Sequencing of SARS-CoV-2 RNA Fragments in Wastewater Detects the Spread of New Variants during Major Events

Damir Zhakparov; Yves Quirin; Yi Xiao; Nicole Battaglia; Michael Holzer; Martin Bühler; Walter Kistler; Doortje Engel; Jon Paulin Zumthor; Alexa Caduff; Katja Baerenfaller

doi:10.3390/microorganisms11112660

Sequencing of SARS-CoV-2 RNA Fragments in Wastewater Detects the Spread of New Variants during Major Events

Microorganisms. 2023 Oct 30;11(11):2660. doi: 10.3390/microorganisms11112660.

Authors

Damir Zhakparov^{1

2}, Yves Quirin³, Yi Xiao^{1

2}, Nicole Battaglia⁴, Michael Holzer³, Martin Bühler⁵, Walter Kistler⁶, Doortje Engel⁷, Jon Paulin Zumthor⁴, Alexa Caduff⁵, Katja Baerenfaller^{1

2}

Affiliations

¹ Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland.
² Swiss Institute of Bioinformatics (SIB), 1005 Lausanne, Switzerland.
³ Cantonal Office for Nature and Environment, 7000 Chur, Switzerland.
⁴ Cantonal Office for Food Security and Animal Health, 7000 Chur, Switzerland.
⁵ Cantonal Office for Military and Civil Protection, 7000 Chur, Switzerland.
⁶ Hospital Davos, 7270 Davos, Switzerland.
⁷ Cantonal Office for Health, 7000 Chur, Switzerland.

Abstract

The sequencing of SARS-CoV-2 RNA in wastewater is an unbiased method to detect the spread of emerging variants and to track regional infection dynamics, which is especially useful in case of limited testing and clinical sequencing. To test how major international events influence the spread of new variants we have sequenced SARS-CoV-2 RNA in the wastewater samples of Davos, Landquart, Lostallo, and St. Moritz in the Swiss canton of Grisons in the time around the international sports competitions in Davos and St. Moritz in December 2021, and additionally in May 2022 and January 2023 in Davos and St. Moritz during the World Economic Forum (WEF) in Davos. The prevalence of the variants identified from the wastewater sequencing data showed that the Omicron variant BA.1 had spread in Davos and St. Moritz during the international sporting events hosted there in December 2021. This spread was associated with an increase in case numbers, while it was not observed in Landquart and Lostallo. Another instance of new variant spread occurred during the WEF in January 2023, when the Omicron variant BA.2.75 arrived in Davos but not in St. Moritz. We can therefore conclude that major international events promote the spread of new variants in the respective host region, which has important implications for the protective measures that should be taken.

Keywords: COVID-19 pandemic; SARS-CoV-2; amplicon sequencing; epidemiological surveillance; relative prevalence; variant mapping; wastewater.

Grants and funding

This research was funded by the Swiss Institute of Allergy and Asthma Research (SIAF), by the Center for Data Analysis, Visualization and Simulation (DAViS), and by the Swiss canton of Grisons.