COVID-19 için tanısal yaklaşımlar

Coronavirus hastalığı-2019 (COVID-19), Aralık 2019'daÇin'in Hubei Eyaletinde ortaya çıkmış ve tüm dünyaya yayılmıştır. Hastalığın etkeni olan SARS-CoV-2'nin hızlı ve doğrulaboratuvar testleri tespit edilebilmesi erken tanı, hızlı raporlama, karantina tedbirlerinin alınması, erken tedavininuygulanması ve bulaşma yolunun kesilmesinde önem arzetmektedir. COVID-19 hastalarında gözlenen semptomlarspesifik semptomlar olmadığı için kesin tanıda bunlardanyararlanılamamaktadır. Günümüzde, COVID-19 tanısı, RTPCR, serolojik testler ve bilgisayarlı tomografi ile yapılmaktadır, ayrıca LAMP, RT-LAMP, CRISPR vb. gibi alternatifteknolojiler de geliştirme aşamasındadır ve yakın zamandaCOVID-19 tanısında kullanılacağı düşünülmektedir. Bu derlemede, SARS-CoV-2 tanısı amacıyla örnek toplama, kullanılannükleik asit testleri, serolojik testler ve bilgisayarlı tomografiyanı sıra alternatif teknikler hakkında bilgi vermek amaçlanmıştır. COVID-19’un dünya çapındaki yayılımı göz önünealındığında, hızlı, güvenilir ve ucuz alternatif tanı testlerininde geliştirilmesine acil ihtiyaç duyulmaktadır ve bu yöntemlerin geliştirilmesi gelecekteki salgınları önlemek açısındanda faydalı olacaktır

Diagnostic approaches for COVID-19

Coronavirus disease-2019 (COVID-19) emerged in Hubei Province of China in December 2019 and spread all over the world. Fast and accurate laboratory tests of SARS-CoV-2, the cause of the disease, are important in early diagnosis, early reporting, taking early quarantine measures, applying early treatment and stopping the transmission path. Since the symptoms observed in COVID-19 patients are not specific symptoms, they cannot be utilized in the definitive diagnosis. Currently, the diagnosis of COVID-19 is made by RT-PCR, serological tests and computed tomography, also alternative technologies such as rapid diagnostic kits, LAMP, RT-LAMP, CRISPR etc., are under development and are thought to be used in the diagnosis of COVID-19 in the future. In this review, it is aimed to give information about sample collection, nucleic acid tests, serological tests and computed tomography as well as alternative techniques for the diagnosis of SARS-CoV-2. Given the worldwide spread of COVID-19, there is an urgent need to develop fast, reliable and inexpensive alternative diagnostic tests, and the development of these methods will also be useful in preventing future epidemics.

___

  • Abd El Wahed A, Patel P, Heidenreich D, Hufert et al., 2013. Reverse Transcription Recombinase Polymerase Amplification Assay for the Detection of Middle East Respiratory Syndrome Coronavirus. PLoS Curr 5.
  • Ahmed W, Angel N, Edson J, Bibby K, et al., 2020. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community. Sci Total Environ 728, 138764.
  • Ai T, Yang Z, Hou H, Zhan C, et al., 2020. Correlation of Chest CT and RT-PCR Testing for Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases. Radiology 296, E32–E40.
  • Alpaslan-Kocamemi B, Kurt H, Sait A, Sarac F, et al., 2020. SARS-CoV-2 Detection in Istanbul Wastewater Treatment Plant Sludges. medRxiv
  • Beltrán-Pavez, C, Márquez CL, Muñoz G, Valiente-Echeverría F, et al., 2020. SARS-CoV-2 detection from nasopharyngeal swab samples without RNA extraction. bioRxiv
  • Bernheim A, Mei X, Huang M, Yang Y, et al., 2020. Chest CT Findings in Coronavirus Disease-19 (COVID-19): Relationship to Duration of Infection. Radiology 295, 200463.
  • Broughton JP, Deng X,Yu G, Fasching CL, et al., 2020. CRISPR– Cas12-based detection of SARS-CoV-2. Nat Biotechnol 38, 870-874.
  • CDC, 2020a. 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel. Erişim Tarihi: 07.08.2020
  • CDC, 2020b. CDC 2019-Novel Coronavirus (2019-nCoV) RealTime RT-PCR Diagnostic Panel. Erişim Tarihi: 07.08.2020
  • CDC, 2020c. Discontinuation of Transmission-Based Precautions and Disposition of Patients with COVID-19 in Healthcare Settings (Interim Guidance) https://www.cdc.gov/ coronavirus/2019-ncov/hcp/disposition-hospitalized-patients.html. Erişim Tarihi: 07.08.2020
  • CDC, 2020d. Preparation Of Viral Transport Medium https:// www.cdc.gov/coronavirus/2019-ncov/downloads/ViralTransport-Medium.pdf Erişim Tarihi: 07.10.2020
  • Chen W, Lan Y, Yuan X, Deng, 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.
  • Chu DKW, Pan Y, Cheng SMS, Hui KPY, et al., 2020. Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia Clin Chem 66, 549–555.
  • Corman VM, Landt O, Kaiser M, Molenkamp R, et al., 2020. Detection of 2019 novel coronavirus (2019-nCoV) by realtime RT-PCR. Eurosurveillance 25, 1–8.
  • Daughton, C, 2020. The international imperative to rapidly and inexpensively monitor community-wide Covid-19 infection status and trends. Sci Total Environ 726, 138149.
  • Ding S, Liang TJ, 2020. Is SARS-CoV-2 also an enteric pathogen with potential fecal–oral transmission? A COVID-19 virological and clinical review. Gastroenterology 159, 53-61.
  • Fakruddin M, Mannan K Bin, Hossain M, Islam S, et al., 2013. Nucleic acid amplification: Alternative methods of polymerase chain reaction. J Pharm Bioallied Sci 5, 245.
  • Fang Y, Zhang H, Xie J, Lin M, et al., 2020. Sensitivity of Chest CT for COVID-19: Comparison to RT-PCR. Radiology 296, E115–E117.
  • Fehr AR, Perlman S, 2015. Coronaviruses: An Overview of Their Replication and Pathogenesis, in: Coronaviruses: Methods and Protocols. Ed: Maier HJ, Bickerton E, Britton P. Humana Press, New York, NY, pp. 1–23.
  • Freeman B, Lester S, Mills L, Rasheed MAU, et al., 2020. Validation of a SARS-CoV-2 spike protein ELISA for use in contact investigations and serosurveillance. bioRxiv GISAID, 2020. Genomic epidemiology of hCoV-19, https:// www.gisaid.org/epiflu-applications/next-hcov-19-app/ Erişim Tarihi: 07.08.2020
  • Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, et al., 2017. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356, 438–442.
  • Guan W, Ni Z, Hu Y, Liang W, et al., 2020. Clinical characteristics of coronavirus disease 2019 in China. N Engl J Med 382, 1708–1720.
  • HKU, 2019. Detection of 2019 novel coronavirus (2019- nCoV) in suspected human cases by RT-PCR. Erişim Tarihi: 08.08.2020
  • Holshue ML, DeBolt C, Lindquist S, Lofy KH, et al., 2020. First Case of 2019 Novel Coronavirus in the United States. N Engl J Med 382, 929–936.
  • Huang P, Wang H, Cao Z, Jin H, et al., 2018. A Rapid and Specific Assay for the Detection of MERS-CoV. Front Microbiol 9, 1101.
  • Huang WE, Lim B, Hsu C, Xiong D, et al., 2020. RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2. Microb Biotechnol 13, 950–961. ICTV, https://talk.ictvonline.org/ictv-reports/ictv_9th_report/positive-sense-rna-viruses-2011/w/posrna_viruses/222/coronaviridae Erişim Tarihi: 03.08.2020
  • Jalandra R, Yadav AK, Verma D, Dalal N, et al., 2020. Strategies and perspectives to develop SARS-CoV-2 detection methods and diagnostics. Biomed Pharmacother 129, 110446.
  • Kriegova E, Fillerova R, Kvapil P, 2020. Direct-RT-qPCR detection of SARS-CoV-2 without RNA extraction as part of a COVID-19 testing strategy: from sample to result in one hour. Diagnostics 8, 605.
  • Khunti K, 2010. Near-patient testing in primary care. Br J Gen Pract 60, 157–158.
  • Kitajima M, Ahmed W, Bibby K, Carducci A, et al., 2020. SARSCoV-2 in wastewater: State of the knowledge and research needs. Sci Total Environ 739, 139076.
  • Kocamemi BA, Kurt H, Hacıoglu S, Yaralı C, et al., 2020. First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey. medRxiv 2–11.
  • Kroiss SJ, Ahmadzai M, Ahmed J, Alam MM, et al., 2018. Assessing the sensitivity of the polio environmental surveillance system. PLoS One 13, e0208336.
  • Li Q, Liu Q, Huang W, Li X et al., 2018. Current status on the development of pseudoviruses for enveloped viruses. Rev Med Virol 28, e1963.
  • Lodder W, de Roda Husman AM, 2020. SARS-CoV-2 in wastewater: potential health risk, but also data source. Lancet Gastroenterol Hepatol 5, 533–534.
  • Lu R, Zhao X, Li J, Niu P, et al., 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395, 565–574.
  • Lv H, Wu NC, Tsang OT-Y, Yuan M, et al., 2020. Cross-reactive Antibody Response between SARS-CoV-2 and SARS-CoV Infections. Cell Rep 31, 107725.
  • Nao N, Shirato K, Harutaka K, Shutoku M, et al., 2019. Detection of second case of 2019-nCoV infection in Japan. Erişim Tarihi: 08.08.2020
  • National Health Commission of China., 2019. COVID-19 : Laboratory Testing Guideline 2019, 1–8. Erişim Tarihi: 09.08.2020
  • Nie J, Li Q, Wu J, Zhao C,et al., 2020. Establishment and validation of a pseudovirus neutralization assay for SARS-CoV-2. Emerg Microbes Infect 9, 680-686.
  • Pan Y, Zhang D, Yang P, Poon LLM, et al., 2020. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect Dis 20, 411– 412.
  • Park G-S, Ku K, Baek S-H, Kim S-J, et al., 2020. Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). J Mol Diagnostics 22, 729–735.
  • Pasteur Institut, 2020. Protocol : Real-time RT-PCR assays for the detection of SARS-CoV-2. Erişim Tarihi: 12.08.2020
  • Petersen E, Koopmans M, Go U, Hamer DH, et al., 2020. Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics. Lancet Infect Dis 3099, 1–7.
  • Roy N, Kashyap J, Verma D, Tyagi RK, et al., 2020. Prototype of a Smart Microfluidic Platform for the Evaluation of SARS-Cov-2 Pathogenesis, Along with Estimation of the Effectiveness of Potential Drug Candidates and Antigen– Antibody Interactions in Convalescent Plasma Therapy. Trans. Indian Natl Acad Eng 5, 241–250.
  • Shephard M, 2013. Point-of-Care Testing in Australia. Point Care J. Near-Patient Test. Technol 12, 41–45.
  • Smyrlaki I, Ekman M, Lentini A, de Sousa NR, et al., 2020.Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR. Nat Commun 11, 4812. https://doi.org/10.1038/s41467-020-18611-5
  • Tan CW, Chia WN, Qin X, Liu P, et al., 2020. A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2–spike protein–protein interaction. Nat Biotechnol 9, 1-6.
  • T.C. Sağlık Bakanlığı, 2020. COVID-19 (SARS-CoV-2 Enfeksiyonu) Genel Bilgiler, Epidemiyoloji Ve Tanı. https:// covid19.saglik.gov.tr/Eklenti/38597/0/covid-19rehberigenelbilgilerepidemiyolojivetanipdf.pdf. Erişim Tarihi: 08.08.2020.
  • Thai HTC, Le MQ, Vuong CD, Parida M, et al., 2004. Development and Evaluation of a Novel Loop-Mediated Isothermal Amplification Method for Rapid Detection of Severe Acute Respiratory Syndrome Coronavirus. J Clin Microbiol 42, 1956–1961.
  • Thailand Department of Medical Sciences Ministry of Public Health, 2020. Diagnostic detection of novel coronavirus 2019 by real time RT-PCR. https://www.who.int/docs/default-source/coronaviruse/conventional-rtpcr-followedby-sequencing-for-detection-of-ncov-rirl-nat-inst-healtht.%0Apdf Erişim Tarihi: 08.08.2020
  • Udugama B, Kadhiresan P, Kozlowski HN, Malekjahani A, et al., 2020. Diagnosing COVID-19: the disease and tools for detection. ACS Nano 14, 3822–3835.
  • US CDC, 2020. 2019-Novel Coronavirus ( 2019-nCoV ) Realtime rRT-PCR Panel Primers and Probes, Division of Viral Diseases. Centers for Disease Control and Prevention.
  • Venugopal A, GanesanH, Sudalaimuthu Raja SS, Govindasamy V, et al., 2020. Novel wastewater surveillance strategy for early detection of coronavirus disease 2019 hotspots. Curr Opin Environ Sci Heal 17, 8–13.
  • Wang B, Potter SJ, Lin Y, Cunningham AL, et al., 2005. Rapid and sensitive detection of severe acute respiratory syndrome coronavirus by rolling circle amplification. J Clin Microbiol 43, 2339–2344.
  • WHO, 2020a. Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases, Interim Guidance. Erişim Tarihi: 14.08.2020
  • WHO, 2020b. Water , sanitation , hygiene , and waste management for SARS-CoV-2 , the virus that causes COVID-19. Erişim Tarihi: 14.08.2020
  • WHO, 2020c. Novel-coronavirus-2019. Situation report. https://www.who.int/emergencies/diseases/novel-coronavirus-2019 Erişim Tarihi: 14.08.2020
  • Woo PCY, Huang Y, Lau SKP, Yuen K-Y, 2010. Coronavirus genomics and bioinformatics analysis. Viruses 2, 1804–1820.
  • Wu F, Xiao A, Zhang J, Gu X, et al., 2020a. SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases. medRxiv.
  • Wu F, Zhao S, Yu B, Chen Y-M, et al., 2020b. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269.
  • Wu Y, Guo C, Tang L, Hong Z, et al., 2020c. Prolonged presence of SARS-CoV-2 viral RNA in faecal samples. Lancet Gastroenterol Hepatol 5, 434–435.
  • Wu Z, McGoogan JM, 2020. Characteristics of and Important lessons from the coronavirus disease 2019 (COVID-19) outbreak in china. JAMA 323, 1239-1242.
  • Wurtzer S, Marechal V, Mouchel J-M, Maday Y, et al., 2020. Evaluation of lockdown impact on SARS-CoV-2 dynamics through viral genome quantification in Paris wastewaters. medRxiv.
  • Xiang J, Yan M, Li H, Liu T, et al., 2020. Evaluation of enzymelinked immunoassay and colloidal gold- immunochromatographic assay kit for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19). MedRxiv.
  • Xu Y, Li X, Zhu B, Liang H, et al., 2020. Characteristics of pediatric SARS-CoV-2 infection and potential evidence for persistent fecal viral shedding. Nat Med 26, 502–505.
  • Yan L, Zhou J, Zheng, Y, Gamson AS, et al., 2014. Isothermal amplified detection of DNA and RNA. Mol Biosyst 10, 970.
  • Yan Y, Chang L, Wang L, 2020. Laboratory testing of SARSCoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV): Current status, challenges, and countermeasures. Rev Med Virol 30, 1–14.
  • Yang W, Yan F, 2020. Patients with RT-PCR-confirmed COVID-19 and normal chest CT. Radiology 295, E3–E3.
  • Zhang F, Abudayyeh OO, Gootenberg JS, Sciences C, et al., 2020a. A protocol for detection of COVID-19 using CRISPR diagnostics, Bioarchive. https://www.broadinstitute.org/ files/publications/special/COVID-19%20detection%20 (updated).pdf Erişim Tarihi:11.08.2020
  • Zhang W, Du R-H, Li B, Zheng X-S, et al., 2020b. Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes. Emerg Microbes Infect 9, 386–389.
  • Zhou P, Yang X Lou, Wang XG, Hu B, et al., 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273.
  • Zhu N, Zhang D, Wang W, Li X, et al., 2020. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 382, 727–733.