Computational protocol: Genetic Characterization of Foot-and-Mouth Disease Viruses, Ethiopia, 1981–2007

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Protocol publication

[…] Total RNA was extracted from 81 FMD viruses in Ethiopia, and each VP1-coding region was successfully amplified by RT-PCR. The PCR products were directly sequenced on both strands to obtain the complete VP1 sequences, which were compared with the other relevant FMDV VP1 sequences within the same serotype (see Figures 1–5 for database accession numbers).VP1 nucleotide sequences were aligned by using BioEdit () and Clustal W (). These alignments were used to construct distance matrices by using the Kimura 2-parameter nucleotide substitution model in the program MEGA 4.0 (). Some previously published sequences of serotype O were incomplete at the 5′ end of the VP1 gene and consisted of 495 nucleotides rather than the full-length 639 nucleotides. Midpoint-rooted neighbor-joining trees were then constructed with MEGA 4.0 software. The robustness of the tree topology was assessed with 1,000 bootstrap replicates by using the model in MEGA 4.0. The serotype C sequences labeled PD-FMD in were supplied by the Project Directorate on FMD, Mukteswar, India (). […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA
Application Phylogenetics
Diseases Foot-and-Mouth Disease, Mouth Diseases