Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
Department of Pathology, Faculty of Medicine, Ramathibodhi Hospital, Mahidol University, Bangkok, Thailand.
PLoS One. 2015 Apr 13;10(4):e0122812. doi: 10.1371/journal.pone.0122812. eCollection 2015.
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.
流感病毒（IFV）能够快速进化，导致基因漂移和转变，从而引发人类和动物的流感疫情和大流行。导致 2009 年甲型 H1N1 流感大流行的基因转变源自禽、猪和人流感病毒的三重基因重组。基因漂移中较小的遗传改变可能导致流感药物耐药性，如与奥司他韦耐药相关的 H274Y 突变。因此，快速检测 IFV 突变和新的毒力菌株出现的工具可以更好地为季节性流感爆发以及潜在的大流行做好准备。此外，通过仔细检查 IFV 序列中的单核苷酸多态性（SNP）来确定特定的突变，对于鉴定与潜在危险 IFV 表型相关的潜在遗传标记至关重要。在这项研究中，我们开发了一种名为“SNPer”的新型 R 库，用于分析 IFV 亚群中 SNP 的定量变异。计算 SNPer 程序应用于已发表的 IFV 基因组信息的三个不同亚群。SNPer 查询 SNP 数据，并将 SNP 分为（1）通用 SNP，（2）可能常见的 SNP，和（3）独特的 SNP。与手动可视化相比，SNPer 在时间和劳动力方面表现更优。与手动可视化相比，SNPer 在 SNP 比较事件中只需要三秒钟，没有错误，而手动可视化则需要 40 小时，并且存在错误。SNPer 工具可以加快捕获新的和潜在危险的 IFV 菌株的能力，以减轻未来的流感爆发。
