Computational protocol: Human to animal transmission of influenza A(H1N1)pdm09 in a turkey breeder flock in Norway

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Protocol publication

[…] All turkey samples were analysed at the Norwegian Veterinary Institute. Blood samples were tested for antibodies against IAV using a blocking ELISA from IDvet (ID Screen influenza A antibody competition multi-species), and an indirect ELISA from IDEXX (IDEXX AI Ab test). For confirmation, positive samples were followed up with subtype specific haemagglutination inhibition (HI) tests []. Inactivated virus antigens and positive control sera for AI subtypes were obtained from the EU Reference Laboratory for Avian Influenza, Animal and Plant Health Agency, UK, and were as follows: H5N1 A/chicken/Scotland/59; H5N2 A/Ostrich/Denmark/72420/96; H5N3 A/teal/England/7394-2805/06; H5N7A/Mallard/Denmark/64650/03; H7N1 A/African starling/England/983/79; H7N7 A/turkey/England/647/77 []. Inactivated virus antigens and positive control sera for H1N1pdm09 were purchased from the University of Gent, Belgium (H1N1 A/Swine/California/07/09). Antibodies from egg yolk were extracted with chloroform, as described by Mohammed []. Turkey cloacal and oropharyngeal swabs and tissue samples were tested with a pan-influenza A real-time RT-PCR (rRT-PCR) [], and subtype specific rRT-PCRs for H5, H7 and H1N1pdm09 [–]. HA gene sequences from positive samples were based on PCR fragments generated as previously described [].Human samples were tested at the Norwegian Institute for Public Health. Nucleic acid from human nasopharyngeal swabs were typed [] and H1 subtyped [] by rRT-PCR. The HA gene was sequenced by dye-terminator Sanger sequencing (PCR and sequencing primers available upon request). Nucleotide sequences were further analysed by BioNumerics (AppliedMaths, Belgium), BioEdit [], and MEGA 6 software []. Phylogenetic trees were constructed with the neighbour-joining method, using Kimura2-parametre pairwise distances. Viral nucleotide sequences from the turkey sample (A/Turkey/Norway/1051/2016) and the human sample (A/Norway/1728/2016) were submitted to GISAID with the accession numbers: 11,046,376 and 1,046,371, respectively. […]

Pipeline specifications

Software tools BioNumerics, BioEdit, MEGA
Application Phylogenetics
Organisms Homo sapiens, Meleagris gallopavo, Human poliovirus 1 Mahoney
Diseases Infection, Influenza, Human, HIV Infections