A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant
The spread of new SARS-CoV-2 variants represents a serious threat worldwide, thus rapid and cost-effective methods are required for their identification. Since November 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific) has been used to identify viral strains of the new lineage B.1.1.7, si...
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The Journal of Infection in Developing Countries
2021-03-01
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| Series: | Journal of Infection in Developing Countries |
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| Online Access: | https://jidc.org/index.php/journal/article/view/14972 |
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| author | Gabriele Ibba Rosangela Sau Flavia Angioj Marcello Abbondio Salvatore Rubino Sergio Uzzau |
| author_facet | Gabriele Ibba Rosangela Sau Flavia Angioj Marcello Abbondio Salvatore Rubino Sergio Uzzau |
| author_sort | Gabriele Ibba |
| collection | DOAJ |
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The spread of new SARS-CoV-2 variants represents a serious threat worldwide, thus rapid and cost-effective methods are required for their identification. Since November 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific) has been used to identify viral strains of the new lineage B.1.1.7, since it fails to detect the S-gene with the ∆69/70 deletion. Here, we proposed S-gene mutations screening with the Allplex SARS-CoV-2 assay (Seegene), another widely used RT-PCR test that targets Sarbecovirus E, SARS-CoV-2 N, and RdRp/S genes. Accordingly, we evaluated the S gene amplification curve pattern compared to those of the other genes. Exploiting an Allplex assay-generated dataset, we screened 663 RT-PCR digital records, including all SARS-CoV-2 respiratory samples tested in our laboratory with the Allplex assay between January 1st and February 25th, 2021. This approach enabled us to detect 64 samples with peculiar non-sigmoidal amplification curves. Sequencing a selected group of 4 RNA viral genomes demonstrated that those curves were associated with B.1.1.7 variant strains. Our results strongly suggest that B.1.1.7 variant spread has begun in this area at least since January and imply the potential of these analytical methods to track and characterize the spread of B.1.1.7 strains in those areas where Allplex SARS-CoV-2 datasets have been previously recorded.
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| format | Article |
| id | doaj-art-dac06aa20fc247f398a8fc542755ecb5 |
| institution | OA Journals |
| issn | 1972-2680 |
| language | English |
| publishDate | 2021-03-01 |
| publisher | The Journal of Infection in Developing Countries |
| record_format | Article |
| series | Journal of Infection in Developing Countries |
| spelling | doaj-art-dac06aa20fc247f398a8fc542755ecb52025-08-20T02:27:22ZengThe Journal of Infection in Developing CountriesJournal of Infection in Developing Countries1972-26802021-03-01150210.3855/jidc.14972A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variantGabriele Ibba0Rosangela Sau1Flavia Angioj2Marcello Abbondio3Salvatore Rubino4Sergio Uzzau5Department of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, 07100 Sassari, ItalyDepartment of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, 07100 Sassari, ItalyMicrobiologia e Virologia, Azienda Ospedaliera Universitaria, 07100 Sassari, ItalyDepartment of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, 07100 Sassari, ItalyDepartment of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, 07100 Sassari, ItalyDepartment of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, 07100 Sassari, Italy The spread of new SARS-CoV-2 variants represents a serious threat worldwide, thus rapid and cost-effective methods are required for their identification. Since November 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific) has been used to identify viral strains of the new lineage B.1.1.7, since it fails to detect the S-gene with the ∆69/70 deletion. Here, we proposed S-gene mutations screening with the Allplex SARS-CoV-2 assay (Seegene), another widely used RT-PCR test that targets Sarbecovirus E, SARS-CoV-2 N, and RdRp/S genes. Accordingly, we evaluated the S gene amplification curve pattern compared to those of the other genes. Exploiting an Allplex assay-generated dataset, we screened 663 RT-PCR digital records, including all SARS-CoV-2 respiratory samples tested in our laboratory with the Allplex assay between January 1st and February 25th, 2021. This approach enabled us to detect 64 samples with peculiar non-sigmoidal amplification curves. Sequencing a selected group of 4 RNA viral genomes demonstrated that those curves were associated with B.1.1.7 variant strains. Our results strongly suggest that B.1.1.7 variant spread has begun in this area at least since January and imply the potential of these analytical methods to track and characterize the spread of B.1.1.7 strains in those areas where Allplex SARS-CoV-2 datasets have been previously recorded. https://jidc.org/index.php/journal/article/view/14972SARS-CoV-2 B.1.1.7 variantRT-PCRMolecular Diagnostics |
| spellingShingle | Gabriele Ibba Rosangela Sau Flavia Angioj Marcello Abbondio Salvatore Rubino Sergio Uzzau A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant Journal of Infection in Developing Countries SARS-CoV-2 B.1.1.7 variant RT-PCR Molecular Diagnostics |
| title | A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant |
| title_full | A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant |
| title_fullStr | A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant |
| title_full_unstemmed | A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant |
| title_short | A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant |
| title_sort | straightforward molecular strategy to retrospectively investigate the spread of sars cov 2 voc202012 01 b 1 1 7 variant |
| topic | SARS-CoV-2 B.1.1.7 variant RT-PCR Molecular Diagnostics |
| url | https://jidc.org/index.php/journal/article/view/14972 |
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