CAPS genomic subtyping on orthomyxoviridae

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


研究成果: Conference contribution同行評審


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.

主出版物標題Emerging Intelligent Computing Technology and Applications - 5th International Conference on Intelligent Computing, ICIC 2009, Proceedings
出版狀態Published - 2009
事件5th International Conference on Intelligent Computing, ICIC 2009 - Ulsan, Korea, Republic of
持續時間: 16 9月 200919 9月 2009


名字Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
5754 LNCS


Conference5th International Conference on Intelligent Computing, ICIC 2009
國家/地區Korea, Republic of


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