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Open Access Highly Accessed Research

A mobile genetic element with unknown function found in distantly related viruses

Torstein Tengs1*, Anja Bråthen Kristoffersen1, Tsvetan R Bachvaroff2 and Christine Monceyron Jonassen1

Author Affiliations

1 National Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway

2 Institute for Marine and Environmental Technology, 701 E. Pratt St, Baltimore, MD 21202, USA

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Virology Journal 2013, 10:132  doi:10.1186/1743-422X-10-132

Published: 25 April 2013

Abstract

Background

The genetic element s2m seems to represent one of very few examples of mobile genetic elements in viruses. The function remains obscure and a scattered taxonomical distribution has been reported by numerous groups.

Methods

We have searched GenBank in order to identify all viral accessions that have s2m(−like) sequence motifs. Rigorous phylogenetic analyses and constrained tree topology testing were also performed in order to investigate the apparently mobile nature of s2m.

Results

The stem-loop s2m structure can be found in four families of + ssRNA viruses; Astroviridae, Caliciviridae, Picornaviridae and Coronaviridae. In all of these virus families, with the possible exception of Caliciviridae, multiple gains and/or losses of s2m would have to be postulated in order to explain the distribution of this character.

Conclusions

s2m appears to be a mobile genetic element with a unique evolutionary history in all of the four virus families where it can be found. Based on our findings and a review of the current literature on s2m, a hypothesis implying an RNAi-like function for the s2m element is also outlined.

Keywords:
Astroviruses; Caliciviruses; Picornaviruses; Coronaviruses; Mobile genetic element; s2m