Phylogeographic and phylodynamic analyses
To infer significant transition rates between epidemiologic features (known as ‘traits’) of PB2 sequences along phylogenetic tree branches, including (a) geographic location, (b) host species, and (c) HA and Neuraminidase (NA) subtypes, and evaluate continuous virus diffusion (rate of movement in km/year) among host taxa, joint discrete and continuous trait Bayesian phylogeographic and phylodynamic analyses were performed using BEAST v.1.10.4 (Suchard et al., 2018). An asymmetric substitution model with Bayesian stochastic search variable selection (BSSVS) and a strict clock model were used to estimate diffusion between discrete states (Lemey, Rambaut, Drummond, & Suchard, 2009). Statistical significance for diffusion between discrete states was determined by the following Bayes Factors (BF): 3 ≤ BF < 20, 20 ≤ BF <150, and BF ≥ 150, denoting positive, strong, and very strong support, respectively (Kass & Raftery, 1995). To quantify transitions among geographic, host, or HA/NA subtype states (Markov jumps, i.e. the frequency of transitions from one geographic or host state to another along phylogenetic branches) and the duration of time viruses spend in each state (Markov rewards), posterior inference of the complete Markov jump history through time was included (Hong, Lemey, Suchard, & Baele, 2021).
Continuous Bayesian phylogeographic analyses were performed by annotating the empirical tree with latitude and longitude locations of all sampling sites via www.geonames.org to infer and visualize the evolutionary and geographic relationships between global sequences. Sequences between 1978 and 2008 were masked so that they contributed to the overall tree structure but were not included in the calculation of diffusion rates globally or within Iceland (Hicks, Dimitrov, Afonso, Ramey, & Bahl, 2019). A Cauchy relaxed random walk (RRW) model and an uncorrelated relaxed lognormal clock were used and a random jitter of 0.001 was applied to isolates with matching geographic latitude and longitude coordinates (Lemey et al., 2010). Host-specific diffusion rates, the rate of virus movement (in kilometers per year), were calculated (Dellicour, Rose, & Pybus, 2016; Minin & Suchard, 2008; Trovão, Suchard, Baele, Gilbert, & Lemey, 2015). GIS mapping was performed using QGIS v.3.16.3 (QGIS Development Team, 2020).