Abstract
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.
Highlights
Rhinoviruses (RV) are the most frequently infecting human pathogens causing common cold infections
The RV belong to the genus Enterovirus of the family Picornaviridae and there are three species such as RV-A, -B and -C
In order to assess the performance of web server, true positive (TP) and negative (TN) data sets were compiled such that there is no overlap with the reference data set
Summary
Rhinoviruses (RV) are the most frequently infecting human pathogens causing common cold infections. RV are the principle agents of acute respiratory tract illness and are increasingly being associated with more severe diseases such as acute otitis media, pneumonia, recurrent whizzing, asthma and bronchiolitis [1,2,3]. The RV belong to the genus Enterovirus of the family Picornaviridae and there are three species such as RV-A, -B and -C. They are small, non-enveloped, single-stranded RNA viruses containing a copy of positive sense genome (~7200 nt). RV-C is known to cause majority of asthma attacks in children, as compared to RV-A and -B [3]. RV-C has become a PLOS ONE | DOI:10.1371/journal.pone.0149350 February 12, 2016
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