Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes
Since the beginning of 2020, the betacoronavirus SARS-CoV-2 is causing a global pandemic of an acute respiratory disease termed COVID-19. The diagnostics of the novel disease is primarily based on direct virus detection by RT-PCR; however, the availability of test kits may become a major bottleneck,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-11-01
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| Series: | Diseases |
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| Online Access: | https://www.mdpi.com/2079-9721/9/4/84 |
| _version_ | 1797505412372627456 |
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| author | Sabine Bock Bernd Hoffmann Martin Beer Kerstin Wernike |
| author_facet | Sabine Bock Bernd Hoffmann Martin Beer Kerstin Wernike |
| author_sort | Sabine Bock |
| collection | DOAJ |
| description | Since the beginning of 2020, the betacoronavirus SARS-CoV-2 is causing a global pandemic of an acute respiratory disease termed COVID-19. The diagnostics of the novel disease is primarily based on direct virus detection by RT-PCR; however, the availability of test kits may become a major bottleneck, when millions of tests are performed per week. To increase the flexibility of SARS-CoV-2 diagnostics, three real-time RT-PCR assays listed on the homepage of the World Health Organization were selected and investigated regarding their compatibility with three different RT-PCR kits. Furthermore, the reaction volume of the PCR chemistry was reduced up to half of the original protocol to make the individual reactions more cost- and resource-effective. When testing dilution series of culture-grown virus, nearly identical quantification cycle values (Cq) were obtained for all RT-PCR assay/chemistry combinations. Regarding the SARS-CoV-2 detection in clinical samples, agreeing results were obtained for all combinations for virus negative specimens and swabs containing high to medium viral genome loads. In cases of very low SARS-CoV-2 genome loads (Cq > 36), inconsistent results were observed, with some test runs scoring negative and some positive. However, no preference of a specific target within the viral genome (E, RdRp, or N) or of a certain chemistry was seen. In summary, a reduction of the reaction volume and the type of PCR chemistry did not influence the PCR sensitivity. |
| first_indexed | 2024-03-10T04:18:16Z |
| format | Article |
| id | doaj.art-b8cc58e915c0485380f35c35f615fe90 |
| institution | Directory Open Access Journal |
| issn | 2079-9721 |
| language | English |
| last_indexed | 2024-03-10T04:18:16Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diseases |
| spelling | doaj.art-b8cc58e915c0485380f35c35f615fe902023-11-23T07:55:55ZengMDPI AGDiseases2079-97212021-11-01948410.3390/diseases9040084Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction VolumesSabine Bock0Bernd Hoffmann1Martin Beer2Kerstin Wernike3Berlin-Brandenburg State Laboratory, 15236 Frankfurt, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald, GermanySince the beginning of 2020, the betacoronavirus SARS-CoV-2 is causing a global pandemic of an acute respiratory disease termed COVID-19. The diagnostics of the novel disease is primarily based on direct virus detection by RT-PCR; however, the availability of test kits may become a major bottleneck, when millions of tests are performed per week. To increase the flexibility of SARS-CoV-2 diagnostics, three real-time RT-PCR assays listed on the homepage of the World Health Organization were selected and investigated regarding their compatibility with three different RT-PCR kits. Furthermore, the reaction volume of the PCR chemistry was reduced up to half of the original protocol to make the individual reactions more cost- and resource-effective. When testing dilution series of culture-grown virus, nearly identical quantification cycle values (Cq) were obtained for all RT-PCR assay/chemistry combinations. Regarding the SARS-CoV-2 detection in clinical samples, agreeing results were obtained for all combinations for virus negative specimens and swabs containing high to medium viral genome loads. In cases of very low SARS-CoV-2 genome loads (Cq > 36), inconsistent results were observed, with some test runs scoring negative and some positive. However, no preference of a specific target within the viral genome (E, RdRp, or N) or of a certain chemistry was seen. In summary, a reduction of the reaction volume and the type of PCR chemistry did not influence the PCR sensitivity.https://www.mdpi.com/2079-9721/9/4/84SARS-CoV-2COVID-19coronavirusdiagnosticsvirus detectionswab |
| spellingShingle | Sabine Bock Bernd Hoffmann Martin Beer Kerstin Wernike Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes Diseases SARS-CoV-2 COVID-19 coronavirus diagnostics virus detection swab |
| title | Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes |
| title_full | Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes |
| title_fullStr | Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes |
| title_full_unstemmed | Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes |
| title_short | Saving Resources: SARS-CoV-2 Diagnostics by Real-Time RT-PCR Using Reduced Reaction Volumes |
| title_sort | saving resources sars cov 2 diagnostics by real time rt pcr using reduced reaction volumes |
| topic | SARS-CoV-2 COVID-19 coronavirus diagnostics virus detection swab |
| url | https://www.mdpi.com/2079-9721/9/4/84 |
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