SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron
The continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. The aim of this work was to characterize SARS-CoV-2 genetic variability during the Delta–Omicron shift in patients and in a neighboring wastewat...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Biomedicines |
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| Online Access: | https://www.mdpi.com/2227-9059/10/9/2080 |
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| author | Ahlam Chaqroun Cédric Hartard Thomas Josse Audrey Taverniers Hélène Jeulin Christophe Gantzer John M. Murray Obepine Consortium Isabelle Bertrand Evelyne Schvoerer |
| author_facet | Ahlam Chaqroun Cédric Hartard Thomas Josse Audrey Taverniers Hélène Jeulin Christophe Gantzer John M. Murray Obepine Consortium Isabelle Bertrand Evelyne Schvoerer |
| author_sort | Ahlam Chaqroun |
| collection | DOAJ |
| description | The continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. The aim of this work was to characterize SARS-CoV-2 genetic variability during the Delta–Omicron shift in patients and in a neighboring wastewater treatment plant (WWTP) in the same urban area. The surveillance of SARS-CoV-2 was performed by routine screening of positive samples by single nucleotide polymorphism analysis within the S gene. Moreover, additionally to national systematic whole genome sequencing (WGS) once a week in SARS-CoV-2-positive patients, WGS was also applied when mutational profiles were difficult to interpret by routine screening. Thus, WGS was performed on 414 respiratory samples and on four wastewater samples, northeastern France. This allowed us to report (i) the temporally concordant Delta to Omicron viral shift in patients and wastewaters; (ii) the characterization of 21J (Delta) and 21K (Omicron)/BA.1-21L (Omicron)/BA.2-BA.4 mixtures from humans or environmental samples; (iii) the mapping of composite mutations and the predicted impact on immune properties in the viral Spike protein. |
| first_indexed | 2024-03-10T00:40:41Z |
| format | Article |
| id | doaj.art-cc3b63331c384c3c99093553296c4b66 |
| institution | Directory Open Access Journal |
| issn | 2227-9059 |
| language | English |
| last_indexed | 2024-03-10T00:40:41Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomedicines |
| spelling | doaj.art-cc3b63331c384c3c99093553296c4b662023-11-23T15:08:50ZengMDPI AGBiomedicines2227-90592022-08-01109208010.3390/biomedicines10092080SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to OmicronAhlam Chaqroun0Cédric Hartard1Thomas Josse2Audrey Taverniers3Hélène Jeulin4Christophe Gantzer5John M. Murray6Obepine ConsortiumIsabelle Bertrand7Evelyne Schvoerer8CNRS, LCPME, Université de Lorraine, F-54000 Nancy, FranceCNRS, LCPME, Université de Lorraine, F-54000 Nancy, FranceLaboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, FranceLaboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, FranceCNRS, LCPME, Université de Lorraine, F-54000 Nancy, FranceCNRS, LCPME, Université de Lorraine, F-54000 Nancy, FranceSchool of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052, AustraliaCNRS, LCPME, Université de Lorraine, F-54000 Nancy, FranceCNRS, LCPME, Université de Lorraine, F-54000 Nancy, FranceThe continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. The aim of this work was to characterize SARS-CoV-2 genetic variability during the Delta–Omicron shift in patients and in a neighboring wastewater treatment plant (WWTP) in the same urban area. The surveillance of SARS-CoV-2 was performed by routine screening of positive samples by single nucleotide polymorphism analysis within the S gene. Moreover, additionally to national systematic whole genome sequencing (WGS) once a week in SARS-CoV-2-positive patients, WGS was also applied when mutational profiles were difficult to interpret by routine screening. Thus, WGS was performed on 414 respiratory samples and on four wastewater samples, northeastern France. This allowed us to report (i) the temporally concordant Delta to Omicron viral shift in patients and wastewaters; (ii) the characterization of 21J (Delta) and 21K (Omicron)/BA.1-21L (Omicron)/BA.2-BA.4 mixtures from humans or environmental samples; (iii) the mapping of composite mutations and the predicted impact on immune properties in the viral Spike protein.https://www.mdpi.com/2227-9059/10/9/2080SARS-CoV-2 variabilityshiftDeltaOmicronimmune modulation |
| spellingShingle | Ahlam Chaqroun Cédric Hartard Thomas Josse Audrey Taverniers Hélène Jeulin Christophe Gantzer John M. Murray Obepine Consortium Isabelle Bertrand Evelyne Schvoerer SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron Biomedicines SARS-CoV-2 variability shift Delta Omicron immune modulation |
| title | SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron |
| title_full | SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron |
| title_fullStr | SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron |
| title_full_unstemmed | SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron |
| title_short | SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron |
| title_sort | sars cov 2 variability in patients and wastewaters potential immuno modulation during the shift from delta to omicron |
| topic | SARS-CoV-2 variability shift Delta Omicron immune modulation |
| url | https://www.mdpi.com/2227-9059/10/9/2080 |
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