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

Similar protocols

Protocol publication

[…] Preliminary analyses of the genotypes were performed in Norovirus Genotyping Tool v.1.0 (http://www.rivm.nl/norovirus/typingtool) []. 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) (https://www.rcsb.org/), 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