SARS-CoV-2 Variability in Patients and Wastewaters-Potential Immuno-Modulation during the Shift from Delta to Omicron

Ahlam Chaqroun; Cédric Hartard; Thomas Josse; Audrey Taverniers; Hélène Jeulin; Christophe Gantzer; John M Murray; Obepine Consortium; Isabelle Bertrand; Evelyne Schvoerer

doi:10.3390/biomedicines10092080

SARS-CoV-2 Variability in Patients and Wastewaters-Potential Immuno-Modulation during the Shift from Delta to Omicron

Biomedicines. 2022 Aug 25;10(9):2080. doi: 10.3390/biomedicines10092080.

Authors

Ahlam Chaqroun^{1

2}, Cédric Hartard^{1

2}, Thomas Josse², Audrey Taverniers², Hélène Jeulin^{1

2}, Christophe Gantzer¹, John M Murray³, Obepine Consortium, Isabelle Bertrand¹, Evelyne Schvoerer^{1

2}

Affiliations

¹ CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France.
² Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France.
³ School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052, Australia.

Abstract

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.

Keywords: Delta; Omicron; SARS-CoV-2 variability; immune modulation; shift.

Grants and funding

This work was performed in the virology laboratory of the University Hospital of Nancy-France, according to the recommendations from the French Health Authorities (Santé publique, France, EMERGENdb and Caisse Nationale d’Assurance Maladie (CNAM), the National Nealth Insurance Funds). Moreover, we acknowledge the Association des Chefs de Service (ACS, University Hospital of Nancy, Brabois Hospital, 54500 Vandoeuvre les Nancy, France) for financial support on laboratory reagents. Ahlam Chaqroun received a fellowship from the Université de Lorraine France (Ph.D. funding, Pôle Scientifique Chimie et Physique Moléculaire) and by the network Zone Atelier Moselle (ZAM), Université de Lorraine, France.