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Hi all and a happy new year ! As I have already mentioned to some colleagues, we are interested on sequencing our Brazilian FV3 isolates, so Thomas' proposal sounds exellent. Actually we have ethanol preserved samples, extracted DNA and of course infected live tadpoles and frogs. We will make arrangements about which samples will be more suitable and how to ship them. Besides Next-Gen sequencing we also discussed about some kind of collaborative research on getting a "Gold standard" for RV detection. We have seen during presentations and posters, as well as at the discussion group on “Diagnostic” that several methods are being used (qPCR-RTPCR, conventional PCR). However, it looks like nobody is using OIE protocols. So we have the possibility of performing an experiment to compare sensitivity and specificity of available methods for different RV isolates and strains to suggest OIE a new “Gold Standard” for all RVs or recommended methods to be applied on specific strains/species. Best regards for all Rolando On Sun, Jan 5, 2014 at 8:10 PM, Thomas Waltzek <[log in to unmask]> wrote: > Hi Matt/Amanda, > Happy New Year! Please post the attached message to the GRC. I've > also copied the message below. All the best and cheers - Tom > > > > Hello Everyone and Happy New Year! > > > > At the 2013 International Ranavirus Symposium several of us (Brunner, > Storfer, Pessier, Jancovich, Garner, Wellehan, and Waltzek) met to discuss > the genomic sequencing of ranavirus isolates. The outcome of our informal > discussion was that each of the individual parties was going to sequence > their own isolates for their respective projects and then we would > reconvene to combine the datasets into a final global analysis. Toward that > end, a UF PhD student (Sieara Claytor – many of you met her at the meeting) > working under Drs. Susan Cameron Devitt, James Wellehan, and myself has > made great progress toward sequencing North American FV3 isolates. > > > > The objectives of her study are to investigate the phylogeographic > structure of FV3 across its range, determine any patterns among hosts > and/or geography, to determine the origin of introductions, and to evaluate > climatic correlates of FV3. She has surveyed phylogenetically informative > loci (31 loci including hypervariable and conserved regions) from FV3-like > isolates across diverse host and temporospatial scales (2 bull frogs, 4 > wood frogs, pig frog, Columbia spotted frog, tiger frog, leopard frog, > common midwife toad, pallid sturgeon, white sturgeon, soft-shell turtle, 2 > box turtles, Smoky Mountain salamander, 3 yellow-spotted salamanders, and > Chinese giant salamander). Sieara’s next step is sequence an additional 20 > North American isolates we have grown up and purified for genomic > sequencing on our NextGen MiSeq machine (Russian sturgeon, fathead minnow, > Northern pike, walleye, green frog, 3 more box turtles, 2 gopher tortoises, > sulcata tortoise, etc). > > > > We are asking for all those interested in collaborating to provide FV3 and > FV3-like isolates to extend the geographic and taxonomic scope of the > project. If anyone has material (e.g. isolates, infected tissues, or > infected tissue DNA) that you would be willing to share in exchange for > authorship with this project, please let me know and I can help arrange > shipping of the samples. A special thanks to all those that have already > provided input and isolates as collaborators on this project (Matt Gray, > Debra Miller, James Jancovich, Jesse Brunner, James Wellehan, April > Johnson, Matt Allender, and Ellen Ariel). > > > > We are hoping to have all samples by February 31st in order to begin > sequencing the new material. > > > > > > Sincerely, > > Thomas B. Waltzek > > [log in to unmask] > 530-574-2976 > > > > -- > Thomas B. Waltzek, MS, DVM, PhD > Assistant Professor > Infectious Diseases and Pathology > College of Veterinary Medicine > Bldg #1379, Mowry Road > Gainesville, FL 32610 > Work: 352-273-5202 > Cell: 530-574-2976 > Fax: 352-392-4707 > Email: [log in to unmask] > -- Rolando Mazzoni DVM/PhD Pesquisador de Pós-doutorado CPA/EVZ/UFG Tel: (62) 35211576 Cel: (62) 81786489