Umatilla Virus Genome Sequencing and Phylogenetic Analysis: Identification of Stretch Lagoon Orbivirus as a New Member of the Umatilla virus Species

Manjunatha N Belaganahalli,Robert Tesh,Narender S Maan,Peter P C Mertens,Houssam Attoui,Sushila Maan,Anthony R Fooks

doi:10.1371/journal.pone.0023605

Manjunatha N Belaganahalli, Robert Tesh + Show 5 more

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https://doi.org/10.1371/journal.pone.0023605

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Abstract

The genus Orbivirus, family Reoviridae, includes 22 species of viruses with genomes composed of ten segments of linear dsRNA that are transmitted between their vertebrate hosts by insects or ticks, or with no identified vectors. Full-genome sequence data are available for representative isolates of the insect borne mammalian orbiviruses (including bluetongue virus), as well as a tick borne avian orbivirus (Great Island virus). However, no sequence data are as yet available for the mosquito borne avian orbiviruses.We report full-length, whole-genome sequence data for Umatilla virus (UMAV), a mosquito borne avian orbivirus from the USA, which belongs to the species Umatilla virus. Comparisons of conserved genome segments 1, 2 and 8 (Seg-1, Seg-2 and Seg-8) - encoding the polymerase-VP1, sub-core ‘T2’ protein and core-surface ‘T13’ protein, respectively, show that UMAV groups with the mosquito transmitted mammalian orbiviruses. The highest levels of sequence identity were detected between UMAV and Stretch Lagoon orbivirus (SLOV) from Australia, showing that they belong to the same virus species (with nt/aa identity of 76.04%/88.07% and 77.96%/95.36% in the polymerase and T2 genes and protein, respectively). The data presented here has assisted in identifying the SLOV as a member of the Umatilla serogroup. This sequence data reported here will also facilitate identification of new isolates, and epidemiological studies of viruses belonging to the species Umatilla virus.

Highlights

The genus Orbivirus is the largest of 15 genera within the family Reoviridae and currently contains 22 recognized virus species, as well as 13 unclassified or ‘unassigned’ viruses, some of which may represent additional species [1,2,3,4,5]
This paper reports full genome sequence-analysis of Umatilla virus (UMAV), isolated from a pool of mosquitoes in North America, and comparisons of its polymerase (Pol), that VP2 (T2)-subcoreprotein, and T13-core-proteins to different orbiviruses, including Stretch Lagoon orbivirus, indicating that UMAV and SLOV both belong to the species Umatilla virus
In contrast BTV, Epizootic haemorrhagic disease virus (EHDV), African horse sickness virus (AHSV), encephalosis virus (EEV) and Peruvian horse sickness virus (PHSV) all show basically similar 3-3-3-1 migration patterns, and PALV show 3-3-4 migration pattern confirming that UMAV belongs to a different species

Summary

Introduction

The genus Orbivirus is the largest of 15 genera within the family Reoviridae and currently contains 22 recognized virus species, as well as 13 unclassified or ‘unassigned’ viruses, some of which may represent additional species [1,2,3,4,5]. Members of the different Orbivirus species that are currently recognised, were initially distinguished by a lack of cross-reaction in serological assays, including agarose gel immunodifusion, complement fixation and (more recently) enzyme linked immunosorbent assays (ELISA)[2]. The components of the virus core-particle and at least two of the non-structural proteins are highly conserved between isolates of the same Orbivirus species, showing high level serological cross-reactions in virus species/serogroup-specific assays. The nucleotide and amino acid sequences of these conserved genes and proteins (Polymerase and T2 protein) show variations that primarily reflect the virus serogroup/species. Within each virus species, they show variations that reflect the geographic origin of the virus isolate (topotype) [6,7,8,9,10]

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