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5
OCT
2020

SARS-CoV-2 virus genome data are used for epidemiological surveillance and control of Covid-19 in Latvia


Scientists from the Latvian Biomedical Research and Study Center in cooperation with the Latvian Centre for Disease Prevention and Control, E. Gulbis Laboratory, Central Laboratory and The Latvian Centre of Infectious Diseases has been studying the SARS-CoV-2 virus genome since April, therefore obtaining significant information on the diversity and variability of the virus in Latvia. With the financial support from the Ministry of Education and Science and the EU Structural Funds, full genome sequences of 133 isolates of SARS-CoV-2 virus circulating in Latvia have been studied, which represent 9.2% of all infection cases in Latvia. After this indicator, Latvia is in one of the first places in the world in virus research. Obtained information about the virus similarity at the genome level is used for epidemiological investigation of Covid-19 infection cases at the Latvian Centre for Disease Prevention and Control.

In order to identify the mutations of viruses in Latvia, the SARS-CoV-2 genome sequences were compared with the Wuhan virus reference genome, which allows us to evaluate the variability of the virus from the beginning of the outbreak in December 2019. Scientists from Latvian Biomedical Research and Study Centre have discovered 247 different mutations. In general, however, researchers have determined that the divergence of the virus is slow - a new mutation occurs on average once in two weeks, so it can be concluded that the number of mutations in most viral isolates will be small during the year - about 22-23. The results of the SARS-CoV-2 genome analysis revealed that viruses circulating in Latvia are highly related to the ones identified in Europe. The results of phylogenetic analysis obtained in September indicate that the virus has entered Latvia several times from different continents, and so far there is no evidence of widespread infection within Latvia. Since the beginning of July, scientists have been able to identify only several isolates that are related to those described before. The data obtained in September 2020 confirm that most of the newly detected cases have been imported from abroad, which indicates the positive effect of Covid-19 control measures in Latvia. To date, not enough research has been done worldwide focusing on the mutations in the virus and their association with aggressiveness or infectivity of the virus, but it is now thought that a particular mutation (D614G) in protein S (Spike) could s infectivity. This strain of the virus has spread rapidly across all continents since its appearance in late January (the mutation was found in almost 80% of virus isolates worldwide). The data obtained so far show that in Latvia, too, this specific mutation could be present in at least 95% of cases. Given that the analysis of the viral genome allows us to trace the routes of infection, the results of phylogenetic analysis are regularly reported to the Center for Disease Prevention and Control, which further provides information on epidemiological surveillance.

The research is implemented within the framework of ERDF project No.1.1.1.5/17/I/002 “Integrated national level measures for strengthening interest representations for research and development of Latvia as part of European Research Area”. Detailed research results have been published: https://doi.org/10.1101/2020.09.08.20190504.

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Mājas lapas izstrādi finansēja ERAF 2.1.1.2. aktivitātes projekts Nr. 2010/0196/2DP/2.1.1.2.0/10/APIA/VIAA/004 "Latvijas biomedicīnas pētījumu integrācija Eiropas zinātnes telpā".