## 4 Discussion
The situation was the opposite in western Lithuania, and it is likely that such regional differences were due to restrictions on movement between municipalities. Q.1 (Lithuanian sub-lineage) was pushed out of the country not long after its parent B.1.1.7, which spread rapidly due to frequent internal outbreaks. Q.1 is a local version of B.1.1.7 n. This lineage circulated and dominated before other lineages until the appearance of Delta in June 2021, which, one month later, accounted for 95% of all sequenced samples. The Delta lineage accounted for more than 90% of all virus lineage detections for 6 months. During this period, A.Y.4, A.Y.122, A.Y.111, and A.Y.36--different delta sub-lineages--were the most observed, of which variants of sub-lineage AY.4 accounted for the largest percentage during the whole period. The Delta AY.4.5 local lineage out-dominated other Delta sub-lineages. In contrast to the case with Q.1 and its parental lineages, A.Y.4.5 differs from its predecessor lineages by a mutation in the S protein, S:D1259Y. Even though this mutation has not been fully characterized, there are possibilities that it provided infectivity advantages for the virus [27]. This could be supported by a slightly higher R0 value compared to A.Y.4. However, after its peak, the fraction of A.Y.4.5 cases started slowly decreasing, while other Delta sub-lineages started to increase. Hypothetically, if the Omicron variant would have never arisen, we would have different Delta sub-lineages coexisting at a similar measure. Omicron was first identified in December 2021 and quickly became the dominant strain. The BA.1 Omicron subtype was the fastest growing in Lithuania, following with a vast increase in BA.2, observed at the end of January and increasing by about 10% each week, leading to rapid over-domination [28] (Figure A4). Many lineages of SARS-CoV-2 imported to Lithuania from abroad did not spread throughout the country, as shown in Figures 2 and 5; Q.1 and its paternal lineage B.1.1.7 being the exceptions. At the beginning of its arrival/detection, Q.1 rapidly started to spread, and the number of cases grew even faster than the parental Alpha variant (Figure 3). However, it was noted that B.1.1.7 became more prevalent and replaced the previously dominating Q.1 sub-lineage. It is highly likely that the lifting of certain pandemic and travel restrictions in the country is the reason behind the spread. Therefore, we can conclude that travel restrictions have a considerable influence on the spread of various SARS-CoV-2 sub-variants. However, it is worth mentioning that it has a minimal effect on the viral sub-lineages that were imported the most, such as B.1.1.529, B.1.617.2, and B.1.258, due to the fact that they did not contain distinguished traits that could increase their ability to spread. At the time the Delta variant became present in Lithuania, the A.Y.4.5 sub-lineage started to spread rapidly, influenced by large local outbreaks; however, since July the number of cases has declined compared to other sub-lineages. A.Y.4.5 is unlikely to have a significant biological advantage, with additional mutations in S:E156G and S:D1259Y in the SARS-CoV-2 genome. Large initial growth at the beginning of the lineages presence was determined as a result of the founder effect and other Delta mutations. While analysing the variety of lineages, we noticed that increased traveling during the summer holidays and the easing of quarantine restrictions affected the diversity of the different lineages. We decided to verify this hypothesis by comparing the number of emigrants in the country with countries from which different virus lineages were usually imported by relying on the assumption that the countries that most Lithuanian people have emigrated to would import the highest number of different lineages. This notion was confirmed, and we discovered that the amount of emigration significantly correlated with the amount of different lineages present.