Approximately 20,000 COVID-19 genomes sequenced in the HUS area
Keywords:Sequencing is still needed even if the COVID-19 pandemic weakens. In the future, sequencing of microbes may play a major role also in the examination of patients.
A laboratory worker examining a sample for COVID-19 sequencing.
Sequencing is used to determine the exact order of the bases of the viral genome. This allows us to detect genetic variation of virus strains. In the HUS area, approximately 400 COVID-19 samples are randomly selected for sequencing every week. 400–600 samples collected by the Finnish Institute for Health and Welfare (THL) arrive from elsewhere in Finland. In the HUS area, approximately 20,000 COVID-19 genomes have been sequenced so far. More than 35,000 sequencing processes have been completed in the entire country.
Sequencing helps to determine which of the COVID-19 virus strains are prevalent at a specific time, for example. Last year, a significant share of the samples still came from the border. Now, a majority of the samples comes from COVID-19 testing in the public sector.
“The amount of sequencing in Finland is at the European average”, says Maija Lappalainen, Head of Clinical Microbiology in Diagnostic Center.
The amount has increased since the beginning of the COVID-19 pandemic. When alpha, the first variant of COVID-19, developed, regular collection of samples was started. Collection of samples takes approximately one week, followed by a one-week analysis.
Future outlook of sequencing
Before the COVID-19 pandemic, sequencing was mainly carried out in Finland as part of medical research. In the future, sequencing of microbes may play a major role also in the examination of patients.
“Sequencing is likely to become more common in diagnostics for communicable diseases”, says Lappalainen.
At the moment, sequencing is rarely used in patient care.
Samples collected by HUS and THL are processed and sent, without patient identification information, for sequencing with the large sequencing equipment of the Institute for Molecular Medicine Finland (FIMM). The institute then forwards the raw data, which is analysed to identify new variations of COVID-19, and to learn how they function, for example.
The data analysis is carried out with the supercomputers of the CSC - IT Center for Science. HUS and the University of Helsinki cooperate in this matter. Researcher Teemu Smura analyses raw data produced by sequencing in the University of Helsinki under research funding from HUS.
“I believe that the pandemic has demonstrated the value of genetic monitoring of viruses. In several countries, hopefully also in Finland, the monitoring of viral genomes will be extended to other respiratory viruses, such as influenza viruses”, says Smura.
Sequencing resources will be needed even if the COVID-19 pandemic weakens.
“In the future, we will also need capacity for unexpected situations”, reminds Smura.
Not enough sequencing is carried out in poorer countries
Anonymous genome data from a data analysis is sent from Finland to a database where practically every sequencing laboratory in the world sends their genomes. The database already contains approximately 8.5 million COVID-19 genomes.
Sequencing is basically carried out in the same way all over the world. The big question is where in the world will sequencing take place in the future and to what extent.
“At the moment, massive sequencing takes place in practice in the rich Western countries. The most rational use of resources would be to distribute sequencing to poorer countries. There are plenty of infections in poorer countries, and the most concerning variations in the virus genome also take place in these countries", says Smura.