Table 1.

Allele Frequency Changes Between the Severe Acute Respiratory Syndrome Coronavirus 2 Genomes in Patient 1

Gene	Protein	Nucleotide Change	Amino Acid Change	Variant Allele Frequency (%)
				Initial Infection		Reinfection
				Initial Diagnosis	Follow-up
5’UTR		241C>Ta		.0	.0	79.4
ORF1ab	nsp1	526G>T	Q87D	99.9	99.1	19.0
ORF1ab	nsp1	635C>T	R124C	.0	.0	28.6
ORF1ab	nsp2	1059C>T	T85I	.0	.0	66.0
ORF1ab	nsp3	3037C>Ta	F106=	.0	.0	88.7
ORF1ab	nsp3	4951G>C	L744F	.0	.0	20.5
ORF1ab	nsp3	5572G>T	M951I	99.9	NAb	45.7
ORF1ab	nsp3	5822C>T	L1035F	.0	NAb	23.3
ORF1ab	nsp3	6262T>C	N1181=	99.9	99.8	26.7
ORF1ab	nsp3	6719A>G	T1334A	99.8	99.9	24.9
ORF1ab	nsp4	9773delT	V407fs	.0	.0	25.2
ORF1ab	nsp4	9996C>T	S481L	.0	.0	23.3
ORF1ab	nsp6	11083G>Tc	L37F	99.5	99.2	8.0
ORF1ab	nsp9	12810T>C	L42P	.0	.0	32.0
ORF1ab	nsp12	14408C>Ta	P323L	.0	.0	92.1
ORF1ab	nsp12	14805C>T	Y455=	99.7	99.4	59.4
ORF1ab	nsp13	16580C>T	T115I	.0	.0	34.5
S	S	23403A>Ga	D614G	.0	.0	84.8
ORF3a	ORF3a	25563G>Ta	Q57H	.0	.0	80.0
ORF3a	ORF3a	26060C>T	T223I	99.8	99.5	10.0
ORF3a	ORF3a	26144G>Tc	G251V	99.9	98.6	10.0
N	N	28768A>G	T165=	.0	.0	47.5

Abbreviation: NA, not available.

^aThe variant that characterizes the clade G.

^bNot available because the region between 5214 and 5931 of the reference genome was not well covered by aligned sequencing reads.

^cThe variant that characterizes the clade V.