Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses

Perovic, Vladimir

doi:10.1007/s10910-013-0212-1

Cited by 11 publications

(11 citation statements)

References 43 publications

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“…Effect of ADE varies according the Ebola virus species (Takada et al, 2003 ) indicating that properties of GP1 which correspond to information represented by the IS frequency F (0.338) may also differ between species. In order to analyze this variation we performed the ISM-based phylogenetic analysis of all non-redundant sequences of GP1 in GenBank and UniProt databases of Ebola viruses collected between 1976 and 2014 (Data Sheet 1 ) as described before (Perovic, 2013 ; Perovic et al, 2013 ). The amplitude at the frequency F (0.338) as an parameter in the ISM-based phylogenetic analysis was used (Perovic et al, 2013 ) (Figure 5 ).…”

Section: Resultsmentioning

confidence: 99%

In silico analysis suggests interaction between Ebola virus and the extracellular matrix

et al. 2015

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The worst Ebola virus (EV) outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trend lines in this crisis are grave, and now represents a global public health threat concern. Limited therapeutic and/or prophylactic options are available for people suffering from Ebola virus disease (EVD) and further complicate the situation. Previous studies suggested that the EV glycoprotein (GP) is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM), a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM) was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs) are involved in interaction between GP and ECM. This finding could contribute to a better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.

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Section: Resultsmentioning

confidence: 99%

In silico analysis suggests interaction between Ebola virus and the extracellular matrix

et al. 2015

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“…This algorithm was previously described in detail 5 (for access to ISTRE we refer the reader to http://istree.bioprotection.org). Here, we used the ISM distance measure d defined on the specific frequency F = 0.299.…”

Section: Methodsmentioning

confidence: 99%

Prediction of influenza vaccine effectiveness for the influenza season 2017/18 in the US

Paessler

Veljković

2017

F1000Res

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Vaccination against seasonal influenza viruses is the most effective way to prevent infection. A key factor in the effectiveness of the seasonal influenza vaccine is its immunological compatibility with the circulating viruses during the season. The high evolutionary rate, antigenic shift and antigenic drift of influenza viruses, represents the main obstacle for correct prediction of the vaccine effectiveness for an upcoming flu season. Conventional structural and phylogenetic approaches for assessment of vaccine effectiveness have had a limited success in prediction of vaccine efficacy in the past. Recently, a novel bioinformatics approach for assessment of effectiveness of seasonal influenza vaccine was proposed. Here, this approach was used for prediction of the vaccine effectiveness for the influenza season 2017/18 in US.

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“…We used ISM-based phylogenetic algorithm ISTREE [8,9] to analyze hemagglutinin subunit 1 (HA1) from H1N1 SIV (for access to ISTREE, we refer the reader to http://istree.bioprotection.org). Using ISM distance measure d 2 defined as the ratio of specific frequencies correlating with human and swine propensity of H1N1 AIV [5], we generate phylogenetic tree by the following algorithm:…”

Section: Methodsmentioning

confidence: 99%

Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China

Veljković

Paessler

et al. 2016

PLoS ONE

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Influenza A virus (IAV) subtypes against which little or no pre-existing immunity exists in humans represent a serious threat to global public health. Monitoring of IAV in animal hosts is essential for early and rapid detection of potential pandemic IAV strains to prevent their spread. Recently, the increased pandemic potential of the avian-like swine H1N1 IAV A/swine/Guangdong/104/2013 has been suggested. The virus is infectious in humans and the general population seems to lack neutralizing antibodies against this virus. Here we present an in silico analysis that shows a strong human propensity of this swine virus further confirming its pandemic potential. We suggest mutations which would further enhance its human propensity. We also propose conserved antigenic determinants which could serve as a component of a prepandemic vaccine. The bioinformatics tool, which can be used to further monitor the evolution of swine influenza viruses towards a pandemic virus, are described here and are made publically available (http://www.vin.bg.ac.rs/180/tools/iav_mon.php; http://www.biomedprotection.com/iav_mon.php).

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Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses

Cited by 11 publications

References 43 publications

In silico analysis suggests interaction between Ebola virus and the extracellular matrix

In silico analysis suggests interaction between Ebola virus and the extracellular matrix

Prediction of influenza vaccine effectiveness for the influenza season 2017/18 in the US

Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China

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