Computational protocol: Evolutionary Phylodynamics of Korean Noroviruses Reveals a Novel GII.2/GII.10 Recombination Event

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Protocol publication

[…] Amplified PCR products were cleaned using a QIAquick PCR purification kit (Qiagen, Westburg, Germany) and then sequenced using a BigDye Terminator Cycle Sequencing Kit and an automated DNA sequencer (Model 3730, Applied Biosystems, Foster City, CA, USA). The resulting nucleotide sequences were aligned using CLUSTAL-X 2.1 program with parameters set against the corresponding NoV sequences from the NCBI GenBank database . The nucleotide sequences of the capsid and RdRp genes from the study strains were compared with cogent genes of NoVs available in the public database. Phylogenetic trees were constructed using neighbor-joining algorithms from the PHYLIP suite and the Kimura two-parameter model using MEGA6 software. Evolutionary distances for neighbor-joining analyses were based on the model developed by Jukes and Cantor . Tree topology was evaluated using the bootstrap resampling method with 1,000 replicates of the neighbor-joining dataset with the CONSENSE and SEQBOOT programs from the PHYLIP suite. The recombination nucleotide sequences obtained in this study were deposited in the GenBank under the accession numbers KC110854 (4CAU-14), KC10855 (Gil-67), KC110856 (Gil-70), and KC110857 (4CAU-38). […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Organisms Homo sapiens
Diseases Virus Diseases