Within the VDD program the complete or draft genomes of various organisms have been elucidated. The reason for determining the full genome of an organism or isolate could stem from either epidemiology, vaccine development or assist in development of novel diagnostic assays. The majority of the sequencing were done on either the Illumina MiSeq or HiSeq2500 at the ARC-Biotech platform. Full genomes of the following organisms have been determined or is in the process of being completed.
Viruses
The complete genomes of the following veterinary viruses have been sequenced.
African horse sickness virus is an Orbivirus in the family Reoviridae. Its genome consist of ten double-stranded RNA segments (± 19kbp in total).
African swine fever
African swine fever virus is the only known double-stranded DNA arbovirus. Its linear genome consist of about 150 genes (± 190kbp in total).
Avian influenza
Influenza A viruses have a negative-sense, single-stranded, segmented genome. The eight segments encode for 11 proteins, among them 18 different Hemagglutinin (H1 to H18) and 11 different Neuraminidase antigens (N1 to N11) (± 14kbp in total).
Bluetongue
Bluetongue is the type Orbivirus in the family Reoviridae. Its genome consist of ten double-stranded RNA segments (± 19kbp in total).
Epizootic hemorrhagic disease
Epizootic hemorrhagic disease virus is an Orbivirus in the family Reoviridae. Its genome consist of ten double-stranded RNA segments (± 19kbp in total).
Equine encephalitis virus
Equine encephalitis virus is an Orbivirus in the family Reoviridae. Its genome consist of ten double-stranded RNA segments (± 19kbp in total).
Foot and mouth disease
Foot and mouth disease virus is prototype Aphthovirus in the family Picornaviridae. Its genome consist of a positive-sense, single stranded RNA segment (± 9kbp in total).
Lumpy skin disease
Lumpy skin disease virus is in the genus Capripoxvirus in the family Poxviridae. It is a double-stranded DNA genome encoding at least 155 genes (± 150kbp in total).
Newcastle disease
Newcastle disease virus is a variant of avian paramyxovirus 1 (APMV-1) and belongs to the genus Avulavirus in the family Paramyxoviridae. It has a negative-sense, single stranded RNA genome (± 15kbp in total).
Rift Valley fever
Rift valley fever virus is in the genus Phlebovirus in the family Bunyaviridae. Its genome consist of three negative single stranded RNA segments (± 15kbp in total).
Viral vectors
VanSchalkwykA1@arc.agric.za
We are currently in the process of generating a draft genome for the biting midge Culicoides imicola. It transmits arboviruses such as AHSV, BTV, EHDS and EEV. Even though it has been recorded in Africa, Asia and Europe, it is the most prevalent species in South Africa. Its haplotype genome consist of three homomorphic chromosomes (2n=6) (± 200Mbp in total). The draft genome would be used as template for subsequent transcriptomic experiments.
Bacterial genomics and transcriptomics
LiebenbergJ@arc.agric.za
Heartwater is caused by the obligate intracellular bacterium, Ehrlichia ruminantium, in the family Anaplasmataceae, order Rickettsiales. The circular genome is 1.5 Mb in length with a low G+C content of 27.5%. Draft genome sequences of 20 South African isolates of E. ruminantium have been generated. The genome sequences enable us to select heartwater vaccine candidates that are conserved among isolates and to develop improved molecular diagnostic tools.
Transcriptome sequencing is utilised to study the mRNA profiles of E. ruminantium in different cell cultures, and in host or vector tissues. We use the data to elucidate the interaction of the bacterium with its ruminant host and tick vector to aid the development of novel vaccines.
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