Streamlining laboratory procedures, bioinformatics and integrating use of genomic data in infectious disease surveillance in Finland (HaD_SinGen)

National technical resources for genomic surveillance of SARS-CoV-2 and other infectious diseases were improved in the HERA funded project “Enhancing Whole Genome Sequencing (WGS) and/or Reverse Transcription Polymerase Chain Reaction (RT-PCR) national infrastructures and capacities to respond to the Covid-19 pandemic in Finland” The aim of the current project is to take improved technical resources into routine use.

Aims of the project

1.   Routine use of enhanced infrastructure.
2.   Increased sequencing of selected microbes.
3.   Development of respiratory surveillance methods.
4.   National bioinformatics collaboration network.
5.   National WGS data collection.
6.   WGS support to clinical microbiology laboratories.
7.   Improved sentinel surveillance system for respiratory viruses.
8.   Pilot for integration of sequence data to surveillance system.

Implementation

The project is divided in four work packages (WP) progressing in parallel.

WP1 takes care of the management and evaluation of the project.
In WP2 Laboratory methodology and procedures we aim to develop and harmonize methodology for genetic surveillance of microbial infections including viruses and bacteria.
In WP3 Public health microbiology bioinformatics network in Finland we will support clinical microbiology laboratories for setting up NGS methods and streamline processes for genetic data analyses including data collection, transfer, storage, bioinformatical analysing and dissemination of results.
In WP4 Surveillance systems we will integrate the produced and collected genetic data to surveillance systems and enhanced utilization in outbreak investigations, communication, and modelling.

More information about the work packages

Collaborators

The Expert Microbiology Unit in the Finnish Institute for Health and Welfare (THL) will be responsible for the project lead with clinical microbiology laboratories in Finland acting as associated partners.