Recherche immunitaire
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Genotyping of Mumps viruses based on SH gene: Develop-ment of a server using alignment-free and alignment-based methods

Pandurang S Kolekar, Mohan M Kale, Urmila Kulkarni-Kale

Background
Mumps is an acute infectious childhood disease caused by mumps virus (MuV), a member of genus Rubu-lavirus, family Paramyxoviridae. Based on the genetic variability in small hydrophobic (SH) genes, cur-rently MuVs have been divided into twelve confirmed genotypes designated as A-L and one proposed genotype, M. Despite successful vaccination program, a few genotypes are observed to co-circulate amongst vaccinated population. Furthermore, lack of cross protection between different genotypes is re-ported and hence, as a part of epidemiological surveillance, WHO has recommended genotyping of MuV. Currently genotyping is carried out using molecular phylogeny analysis (MPA) of SH genes and no geno-typing server is available for MuV. The present study reports development of a genotyping server for the same, which employs three independent methods. The server uses two conventional methods viz., BLAST, MPA and a novel method based on Return Time Distribution (RTD), which is developed in-house.
Results
A server for genotyping of mumps virus is developed and made available at http://bioinfo.net.in/muv/homepage.html. RTD-based alignment-free method was initially developed for MPA and is applied for genotyping of MuV for the first time. It is found to have 98.95% of accuracy when measured using leave-one-out cross validation method on reference and test datasets. In addition to RTD, the server also imple-ments BLAST and MPA for genotyping of MuV. All the three methods were found to be highly reliable as evident from consensus predictions.
Conclusions
A server for genotyping of MuV, which implements sequence-based bioinformatics approaches is devel-oped and validated using SH gene sequences of known genotypes. This server will be useful for epidemiol-ogical surveillance and to monitor the circulation of MuV genotypes within and across geographic areas. This will also facilitate phylodynamics studies of mumps viruses.