COVID-19 Projects at FIMM

The COVID-19 host genetics initiative brings together the human genetics community to generate, share, and analyze data to learn the genetic determinants of COVID-19 susceptibility, severity, and outcomes. Such discoveries could help to generate hypotheses for drug repurposing, identify individuals at unusually high or low risk, and contribute to global knowledge of the biology of SARS-CoV-2 infection and disease.

The initiative was launched by FIMM-EMBL Group Leader Andrea Ganna with the support of the Director of FIMM, Mark Daly. In a month, more than 130 studies and 600 researchers have already joined.

More information:

Covid-19 Host Genetics Initiative Website

UH Press release

Article in Science

Blog post from Broad Institute

FIMM is also participating in a Finnish COVID-19 research project (COVIDprog) led by Professor Markus Perola / THL). COVIDprog studies the individual properties, such as genetics, other diseases and medication usage, that might explain the severity of COVID-19 infection symptoms. THL has started recruiting Finnish patients to this study in collaboration with the Finnish biobanks. FIMM Genotyping Unit will genotype the patient samples. 

More information:

COVIDProg project website

The population-based GeneRISK study cohort (n=7350) collected by FIMM and consented for recontacting will be asked to participate in a questionnaire-based study screening for COVID-19 symptoms. Later, some of the participants will be asked to provide samples for serological tests. The study aims to understand the role of HLA, common genetic variants and epidemiological factors in COVID-19 severity and suspectibility.

More information:

The focus of this project is to set up a national functional drug response profiling platform for SARS-CoV-2 for drug repurposing. Our first goal is to repurpose approved drugs to prevent and treat COVID-19 and to translate these findings into clinical trials in Finland. To this aim, we create a standardized drug testing platform, which will be available for national or international partners to carry out drug testing against SARS-CoV-2, with flexibility in the assay set-up (antibodies against viral receptors/interacting proteins, novel compounds or probes, addition of CRISPR/Cas9 or siRNAs etc.) and assay readouts (cell viability, high-content imaging e.g. of virus/viral replication/proteins in 2D and 3D cell cultures). Our ultimate goals are to create an open-access database of the results and to find novel antiviral therapies. From FIMM, Päivi Tammela, Kallioniemi group, FIMM HTB Unit and FIMM HCA Unit are involved.

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By studying the SARS-CoV-2 virus genome, we can acquire information regarding the rate of change of the virus or the size of its geographical distribution. This information will help in preparing for future outbreaks. 

Researchers are planning to sequence the SARS-CoV-2 virus genome from nearly all positive COVID-19 samples from the Helsinki University Hospital (HUS) region. The sequencing information will be published quickly in open source databases to share information with other researchers and expert organisations. The SARS-CoV-2 genome is currently being studied simultaneously in many countries, which enables mutations to be followed almost in real time.

FIMM Next Generation Sequencing Unit is conributing to the sequencing efforts led by researchers from the Viral Zoonoses group.

More information:

Virus sequencing project

Open ses­ame coronavirus – re­search­ers map the SARS-CoV-2 virus gen­ome

While many SARS-COV-2 RNA tests already exist and are most commonly RT-PCR-based strategies, several challenges remain to be solved. The exact spatio-temporal secretion pattern of the virus at different points of infection is uncertain and raises questions about the best sample sources for testing. The goal of this project is to identify the best sampling procedures and the impact of viral load and mutations to help to design future RNA tests.

From FIMM, Maija Puhka, Pirkko Mattila, FIMM Hi-Prep Core and FIMM Single Cell Analytics Unit are involved.

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Antibody tests with high specificity and sensitivity are urgently needed to measure the existing immunity against the SARS-CoV2, to follow how intended vaccines work, and to perform serodiagnostic surveys. To tackle these important aspects of current pandemia, we aim to establish a rapid and accurate high-capacity method to measure the general population immunity against SARS-CoV2. The assay is a next-generation version of the indirect immunofluorescence assay (IFA) commonly applied in viral serodiagnostics, since it enables automated detection of up to three immunoglobulin (Ig) classes from a single sample. This project is done in collaboration with the Department of Virology.

From FIMM, Peter Horvath, Vilja Pietiäinen, FIMM HTB Unit and FIMM HCA Unit are involved.

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The aim of this study is to modify and combine a previously developed mobile digital microscopy scanner with a DNA-microarray-based detection of SARS-CoV-2 and to perform evaluation of feasibility and diagnostic accuracy of the method. DNA-microarray assays have previously been widely used in the detection of coronaviruses and allow for analysis of several viral targets in the same assay. However, readout of the microarray results has so far required expensive and bulky instruments, and our proposed combination of technologies decreases the cost per test by orders of magnitude, can be used at the point-of-care and in resource-limited settings.

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This project focuses on looking for rare coding variants predisposing individuals to severe COVID-19 symptoms using exome and HLA sequencing approaches. 

There are younger individuals with no pre-existing conditions that have extremely severe disease and even death as a result of the infection. We will perform exome sequencing on 50-100 such patients at FIMM and search for potential monogenic causes of their extreme response to infection, aligning to known databases of immune deficiency genes. Furthermore, we will comprehensively evaluate the role of MHC variation in disease risk and severity.

Investigators are Mark Daly, Hanna Ollila, Andrea Ganna and Mikko Seppänen (HUS).