Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading
The emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection as a cos...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-02-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/12/2/467 |
| _version_ | 1827655688168407040 |
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| author | Valerio Caputo Giulia Calvino Claudia Strafella Andrea Termine Carlo Fabrizio Giulia Trastulli Arcangela Ingrascì Cristina Peconi Silvia Bardini Angelo Rossini Antonino Salvia Giovanna Borsellino Luca Battistini Carlo Caltagirone Raffaella Cascella Emiliano Giardina |
| author_facet | Valerio Caputo Giulia Calvino Claudia Strafella Andrea Termine Carlo Fabrizio Giulia Trastulli Arcangela Ingrascì Cristina Peconi Silvia Bardini Angelo Rossini Antonino Salvia Giovanna Borsellino Luca Battistini Carlo Caltagirone Raffaella Cascella Emiliano Giardina |
| author_sort | Valerio Caputo |
| collection | DOAJ |
| description | The emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection as a cost-effective method for tracking the Omicron variant in Italy. The study was conducted on patients’ naso-oropharyngeal-swab-derived RNA samples. These samples were subjected to RT-PCR using the TaqPath COVID-19 RT PCR CE IVD kit. Nonparametric testing and polynomial models fitting were used to compare the spreading of Alpha, Delta and Omicron variants. The samples of interest were correctly amplified and displayed the presence of S gene-target failure, suggesting that these patients carry the Omicron variant. The trend of diffusion was found to be significantly different and more rapid compared with that of the Alpha and Delta variants in our cohorts. Overall, these results highlight that the S gene target failure was a very useful tool for the immediate and inexpensive tracking of Omicron variant in the three weeks from the first detection. Thus, our approach could be used as a first-line screening to reduce the time and costs of monitoring strategies, facilitating the management of preventive and counteracting measures against COVID-19. |
| first_indexed | 2024-03-09T22:10:12Z |
| format | Article |
| id | doaj.art-3764f8d05a1b45499ac80fa4782cdbb9 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-09T22:10:12Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-3764f8d05a1b45499ac80fa4782cdbb92023-11-23T19:32:32ZengMDPI AGDiagnostics2075-44182022-02-0112246710.3390/diagnostics12020467Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants SpreadingValerio Caputo0Giulia Calvino1Claudia Strafella2Andrea Termine3Carlo Fabrizio4Giulia Trastulli5Arcangela Ingrascì6Cristina Peconi7Silvia Bardini8Angelo Rossini9Antonino Salvia10Giovanna Borsellino11Luca Battistini12Carlo Caltagirone13Raffaella Cascella14Emiliano Giardina15Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyData Science Unit, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyData Science Unit, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyMedical Services, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyMedical Services, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyNeuroimmunology Unit, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyNeuroimmunology Unit, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyDepartment of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyGenomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, ItalyThe emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection as a cost-effective method for tracking the Omicron variant in Italy. The study was conducted on patients’ naso-oropharyngeal-swab-derived RNA samples. These samples were subjected to RT-PCR using the TaqPath COVID-19 RT PCR CE IVD kit. Nonparametric testing and polynomial models fitting were used to compare the spreading of Alpha, Delta and Omicron variants. The samples of interest were correctly amplified and displayed the presence of S gene-target failure, suggesting that these patients carry the Omicron variant. The trend of diffusion was found to be significantly different and more rapid compared with that of the Alpha and Delta variants in our cohorts. Overall, these results highlight that the S gene target failure was a very useful tool for the immediate and inexpensive tracking of Omicron variant in the three weeks from the first detection. Thus, our approach could be used as a first-line screening to reduce the time and costs of monitoring strategies, facilitating the management of preventive and counteracting measures against COVID-19.https://www.mdpi.com/2075-4418/12/2/467omicron variantCOVID-19molecular diagnosisnaso-oropharyngeal swabsRT-PCRSARS-CoV-2 |
| spellingShingle | Valerio Caputo Giulia Calvino Claudia Strafella Andrea Termine Carlo Fabrizio Giulia Trastulli Arcangela Ingrascì Cristina Peconi Silvia Bardini Angelo Rossini Antonino Salvia Giovanna Borsellino Luca Battistini Carlo Caltagirone Raffaella Cascella Emiliano Giardina Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading Diagnostics omicron variant COVID-19 molecular diagnosis naso-oropharyngeal swabs RT-PCR SARS-CoV-2 |
| title | Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading |
| title_full | Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading |
| title_fullStr | Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading |
| title_full_unstemmed | Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading |
| title_short | Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading |
| title_sort | tracking the initial diffusion of sars cov 2 omicron variant in italy by rt pcr and comparison with alpha and delta variants spreading |
| topic | omicron variant COVID-19 molecular diagnosis naso-oropharyngeal swabs RT-PCR SARS-CoV-2 |
| url | https://www.mdpi.com/2075-4418/12/2/467 |
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