Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus

Xia, Zhen; Jin, Gulei; Zhu, Jun; Zhou, Ruhong

doi:10.1093/bioinformatics/btp423

Cited by 36 publications

(43 citation statements)

References 42 publications

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“…We demonstrated that the informatics framework PREDAC we developed can effectively infer antigenic clusters from HA sequences, and thus can provide a very important tool in the influenza surveillance and vaccine strain recommendation when coupled with large-scale HA sequencing. Previously, many computational approaches were designed to either predict antigenic variants 18,[30][31][32][33][34][35][36] or to model evolutionary patterns for the H3N2 virus [19][20][21]23,24 . In our study, the prediction of antigenic variants and the modeling of antigenic evolutionary patterns are integrated into one computational framework, PREDAC.…”

Section: Discussionmentioning

confidence: 99%

Mapping of H3N2 influenza antigenic evolution in China reveals a strategy for vaccine strain recommendation

et al. 2012

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one of the primary efforts in influenza vaccine strain recommendation is to monitor through gene sequencing the viral surface protein haemagglutinin (HA) variants that lead to viral antigenic changes. Here we have developed a computational method, denoted as PREDAC, to predict antigenic clusters of influenza A (H3n2) viruses with high accuracy from viral HA sequences. Application of PREDAC to large-scale HA sequence data of H3n2 viruses isolated from diverse regions of mainland China identified 17 antigenic clusters that have dominated for at least one season between 1968 and 2010. By tracking the dynamics of the dominant antigenic clusters, we not only find that dominant antigenic clusters change more frequently in China than in the united states/Europe, but also characterize the antigenic patterns of seasonal H3n2 viruses within China. Furthermore, we demonstrate that the coupling of large-scale HA sequencing with PREDAC can significantly improve vaccine strain recommendation for China.

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Section: Discussionmentioning

confidence: 99%

Mapping of H3N2 influenza antigenic evolution in China reveals a strategy for vaccine strain recommendation

et al. 2012

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“…The use of the MI has already been applied to study the genetic drift of influenza A/H3N2 virus [28]. The MI concept is useful when analyzing symbolic RNA or DNA sequences.…”

Section: Introductionmentioning

confidence: 99%

Flow of Information during an Evolutionary Process: The Case of Influenza A Viruses

Serrano-Solis¹,

José²

2013

Entropy

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Abstract:The hypothesis that Mutual Information (MI) dendrograms of influenza A viruses reflect informational groups generated during viral evolutionary processes is put forward. Phylogenetic reconstructions are used for guidance and validation of MI dendrograms. It is found that MI profiles display an oscillatory behavior for each of the eight RNA segments of influenza A. It is shown that dendrograms of MI values of geographically and historically different segments coming from strains of RNA virus influenza A turned out to be unexpectedly similar to the clusters, but not with the topology of the phylogenetic trees. No matter how diverse the RNA sequences are, MI dendrograms crisply discern actual viral subtypes together with gain and/or losses of information that occur during viral evolution. The amount of information during a century of evolution of RNA segments of influenza A is measured in terms of bits of information for both human and avian strains. Overall the amount of information of segments of pandemic strains oscillates during viral evolution. To our knowledge this is the first description of clades of information of the viral subtypes and the estimation of the flow content of information, measured in bits, during an evolutionary process of a virus.

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“…With entropy, a simple informational index was proposed in [17] to reveal the patterns of synonymous codon usage bias. Further, mutual information was utilized in the construction of site transition network based on 4064 HA1 of A/H3N1 sequences from 1968 to 2008, which was able to model the evolutionary path of the influenza virus and to predict seven possible HA mutations for the next antigenic drift in the 2009-2010 season [18]. Recently, entropy and mutual information were also applied to indentify critical positions and co-mutated positions on HA for predicting the antigenic variants [19].…”

Section: Introductionmentioning

confidence: 99%

Correlated mutations in the four influenza proteins essential for viral RNA synthesis, host adaptation, and virulence: NP, PA, PB1, and PB2

Hu¹

2010

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The NP, PA, PB1, and PB2 proteins of influenza viruses together are responsible for the transcription and replication of viral RNA, and the latter three proteins comprise the viral polymerase. Two recent reports indicated that the mutation at site 627 of PB2 plays a key role in host range and increased virulence of influenza viruses, and could be compensated by multiple mutations at other sites of PB2, suggesting the association of this mutation with those at other sites. The objective of this study was to analyze the co-mutated sites within and between these important proteins of influenza. With mutual information, a set of statistically significant comutated position pairs (P value = 0) in NP, PA, PB1, and PB2 of avian, human, pandemic 2009 H1N1, and swine influenza were identified, based on which several highly connected networks of correlated sites in NP, PA, PB1, and PB2 were discovered. These correlation networks further illustrated the inner functional dependence of the four proteins that are critical for host adaptation and pathogenicity. Mutual information was also applied to quantify the correlation of sites within each individual protein and between proteins. In general, the inter protein correlation of the four proteins was stronger than the intra protein correlation. Finally, the correlation patterns of the four proteins of pandemic 2009 H1N1 were found to be closer to those of avian and human than to swine influenza, thus rendering a novel insight into the interaction of the four proteins of the pandemic 2009 H1N1 virus when compared to avian, human, and swine influenza and how the origin of these four proteins might affect the correlation patterns uncovered in this analysis.

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Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus

Abstract: All code and data are available at http://ibi.zju.edu.cn/birdflu/.

Cited by 36 publications

References 42 publications

Mapping of H3N2 influenza antigenic evolution in China reveals a strategy for vaccine strain recommendation

Mapping of H3N2 influenza antigenic evolution in China reveals a strategy for vaccine strain recommendation

Flow of Information during an Evolutionary Process: The Case of Influenza A Viruses

Correlated mutations in the four influenza proteins essential for viral RNA synthesis, host adaptation, and virulence: NP, PA, PB1, and PB2

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