Genomics Inform.
2020 Mar;18(1):e5. 10.5808/GI.2020.18.1.e5.
PAIVS: prediction of avian influenza virus subtype
- Affiliations
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- 1Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- 2Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- 3Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- 4Chungbuk Veterinary Service Laboratory, Chungju 27336, Korea
- 5Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- 6Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- KMID: 2501325
- DOI: http://doi.org/10.5808/GI.2020.18.1.e5
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.
