Computational protocol: Migratory Whooper Swans Cygnus cygnus Transmit H5N1 Virus between China and Mongolia: Combination Evidence from Satellite Tracking and Phylogenetics Analysis

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Protocol publication

[…] Tracheal and cloacal swab samples were taken from the 61 captured whooper swans for laboratory testing. Field work was also carried out in March and April 2015 to collect fecal samples along the routes of the satellite tracked swans. All samples were stored at −80 °C and inoculated into 10-day-old embrocated specific-pathogen free (SPF) chicken eggs for virus isolation at the National Avian Influenza Reference Laboratory of China.Hemagglutinin (HA) gene sequences of HPAI H5N1 viruses were obtained from the GenBank hosted by the National Center for Biotechnology Information (NCBI) as of 10 November 2016. Sequences were aligned with MAFFT v7.127b and trimmed to a length of 1716 bp. An approximate maximum likelihood tree was constructed by FastTree v2.1.4 as the setting of GTR + Gamma with SH-like local-bootstrap support values to estimate the reliability of each split in the tree. The tree was rooted at A/goose/Guangdong/1/96 and structured according to the unified nomenclature system and virus clades for the HPAI H5N1 viruses of the World Health Organization. […]

Pipeline specifications

Software tools MAFFT, FastTree
Application Phylogenetics
Organisms Cygnus cygnus, Human poliovirus 1 Mahoney