Computational protocol: Molecular epidemiology and temporal evolution of norovirus associated with acute gastroenteritis in Amazonas state, Brazil

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Protocol publication

[…] Preliminary analyses of the genotypes were performed in Norovirus Genotyping Tool v.1.0 ( []. Phylogenetic analyses were performed using Maximum-Likelihood with IQTree program v.1.3.0 [] by Ultrafast Bootstrapping (UFboot) []. The statistical significance of phylogenies constructed was estimated with 1000 replicates. Edits on the phylogenetic trees were done with the program FigTree v.1.4.2 [].Analysis of the epitopes of the P2 region was done in the MEGA 6 program []. The prototype sequences were obtained from GenBank database of the National Center for Biotechnology Information (NCBI). The recombination analyses were performed using the Simplot v. 3.5.1 program []. [...] In order to conduct time-measured phylogenetic analysis, P2 subdomain sequences were tested by the Bayesian Markov Chain Monte Carlo (MCMC) method implemented in Bayesian Evolutionary Analysis Sampling Trees (BEAST) v1.8.2 []. The most recent common ancestors (TMRCA) were estimated by a relaxed clock, uncorrelated log-normal molecular clock model []. TMRCA was determined using the Coalescent Piecewise Bayesian Skyride Plot method [] with 100 million replicates (more details in Additional file : Table S1). Nucleotide variations within and between clusters were examined by applying the maximum likelihood based on the GTR + I + G nucleotide substitution model, chosen by jModelTest v. 2.1 []. [...] The 3D structure was built using protein homology modeling. The initial search and selection were done using templates from Protein Database Bank (PDB) (, using the norovirus capsid. The selected templates were 1IHM and 4OP7. The MODELLER© v. 9.15 software was used to build the 3D models. After protein modeling, the results were validated using the PROCHECK [] and VERIFY3D programs [] in order to check the biochemical parameter quality. A visual inspection was performed using the PyMOL Molecular Graphics System v. 1.8 (Schrödinger, LLC). […]

Pipeline specifications

Software tools FigTree, MEGA, SimPlot, BEAST, jModelTest, MODELLER, PROCHECK, VERIFY3D, PyMOL
Applications Phylogenetics, Protein structure analysis
Organisms Homo sapiens
Diseases Dysentery