SARS-CoV-2 detection by extraction-free qRT-PCR for massive and rapid COVID-19 diagnosis during a pandemic in Armenia

• Published in: Journal of virological methods Vol. 295; p. 114199
• Main Authors: Avetyan, Diana, Chavushyan, Andranik, Ghazaryan, Hovsep, Melkonyan, Ani, Stepanyan, Ani, Zakharyan, Roksana, Hayrapetyan, Varduhi, Atshemyan, Sofi, Khachatryan, Gisane, Sirunyan, Tamara, Davitavyan, Suren, Martirosyan, Gevorg, Melik-Andreasyan, Gayane, Sargsyan, Shushan, Ghazazyan, Armine, Aleksanyan, Naira, Yin, Xiushan, Arakelyan, Arsen
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.09.2021; Published by Elsevier B.V
• Subjects: Armenia; Armenia - epidemiology; COVID-19; COVID-19 - diagnosis; COVID-19 - epidemiology; COVID-19 - virology; COVID-19 infection; COVID-19 Nucleic Acid Testing - methods; Direct sample qRT-PCR; disease control; health services; Heat-Inactivation; Humans; Mass Screening - methods; pandemic; Pelleting; Reverse Transcriptase Polymerase Chain Reaction; RNA; RNA, Viral - genetics; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Specimen Handling; Viral Load; Virus detection; Virus Inactivation; Armenia; COVID-19; SARS-CoV-2; Virus detection; Direct sample qRT-PCR; Pelleting; Heat-Inactivation
• ISSN: 0166-0934; 1879-0984; 1879-0984
• DOI: 10.1016/j.jviromet.2021.114199

•COVID-19 pandemic urges for a rapid and efficient test for infection screening.•Omitting the isolation step enables significant expansion of the testing capacity.•The protocol for COVID-19 qRT-PCR testing on direct swab samples was optimized.•Direct testing has lower sensitivity, but enables testing capacity expansion.•Direct sample sensitivity depends on the transport media type. COVID-19 pandemic severely impacted the healthcare and economy on a global scale. It is widely recognized that mass testing is an efficient way to contain the spread of SARS-CoV-2 infection as well as aid in the development of informed policies for disease management. However, the current COVID-19 worldwide infection rates increased the demand for rapid and reliable screening of infection. We compared the performance of qRT-PCR in direct heat-inactivated (H), heat-inactivated and pelleted (HC) samples against RNA in a group of 74 subjects (44 positive and 30 negative). Then we compared the sensitivity of HC in a larger group of 196 COVID-19 positive samples. Our study suggests that HC samples show higher accuracy for SARS-CoV-2 detection PCR assay compared to direct H (89 % vs 83 % of the detection in RNA). The sensitivity of detection using direct samples varied depending on the sample transport and storage media as well as the viral loads (as measured by qRT-PCR Ct levels). Altogether, all the data suggest that purified RNA provides more accurate results, however, direct sample testing with qRT-PCR may help to significantly increase testing capacity. Switching to the direct sample testing is justified if the number of tests is doubled at least.