Transboundary and Emerging Diseases

Research Article

Predicting Potential PRRSV-2 Variant Emergence through Phylogenetic Inference

Table 1

The best fit model for each success aspect and predicted period.


Success aspect	Measure of success	Scenario (model)	Model p-value (LRT)	Predictor	p-value	Coefficient	Raw OR	Adjusted OR	Predictor’s lower upper quartiles	Training set	Test set
Success aspect	Measure of success	Scenario (model)	Model p-value (LRT)	Predictor	p-value	Coefficient	Raw OR	Adjusted OR	Predictor’s lower upper quartiles	Concordance	Sensitivity	Specificity	PPV^†	NPV^††	F1 score	Balanced accuracy

Population expansion	Absolute increase in number of taxa	12-t-12	0.002	Branch length	0.098	−1,423.0	7.9 × 10⁻⁶³	0.12	0.00–0.02	0.875	0.75	0.58	0.38	0.88	0.500	0.667
				Average clade rate	0.808	−200.0	1.3 × 10⁻⁸⁷	0.4	0.00–0.01
				LBI		8.1	3.3 × 10³	12.12	0.03–0.333
				Amino acid distance	0.159	20.9	1.1 × 10⁹	3.15	0.020–0.075
				N-gly similarity	0.410	1.4	4.0	1.79	0.333–0.750
		24-t-24	0.001	Branch length	0.120	−220.4	1.8 × 10⁻⁹⁶	0.08	0.002–0.013	0.810	1.00	0.50	0.40	1.00	0.571	0.750
				Ancestral rate	0.446	268.9	6.1 × 10¹¹⁶	3.65	0.002–0.007
				LBI		8.9	7.2 × 10³	12.67	0.000–0.286
				Amino acid distance	0.652	7.7	2.2 × 10³	1.42	0.030–0.075
				N-gly similarity	0.939	0.2	1.2	1.09	0.333–0.750

Spatial distribution	Relative increase in maximum between-county geodetic distance	12-t-12	0.006	Branch length	0.587	19.9	4.3 × 10⁸	1.34	0.003–0.018	0.729	0.75	0.42	0.30	0.83	0.429	0.583
				Ancestral rate		−898.7	0	0	0.001–0.007
				LBI	0.116	5.8	3.5 × 10²	6.04	0.026–0.333
				Amino acid distance	0.725	5.9	3.5 × 10²	1.38	0.020–0.075
				N-gly similarity	0.081	2.8	1.7 × 10¹	3.24	0.333–0.750
		12-t-24	0.029	Branch length		−170.7	7.5 × 10⁻⁷⁵	0.1	0.003–0.017	0.792	0.50	0.83	0.50	0.83	0.500	0.667
				Ancestral rate	0.136	−309.4	4.3 × 10⁻¹³⁵	0.17	0.002–0.008
				LBI	0.293	5.5	2.5 × 10²	5.13	0.026–0.322
				Amino acid distance		53.4	1.6 × 10²³	14.47	0.025–0.075
				N-gly similarity	0.620	0.8	2.2	1.39	0.333–0.750

Genetic diversity	Absolute increase in 95^th percentile pairwise nucleotide distance	12-t-12	<0.001	Branch length		108.1	8.6 × 10⁴⁶	4.92	0.003–0.018	0.917	1.00	0.58	0.44	1.00	0.615	0.792
				Ancestral rate	0.603	−141.6	3.2 × 10⁻⁶²	0.42	0.001–0.007
				LBI	0.758	−1.2	2.9 × 10⁻¹	0.69	0.026–0.333
				Amino acid distance	0.909	2.1	7.9	1.12	0.020–0.075
				N-gly similarity	0.779	0.6	1.7	1.27	0.333–0.750
		24-t-24	0.006	Branch length	0.119	62.1	9.4 × 10²⁶	2.07	0.002–0.013	0.857	1.00	0.33	0.33	1.00	0.500	0.667
				Ancestral rate	0.880	−46.6	5.9 × 10⁻²¹	0.8	0.002–0.007
				LBI	0.958	−0.2	8.2 × 10⁻¹	0.95	0.000–0.286
				Amino acid distance		42.5	2.9 × 10¹⁸	6.78	0.030–0.075
				N-gly similarity	0.535	1.8	5.8	2.09	0.333–0.750

, ^†positive predictive value, ^††negative predictive value.