期刊
BMC BIOINFORMATICS
卷 23, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s12859-022-04885-7
关键词
Influenza A virus; Host specificity; Amino acid signatures; Adjusted entropy
In this study, we propose an improved entropy-based method for identifying host-specific signatures using a similarity coefficient. Validation with H5N1 PB2 sequences shows that the adjusted entropy has a lower false negative rate compared to unadjusted entropy. Simulations across different levels of sequence divergence demonstrate that adjusted entropy has lower false negative and false positive rates. Additionally, adjusted entropy successfully identifies important mutations in H1N1pdm PB2.
Background Influenza A viruses (IAV) exhibit vast genetic mutability and have great zoonotic potential to infect avian and mammalian hosts and are known to be responsible for a number of pandemics. A key computational issue in influenza prevention and control is the identification of molecular signatures with cross-species transmission potential. We propose an adjusted entropy-based host-specific signature identification method that uses a similarity coefficient to incorporate the amino acid substitution information and improve the identification performance. Mutations in the polymerase genes (e.g., PB2) are known to play a major role in avian influenza virus adaptation to mammalian hosts. We thus focus on the analysis of PB2 protein sequences and identify host specific PB2 amino acid signatures. Results Validation with a set of H5N1 PB2 sequences from 1996 to 2006 results in adjusted entropy having a 40% false negative discovery rate compared to a 60% false negative rate using unadjusted entropy. Simulations across different levels of sequence divergence show a false negative rate of no higher than 10% while unadjusted entropy ranged from 9 to 100%. In addition, under all levels of divergence adjusted entropy never had a false positive rate higher than 9%. Adjusted entropy also identifies important mutations in H1N1pdm PB2 previously identified in the literature that explain changes in divergence between 2008 and 2009 which unadjusted entropy could not identify. Conclusions Based on these results, adjusted entropy provides a reliable and widely applicable host signature identification approach useful for IAV monitoring and vaccine development.
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