Something that worries viral researchers sequencing the coronavirus genome in Lithuania

Who does sequencing serve?

Sequencing is the exploration of the genetic code (DNA or RNA) of a virus or an organism, that is, the determination of which letters (nucleotides) and in what order make up the genome of an organism.

“We are pleased that the biotechnology leader ‘Thermo Fisher Scientific Baltics’ is contributing to applied science in Lithuania and, together with specialists from the VUL Santara clinics, is conducting nationally important viral genome research. The pandemic has shown that we have many high-level experts in Lithuania, and the synergy of medicine and biotechnology gives fast, high-quality results, ”said Daniel Naumov, director of the Santara Clinics Biobank and senior medical biologist.

Over the past decade, the sequencing of the genomes of infectious agents has become an integral part of the fight against communicable diseases, helping to identify, understand, and control infectious disease outbreaks. Monitoring of genetic changes in infectious agents provides a wealth of valuable information for decision makers important to the state. Therefore, near real-time data analysis has a direct impact on public health and life.

Genome sequencing has already been instrumental in managing the COVID-19 pandemic. She helped:

• identify SARS-CoV-2 as a cause of COVID-19;

• start to implement new diagnostic methods;

• develop new treatments and vaccines;

• determine the date the virus first entered the human body and determine the origin of the virus;

• distinguish chronic disease from reinfection;

• distinguish the local spread of the disease from the many cases introduced in the early stages of the epidemic;

• detect new varieties with modified properties;

• Recognize virus flows: between hosts, between geographic locations.

What can you see in the latest sequencing data?

The virus researcher Gytis Dudas, to describe the dominant strains of the virus in Lithuania (Vilnius), says that currently two main ones are being identified: B.1.1.280 (Lithuanian) and B.1.177 (Spanish, more precisely, the Version ” Lithuanian “of the latter).

“In my opinion, such a limited image of dominant varieties is not the worst option, because it shows that the additional varieties that have entered our country have not been able to expand more widely, otherwise we would have an even larger mosaic of varieties,” G Doubts comments.

According to Daniel Naumov, the dominant strains of B.1.1.280 and B.1.177.LTU in Lithuania are not very special, which means that they have no worrisome mutations, not to mention English, Brazilian or South African.

What is the most worrisome?

G. Dud points to the phylogenetic tree of SARS-CoV-2 genomes.

“By looking at the phylogenetic tree of the SARS-CoV-2 genomes, you can see a small and hitherto known B.1.1.7 genome from Lithuania (see the dot surrounded by red in the graph).

We are in a situation in which statistical analysis is no longer necessary, since every week the same image is opened where B.1.1.7 is found, a rapid replacement of all the varieties that previously circulated through it. We have seen it in the UK, in Denmark and now we are seeing it everywhere.

Currently ~ 35% in Europe. COVID-19 cases in sequencing countries belong to this variety, so it would be naive to expect that we won’t see it in Lithuania. The least we can do is be prepared, “said the scientist.

The Santara clinics see a great need to monitor the epidemiological situation and therefore continue to track the SARS-CoV-2 genomes.