Whole genome sequencing strategies and development of orbivirus sequence database: Implications for novel dsRNA virus detection

The genus Orbivirus is the largest of the genera within the family Reoviridae, containing 22 recognised virus species as well as 15 unclassified ‘orbiviruses’, which could potentially represent further new species. The orbiviruses are transmitted by both ticks and/or haematophagous insect vectors. They have a wide host range that includes domestic and wild ruminants, equines, marsupials, sloths, bats, birds and humans. Low-level serological cross-reactions between different species of orbiviruses and lack of reference strains/antisera for existing Orbivirus species make serological identification of new virus isolates difficult. Recently, whole genome sequence data (WGS) has become an important tool for the detection, classification and epidemiological investigations of different pathogens. This study presents full genome sequence database of all known 22 Orbivirus species (including 5 unclassified viruses). Development of novel sequencing strategies and phylogenetic analysis of the orbiviruses using this database has identified five novel Orbivirus species and has facilitated development of a pan-orbivirus RT-PCR assay that can be used to identify the RNA of any Orbivirus species. These techniques will support Orbivirus discovery with greater accuracy than before and can be used for definitive diagnosis of suspected Orbivirus infection.