Computational protocol: Genetic Diversity and Distribution of Human Norovirus in China (1999–2011)

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Protocol publication

[…] The genogroups, genotypes, and GII.4 variants of the NoV sequences were determined by the online-based typing-tool (http://www.rivm.nl/mpf/norovirus/typingtool) [].Nucleotide sequences were aligned using the ClustalW program. Phylogenetic analysis was performed with MEGA 5.1 package based on partial ORF1 (1029 nt) and ORF2 (811 nt) sequences. Phylogenetic trees were reconstructed using the Tamura-Nei model and maximum-likelihood method. Bootstrap was calculated with 1000 pseudoreplicate data sets. The distance scale represents the number of nucleotide substitution per position. A phylogenetic tree was first constructed using all of the GII.4 ORF1 sequences (n = 327) and the reference sequences retrieved from the NCBI database. Then, to simplify and clarify the complicated tree, a total of 41 representative sequences, which revealed, respectively, high similarity to other sequences grouped in the same cluster, were chosen to reconstruct the tree. Like the ORF1 tree, a total of 399 ORF2 sequences were analyzed initially, and then 108 representative sequences were used to reconstruct the phylogenetic tree. [...] To detect recombination events, sequences were aligned using ClustalW and adjusted manually using SeqMan and BioEdit. The reference strains used were the same as those described above. The suspected recombinant strains were defined as recombinants if they were grouped into different genotypic clusters on the phylogenetic trees reconstructed using the 3′ end of ORF1 and the 5′ end of ORF2, respectively []. Phylogenetic analysis was performed as described above with the exception of 231 nt of ORF1 and 259 nt of ORF2 sequences.SimPlot method was used to identify the breakpoint recombination site and to confirm the NoV recombinants []. The bootstrap values were plotted for a window of 300 bp, moving in increments of 10 bp along the alignment []. […]

Pipeline specifications

Software tools Clustal W, MEGA, BioEdit, SimPlot
Application Phylogenetics
Organisms Homo sapiens
Diseases Communicable Diseases