Virus Sequencing

Finnish SARS-CoV-2 sequences

Below are links to information regarding SARS-CoV-2 sequences that are the result of work done at the  viral zoonoses research unit (VZRU) and emerging infections research group (EIRG) at University of Helsinki, Finland. The people responsible for this site and these sequences are Ravi Kant and Teemu Smura.

In Finland, virus sequencing has been developed at the University of Helsinki’s Department of Virology by Professor Olli Vapalahti’s research unit specialised in viral zoonoses, where coronavirus sequencing has been carried out ever since the first Covid-19 diagnosis. Since last autumn, these efforts have been supported by the Institute for Molecular Medicine Finland (FIMM). As the new, more transmissible coronavirus variants have arrived in Finland, we plan to sequence about 1000 SARS-CoV-2 sequences weekly (Read more). We submit most of these sequences to GISAID.

Visualization of the Finnish SARS-CoV-2 dataset is powered by auspice. This includes 783 sequences from Finnish Covid-19 patients, assembled between February, 2020 and June, 2020. All sequences are at least 95% complete (i.e., at most 5% of sites have an ambiguous 'N' nucleotide).

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 in real time. Now we are joining forces with the Institute for Molecular Medicine Finland (FIMM) and with the Institute of Biotechnology (BI). This will enables us to sequence all samples available to us.

Kindly contact if you would like to obtain the  full-genome sequences (FASTA) and the TAB-separated metadata for the VZRU-produced sequences used in the production of the above visualization. 

Please note

This page exists solely to provide you with early access to unpublished SARS-CoV-2 sequences assembled by VZRU, department of virology, University of Helsinki. 

Sequence assembly can be time-intensive and may require several rounds of careful laboratory and computational work. The sequences released here should be regarded as current best-effort drafts, subject to change, and minor changes should be expected. These can occur for a variety of reasons such as re-sequencing samples to resolve ambiguous nucleotides or to clarify the impact of minority variants on consensus sequences, or re-analysis to identify likely sequencing or computational errors.

If you plan to use these sequence as part of a publication, please contact us to check for additional details regarding planned sequence updates, specific nucleotide uncertainties, or for additional sample metadata that we may have available.

(Hosted through CSC server - thanks to Kimmo Mattila)