First report on the Latvian SARS-CoV-2 isolate genetic diversity

Abstract

Remaining a major healthcare concern with nearly 27 million confirmed cases worldwide at the time of writing, novel severe acute respiratory syndrome coronavirus - 2 (SARS-CoV-2) has caused more than 880 thousand deaths since its outbreak in China, December 2019. First case of a person testing positive for SARS-CoV-2 infection within the territory of the Republic of Latvia was registered on 2nd of March 2020, nine days prior to the pandemic declaration by WHO. Since then, more than 230 000 tests were carried out confirming a total of 1330 cases of COVID-19 in the country as of 20th of August 2020. Rapidly reacting to the spread of the infection, an ongoing sequencing campaign was started mid-March in collaboration with the local testing laboratories, with an ultimate goal in sequencing as much local viral isolates as possible, resulting in first full-length SARS-CoV-2 isolate genome sequences from the Baltics region being made publicly available in early April. With 109 viral isolates representing ~8.2% of the total COVID-19 cases in the country being completely sequenced as of today, here we provide a first report on the genetic diversity of Latvian SARS-CoV-2 isolates.

First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity

“…The authors acknowledge the use of infrastructure provided by High-Performance Computing Center of Riga Technical University. We are also thankful to the medRxiv preprint server for health sciences for allowing us to post-previous versions of this manuscript ( 60 ) as a preprint.…”

Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and High-Frequency mutation N501Y in different levels of control measures

“…This finding highlights the importance of rapid identification of other mutations of concern and characterization on their dynamics. Some of the MF and LF mutations that we observed have been less reported, described only in particular countries or regions [24,25,26], or not reported, such as K997Q on nsp3 and S202C on N protein. We think that it is also important to study MF and LF mutations because they are present in several months throughout the pandemic and we did not observe the extinction of any of these mutations (relative frequency of 0 or near to 0 in two or more months) (Fig.…”

Epidemiological Characterization of SARS-CoV-2 Variants in Children Over the Four COVID-19 Waves and Correlation with Clinical Presentation

“…By the end of August, 20E (EU1) sequences had also been detected in most of European countries, including Italy [31]. The 17.4% of 20E sequences circulating in children were also involved in local transmission clusters, one of them composed by 24 sequences characterized by 5 SNPs, some of them previously described in Northern Europe [41] and as of 3 December 2021 not related with transmission or pathogenicity alterations. Among the variants rapidly causing concerns, P.1 (gamma clade), B.1.1.7 (alpha clade), and B.1.617 (delta clade) raised in paediatric population between March and July 2021.…”