The Norwegian Institute of Public Health (NIPH) is the national infection control institute in Norway and is the national reference laboratory for a total of 30 bacteria and viruses. Microbial surveillance is an essential part of the NIPH laboratory activity. The role as reference laboratory covers research, laboratory-based surveillance and characterization of pathogens, outbreak investigations and response, as well as specialized microbiological assays.
The Covid-19 pandemic led to a great demand for whole genome sequencing (WGS). NIPH is responsible for surveillance of the Covid-19 pandemic at a national level and has implemented WGS protocols for SARS-CoV-2, enabling monitoring of the epidemic in Norway. Different protocols have been implemented to ensure quality and robustness of WGS as new variants emerge. And as of September 2022, we have processed and sequenced close to 70,000 samples and deposited the corresponding consensus sequences on GISAID.
At NIPH, WGS was already implemented in 2018 as part of the microbial analysis portfolio, and by postponing most of our other activities we were able to sequence and analyse a sufficient number of SARS-CoV-2 samples to support national and international surveillance. Through the HERA grant we have successfully implemented solutions that make our SARS-CoV-2 WGS analysis workflow less labour intensive by automating and digitalising our lab flow and data capture. However, the HERA grant focused specifically on the lab infrastructure related to handling of SARS-CoV-2 samples.
WGS is increasingly important both in routine surveillance and preparedness to future outbreaks also for other pathogens. Therefore, we need to consolidate the HERA initiative and prepare for the implementation of the SARS-CoV-2 solutions to other pathogens, as well as further strengthening our level of automation in acquiring and reporting data. This includes visualisation, publishing, and reporting of SARS-CoV-2 WGS results and expanding the automation and WGS data capture to other agents with established WGS protocols at NIPH. In preparedness for future outbreaks, we also have a need to expand the WGS technology and analysis pipelines to new and potentially novel or unknown pathogens.
The general objective of this project is therefore to further strengthen and expand our microbial WGS analysis. We will do this by automation of our laboratory workflow, including digitalisation of instrument data, expanding the current WGS activity to other pathogens, and develop downstream visualisation and reporting platforms. This will allow us to more rapidly and efficiently respond to the Covid-19 pandemic, as well as enhance our preparedness for future pathogens and other cross-border threats.