. 2023 Mar 15;131:65–70. doi: 10.1016/j.ijid.2023.03.014

Table 2.

Sequence profiles from the analysis of aliquot 1 from primary sample. Mutations below 70% are reported. Most mutations are referable either to Delta (italics) or Omicron (bold). The mutational pattern in the primary sample is consistent with the presence of two separate viral lineages within the specimen.

Sequence 1
gene	protein	depth	var fraction %	gene	protein	depth	var fraction %	gene	protein	depth	var fraction %
				*Spike*	Thr19Arg	26	800
*ORF1ab*	Ile695Val	69	2025		Ala67Val	73	1323	*ORF3a*	Ser26Leu	34	815
	Lys856Arg	35	1214		His69_Val70del	73	1323		Thr64=	66	1102
	Phe924=	100	2096		Thr95Ile	100	2156		Asp155Tyr	41	2114
	Gly934Val	58	2094		Gly142_Tyr145delinsAsp	1211	100
	Asn1076=	36	598		Glu156_Arg158delinsGly	334	98	*E gene*	Thr9Ile	60	602
	Ala1306Ser	40	2672		Gly339Asp	64	4471
	Ala1707=	66	739		Ser371Pro	67	109	*M gene*	Asp3Gly	62	2196
	Pro2046Leu	66	1148		Ser371Phe	67	109		Gln19Glu	63	1996
	Pro2287Ser	69	2533		Ser373Pro	67	109		Ala63Thr	56	1982
	Ala2529Val	68	1501		Ser375Phe	65	109		Ile82Thr	45	1983
	Ala2710Thr	37	696		Lys417Asn	58	952
	Asp2907=	64	2293		Leu452Arg	100	159	*ORF6*	Arg20=	48	591
	Thr3255Ile	100	1690		Thr478Lys	100	314
	Pro3395His	34	2457		Thr547Lys	50	3938	*ORF7a*	Thr120Ile	50	2243
	Ala3645=	68	3282		Asp614Gly	100	2780
	Thr3646Ala	68	3282		His655Tyr	49	4559	*ORF7b*	Leu18=	57	3203
	Leu3674_Gly3676del	744	100		Asn679Lys	53	2032	*ORF7b*	Thr120Ile	27	961
	Val3689=	100	746		Pro681Arg^a	47	949
	Ile3758Val	43	1940		Pro681His^a	53	1079	*N gene*	Pro13Leu	45	7798
	Val4310=	36	3859		Asn764Lys	57	1805		Asp63Gly	53	1143
	Pro4715Leu	100	2651		Asn856Lys	62	3616		Arg203Met^a	58	1949
	Asn4992=	29	2756		Asp950Asn	80	649		Arg203Lys^a	42	1389
	Gly5063Ser	73	6005		Gln954His	20	650		Gly204Arg	42	3339
	Pro5401Leu	74	5086		Asn969Lys	58	1121		Gly215Cys	58	8679
	Ile5967Val	32	1998		Leu981Phe	57	1124		Asp377Tyr	51	4223
					Asp1146=	66	1679

^⁎

In two instances, we were able to identify the simultaneous presence of two marker mutations, respectively for Delta and Omicron, at the same genomic position.