Abstract
Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype cause HPAI. Therefore, sensitive and accurate subtyping of AIV is important to prepare and prevent for the spread of HPAI. Next-generation sequencing (NGS) can analyze the full-length sequence information of entire AIV genome at once, so this technology is becoming a more common in detecting AIVs and predicting subtypes. However, an analysis pipeline of NGS-based AIV sequencing data, including AIV subtyping, has not yet been established. Here, in order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end users.
Highlights
The avian influenza virus (AIV) genome comprises eight segments that encoded up to 11 proteins [1]
Most of them are of low pathogenicity and cause mild infections in birds, some AIV combinations including HA H5 and H7 cause highly pathogenic avian influenza (HPAI), which is characterized by high morbidity and mortality [3,4]
We introduce the prediction of avian influenza virus subtype (PAIVS) which is a user-friendly tool with multiple functions that support the pre-processing of Next-generation sequencing (NGS) data, reference-guided AIV subtyping, de novo assembly, variant calling, and identifying the closest full-length sequences by BLAST and provide the graphical summary to the end users
Summary
The avian influenza virus (AIV) genome comprises eight segments (polymerase basic 2, polymerase basic 1, polymerase acidic, hemagglutinin [HA], nucleoprotein, neuraminidase [NA], matrix, nonstructural) that encoded up to 11 proteins [1]. In contrast to these methods, NGS can analyze the full-length sequence information of all eight AIV segments at once, so it can identify subtypes sensitively and accurately. We developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS), to support the pre-processing of NGS data and its interpretation.
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