Pandemic response

In the early days of the SARS-CoV-2 pandemic in 2020, we thought about how we could contribute to the mounting health crisis caused by SARS-CoV-2. Our host institution CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences  had no BSL3 labs nor was it seeing patients. With long-term interests in viral evolution and one of the best national sequencing facilities in house, and no SARS-CoV-2 genomes available from Austria yet, we decided in mid March 2020 to sequence this emerging zoonotic pathogen. We started the project “Mutational Dynamics of SARS-CoV-2 in Austria” in close collaboration with Dr. Christoph Bock and the CeMM Biomedical Sequencing Facility, and with the support of the CeMM directors Dr. Giulio Superti-Furga and Anita Ender. On April 3 2020, in the midth of the first strict lockdown, we published the first 21 SARS-CoV-2 genomes from Austria and deposited them in the public database GISAID.

Picture 1From the start and through several lockdowns, it was a tremendous team effort by many scientists in our lab and at CeMM to set up the logistics, sequencing and data analysis pipelines. This was soon to be complemented by collaborations with institutions across Austria and beyond. Foremost, this included the Center of Virology at the Medical University of Vienna, the Austrian Agency of Health and Food Safety (AGES) and collaboration partners from the Medical University of Innsbruck, the Klinikum Favoriten, TU Vienna, University of Innsbruck, University of Vienna and Harvard University. Additional collaborations with e.g. the Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Institute Pasteur in Paris, Erasmus MC Rotterdam and others would follow. The early work was supported mostly by CeMM as well as by funding from the Vienna Science and Technology Fund (WWTF), which was later complemented by a collaboration with the AGES and a grant of the Austrian Science Fund (FWF).

The following paragraphs aim to briefly summarize and contextualize our contributions to the pandemic responses from March 2020 until April 2022.

12573_toc_D1Science: The pandemic provided the opportunity to initiate and intensify collaborations with inspiring colleagues from all walks of science including virology, immunology, evolution biology, biomathematics, infection epidemiology, modeling and public health. From January 2021 onwards, we intensified our collaboration with the AGES and began to sequence several hundred SARS-CoV-2 genomes per week. This amounted to more than 70% of all whole genomes sequenced in Austria by March 2022. Next to this, we strategically chose research topics of relevance and where our setup of sequencing and close interactions with all national stakeholders would proof valuable. This led to a study about fundamental properties of SARS-CoV-2 in the context of early superspreading events in Austria (Popa AM, Genger JM et al. Science Translational Medicine 2020). We also were blessed to collaborate with the Judith Aberle and Johannes Huppa laboratories (Medical University of Vienna) and contribute to questions on viral escape from CD8 T cell epitopes (Agerer B, Koblischke M, Gudipati V et al. Science Immunology 2021). Early on, we also focused our efforts on pathogen surveillance in wastewater. This turned out to be another demonstration of the strengths of interdisciplinary collaborations, as we broke new grounds towards the -until then for us entirely unknown- world of wastewater research. This was achieved together with the laboratories of Norbert Kreuzinger (TU Vienna), Heribert Insam (University of Innsbruck) and Herbert Oberacher (Medical University of Innsbruck). We contributed to the establishment of a national-wide surveillance of viral variants from wastewater in Austria and developed and validated new methodology to deconvolute SARS-CoV-2 variants from wastewater (Amman F, Markt R et al. bioRxiv 2022). This became part of a national surveillance system from wastewater. Beyond, we supported numerous collaborations which led to 12 co-authored publications and more pending.

d86410aa-e0d3-4e4c-932e-8d6825ca7a66Advisory roles: 
With the advent of the first variants of Alpha and Beta in late December 2020/January 2021, the attributed relevance of SARS-CoV-2 genome sequencing changed rapidly. Over the Holiday Season we sequenced selected samples, which turned out to be the first confirmed Alpha and Beta variants in Austria. The results were available on January 3 and communicated the following day together with the Federal Minister of Health and the head of the AGES. As the evolution of the pandemic SARS-CoV-2 became an ever more important parameter for pandemic management, we were increasingly asked for scientific advice. This included advisory roles of Dr. Bergthaler to e.g. the Federal Minister(s) for Social Affairs, Health, Care and Consumer Protection and the Federal Chancellor(s) of the Republic of Austria. In addition, ad hoc advisory services were requested given to other advisory boards (e.g. Ampelkommission, Oberste Sanitätsrat), the Federal President of the Republic of Austria, provincial governors, political parties of the opposition and others. Dr. Bergthaler is actively involved in the Health Working Group of the COVID-19 Future Operations Platform, which fosters interdisciplinary expert exchange and prepares forward-looking Expert Opinions. In May 2022, this culminated in a two-days international conference entitled “Science for resilience – Learnings from the Pandemic”. From end of November 2021 to January 2022, Dr. Bergthaler co-authored 8 weekly Omicron reports with Dr. Ulrich Elling, Dr. Arne Bathke and Dr. Peter Klimek, which were widely distributed among the stakeholders and received by health authorities and political institutions. Since December 2022, Dr. Bergthaler is founding member of the top governmental advisory board for pandemic management GECKO. These advisory roles are served on a voluntary basis and are not remunerated.

Screenshot 2021-11-04 at 16.01.24Public Engagement: 
Throughout the pandemic, we took considerable efforts to explain to a wide audience how SARS-CoV-2 evolves and its potential implications for pandemic management strategies and vaccines. This includes a dedicated project website with explanations of our work and tools such as Nextstrain Austria, social media and podcast activities, >80 presentations to diverse lay and scientific audiences and 980 interviews for national and international print and TV media in 2020-2022. A. Bergthaler pursues long-term interests in science communication within high schools. During the pandemic, he was involved in several workshops with high Plakat_Krisenbewltigungschool and university students (e.g. at the International Academy Traunkirchen). In addition, together with the Austrian Red Cross, A. Bergthaler co-initiated and moderated the Live webinar series #BreakingtheWave targeting pupils, parents and teachers ( This led to eight live webinars about the pandemic and the use of vaccines together with expert panels from medicine, epidemiology, education and journalism from November 2021 to January 2022. Of note, this included dedicated webinars for non-German speakers in Arabic, Bosnian-Serbian-Croatian and Turkish language. These #BreakingtheWave webinars reached >12.000 pupils live as well as a wider audience through the recorded webinars on Youtube / Facebook and extended media coverage. 05/2022-ab

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