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Revista Cubana de Ciencias Informáticas

On-line version ISSN 2227-1899


JIMENEZ GARI, Jorge Alejandro et al. Preliminary analysis of the potentiality of the different genomic subregions of SARS-Cov-2 for their use as phylogenetic markers. Rev cuba cienc informat [online]. 2021, vol.15, n.4, suppl.1, pp. 101-119.  Epub Dec 01, 2021. ISSN 2227-1899.

The use of phylogenetic tools could be key in making decisions in the management of epidemics. Phylogenetic reconstruction requires appropriate markers, which contain the necessary information and allow reconstructing the evolutionary history of the pathogen. For the study of SARS-Cov-2 at the international level, multiple complete genomes of the virus have been sequenced starting from isolates from several countries. This information, available in international databases, has facilitated phylogenomic studies. In the case of Cuba, technological capabilities do not allow complete genomes to be sequenced, which makes it necessary to evaluate the different SARS-Cov-2 genomic regions for their potential use as sources of information. This work describes an analysis, carried out at the beginning of the pandemic, of the genomic regions of SARS-Cov-2, to evaluate their possible use as phylogenetic markers. For this, sequences and public tools were used, taking into account their variability, tendency to saturation and presence of noise, in addition to evaluating their ability to reconstruct the same phylogenetic relationships as those obtained with the analysis of the entire genome. Due to the relatively low evolutionary rate of the virus, and the short time that has elapsed since the beginning of the transmission of SARS-Cov-2 in humans at the time of the study, it is observed that the variability in the individual genomic regions does not contribute the same level of information, that the complete genome, and that the length of the selected segment and the taxonomic sampling are decisive in the resolution capacity of the phylogenetic methods used.

Keywords : SARS-Cov-2; phylogenetics; phylogenetic signal; phylogenetic marker; saturation.

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