The Bayesian reconstruction and the evolutionary history of Salivirus type 1 and type 2: the worldwide spreading.

Silvia Angeletti,Giancarlo Ceccarelli,Massimo Ciccozzi,Domenico Benvenuto,Boban Mugosa,Ivana Maida,Marta Fogolari,Cecilia De Flora,Riccardo Bazzardi,Stefano Pascarella,Silvia Spoto

doi:10.3855/jidc.12141

Abstract

Salivirus (SalV) represents an emerging problem in public health especially during the recent years. In this study, the Bayesian evolutionary history and the spread of the virus through the different countries have been reported. a database of 81 sequences of SalV structural VP1 fragment were downloaded from GenBank, aligned and manually edited by Bioedit Software. ModelTest v. 3.7 software was used to estimate the simplest evolutionary model fitting the sequence dataset. A Maximum-Likelihood tree has been generated using MEGA-X to test the "clockliness" signal using TempEst 1.5.1. The Bayesian phylogenetic tree was built by BEAST. Homology modelling was performed by SWISS-Model and protein variability evaluated by ConSurf server. the phylogenetic tree showed a clade of SalV A2 and three main clades of SalV A1, revealing several infections in humans in South Korea, India, Tunisia, China, Nigeria, Ethiopia and USA. The Bayesian maximum clade credibility tree and the time of the most common recent ancestor dated back the root of the tree to the year 1788 with the probable origin in USA. Selective pressure analysis revealed two positive selection sites, His at 100th and Leu at 116th positions that at the homology modelling resulted important to guarantee protein stability and variability. This could contribute to the development of new mutations modifying the clinical features of this evolving virus. Bayesian phylogenetic and phylodynamic represented a useful tool to follow the transmission dynamic of SalV and to prevent new epidemics worldwide.

Highlights

Salivirus (SalV) represents an emerging problem in public health especially during the recent years
The Pairwise Homoplasy index (Phi) test did not detect any significant signal of recombination (p-value = 0.104)
In sequences from Nigeria, Ethiopia, Usa, China, Guatemala, Spain and Thailand at the 100th position the presence of Histidine has been found, while in the other sequences the most prevalent amino acid was Arginine. This difference in the 100th position is present in the sanitation-resistant sequence isolated from sewage water in Bangkok (JQ898343.1), in the sequence isolated in the nasal swab of a child in china (KT182636.1) and in the sequences isolated in stool samples from Nigerian children suffering from nonpolio acute flaccid paralysis (AFP) (GQ179640.3, GQ507022.1)

Summary

Introduction

Salivirus (SalV) represents an emerging problem in public health especially during the recent years. Selective pressure analysis revealed two positive selection sites, His at 100th and Leu at 116th positions that at the homology modelling resulted important to guarantee protein stability and variability. This could contribute to the development of new mutations modifying the clinical features of this evolving virus. Conclusions: Bayesian phylogenetic and phylodynamic represented a useful tool to follow the transmission dynamic of SalV and to prevent new epidemics worldwide. Salivirus (SalV), previously named Klassevirus, a non-enveloped single-strand RNA virus with a genome length of 7.4 kb belonging to the Picornaviridae family, was recently described as an emerging problem in public health. SalV as causal agent of acute gastroenteritis was described in 0.2-8.7 % of cases

Methods

Results

Discussion

Conclusion