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Pandemic Preparedness Capabilities

Enhancing Pandemic Laboratory Preparedness through Rapid Biopsy Sample Handling

PI(s)/Head responsible for the resource:

Annika Karlsson

Host organisation(s):

Department of Laboratory Medicine, Karolinska Institutet

Resource description:

“In this proposal we aim to extend our ongoing RAPID-SEQ project on pandemic laboratory preparedness for SARS-CoV-2 and metagenomics to include research and surveillance on enteroviruses, which have the capacity to cause large worldwide outbreaks. Historically, poliomyelitis is the most well-known and feared enterovirus disease, but many other disease outbreaks have been caused enteroviruses. This includes recent reports on neonatal cases with fulminant and fatal hepatitis due to echovirus 11, polio-like acute flaccid myelitis due to enterovirus D68 (EV-D68), myocarditis due to coxsackie B3 and B4 and neonatal sepsis and meningoencephalitis. Despite the serious consequences and threats from enterovirus infections, Sweden lacks a comprehensive program for surveillance of enteroviruses, apart from the WHO mandated surveillance for poliovirus.

This proposal aims to build capacity and preparedness for comprehensive laboratory surveillance of enteroviruses by:

  1. Implementing NGS-based methods for partial and whole genome sequencing (WGS) of enteroviruses and rhinoviruses.
  2. Performing enterovirus genotyping on respiratory specimens.
  3. Analysing (i) genotypes from patients sampled at an intensive care unit vs other unit, (ii) circulating genotypes over time, and (iii) genotypes across age groups.

Our laboratory is excellently suited to take on the above tasks as being the largest clinical microbiology laboratory in Sweden with continuous access to large numbers of patient samples and results from routine diagnostics. In addition, we are the national reference laboratory for non-polio enteroviruses and a partner in the European non-polio enterovirus network (ENPEN). Within ENPEN we have contributed to several studies on EV-D68. In this proposal we will extend this work to other species and types of enteroviruses and rhinoviruses. We will build on the capacity in our current PLP project (RAPID-SEQ) by adapting the workflow for SARS-CoV-2 to another pathogen.”

Contact information:

Annika Karlsson