Abstract
BackgroundThe pandemic threat of influenza has attracted great attention worldwide. To assist public health decision-makers, new suites of tools are needed to rapidly process and combine viral information retrieved from public-domain databases for a better risk assessment.ResultsUsing our recently developed FluConvert and IniFlu software, we automatically processed and rearranged sequence data by standard viral nomenclature, determined the group-related consensus sequences, and identified group-specific polygenic signatures. The software possesses powerful ability to integrate viral, clinical, and epidemiological data. We demonstrated that both multiple basic amino acids at the cleavage site of the HA gene and also at least 11 more evidence-based viral amino acid substitutions present in global highly pathogenic avian influenza H5N2 viruses during the years 2009–2016 that are associated with viral virulence and human infection.ConclusionsFluConvert and IniFlu are useful to monitor and assess all subtypes of influenza viruses with pandemic potential. These programs are implemented through command-line and user-friendly graphical interfaces, and identify molecular signatures with virological, epidemiological and clinical significance. FluConvert and IniFlu are available at https://apps.flutures.com or https://github.com/chinrur/FluConvert_IniFlu
Highlights
The pandemic threat of influenza has attracted great attention worldwide
Given the fact that multiple mutations across gene segments of influenza viruses can exist and the genomic stability might be influenced by a particular mutation over time [5], new suites of tools are needed to integrate these databases for a better alignment of virological, epidemiological and clinical data in a real-time manner
In addition to these multiple basis amino acid residues in the HA, we demonstrate that several other amino acid substitutions across different gene segments of H5N2 avian influenza viruses could be associated with the viral virulence and mammalian infections based on IniFlu-generated polygenic highly pathogenic avian influenza (HPAI) consensus signature
Summary
To assist public health decision-makers, new suites of tools are needed to rapidly process and combine viral information retrieved from public-domain databases for a better risk assessment. Thereafter, the re-emergence of highly pathogenic avian influenza (HPAI) A H5Ny subtypes that cause widespread infections in poultry farms and in wild birds since 2003 has greatly attracted public health attention. Understanding the viral factors which determine the pathogenicity of H5 AIV by timely integration of virological, immunological and epidemiological information will be helpful to establish effective prevention and control measures to minimize future pandemic threats. The immediate release of the genetic sequences of influenza A viruses combined with collections of tools established for analyzing all types and subtypes of influenza viral sequences have greatly advanced our understanding of the evolution of circulating viruses and their potential risk to animal and human health [4]. Given the fact that multiple mutations across gene segments of influenza viruses can exist and the genomic stability might be influenced by a particular mutation over time [5], new suites of tools are needed to integrate these databases for a better alignment of virological, epidemiological and clinical data in a real-time manner
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