CAPS genomic subtyping on orthomyxoviridae

Sheng Lung Peng*, Yu Wei Tsay, Chih-Sheng Lin, Chuan Yi Tang

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

The Orthomyxoviridae is a family of single strained RNA viruses including five genera: Influenza virus A, Influenza virus B, Influenza virus C, Thogotovirus, and Isavirus. Usually, Influenza viruses are identified by antigenic differences in their nucleoprotein and matrix protein. In this paper, we propose an algorithm to determine a set of suitable restriction enzymes for producing recognizable restriction maps on Orthomyxoviridae. Our method is applied to viral strains of highly pathogenic avian influenza (HPAI), containing potentially homozygous, heterozygous, and various genetic variations. In the analysis of CAPS (Cleaved Amplified Polymorphic Sequence) subtyping, our method outperforms the RNA coding of representative and epidemiologically significant human wild-type viruses, including H3N8, H5N1, H5N9, H7N1, H7N7, and H9N2. These isolates are analyzed by CAPS with enzymes AgeI, EciI, KpnI, and XbaI. The HPAI strains show a different RFLP (Restriction Fragment Length Polymorphism) profile by comparing with other low pathogenic avian influenza (LPAI) strains. We provide a rapid, specific, and reproducible identification of the genotypes on Orthomyxoviridae. It permits us to quickly confirm subtypes of Orthomyxoviridae.

Original languageEnglish
Title of host publicationEmerging Intelligent Computing Technology and Applications - 5th International Conference on Intelligent Computing, ICIC 2009, Proceedings
Pages130-137
Number of pages8
DOIs
StatePublished - 2 Nov 2009
Event5th International Conference on Intelligent Computing, ICIC 2009 - Ulsan, Korea, Republic of
Duration: 16 Sep 200919 Sep 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5754 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference5th International Conference on Intelligent Computing, ICIC 2009
Country/TerritoryKorea, Republic of
CityUlsan
Period16/09/0919/09/09

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