External Sequence Data Analysis
Please email external sequences to [email protected] and the pathologist assigned to the case.
There will be no additional fee for the analysis and dendrogram maintenance for any sequences performed at the U of MN VDL. H1 clades are determined using the Swine H1 Clade Classification available from the NIAID Influenza Research Database (IRD) [Zhang Y, et al. (2017)] through the web site at http://www.fludb.org. For more information on H1 clade information and methodology, please refer to "A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses." Tavis K. Anderson, Catherine A. Macken, et.al, mSphere Dec 2016, 1 (6) e00275-16; DOI: 10.1128/mSphere.00275-16. H3 clades are determined using a public data set of Swine H3 Clade Classification reference strains and the BLASTN 2.2.22 tool available from the NIAID Influenza Research Database (IRD) [Zhang Y, et al. (2017)] through the website at http://www.fludb.org. For more information regarding Swine H3 clade classifications, please refer to "Sequences used in swine H3 clade classification reference tree." Tavis K. Anderson, Catherine A. Macken, et. al. Virus Pathogen Database and Analysis Resource (ViPR) -. N.p., 03 Nov. 2016. Web. 21 Feb. 2017. For a review of influenza in pigs in the USA, read this lay publication on this website: https://www.pig333.com/swine-influenza/the-genetic- diversity-of- contemporary-swine- influenza-a- viruses-in- usa_11593/