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Phylogenetic analysis and molecular detection of coronaviruses
MARHOUNOVÁ, Lucie
The aim of this bachelor thesis was to get acquainted with the creation of phylogenetic trees, which describe the relationships between coronaviruses and compare and assess the suitability of used and designed primers for the detection of a new type of coronavirus SARS-CoV-2. According to phylogenetic trees, it is possible to determine the evolutionary relationship of the studied organisms, which during evolution are subject to changes in their sequences, so-called mutations. These changes determine their development. The theoretical part of the bachelor thesis was focused on general acquaintance with viruses and subsequently coronaviruses and a new type of coronavirus SARS-CoV-2. SARS-CoV-2 has posed and continues to pose a major threat to the world. Furthermore, the issue of phylogenetics and finally the PCR detection method were discussed. In the practical part, phylogenetic trees were created using the computer program MEGA-X using the Neighbor-Joining method, which examined the phylogenetic relationships between coronaviruses focused mainly on SARS-CoV-2. The nearest coronaviruses of this new type of SARS-CoV-2 coronavirus were further compared using special BLAST software, which reported the percent agreement of the studied sequences. During these analyzes, SARS-CoV-2 was found to be most like the bat coronavirus RaTG13. Primers that are commonly used to detect SARS-CoV-2 are not disclosed, therefore primers from the CoVrimer web application have been used, where primers that have been used for scientific research are available. These were compared with the primers designed by the author. The design was performed as part of a bachelor's thesis using a special application Pirmer-BLAST. The primers obtained from the CoVrimer application were not designed to comprehensively distinguish all SARS-CoV-2 variants studied.
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