Pandemic diagnostic tool and accuracy of biomаtеrials for SARS-COV-2 detection
Keywords:diagnostic tool, biological material, types of biological material, nasopharyngeal smear, nasal smear, saliva, RT-PCR, SARS-CoV-2, COVID-19
Background. The new SARS-CoV-2 coronavirus pandemic continues to have an unprecedented impact on the social aspects of society and the world economy. To prevent and control the transmission of COVID-19, infection monitoring, there is a constant need for high-performance technologies to identify the pathogen or its markers. An important tool and the gold standard of today in the diagnosis of coronavirus disease (COVID-19) are molecular genetic technologies, namely the method of polymerase chain reaction with reverse transcription (RT-PCR) to detect markers of ribonucleic acid (RNA) SARS-CoV-2) in samples of different types of biological material, from the most probable sites of the human body available for selection. The biological material of nasal smears (NS), saliva (SS) was studied, although reliable data on their accuracy of use are limited. To do this, we studied the diagnostic value and accuracy of the collected samples of different biological material: nasopharynx/nose /saliva (NPS/NS/SS). Materials and methods. Thirty patients were included after a positive test for SARS-CoV 2 RT-PCR in NPS samples in accordance with the current order № 662 of the Ministry of Health of Ukraine "Guidelines" Procedure for collection, transportation and storage of material for polymerase chain reaction", WHO guidelines for collection, processing and testing of clinical specimens on COVID-19. In comparison with this recommended test method, NPS/NS/SS samples were tested using an automated portable ExiStation 48 detection system (Bioneer Corporation, South Korea) to investigate the feasibility and usefulness of the ExiStation method. 48 and the difference between the types of biological sample samples, specificity and sensitivity were calculated, and three to five samples were taken from each patient over a total study period of 6 to 9 days. Results. 171 sets of NPS/NS/SS samples were selected, of which 122 tested positive for COVID-19 by RT-PCR from NPS biological material. In general, the concordance ratio for biological material types was 82.0%/68.2%/50.4% for NPS/NS/SS samples (ExiStation 48 system); however, for samples collected on the 9th day after the onset of the disease (66 negative and three positive samples), the corresponding figures were 91.7%/80.0%/65.2%. Overall sensitivity estimates were 100.0%/67.5%/37.5% for NPS/NS/SS samples (ExiStation 48 system). For samples up to 7 days after the onset of the disease, the values were 98.0%/84.4%/64.6%. Conclusions. Biological material of samples taken from the lower nasal passage (insert the tip of the tampon into the nostril 2-3 cm from the nostril, touching the anterior nasal cavity and mucous membrane) NS are more reliable than SS samples, and can be an alternative to biological samples NPS collected and delivered in the transport medium for viruses with a lysing component. Therefore, the biological material of the samples taken from the anterior nasal cavity in a special transport medium with a lysing component may be recommended for RT-PCR studies for the diagnosis of COVID-19 during an epidemic or rise in SARS for differential diagnosis.
Chen N, Zhou M, Dong X and others. Epidemiological and clinical characteristics of 99 cases of new coronavirus pneumonia in 2019 in Wuhan, China: a descriptive study. Lancet. 2020; 395 (10223): 507-513. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Sohrabi C, Alsafi Z, O'Neill N, and others. The World Health Organization has declared a state of emergency in the world: a review of the new coronavirus (COVID-19) in 2019. Int J Surg. 2020; 76: 71-76. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Guan WJ, Ni ZY, Hu Y, etc .; Chinese Expert Group on Covid-19 Treatment. Clinical characteristics of coronavirus disease in 2019 in China. N Engl J Med. 2020; 382 (18): 1708-1720. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Zou L, Ruan F, Huang M, etc. SARS-CoV-2 viral load in upper respiratory tract samples from infected patients. N Engl J Med. 2020; 382 (12): 1177-1179. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Wehrhahn MC, Robson J, Brown S and others. Self-collection: an appropriate alternative during a SARS-CoV-2 pandemic. Jay Wedge Virol. 2020; 128: 104417. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
To KKW, Tsang Oty, Leung WS and others. Temporary viral load profiles in posterior oropharyngeal samples and serum antibody responses to SARS-CoV-2 infection: a cohort study. Lancet Infect Dis. 2020; 20 (5): 565-574. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Centers for disease control and prevention. Interim guidelines for the collection, handling and testing of human clinical specimens for coronavirus disease 2019 (COVID-19). Atlanta, Georgia: Centers for Disease Control and Prevention; 2019. [Google Scholar].
Order of the Ministry of Health of Ukraine dated 28.03.2020 № 722 "Organization of medical care for patients with coronavirus disease (COVID-19)" / https://moz.gov.ua/uploads/3/19711-dn_20200328_722.pdf.
Order of the Ministry of Health of Ukraine dated 02.04.2020 № 762 роOn approval of the protocol ‑ Provision of medical care for the treatment of coronavirus disease (COVID-19) || https: //moz.gov.ua/uploads/3/19829-protokol.pdf.
Butler-Laporte G, Lawandi A, Schiller I, and others. Comparison of nucleic acid amplification test in nasopharyngeal smear for SARS-CoV-2 detection: systematic review and meta-analysis. JAMA Intern Med. 2021; 181 (3): 353-358. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Gwet KL. Internal rating reliability. Wiley Encyclopedia of Clinical Trials. Hoboken (NJ): Wiley; 2008 [Google Scholar].
Nishiura H. Reliable statistical AC to assess agreement between observers in reliability studies. Nihon Hoshasen Gijutsu Gakkai Zasshi. 2010; 66 (11): 1485 - 1491. [Crossref], [PubMed], [Google Scholar].
Kanda Yu. Research of freely available easy-to-use software "EZR 'for medical statistics". Bone marrow transplant. 2013; 48 (3): 452-458. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Long QX, Tang XJ, Shi QL and others. Clinical and immunological evaluation of asymptomatic SARS-CoV-2 infections. Nat Med. 2020; 26 (8): 1200 - 1204. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Ferretti L, Wymant C, Kendall M, and others. Quantitative assessment of SARS-CoV-2 transmission involves controlling the epidemic through digital contact tracking. Science. 2020; 368 (6491): eabb6936. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Chen Yu, Chen L, Deng K and others. The presence of SARS-CoV-2 RNA in the feces of patients with COVID-19. J Med Virol. 2020; 92 (7): 833-840. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Tu Yu.P., Jennings R., Hart B. and others. Smears collected by patients or healthcare professionals for testing for SARS-CoV-2. N Engl J Med. 2020; 383 (5): 494-496. [Crossref], [PubMed], [Web of Science ®], [Google Scholar].
Péré H, Podglajen I, Wack M, et al. SARS-CoV-2 nasal swab: a convenient alternative for nasopharyngeal swab deficiency. J Clin Microbiol. 2020; 58 (6): 2 - 3. [Crossref], [Web of Science ®], [Google Scholar].
Pinninti S, Trieu C, Pati SK and others. Comparison of nasopharyngeal and middle nasal smear analysis to detect severe acute coronavirus syndrome 2. Clin Infect Dis. 2020; ciaa882. [Crossref], [PubMed], [Google Scholar].
Ministry of Health of Japan L and W. Guidelines for testing new coronavirus pathogens (covid-19) (version 1). Available at: https://www.mhlw.go.jp/content/000678571.pdf. [Google Scholar].
How to Cite
This work is licensed under a Creative Commons Attribution 4.0 International License.