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

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.

Full Genome Sequencing of Corriparta Virus, Identifies California Mosquito Pool Virus as a Member of the Corriparta virus Species

“…Currently there are also 15 ‘unclassified’ orbiviruses in the genus, which may represent additional species [1]–[6]. The orbivirus genome is composed of 10 segments of linear dsRNA, packaged as one copy of each segment within each of the non-enveloped icosahedral virus particles.…”

Confirmation of Elsey virus infection in a Queensland horse with mild neurologic signs

“…The genome segments coding for the virus core and/or the nonstructural proteins can be used as targets for serogroup (virus species)-specific, reverse transcription (RT)-PCR-based assays. 2,13 In 2011, a 2-year-old horse in northern Queensland, Australia, was showing very mild neurologic signs. The ethylenediamine tetra-acetic acid (EDTA) blood sample collected was submitted to Biosecurity Queensland for a disease investigation.…”

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011

“…Cucumis sativus L., North-European Cucumber, sequence accession FI132140-FI136208, GS765762-GS766880, GS815969-GS874855 [122] Ricinus communis Castor bean organelle genome, sequence accession JF937588(chloroplast), HQ874649 (mitochondria) [123] Stretch Lagoon Orbivirus Umatilla, sequence accession HQ842619 through HQ842628 [124] Gadus morhua Atlantic cod, sequence accession CAEA01000001 through CAEA01554869 [125] Solanum tuberosum L. Potato, sequence accession GS025503 through GS026177 [126] ΦCA82, sequence accession HQ264138 [127] Paramecium caudatumreveals mitochondria, sequence accession NC001324 [128] bacteriophage IME08, sequence accession NC_014260 [129] virus (ILTV), sequence accession HQ_630064 [130] Macropus eugenii Australian kangaroo, sequence accession ABQO000000000 [131] Aichi virus, sequence accession FJ890523 [132] "Candidatus Tremblaya princeps" Strain PCVAL, sequence accession CP002918 [133] an isolate from human gastric mucosa . …”