TABLE 1.

Linear mixed-effects models for association of hospitalization, vaccination and healthcare worker surveillance samples on minor variant richness.

a. Effect of sample Ct value and patient hospitalization status on log10 transformed minor variant richness. Sequencing run is included as a random effect.
	numDF	denDF	F-value	p-value
(Intercept)	1	6090	602.4491	<.0001
Ct	1	6090	1370.695	<.0001
admitted_hospital	1	6090	77.6004	<.0001
Ct:admitted_hospital	1	6090	11.5969	7.00E-04

b. Effect of sample Ct value and patient vaccination status on log10 transformed minor variant richness. Only samples from non-hospitalized patients collected in July 2021 or later are included. Sequencing run is included as a random effect.
	numDF	denDF	F-value	p-value
(Intercept)	1	1346	297.22177	<.0001
Ct	1	1346	152.42258	<.0001
vaccine_status	1	1346	4.52737	0.0335
Ct:vaccine_status	1	1346	4.31531	0.0380

c. Effect of sample Ct value and healthcare worker surveillance sample status on log10 transformed minor variant richness. Only samples from non-hospitalized individuals are included. Sequencing run is included as a random effect.
	numDF	denDF	F-value	p-value
(Intercept)	1	3824	455.9225	<.0001
Ct	1	3824	669.4242	<.0001
surveillance_sample	1	3824	0.1950	0.6588
Ct:surveillance_sample	1	3824	0.0207	0.8857