Direct Sequencing of African Foot-and-Mouth Disease Viruses from Clinical Samples
Unbiased RNASeq successfully produced complete genome sequences of three African Foot-and-Mouth Disease viruses directly from clinical samples, demonstrating the feasibility of direct sequencing from symptomatic animals. Results showed high average coverage with limited gap closure needed in one sample. Potential for unbiased detection of co-infections was highlighted, with targeted approaches offering improved coverage. The study concludes by presenting complete genome sequences obtained from the samples collected in Zambia and Namibia.
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Presentation Transcript
Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses, Directly from Clinical Samples S Van Borm, T Rosseel, A Haegeman, M E Fana, L Seoke, J Hyera, G Matlho, F Vandenbussche, K De Clercq Open Session of the EuFMD - Cascais Portugal 26-28 October 2016
The Study Can unbiased RNASeq produce complete FMDV genome sequences directly from clinical samples? 3 strong positive epithelial samples (CT range 14,63 16,18) from Zambia and Namibia
Results Unbiased RNASeq produces complete genomes with high average coverage in 2/3 samples limited gap closure (Sanger sequencing) needed in 3rd sample due to low coverage (limited % of FMDV reads). Potential for unbiased detection of co-infections If only targeting FMDV, targeted approaches may produce better coverage. e.g. Logan G, Freimanis GL, King DJ, Valdazo-Gonzalez B, Bachanek-Bankowska K, Sanderson ND, Knowles NJ, King DP, Cottam EM. (2014) BMC Genomics 15:828
Conclusion These data demonstrate the feasibility of direct sequencing of complete FMDV coding sequences from samples from symptomatic animals The complete genome sequences of O/ZAM14/2010, SAT1/NAM01/2010 and SAT2/ZAM18/2009 were obtained
