Predicting interspecies transmission of avian influenza virus based on wavelet packet decomposition

Using wavelet packet decomposition, the energy coefficients in the fifth level of viral protein sequences were achieved to predict interspecies transmission. Since avian-origin influenza viruses could have high sequence similarities with human-origin avian influenza virus and could have the phenotype of interspecies transmission, viral data should be filtered to prevent the misconduct of feature selection and false performance of predicting models. Considering the balance of data size, the empirical cut-off value 97% was used to screen avian-origin influenza virus with high sequence similarity. The excellent performances of cross validation show that the SVM model has the best capability of predicting transmission and evaluating the contribution of five amino acid factors. The robust model was finally used to evaluate the filtered data of avian-origin virus and the results confirmed that double check for ambiguous phenotype of avian-origin virus with high sequence similarity was necessary and part of them have the ability to across species barriers.

[1]  Y. Guan,et al.  Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia , 2004, Nature.

[2]  Henry Han,et al.  Derivative component analysis for mass spectral serum proteomic profiles , 2014, BMC Medical Genomics.

[3]  Ian A. Wilson,et al.  A Single Amino Acid Substitution in 1918 Influenza Virus Hemagglutinin Changes Receptor Binding Specificity , 2005, Journal of Virology.

[4]  Zheng Kou,et al.  Prediction of interspecies transmission for avian influenza A virus based on a back-propagation neural network , 2010, Math. Comput. Model..

[5]  N. Cox,et al.  Genetic characterization of the pathogenic influenza A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks in Hong Kong. , 1999, Virology.

[6]  Marion Koopmans,et al.  Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Y. Guan,et al.  Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[8]  N. Cox,et al.  Characterization of an avian influenza A (H5N1) virus isolated from a child with a fatal respiratory illness. , 1998, Science.

[9]  Zehui Shao,et al.  On the Maximum ABC Index of Graphs With Prescribed Size and Without Pendent Vertices , 2018, IEEE Access.

[10]  Xuequn Shang,et al.  An efficient algorithm to identify the optimal one-bit perturbation based on the basin-of-state size of Boolean networks , 2016, Scientific reports.

[11]  Hongjie Yu,et al.  Lethal avian influenza A (H5N1) infection in a pregnant woman in Anhui Province, China. , 2006, The New England journal of medicine.

[12]  Pietro Liò,et al.  Wavelets in bioinformatics and computational biology: state of art and perspectives , 2003, Bioinform..

[13]  R. Webster,et al.  Evolution and ecology of influenza A viruses. , 1992, Current topics in microbiology and immunology.

[14]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[15]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[16]  Jie Dong,et al.  Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus. , 2018 .

[17]  Tin Wee Tan,et al.  Predicting host tropism of influenza A virus proteins using random forest , 2014, BMC Medical Genomics.

[18]  M. Peiris,et al.  Human infection with influenza H9N2 , 1999, The Lancet.

[19]  Theo M Bestebroer,et al.  Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets , 2012, Science.

[20]  W. Atchley,et al.  Solving the protein sequence metric problem. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[21]  He He,et al.  A confirmed severe case of human infection with avian-origin influenza H7N9: A case report , 2014, Experimental and therapeutic medicine.

[22]  Yi Guan,et al.  Human Infection with an Avian H9N2 Influenza A Virus in Hong Kong in 2003 , 2005, Journal of Clinical Microbiology.

[23]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[24]  R. Webster,et al.  Human influenza A H5N1 virus related to a highly pathogenic avian influenza virus , 1998, The Lancet.

[25]  Wei Wang,et al.  Fatal infection with influenza A (H5N1) virus in China. , 2006, The New England journal of medicine.

[26]  Wenbin Liu,et al.  Signaling pathway impact analysis by incorporating the importance and specificity of genes (SPIA-IS) , 2017, Comput. Biol. Chem..

[27]  Gabriele Neumann,et al.  Experimental adaptation of an influenza H5 haemagglutinin (HA) confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets , 2012, Nature.

[28]  Baoping Yan,et al.  Characterization of H5N1 Influenza Viruses Isolated from Migratory Birds in Qinghai Province of China in 2006 , 2007, Avian diseases.

[29]  Zheng Kou,et al.  Using amino acid factor scores to predict avian-to-human transmission of avian influenza viruses: a machine learning study. , 2013, Protein and peptide letters.

[30]  Zheng Kou,et al.  Molecular patterns of avian influenza A viruses , 2008 .