Model fitting with the observed proportion of ELISA(+)PCR(-) in the tested boar.

We fit the model describing (Ri(t)+Vi (t))/Ni(t) by maximising the likelihood shown in Eq 18. The mean estimated proportion of ELISA(+) PCR(-) individual is demonstrated by a solid line. Each dot denotes the observed value of the proportion of ELISA(+)PCR(-) individuals in each week. Arrows denote the vaccine campaigns.</p

Sensitivity analysis with respect to the condition for data extraction.

The required vaccination effort was estimated by varying the data-extraction criteria in terms of the test frequency against CSF. The grids where at least one test was enrolled by every 9, 10, 11, 12, and 13 weeks were analysed (baseline value = 12). Mean estimated vaccination effort for the elimination of CSF is demonstrated by the solid lines. The dashed lines denote 95% confidence intervals of the estimated values. (EPS)</p

Sensitivity analysis with respect to <i>r</i>_<i>y</i>.

The required vaccination effort was estimated by varying the yearly growth rate of wild boar ry from 1.2 to 2.0 (baseline value = 1.6). Mean estimated vaccination effort for the elimination of CSF is demonstrated by the solid lines. The dashed lines denote 95% confidence intervals of the estimated values. (EPS)</p

Time-series change in the number of boar captured and found dead from week 1 to week 61.

The black bar demonstrates the number of dead boar found between week 1 and week 61. The grey bar demonstrates the number of boar captured between the week 1 and week 61. (TIFF)</p

Sensitivity analysis with respect to <i>μ</i>.

The required vaccination effort was estimated by varying the yearly natural mortality rate μ from 0.07 to 0.23 (baseline value = 0.15). Mean estimated vaccination effort for the elimination of CSF is demonstrated by the solid lines. The dashed lines denote 95% confidence intervals of the estimated values. (EPS)</p

Fig 1 -

(A) The location of Gifu Prefecture in Japan and selected grids. The location of Gifu Prefecture in Japan (green) and the selected grids (17 grids; red) are shown. Map base layer of Japan was obtained from Natural Earth (http://www.naturalearthdata.com/about/terms-of-use/) and is available at https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/cultural/ne_10m_admin_0_countries_jpn.zip. Map base layer of Gifu Prefecture was obtained from the digital national land information of Japan (https://nlftp.mlit.go.jp/index.html) and is available at https://nlftp.mlit.go.jp/ksj/gml/datalist/KsjTmplt-N03-v3_0.html#prefecture21. (B) Time-series change in the number of boar tested that resulted in PCR-positive from week 1 to week 61. The red and grey bars demonstrate the number of PCR(+) and PCR(-) boar reported between week 1 and week 61, respectively. Arrows denote the vaccine campaigns. (C) Time-series change in the number of boar tested that resulted in ELISA-positive and PCR-negative from week 1 to week 61. The orange bar demonstrates the number of ELISA(+)PCR(-) boar reported between the week 1 and week 61. The grey bar demonstrates the sum of the number of ELISA(+)PCR(+) boar and that of ELISA(-) boar reported between the week 1 and week 61. Arrows denote the vaccine campaigns. ELISA, enzyme-linked immunosorbent assay; PCR, polymerase chain reaction; RT, reverse transcription.</p

Required vaccination effort for CSF elimination at week 28 compared to the cumulative vaccination effort until week 50 [<i>V</i>_eff,i(50)] with a varied basic reproduction number.

Mean estimated vaccination effort for the elimination of CSF is demonstrated by the solid line. The dashed lines denote 95% confidence intervals of the estimated values.</p

Descriptions of parameters for the estimation.

Descriptions of parameters for the estimation.</p

Change in the proportion of immunised wild boar by the bait vaccination among the total wild boar population at the beginning of vaccination campaign, (<i>V</i>_i (<i>t</i>))/(<i>N</i>_i(28)).

Mean estimated increment of the proportion of ELISA(+) PCR(-) is demonstrated by the solid line. The 95% confidence intervals are shown by dashed lines. The bait vaccination was implemented in the weeks 28–29, weeks 34–35, week 44, and weeks 49–50. Arrows denote the timing of vaccine campaigns.</p

Phylogenic tree for 119 PEDV strains and identified motifs.

<p>(A) Phylogenetic tree based on the genomes of 119 PEDV strains isolated in 2013–2014. Phylogenetic analysis was performed using a maximum-likelihood method with general time reversible nucleotide substitution model and with a bootstrap test using 1000 replicates in the MEGA6 program. Notations on the very left side represent the clades shown by Vlasova et al. (9). (B) The presence of sequence motifs in each strain. (C) Color chart of nucleotides in the sites having inconsistencies within the 119 PEDV strains. Nucleotides in agreement with the sequence of Indiana12.83/USA/2013 are colored with respect to the type of nucleotide (a: red, t: blue, c: green, and g: yellow). To increase the discriminability of motifs, nucleotides in sites with only one inconsistent strain were not colored.</p