SAVANNAH, GA Sept. 23 (GenomeWeb News) - Genome sequence provides some pretty hot information for biologists, but what's in it for Kenyan cattle farmers?
Apparently, quite a lot, according to Evans Taracha, of the International Livestock Research Institute in Nairobi, who spoke at the GSAC conference here during an afternoon symposium on microbial genomics. Taracha heads up the ILRI's end of a multi-continent consortium that is using genomics to attack a attack East Coast fever, a parasitic cattle disease that costs East African farmers to lose a million cattle, and up to $169 million, a year, according to his estimates.
The consortium stemmed from a meeting at a malaria conferencein the late 1990s, between Vishvanath Nane, who was then working at ILRI, and TIGR researcher Malcom Gardner at a malaria conference, Taracha told GenomeWeb News. The two initiated a collaboration to sequence the genome of T. parva, the parasite that causes East Coast fever, and use the genomic information to find novel antigens that could then be tested as vaccine candidates in Kenyan cattle.
Theileria parva is in the same phylum as the common malaria parasite, Plasmodium falciparum, and has a similar life cycle divided between an insect vector--in this case the brown-eared tick, not the mosquito--and the mammalian host. In the mammalian stage, T. parva infects the lymphocytes of the cattle and causes them to rapidly proliferate, in a tumor-like fashion. The cattle are usually dead within two to three weeks without treatment.
While a live vaccine exists for the disease, this vaccine, which costs $10-$20 per animal is cost-prohibitive for most subsistence farmers in east Africa, according to Taracha. And, because it is live it requires refrigeration, as well as post-vaccination treatment--two requirements that are difficult to meet in rural sub-Saharan areas. An effective killed vaccine that targets different antigens in T. parva would be much cheaper to produce and easier to distribute, Taracha said.
Enter TIGR. In the collaboration, the Rockville, MD-based institute put up $1.5 million, and offered its manpower for sequencing. ILRI devoted $300,000 of its budget to the project, the Ludwig Institute for Cancer Research in Belgium offered its own expertise and some funding, and the UK's Department for International Development also offered "generous" funding to support the project, according to Taracha. Additionally, animal health giant Merial has stepped in to collaborate with the partners on the vaccine delivery and manufacturing end.
The genome sequencing stage was a relatively "typical" whole genome shotgun project, Gardner told the GSAC audience in an earlier presentation this afternoon. The group rapidly generated 129,000 good sequences at 629 nucleotides each at an 82 percent success rate, for 9x sequence coverage--"I wish we had started later than we did," Gardner said, as TIGR's fleet of ABI 3730s now generates 800 nucleotides per read at an 86 percent success rate. After shotgun stage, they spent a "great deal of time closing the genome sequence," but eventually covered all four chromosomes of the parasite, aside from two tiny problem areas.
TIGR's bioinformatics staff then used gene finding algorithms to predict the coding regions in the genome. But "there's only so much you can learn from genome gazing," Gardner said. At this step, the TIGR team stepped into the background and the ILRI team started to use the genome to search for antigens that would be vaccine candidates.
At ILRI, Taracha's group developed cDNA libraries from from purified T. parva schizonts (the stage inside the cattle lymphocytes), he said, as well as a cell line from six different cytotoxic T cells in different subtypes of animals. They developed a high-throughput interferon gamma assay using both of these elements. While this random cDNA library screening approach did not generate any hits, they also cloned about 52 genes from a list of 55 predicted genes that TIGR sent them, and put them through the assay pipeline. "We were able to pick up three vaccine candidates," said Taracha.
Currently, ILRI is conducting cattle vaccine trials for two of these antigens on its premises in the rolling ngo, and just terminated one trial today, according to Taracha. The data will then be analyzed by the institute's bioinformatics specialists to see weather the antigen is a viable vaccine candidate, Taracha said. "We expect to have results known of this trial in a week or so, he said, and to test all eight candidates by June of next year."
Once the ILRI researchers have shown that a vaccine candidate works experimentally, Merial will do the manufacturing, quality control, and distribution of the vaccine, Taracha said. The company, he said, plans to sell the vaccine commercially.
Meanwhile, said ILRI researchers attending the conference, the cattle farmers in Kenya are anxiously awaiting the results of this cross-continental genomics collaboration.