title: SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations.
abstract: Influenza virus (IFV) can evolve rapidly leading to genetic drifts and shifts resulting in human and animal influenza epidemics and pandemics. The genetic shift that gave rise to the 2009 influenza A/H1N1 pandemic originated from a triple gene reassortment of avian, swine and human IFVs. More minor genetic alterations in genetic drift can lead to influenza drug resistance such as the H274Y mutation associated with oseltamivir resistance. Hence, a rapid tool to detect IFV mutations and the potential emergence of new virulent strains can better prepare us for seasonal influenza outbreaks as well as potential pandemics. Furthermore, identification of specific mutations by closely examining single nucleotide polymorphisms (SNPs) in IFV sequences is essential to classify potential genetic markers associated with potentially dangerous IFV phenotypes. In this study, we developed a novel R library called "SNPer" to analyze quantitative variants in SNPs among IFV subpopulations. The computational SNPer program was applied to three different subpopulations of published IFV genomic information. SNPer queried SNPs data and grouped the SNPs into (1) universal SNPs, (2) likely common SNPs, and (3) unique SNPs. SNPer outperformed manual visualization in terms of time and labor. SNPer took only three seconds with no errors in SNP comparison events compared with 40 hours with errors using manual visualization. The SNPer tool can accelerate the capacity to capture new and potentially dangerous IFV strains to mitigate future influenza outbreaks.
authors: Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
authors: Unitsa
authors: U
authors: Sangket
authors: Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
authors: Sukanya
authors: S
authors: Vijasika
authors: Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
authors: Hasnee
authors: H
authors: Noh
authors: Department of Pathology, Faculty of Medicine, Ramathibodhi Hospital, Mahidol University, Bangkok, Thailand.
authors: Wasun
authors: W
authors: Chantratita
authors: Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors: Chonticha
authors: C
authors: Klungthong
authors: Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors: In Kyu
authors: IK
authors: Yoon
authors: Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors: Stefan
authors: S
authors: Fernandez
authors: Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors: Wiriya
authors: W
authors: Rutvisuttinunt
mesh_terms: D000465:Algorithms; D000483:Alleles; D019295:Computational Biology / Q000379:methods*; D015723:Gene Library; D040961:Genetic Drift; D023281:Genomics; D006801:Humans; D007251:Influenza, Human / Q000821:virology*; D009975:Orthomyxoviridae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011381:Programming Languages; D012984:Software