The first results of a large-scale coronavirus study in Lithuania: the second wave virus is different

“September 15 In the international virus database, a team of LSMU researchers shared with the world the first coronavirus genome sequence scanned in Lithuania. Since then, LSMU researchers have added more than 150 genome sequences of 5 Lithuanian cities to the database, which is the largest study of coronavirus genomes in the Baltic and neighboring countries, ”says Professor Vaiva Lesauskaitė, LSMU Vice Chancellor for Science.

What is the coronavirus genome in general and why is it so important to study it? Is the virus mutating in Lithuania? What is the difference between first and second wave viruses? We asked these questions of the project’s research researchers: LSMU PhD student Lukas Žemaitis and Cambridge University PhD student, virology bioinformatics department Ingrida Olendraitė.

– How is the coronavirus genome sequence information collected?

Lukas Žemaitis (L.Ž.): – Coronaviruses, like other viruses, are primitive life forms made up of genetic material, an envelope protein coat, and a membrane. The genetic material, the genome, encodes the biological properties of the virus. Genome research is essential for the development of vaccines, drugs or diagnostic methods, and it is also important for molecular epidemiology, since the mutation profile of the virus, like a unique barcode, can accurately track the forms in that the virus spreads and examine the foci of the disease.

The resulting viral genome sequences are processed by various bioinformatic algorithms to assemble the viral genome sequence from a specific sample. In the case of the coronavirus, there are about 30 thousand. nucleotides (letters in the RNA code).

In this study, we used two different sequencing technologies: we performed RNA sequencing based on DNA synthesis, and we tested an innovative nanopore-based assay method.

– Were LSMU researchers the first to publish data from Lithuania?

Prof. Vaiva Lesauskaitė (VL): – To date, only 3 SARS-CoV-2 genome sequences detected in Lithuania have been published in the international GISAID database and scanned by German researchers.

However, LSMU researchers were the first to provide detailed data describing the virus, which was obtained in Lithuania. At the same time, it is gratifying that the LSMU research team has not only successfully applied different sequencing technologies to this type of research, but has also added the largest amount of data to the GISAID database in the Baltic region. and neighboring countries (Latvia has published 135 genomes to date; Estonia 20; Belarus 3 Poland – 117). The research is carried out after LSMU researchers have obtained funding from the Lithuanian Science Council.

– The results of the investigation spread speculation that a “lighter” and “better” version of the virus is spreading in Lithuania. What is the virus that has spread in our country?

Ingrida Olendraitė (IO): – During the first wave, the coronavirus that spread in Lithuania differed from the virus genome sequences by an average of 7 nucleotides from Wuhan, where the pandemic began. Therefore, it can be said that this, compared to other viruses, p. Eg flu, mutates little. Similar data are provided by other scientists around the world.

By comparing the scanned genomes with foreign data, we found that virus variants circulating in the largest points of the pandemic (Italy, New York, Wuhan) also spread in Lithuania in the spring.

Therefore, it cannot be said that a “better” virus is spreading in Lithuania. It is more likely that in our country it was handled better and not spread as much. This shows once again that it is more important to manage outbreaks in a timely manner than to wait for our genetic base or “better” variants of the virus to protect against infection.

– An important place in the study was the analysis of data from samples from Marijampolė. That resulted?

L.Ž .: – Our goal was to assess the causes of the coronavirus outbreak in Marijampolė in March. We investigated whether the same virus was prevalent in the outbreak, or just the coincidence led to the appearance of many infected people in one place. This cannot be determined from PCR studies. It turned out that many of the people studied were infected with the same virus variant, we found similar virus variants in other Lithuanian cities during the same period. This shows that the outbreak of the virus in the district was not controlled in time and from one case probably not only many people in Marijampolė were infected, but the virus spread outside the region.

– Important research finding: a person with this virus can be re-infected. Is strong immunity possible after coronavirus infection?

L. Ž .: – Unexpectedly, we found at least two different variants of the virus in a sample. This indicates that a person infected with the coronavirus can be re-infected. It is likely that such a double infection can complicate the course of the disease, causing further damage to the body. However, it is still very difficult to talk about the immune response to COVID-19 infection.

Today it is known that an infected person develops an immune response in the first weeks, but there is no consensus on the intensity of this. There are cases in which a person with COVID-19 becomes infected a second time. In our study we also evaluated the peculiarities of the formation of the immune response, but it is too early to publish generalized conclusions.

– Are the viruses of the first and second waves in Lithuania different?

IO: – Of all the mutations detected, the D614G mutation in the viral spike protein, which is spreading rapidly in Europe, is of particular concern. This mutation is believed to facilitate the way the virus enters the cell. In the spring, attention was paid to a variant of the virus that spreads in Europe and China, which has an amino acid change: amino acid D is replaced by amino acid G, this virus mutation quickly began to dominate in Europe and later in the US, Canada and Australia.

Some experiments have shown that if the virus contains the amino acid G, the more the virus is detected in the epithelial cells of the human lung, the easier it is to infect the cells (more on this here). However, scientists still disagree on the importance of this mutation.

Of our tested first wave samples, 93 percent had the D amino acid variant, and only 7% had the G mutation, which is likely to spread more easily and lead to more efficient virus replication. Samples tested in Lithuania.

After the studies of the genome of the second wave of coronavirus, we saw that the situation turned around. A 100% G mutation was detected in the second wave samples: this type of virus also became dominant in Lithuania. Of course, this and several other mutations in the virus have caught the attention of our research team, so we will seek a better understanding of their clinical importance in the later stages of the study.

– After conducting such a large-scale research, can you provide any recommendations and prognosis?

L.Ž .: – All the research we’ve done so far confirms an important message: in the absence of a vaccine, it’s critical to focus on controlling the spread of infection. The currently prevalent type of second wave COVID infection virus may be more adapted to spread. We also discovered that one person can be infected with several coronaviruses at the same time, and the example of the Marijampol outbreak showed that even one case can be enough to infect dozens of people.

These facts only confirm that today we must act with great responsibility, follow the recommendations and try to control the spread of the disease as quickly as possible. There is still something investigators need to do to get to know this unsolicited guest better, so we need to focus and collaborate.