Computational protocol: Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013

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Protocol publication

[…] The PCR products were purified using a PCR purification kit (Qiagen, USA) and labeled with a BigDye Terminator v3·1 Cycle Sequencing Kit (Applies Biosystems, USA) according to the manufacturer's instructions and then analyzed on an ABI 3130 automatic DNA sequencer. Nucleotide sequences were assembled using DNASTAR v.8.0, and multiple sequence alignment using H1 numbering was conducted with CLUSTAL X for the major coding regions of HA and NA segments. The sources of sequences in phylogenetic analyses are shown in Figures 3 and 4. Phylogenetic trees were constructed by the maximum likelihood (ML) method with bootstrap-supported values. To quantify the amino acid sequence diversity of each lineage, we used MEGA 5 software package. To find the closest relative, sequences were compared with those in the NCBI database using BLAST. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Diseases HIV Infections
Chemicals Oseltamivir