Kolekar Pandurang S, Waman Vaishali P, Kale Mohan M, Kulkarni-Kale Urmila
Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, 411 007, India.
Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune, 411 007, India.
PLoS One. 2016 Feb 12;11(2):e0149350. doi: 10.1371/journal.pone.0149350. eCollection 2016.
Rhinoviruses (RV) are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus Enterovirus and family Picornaviridae. There are three species of RV (RV-A, -B and -C), with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of Rhinoviruses is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on "return time distribution" (RTD) of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2) to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at http://bioinfo.net.in/RV-Typer/home.html.
越来越多的报告显示，鼻病毒（RV）可引起人类从轻度到重度的呼吸道感染。鼻病毒在抗原性上是肠道病毒属和小核糖核酸病毒科中最多样化的物种。鼻病毒有三个种（RV - A、 - B和 - C），分别有80、32和55个血清型/类型。抗原变异是开发针对鼻病毒的交叉保护疫苗的主要限制因素。鼻病毒的血清分型是在细胞培养中使用交叉中和试验进行的。然而，对于大量菌株来说，这些试验既费力又耗时。另外，鼻病毒的血清分型是通过对VP1的蛋白质和核苷酸序列进行基于比对的系统发育分析来进行的。然而，基于比对的系统发育分析进行鼻病毒血清分型是一个多步骤过程，每次对新分离株进行测序时都需要重复。鉴于对鼻病毒血清分型的需求不断增加，一种基于VP1蛋白中氨基酸残基“返回时间分布”（RTD）的无比对方法已经开发出来，并以名为RV - Typer的网络服务器形式实现。RV - Typer接受核苷酸或蛋白质序列作为输入，并计算二肽（k = 2）的返回时间以指定血清型。RV - Typer的灵敏度和特异性均为100%。它比基于比对的方法快得多。该网络服务器可在http://bioinfo.net.in/RV - Typer/home.html上获取。
