Computational protocol: Characterization of Foot-And-Mouth Disease Viruses (FMDVs) from Ugandan Cattle Outbreaks during 2012-2013: Evidence for Circulation of Multiple Serotypes

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Protocol publication

[…] Descriptive serological data were entered in Microsoft Excel and imported into Stata 9 (Statacorp, Lakeway Drive College Station, Texas, USA) where the analysis was performed using the median and interquartile range as a measure of central tendency and spread respectively. For molecular data, base calling of nucleotide sequences was performed using seqMan Pro software (Lasergene package, DNAstar, Inc., WI, USA). Published sequences relevant to this study were obtained using BLAST searches from NCBI (http://www.ncbi.nlm.nih.gov/)[]. The sequences analyzed correspond to the VP1 coding region and details of the new and previously published sequences are summarised in . Multiple sequences were aligned using MUSCLE (codons) [] incorporated in MEGA 5 []. A phylogenetic tree of these sequences was estimated using the Neighbor-Joining method []. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (2000 replicates) is shown next to the branches []. The tree is drawn to scale with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Tamura 3-parameter method [] and are in the units of the number of base substitutions per site. The rate variation among sites was modelled with a gamma distribution (shape parameter = 1). The analysis for serotype A and SAT 2 involved 24 and 17 different nucleotide (nt) sequences, respectively, and codon positions included were 1st+2nd+3rd. There were a total of 638 and 648 nt positions in the final dataset for serotype A and SAT 2, respectively. Evolutionary analyses were conducted in MEGA 5 []. […]

Pipeline specifications

Software tools DNASTAR Molecular Biology Suite, MUSCLE, MEGA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Bos taurus, Viruses, Human poliovirus 1 Mahoney
Diseases Foot-and-Mouth Disease