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

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.

When the virus replicates in humans, small changes, called mutations, emerge in its genome. Even though the majority of those changes do not affect the virus’s primary characteristics, such as pathogenicity, those changes can be used when we are tracking down the virus’s geographical distribution, mutability and the size of the virus population currently circulating in the human population.

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.

“By looking at the whole virus genome in people who have had confirmed cases of COVID-19, one can monitor changes in the virus on a national scale to understand how the virus is spreading and whether different strains are emerging. We can also better prepare for future epidemics,” says Dr Ravi Kant from the University of Helsinki.

So far, researchers have sequenced over 40 Finnish SARS-CoV-2 virus sequences. In the early time points when SARS-CoV-2 was introduced to Finland, all of the viruses were imported, mainly from Italy. By the second week of March, clear clustering could be seen when comparing sequences, which indicated that the disease had started to spread among the Finnish population.

“By studying these SARS-CoV-2 sequences, we can follow the evolution of different lineages starting from importation with very high resolution. Regarding importations – especially if a second epidemic wave occurs in the future, for example, next autumn, it would be important to distinguish between the local spread and imported cases of the virus which we can easily recognise,” says Dr Teemu Smura, who leads the sequencing work of the Viral Zoonoses group.

Now researchers from the Viral Zoonoses group, led by Professor Olli Vapalahti at the Department of Virology, University of Helsinki, are joining forces with the Institute for Molecular Medicine Finland (FIMM) and with the Institute of Biotechnology (BI).

This enables the sequencing of almost all available samples. Researchers are using high-throughput sequencing, and it takes about two to three days to prepare the sequences.

The COVID-19 website lists researchers’ current projects during the corona crisis

“Researchers around Finland are uniting their efforts against COVID-19,” says Dr Ravi Kant.

The COVID-19 group at the University of Helsinki is one form of co-operation. Their website outlines the effort of researchers and research groups working on the ongoing pandemic COVID-19 in collaboration with Helsinki University Hospital (HUS) and the Finnish Institute for Health and Welfare (THL).

The project website describes several research projects on coronavirus.

Read more: Virus sequencing

Further information:

Teemu Smura, PhD, University of Helsinki
Tel. +358 2941 26480

Ravi Kant, PhD, University of Helsinki
Tel. +358 2941 57054

Read more:
What are we doing to stop the coronavirus crisis?