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.

Research findings:

The project has succeeded in the isolation and characterization of several novel important viruses, e.g. a new β- coronavirus (Grimsö virus) in Swedish bank voles. We have also discovered a novel lineage of Puumala hantavirus (PUUV) in bank voles, currently spreading in Skåne and causing severe human disease. We have further discovered two distinct hantaviruses in Swedish shrews. We have investigated and described the overwintering mechanisms of an imported mosquito-borne virus with African origin in Sweden. We have developed and evaluated unique Luminex-based assays for both SARS-CoV-2 and TBEV and studied antibody responses in various groups of patients, e.g. SARS-CoV-2 infected children and adults with cancer. We have investigated the TBEV seroprevalence and vaccine coverage in Sweden. The effect of the inclusion of the TBE vaccination in the national vaccination program on the Åland Islands have been investigated.

We have shown that both avian influenza virus and SARS-CoV replicate efficient in stable human nose organoids.

We have characterized various most important and emerging variants of avian influenza virus (e.g. H9N2, H5N8 and H5N1) and investigated the diversity of receptor molecules for influenza A in mallard, chicken and tufted duck. We have established methods for SARS-CoV-2 and avian influenza virus single cell transcriptomics inside our BSL-3 lab.

We have established the models for infection of live mosquitoes with risk class 3 viruses inside our BSL-3 lab, and evaluated Swedish Culex pipiens as vectors for both Japanese encephalitis virus and Usutu virus, two emerging viruses. We also value our active participating in the establishment of a nation BSL-3 Network as an important part of the project.

Impact on prepardness for future pandemics:

The discovery of a new variant of PUUV hantavirus in Skåne, 600 km south of the previously known spread in Sweden, and causing severe human disease is highly important for the public health, but also for an improved general understanding of how rodent-borne viruses can suddenly emerge, i.e. highly important for better preparedness. The finding and characterization of a novel beta-Coronavirus in Swedish bank voles revealed a unique model to study how a virus, closely related virus to SARS-CoV-2, can spread and circulate in the nature, which is of high importance regarding preparedness.

Our diagnostic methods for SARS-CoV-2 and TBEV have proven most useful in a better understanding of the serological responses, e.g. in various groups of COVID-19 patients, but also proven that TBEV-infections are much more common in Sweden than previously known. Combined with our work on blood donor samples from Åland, which has proven the positive effect of the vaccine campaign there, will now hopefully and finally change the vaccine strategies in Sweden in a near future.

In collaboration with L. Svensson and M. Hagbom (Linköping Univ.) we have developed stable lines of human nose organoids that are proven to be highly efficient in replicating both SARS-CoV-2 and Influenza A virus. This new tool will be extremely useful for a better pandemic preparedness, due to the unique possibility to directly study the zoonotic potential of viruses from wild life and domestic animals.

Our work on avian influenza is most important for a better understanding of which variants of the virus that are most likely to cause a pandemic in the future.

The establishment of methods for virus infection-experiments in live mosquitoes in our BSL3 is unique for northern Europe and makes a number of experiments on vector-competence and transmission now possible, most important for better preparedness.

The establishment of a National BSL3-lab network is highly important for a better preparedness in the future. The COVID-19 pandemic most clearly proved the lack of active BSL3 laboratories in Sweden, and the severe lack of competent personnel, of course highly important for a better preparedness for future pandemics.

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