Table 2.

Consensus sequence analysis of SARS-CoV-2 in longitudinal specimens.

Patient	Sample #	Days since symptom onset	Ct value	%Ns	Clade (Nextclade/Pangolin)	Number of nt differences relative to first sample
P001	1	Asymptomatic	22.6	0.0	19B/A.1	–
	2	3**	22.2	0.0		4
P003	1	Unknown	18.0	0.0	19B/A.1	–
	2	5**	25.3	0.0		0
P005	1	0*	19.1	0.3	19B/A.1	–
	2	12	30.9	0.0		0
P006	1	Asymptomatic	25.6	0.0	19B/A.1	–
	2	0**	29.7	0.0		0
P007	1	0*	15.8	0.0	19B/A.1	–
	2	6	26.3	0.0		0
P008	1	0*	17.7	0.0	19B/A.1	–
	2	16	29.4	0.0		0
P009	1	0*	25.3	0.0	20C/B.1.21	–
	2	9	21.7	0.0		0
P010	1	− 7	20.7	0.0	19B/A.1	–
	2	4	26.2	0.0		0
	3	7	31.3	0.0		0
	4	15	26.1	0.0		0
P011	1	0	25.3	0.5	20C/B.1.21	–
	2	8	27.7	0.0	20C/B.1.21	0
	3	11	31.6	0.1		0
P012	1	5	21.6	0.7	20C/B.1.21	–
	2	5	19.8	0.0		0
P014	1	Asymptomatic	27.6	0.0	19B/A.1	–
	2	3**	29.2	1.6		0
P015	1	3	18.5	0.0	19B/A.1	–
	2	11	21.1	0.0		0
	3	14	27.9	0.0		0
P016	1	16	23.9	0.0	20C/B.1	–
	2	19	25.3	0.0		0
	3	22	30.9	0.0		0
P017	1	10	24.8	0.0	19B/A.1	–
	2	13	28.6	0.0		0
	3	21	26.6	0.0		0
P018	1	Unknown	15.3	0.0	20B/B.1.1.77	–
	2	3**	17.8	0.0		0
P019	1	Unknown	14.6	0.0	20A/B.1	–
	2	19**	31.1	0.3		0

All patients with less than 2% unknown bases (Ns) are included. The last column indicates nucleotide differences compared to the first sample collected for each respective patient. One asterisk (*) indicates symptoms were present at first time point but exact date of symptom onset is unknown. Two asterisks (**) indicate days since first sample.