Eurosurv. Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023

[tetano]

• Olga Frank¹ , David Acitores Balboa¹ , Maria Novatchkova^1,2 , Ezgi Özkan¹ , Marcus Martin Strobl² , Ramesh Yelagandula¹ , Tanino Guiseppe Albanese³ , Lukas Endler^4,5 , Fabian Amman^4,5 , Vera Felsenstein^1,6 , Milanka Gavrilovic¹ , Melanie Acosta¹ , Timothej Patocka⁶ , Alexander Vogt⁶ , Ido Tamir⁶ , Julia Klikovits⁷ , Alexander Zoufaly^8,9 , Tamara Seitz⁸ , Manuela Födinger^9,10 , Andreas Bergthaler⁴ , Alexander Indra⁷ , Daniela Schmid^7,11 , Peter Klimek¹² , Alexander Stark^2,13 , Franz Allerberger⁷ , Bernhard Benka⁷ , Katharina Reich¹⁴ , Luisa Cochella^2,15 , Ulrich Elling¹

Background

The COVID-19 pandemic was largely driven by genetic mutations of SARS-CoV-2, leading in some instances to enhanced infectiousness of the virus or its capacity to evade the host immune system. To closely monitor SARS-CoV-2 evolution and resulting variants at genomic-level, an innovative pipeline termed SARSeq was developed in Austria.

Aim

We discuss technical aspects of the SARSeq pipeline, describe its performance and present noteworthy results it enabled during the pandemic in Austria.

Methods

The SARSeq pipeline was set up as a collaboration between private and public clinical diagnostic laboratories, a public health agency, and an academic institution. Representative SARS-CoV-2 positive specimens from each of the nine Austrian provinces were obtained from SARS-CoV-2 testing laboratories and processed centrally in an academic setting for S-gene sequencing and analysis.

Results

SARS-CoV-2 sequences from up to 2,880 cases weekly resulted in 222,784 characterised case samples in January 2021–March 2023. Consequently, Austria delivered the fourth densest genomic surveillance worldwide in a very resource-efficient manner. While most SARS-CoV-2 variants during the study showed comparable kinetic behaviour in all of Austria, some, like Beta, had a more focused spread. This highlighted multifaceted aspects of local population-level acquired immunity. The nationwide surveillance system enabled reliable nowcasting. Measured early growth kinetics of variants were predictive of later incidence peaks.

Conclusion

With low automation, labour, and cost requirements, SARSeq is adaptable to monitor other pathogens and advantageous even for resource-limited countries. This multiplexed genomic surveillance system has potential as a rapid response tool for future emerging threats.

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2024.29.23.2300542#html_fulltext