ZSC: National core facility for Pandemic Preparedness

PI(s)/Head responsible for the resource:

Åke Lundkvist, Josef Järhult

Host organisation(s):

Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University; Department of Medical Sciences, Zoonosis Science Center, Uppsala University

Resource description:

1. Clinical study

To understand the virus shedding and further the disease management for COVID-19 patients in intensive care unit (ICU), we have isolated SARS-CoV-2 from nasopharynx samples collected from COVID-19 patients admitted to ICU with severe respiratory failure at the Uppsala University Hospital, between December 2020 and June 2021. The resources are the clinical data from patients who were enrolled in the PronMed study.

2. Virome study

The resources are samples and RNA-sequencing data from important zoonotic reservoirs: Swedish rodents and shrews, as well as mosquitoes and ticks.

3. Factors behind reassortment and recombination, spill-over events to new species and immune responses

To better understand why new variants, some with enhanced transmission and spread, of influenza and coronavirus we have established reverse genetics (RG) systems. To be able to study immune responses at the level of single cells, we have established systems within our own BSL-3 laboratory.

4. Development of diagnostics

We have established highly sensitive and specific Luminex-based systems for studies on antibody responses to Flavi-, Hanta- and coronaviruses, including SARS-CoV-2. These systems can be rapidly up-dated to new virus variants and new emerging viruses.

How this resource can be used for Pandemic Preparedness research:

1. PronMed study: patient clinical information etc.
2. Virome study: identify RNA virus composition from important reservoirs and vectors in Sweden.
3. Spill-over and immune responses: By our research on transmission and maintenance of zoonotic viruses in nature, we will increase the knowledge on potential threats for future endemics and pandemics. How are climate changes increase the risks, which new viruses may be introduced to Sweden?
4. Diagnostics: By our established Luminex-based systems, we are able to study e.g. seroprevalences and vaccine responses. In addition, we can rapidly up-date the systems with new variants or completely new viruses in future endemics or pandemics.

Who is able to access the resource (and under what conditions):

1. The same as the PronMed study.
2. Everyone has access to the Genbank or BioProject, once the RNA-sequencing data and viral genome sequences data will be public.
3. Open access publications.

SOPs, guidelines, publications, etc. describing the resource:

• Ling J, Hickman RA, Frithiof R, Hultström M, Järhult JD, Lundkvist Å, Lipcsey M. Infectious SARS-CoV-2 is rarely present in the nasopharynx samples collected from Swedish hospitalised critically ill COVID-19 patients. Ir J Med Sci (2022). DOI: 10.1007/s11845-022-02961-8
• Wasberg A, Raghwani J, Li J, Pettersson JH, Lindahl J, Lundkvist Å, Ling J. Discovery of a novel coronavirus in Swedish bank voles (Myodes glareolus). bioRxiv (2022). DOI: 10.1101/2022.02.24.481848
• Ling J, Li J, Khan A, Lundkvist Å, Li JP. Is heparan sulfate a target for inhibition of RNA virus infection? Am J Physiol Cell Physiol. 322(4):C605-C613 (2022). DOI: 10.1152/ajpcell.00028.2022.
• Krambrich J, Bringeland E, Hesson JC, Hoffman T, Lundkvist Å, Lindahl JF, Ling J. Usage of FTA® Classic Cards for Safe Storage, Shipment, and Detection of Arboviruses. Submitted (2022).

Contact information:

Åke Lundkvist
Professor
ake.lundkvist@imbim.uu.se