Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants
ABSTRACT The genome of the Omicron variant of concern (VOC) contains more than 50 mutations, many of which have been associated with increased transmissibility, differing disease severity, and the potential to elute immune responses acquired after severe acute respiratory syndrome coronavirus 2 (SAR...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2022-12-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.02133-22 |
| _version_ | 1811290162542411776 |
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| author | Maud Salmona Marie-Laure Chaix Linda Feghoul Nadia Mahjoub Sarah Maylin Nathalie Schnepf Hervé Jacquier Eve-Marie Walle Marion Helary Guillaume Mellon Nathalie Osinski Widad Zebiche Yacine Achili Rishma Amarsy Véronique Mahé Jérôme Le Goff Constance Delaugerre |
| author_facet | Maud Salmona Marie-Laure Chaix Linda Feghoul Nadia Mahjoub Sarah Maylin Nathalie Schnepf Hervé Jacquier Eve-Marie Walle Marion Helary Guillaume Mellon Nathalie Osinski Widad Zebiche Yacine Achili Rishma Amarsy Véronique Mahé Jérôme Le Goff Constance Delaugerre |
| author_sort | Maud Salmona |
| collection | DOAJ |
| description | ABSTRACT The genome of the Omicron variant of concern (VOC) contains more than 50 mutations, many of which have been associated with increased transmissibility, differing disease severity, and the potential to elute immune responses acquired after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination or infection with previous VOCs. Due to a better tropism for the upper respiratory tract, it was suggested that the detection of the Omicron variant could be preferred in saliva, compared to nasopharyngeal swabs (NPS). Our objective was to compare the SARS-CoV-2 levels in saliva fluid and NPS to estimated Ct values, according to the main SARS-CoV-2 variants circulating in France since the beginning of 2021. We analyzed 1,289 positive reverse transcription-polymerase chain reaction (RT-PCR) results during the three major waves: Alpha, Delta, and Omicron. NPS and saliva sampling were performed for 909 (71%) and 380 (29%) cases, respectively. The Ct values were significantly lower in the NPS samples than in the saliva samples for the three main VOCs. Still, the difference was less pronounced with the Omicron variant than for the Alpha and Delta variants. In contrast, in the saliva samples, Ct values were significantly lower for the Omicron variant than for the Delta (difference of −2.7 Ct) and the Alpha (difference of −3.0 Ct) variants, confirming a higher viral load in saliva. To conclude, the higher viral load in saliva was evidenced for the Omicron variant, compared to the Alpha and Delta variants, suggesting that established diagnostic methods might require revalidation with the emergence of novel variants. IMPORTANCE Established methods for SARS-CoV-2 diagnostics might require revalidation with the emergence of novel variants. This is important for screening strategy programs and for the investigation of the characteristics of new variants in terms of tropism modification and increased viral burden leading to its spread. SARS-CoV-2 RT-PCR screening on saliva samples reported lower but acceptable performance, compared to nasopharyngeal samples. Due to a better tropism for the upper respiratory tract, it was suggested that the detection of the Omicron variant could be preferred in saliva, compared to nasopharyngeal swabs. Our study analyzed 1,289 positive RT-PCR results during the three major waves in France: Alpha, Delta, and Omicron. Our findings also showed a higher viral load in saliva for the Omicron variant, compared to the Alpha and Delta variants. |
| first_indexed | 2024-04-13T04:06:57Z |
| format | Article |
| id | doaj.art-bf3a8d24b5424cf5949d04d215904e68 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-13T04:06:57Z |
| publishDate | 2022-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-bf3a8d24b5424cf5949d04d215904e682022-12-22T03:03:13ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-12-0110610.1128/spectrum.02133-22Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral VariantsMaud Salmona0Marie-Laure Chaix1Linda Feghoul2Nadia Mahjoub3Sarah Maylin4Nathalie Schnepf5Hervé Jacquier6Eve-Marie Walle7Marion Helary8Guillaume Mellon9Nathalie Osinski10Widad Zebiche11Yacine Achili12Rishma Amarsy13Véronique Mahé14Jérôme Le Goff15Constance Delaugerre16Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceService de Bactériologie-Hygiène, Hôpitaux Universitaires Saint-Louis - Lariboisière - Fernand Widal, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceÉquipe Opérationnelle d’Hygiène, AP-HP, Hôpital Saint Louis, Paris, FranceÉquipe Opérationnelle d’Hygiène, AP-HP, Hôpital Saint Louis, Paris, FranceÉquipe Opérationnelle d’Hygiène, AP-HP, Hôpital Saint Louis, Paris, FranceService Central de Santé au Travail, AP-HP, Hôpital Saint Louis, Paris, FranceEquipe Opérationnelle d’Hygiène, AP-HP, Hôpitaux Lariboisière-Fernand Widal, Paris, FranceService Central de Santé au Travail, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceLaboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, FranceABSTRACT The genome of the Omicron variant of concern (VOC) contains more than 50 mutations, many of which have been associated with increased transmissibility, differing disease severity, and the potential to elute immune responses acquired after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination or infection with previous VOCs. Due to a better tropism for the upper respiratory tract, it was suggested that the detection of the Omicron variant could be preferred in saliva, compared to nasopharyngeal swabs (NPS). Our objective was to compare the SARS-CoV-2 levels in saliva fluid and NPS to estimated Ct values, according to the main SARS-CoV-2 variants circulating in France since the beginning of 2021. We analyzed 1,289 positive reverse transcription-polymerase chain reaction (RT-PCR) results during the three major waves: Alpha, Delta, and Omicron. NPS and saliva sampling were performed for 909 (71%) and 380 (29%) cases, respectively. The Ct values were significantly lower in the NPS samples than in the saliva samples for the three main VOCs. Still, the difference was less pronounced with the Omicron variant than for the Alpha and Delta variants. In contrast, in the saliva samples, Ct values were significantly lower for the Omicron variant than for the Delta (difference of −2.7 Ct) and the Alpha (difference of −3.0 Ct) variants, confirming a higher viral load in saliva. To conclude, the higher viral load in saliva was evidenced for the Omicron variant, compared to the Alpha and Delta variants, suggesting that established diagnostic methods might require revalidation with the emergence of novel variants. IMPORTANCE Established methods for SARS-CoV-2 diagnostics might require revalidation with the emergence of novel variants. This is important for screening strategy programs and for the investigation of the characteristics of new variants in terms of tropism modification and increased viral burden leading to its spread. SARS-CoV-2 RT-PCR screening on saliva samples reported lower but acceptable performance, compared to nasopharyngeal samples. Due to a better tropism for the upper respiratory tract, it was suggested that the detection of the Omicron variant could be preferred in saliva, compared to nasopharyngeal swabs. Our study analyzed 1,289 positive RT-PCR results during the three major waves in France: Alpha, Delta, and Omicron. Our findings also showed a higher viral load in saliva for the Omicron variant, compared to the Alpha and Delta variants.https://journals.asm.org/doi/10.1128/spectrum.02133-22SARS-CoV-2VOCsalivacycle thresholdOmicron |
| spellingShingle | Maud Salmona Marie-Laure Chaix Linda Feghoul Nadia Mahjoub Sarah Maylin Nathalie Schnepf Hervé Jacquier Eve-Marie Walle Marion Helary Guillaume Mellon Nathalie Osinski Widad Zebiche Yacine Achili Rishma Amarsy Véronique Mahé Jérôme Le Goff Constance Delaugerre Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants Microbiology Spectrum SARS-CoV-2 VOC saliva cycle threshold Omicron |
| title | Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants |
| title_full | Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants |
| title_fullStr | Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants |
| title_full_unstemmed | Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants |
| title_short | Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants |
| title_sort | detection of sars cov 2 in saliva and nasopharyngeal swabs according to viral variants |
| topic | SARS-CoV-2 VOC saliva cycle threshold Omicron |
| url | https://journals.asm.org/doi/10.1128/spectrum.02133-22 |
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