## 4 Discussion  
During the pandemic's first year (2020), several viral lineages were distinguished and were all prevalent at the same time. By the end of the second year of the pandemic (2021), the viral advancement pattern had changes, showing one or more dominant lineages, instead of the high variety noted previously. The first SARS-CoV-2 genomes that were sequenced in Germany (n = 3) had a very similar gene sequence to the Wuhan-hu-1 [19] lineage, differing by an average of 4-5 nucleotides [2; 20]. It is noteworthy that in one of the first cases in Lithuania that were sequenced, a strain with the S:D614 mutation was detected, which was later confirmed to have higher infectivity and promote a faster spread [21; 22]. In April 2020, the first B.53 virus lineages were identified in several samples collected and analysed in Lithuania. This lineage was first detected in February 2020 in the United Arab Emirates and is characterized by S:Y2 BH, ORF:8884L, and N:P344S mutations [23]. According to GISAID data (February 2022), a total of 84 cases were registered worldwide, of which 73.0% were in Lithuania, 24.0% in the United Arab Emirates, 1.0% in India, 1.0% in Belgium, and 1.0% in Australia [2; 23]. It is likely that this lineage was responsible for the first major outbreak that began to be monitored in the second half of March 2020. Due to the low amounts of sampling, it is difficult to evaluate the prevalence of this viral lineage; however, we have observed a wide spread of B.53 at the beginning of the pandemic. In the following spring and throughout the summer, two other Lithuanian SARS-CoV-2 lineages (B.1.1.30 and B.1.1) started to spread. The second widely viral lineage was B.1.1.30, which spread during the period 18 May 2020-3 June 2020. All 13 cases of this lineage were registered in Lithuania, Vilnius district. With a gradual decrease in the number of cases with this lineage, Pango, classified as B.1.1, which is characterized by mutations in S:D614G, N:G204R, N:R203K, NSP2:T332I, and NSP12:P323L, spread at a similar time. It comes as no surprise that both the B.1.1.30 and B.1.1 lineages' most intensive spread to Lithuania was from the United Kingdom (Figure 4), which is the country that hosts most Lithuanian emigrants. The outbreak of this lineage was replaced by the vast spread of B.1.1.280. The viral lineage, which has been present in Lithuania for almost a year, was observed from 30 July 2020 to 12 July 2021, with  
Figure 7: Relationship between frequency of transmission to Lithuania, as inferred from the time-scaled phylogenetic trees, and initial growth rate. On the x-axis, the sum of transmission frequencies from abroad to Lithuania, as inferred from the time-scaled phylogenetic trees, is given, and the y-axis matches the maximum first order derivative of the spline fitted to month fractions of the lineages. the percentage of cases being 92.0% in Lithuania, 3.0% in Norway, and about 1.0% in Germany, the United Kingdom, and Latvia [23]. These figures agree with the data in Figure 4 indicating that the most intensive spread of this lineage to Lithuania was from Norway. This lineage was not related to the changes in the biological characteristics of the virus; therefore, it is likely that the epidemiological factors, such as long-term spread, were the main cause of the wide spread of this strain, rather than the altered viral characteristics. The increase in variety of lineages could be related to summer holidays or similar travels. The first more-pronounced mutation of a single virus line was observed in late autumn, when the number of COVID-19 cases began to rise rapidly. The prevailing Lithuanian virus lineages resulted from the Spain-originated lineage B.1.177, which at that time was the dominating lineage in Europe. Currently, there is limited evidence of increased transmissibility or severity of the infections associated with the B.1.177 lineage [24].