Table 1.

Summary of linear mixed models of nucleotide diversity (π) and synonymous nucleotide diversity (πS) of SARS-CoV-2 in lions as a function of time (π model p = 0.000088; πS model p = 0.00017)

	Nucleotide diversity		Synonymous nucleotide diversity
Predictors	Estimates	p	Estimates	p
(Intercept)	0.000031 **	0.006	0.000031 *	0.012
Time (days after first positive test)	0.000002 ***	<0.001	0.000003 ***	<0.001
Random Effects
σ2	0.000000002600		0.000000003679
τ00	0.000000000210 animal_ID		0.000000000000 animal_ID
ICC	0.074647622901
N	11 animal_ID		11 animal_ID
Observations	54		54
Marginal R2 / Conditional R2	0.249 / 0.305		0.236 / NA

*p < 0.05 **p < 0.01 ***p < 0.001

Time was measured as days since first positive qRT-PCR test. Time was a fixed effect, with animal ID as a random effect to account for repeated measures of the same individual (N = 54 samples from 11 lions) over time. The models were fit with the lmer() function in the ‘lme4’ package, with the ‘lmerTest’ package used to obtain p-values based on Satterthwaite’s degrees of freedom approximation (two-sided). The table was generated with the tab_model() function in the ‘sjPlot’ package in R.