002-7722-5772

Seda Ekici 0000-0002-7982-5261

Büşra Malas 0000-0002-2432-091X

Publication Date August 28, 2020
Acceptance Date August 11, 2020
Published in Issue Year 2020 Volume: 11 Issue: 2

Cite

APA Semen, Z., Ekici, S., & Malas, B. (2020). COVID-19 İÇİN MOLEKÜLER TANI YÖNTEMLERİNE GENEL BAKIŞ. Veteriner Farmakoloji Ve Toksikoloji Derneği Bülteni, 11(2), 72-79. https://doi.org/10.38137/vetfarmatoksbulten.772452