Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach.

Nabil Abid,Giovanni Chillemi,Marco Salemi

doi:10.3390/genes11010028

Abstract

Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.

Highlights

IntroductionRotavirus A (RVA) is a double-stranded RNA (dsRNA) virus of the Reoviridae family
Rotavirus A (RVA) is a double-stranded RNA virus of the Reoviridae family.It is a significant cause of childhood gastroenteritis and accounts for ≈450,000 deaths annually, most occurring in developing countries [1]
The substitutional process underlying the evolution of RVA genes seems to be similar, following the General Time-Reversible (GTR) model with invariant sites (I) and with Gamma-distributed among site rate variation (G) based upon the results of Bayesian information criterion (BIC) scores as implemented in PartitionFinder

Summary

Introduction

Rotavirus A (RVA) is a double-stranded RNA (dsRNA) virus of the Reoviridae family It is a significant cause of childhood gastroenteritis and accounts for ≈450,000 deaths annually, most occurring in developing countries [1]. Studies have revealed numerous distinct genotypes of RVs; some are found throughout the world while others seem to remain regional, and yet others can be seen to emerge, disappear, only to re-emerge later [7,8]. According to this classification, two virus genogroups

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