Table 2.

Non-synonymous mutations with >100× position coverage that are present in January 2021, but absent in July 2020. RdRp = RNA-dependent RNA polymerase. The entirety of the GISAID database was searched on June 17, 2021. Acknowledgement for contributions to GISAID are included in Supplementary Dataset S8.

Nucleotide	Mutation in product	Coverage	SRA counts	GISAID	GISAID filtereda
Orf1ab polyprotein
6032	NSP3_A1105T	129	0	797	5
8083	NSP3_M1788I	116	120	>10 k	128
9928	NSP4_M458I	163	42	8321	61
11,085	NSP6_Y38F	124	0	218	1
12,986	NSP9_M101V	106	0	430	1
14,805	RdRp_T455I	102	0b	0b	0
16,175	RdRp_L912F	138	0	0	0
Other
21,707	Surface glycoprotein	217	51	4923	1
27,964	ORF8 protein	107	2544	0c	0c

^aLocation filtered by South Carolina and Collection date between January 1 and January 31, 2021, inclusive.

^bAbsent from database search results, but present in the literature (Bui et al., 2021; Zeng et al., 2020).

^cGISAID not searchable by ORF8 substitutions.