Predicting the Evolutionary Variability of the Influenza A Virus

Тимофеева, Т. А.; Asatryan, M. N.; Altstein, A. D.; Narodisky, B S; Gintsburg, Alexander L.; Каверин, Н. В.

doi:10.32607/20758251-2017-9-3-48-54

Cited by 7 publications

(4 citation statements)

References 39 publications

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“…Previously we studied the effects of amino acid substitutions in the HA molecule of the H5 influenza virus on the phenotypic traits of escape mutants (resistant to the neutralizing effect of any monoclonal antibody) [ 12 , 18 ]. One of manifestations of the evolutionary variability of highly pathogenic H5N1 influenza viruses during their adaptation to a new host and/or reproduction conditions is associated with HA changes in antigenic sites, receptor-binding sites (RBS), HA glycosylation, and cutting 1 sites [ 19 ]. On the threshold of a possible pandemic caused by the H5 influenza viruses, the efforts of scientists are focused on the search of mutations that may be genetic markers of adaptation of these viruses to mammals and their spread among humans.…”

Section: Discussionmentioning

confidence: 99%

The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses

Тимофеева

Садыкова

et al. 2020

Mol Biol

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Section: Discussionmentioning

confidence: 99%

The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses

Тимофеева

Садыкова

et al. 2020

Mol Biol

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“…2013) and allowed researchers to create progressively more detailed viral phylogenies in an effort to identify regions under selection (Anderson et al. 2016; Timofeeva et al. 2017).…”

Section: Introductionmentioning

confidence: 99%

Influenza passaging annotations: what they tell us and why we should listen

et al. 2019

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Influenza databases now contain over 100,000 worldwide sequence records for strains influenza A(H3N2) and A(H1N1). Although these data facilitate global research efforts and vaccine development practices, they also represent a stumbling block for researchers because of their confusing and heterogeneous annotation. Unclear passaging annotations are particularly concerning given the recent work highlighting the presence and risk of false adaptation signals introduced by cell passaging of viral isolates. With this in mind, we aim to provide a concise outline of why viruses are passaged, a clear overview of passaging annotation nomenclature currently in use, and suggestions for a standardized nomenclature going forward. Our hope is that this summary will empower researchers and clinicians alike to more easily understand a virus sample’s passage history when analyzing influenza sequences.

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“…The analysis of the nucleotide sequences of HA and NA genes of the viruses isolated from patients in different parts of the globe is widely used to predict the evolutionary variability of the influenza virus as well as to predict the emergence of new epidemic strains using mir-journal.org Selection pressure on the NA gene bioinformatics methods, in particular by phylogenetic analysis [8]. In recent years, phylogenetic analysis has become one of the main components of epidemiological surveillance, which is used to determine the relationship and evolution of influenza viruses [9].…”

Section: Introductionmentioning

confidence: 99%

The selection pressure on the neuraminidase gene of influenza viruses isolated in Ukraine from 2009 to 2015

Бабій

Лейбенко

Radchenko

et al. 2019

Microbiology Independent Research Journal (MIR Journal)

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A broad range of naturally occurring antigenic variants of the influenza virus is caused by its rapid evolutionary variability. The survival of viable influenza virus variants occurs through natural selection. The treatment of influenza infection with modern antiviral drugs-neuraminidase (NA) inhibitors-leads to the occurrence of mutations in the NA gene, which thereby result in the emergence of virus resistance to these drugs. The goal of this study was to determine the selection pressure on the NA protein of influenza viruses isolated in Ukraine from 2009 to 2015. The main method for assessing the selection pressure on proteins is to quantify the ratio of substitution rates at nonsynonymous (dN) and synonymous (dS) sites. With the help of this method, we showed that only a few codons in the NA gene were under positive selection resulting in mutations at the following sites: for influenza A viruses of the A(H1N1)pdm09 subtype-site 40, for viruses of the A(H3N2) subtype-sites 93 and 402, for Influenza B viruses of the B/Yamagata lineage-sites 74, 99, and 268, and for the viruses of the B/Victoria lineage-sites 358, 288, and 455. These sites are not associated with the NA active site, transmembrane domain, or the antigenic sites of this protein. We concluded that NA inhibitors are not a significant factor in the process of selection of the influenza viruses in Ukraine because the sites associated with the resistance of influenza viruses to NA inhibitors were not affected by positive selection. This finding could be explained by the limited use of NA inhibitors for the treatment of influenza infections in Ukraine.

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Predicting the Evolutionary Variability of the Influenza A Virus

Cited by 7 publications

References 39 publications

The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses

The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses

Influenza passaging annotations: what they tell us and why we should listen

The selection pressure on the neuraminidase gene of influenza viruses isolated in Ukraine from 2009 to 2015

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