Fig 1.
A map of Canada and insert showing the location of the southwestern Ontario study area.
Grey lines define county boundaries and the 11 counties included in the study are identified. Cities and major bodies of water are also labelled.
Fig 2.
Panel A. Summary of rabies cases due to the AFX variant in 11 counties of southwestern Ontario 1990 to May 2018. The inset shows the recent case data from 2010 onwards at a different scale. Panel B. Total submissions and the percentage of all submissions testing rabies positive by year for the red fox (RFX) and skunk (SSK) hosts within the study zone. Data beyond 2014 are not shown as submissions in recent years were extremely low and sporadic.
Fig 3.
A ML tree generated using WGS for 133 AFX RABVs.
The tree was generated using the GTR+G nucleotide substitution model best supported by the data with 200 bootstrap replicates. Bootstrap values for all major nodes having values ≥ 80% are indicated and a distance scale is shown below the tree. Groups and clades as described in the text are identified to the right of the tree. Sample names are color-coded according to the host species thus: red fox, red; skunk, black; domestic animals, blue; arctic fox, grey.
Fig 4.
Maps of the study area showing the locations of all RABV variants over four time periods (panel A). Maps were generated using ARC-GIS software, v. 10. RABV variants and sub-variants are identified by colour-coding as illustrated in the time-scaled MCC tree generated using the BEAST software package (panel B).
Table 1.
AFX RABV ORFs and notable amino acid substitutions in Ontario RABV samples compared to a virus of the A3 sub-lineage.