RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach

PLoS One. 2016 Feb 12;11(2):e0149350. doi: 10.1371/journal.pone.0149350. eCollection 2016.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Capsid Proteins / genetics
  • Genes, Viral
  • Humans
  • Internet
  • Phylogeny*
  • Picornaviridae Infections / virology*
  • Rhinovirus / classification*
  • Rhinovirus / genetics*
  • Serotyping / methods*
  • Software

Substances

  • Capsid Proteins

Grants and funding

This work was supported under the Centre of Excellence (COE) Grant by the DBT, Government of India to the Bioinformatics Centre, Savitribai Phule Pune University, Pune (India). PSK acknowledges the BioInformatics National Certification (BINC) fellowship awarded by the Department of Biotechnology (DBT), Government of India. VPW acknowledges DBT fellowship. UKK acknowledges the Centre of Excellence (COE) Grant by the DBT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.