Computational protocol: Influenza Herd-Level Prevalence and Seasonality in Breed-to-Wean Pig Farms in the Midwestern United States

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Protocol publication

[…] Hemagglutinin gene (HA) sequences were annotated for completeness and functionality using the influenza virus sequence annotation tool (FLAN) (). H1 clade classification was done using the swine H1 clade classification tool in the Influenza Research Database (IRD) ().For H3 cluster classification, reference strains were obtained from the Influenza Virus Resource at the National Center for Biotechnology Information (NCBI) (). Included H3 reference strains were under the following GenBank reference numbers: JX092535 (H3 IV C), JX092307 (H3 IV D), JN652493 (H3 IV F), JN638733 (H3 IV A), JF812276 (H3 IV E), CY114592 (H3 IV B), CY095675 (H3 I), CY006475 (H3 III), CY002120 (H3 II), and KC306165 (H3 humSea11).Alignment of 1,698-nucleotide-length HA sequences was done using the ClustalW algorithm. Phylogenetic trees were generated using a neighbor joining method and a Hasegawa, Kishino, and Yano (HKY) substitution model in Geneious version 8.1.8 (). H3 cluster was inferred according to the clustering of each isolate in the corresponding trees. […]

Pipeline specifications

Software tools FLAN, Clustal W, Geneious
Databases Influenza Virus Resource IRD
Application Phylogenetics
Organisms Sus scrofa
Diseases Influenza, Human