Study area and sample collection
The study was conducted in north-eastern Poland where ASF was introduced
in February 2014, <1 km from the border with Belarus, and has
subsequently spread through the region in wild boar (Podgórski et al.,
2020) and domestic pigs (Taylor et al., 2021). By mid 2016, ASF cases in
wild boar were distributed continuously in the infected region covering
about 4500 km2 and this is where samples used in this
study originate (Fig. 1). The area is mostly field-woodland mosaic
characterized by extensive agriculture and low human population density
(60 people/km2) and relatively high forest cover
(31%). The landscape is flat (highest elevation 298 ms a.s.l.) with no
significant natural or anthropogenic barriers to wild boar movement.
Wild boar are distributed continually throughout the area with densities
at the start of the ASF epidemic ranging between 0.5 and 5
ind./km2 at the forest district level (Regional
Directorate of State Forests, Białystok, Poland).
Following the introduction of ASF, an intensive surveillance program was
implemented in the affected area. The program conducted laboratory tests
of all hunted wild boar (active surveillance) and all wild boar found
dead (passive surveillance). We used surveillance data routinely
collected by the National Reference Laboratory for ASF at the National
Veterinary Research Institute in Puławy, Poland. Wild boar samples were
classified as ASF-positive (herefater ”case”) if presence of viral DNA
was confirmed in real-time PCR or antibodies were detected using ELISA
test and confirmed with a immunoperoxidase test (IPT). Detailed
description of the surveillance design and laboratory procedures can be
found in (Woźniakowski et al., 2016). A total of 5487 wild boars were
sampled in the study area from February 2014 to July 2016 and 168 of
them tested positive for ASF. It was not technically possible to
genotype all of the sampled individuals. Instead, we selected a
subsample of 1078 individuals (including all ASF-positive) evenly
distributed across the study area for further analyses. However, many
samples, particularly originating from the carcasses, were of poor
quality and yielded too few microsatellite loci (those yielding less
than 13 out of 16 loci were excluded). Finally, we were able to
satisfactorily genotype 323 samples (including 80 ASF cases) which
comprised a final dataset.