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

Table 3.

Sequence profiles from the analysis of aliquot 2 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 2
gene	protein	depth	var fraction %	gene	protein	depth	var fraction %	gene	protein	depth	var fraction %
*ORF1ab*	Ile695Val	74	1702	*Spike*	Thr19Arg	1024	30	*ORF3a*	Ser26Leu	974	39
	Lys856Arg	33	1561		Ala67Val	504	55		Thr64=	1294	62
	Phe924=	100	1765		His69_Val70del	504	55		Asp155Tyr	1839	44
	Gly934Val	61	1773		Thr95Ile	2304	100
	Asn1076=	30	725		Gly142_Tyr145delinsAsp	1181	100	*E gene*	Thr9Ile	788	53
	Ala1306Ser	34	2851		Glu156_Arg158delinsGly	252	100
	Ala1707=	72	922		Arg214_Asp215insGluProGlu	540	67	*M gene*	Asp3Gly	1619	62
	Pro2046Leu	72	1017		Gly339Asp	4855	64		Gln19Glu	1415	60
	Pro2287Ser	74	2874		Ser371Pro	170	65		Ala63Thr	1681	53
	Ala2529Val	74	1633		Ser371Phe	170	65		Ile82Thr	1681	47
	Ala2710Thr	27	897		Ser373Pro	170	65
	Asp2907=	69	2072		Ser375Phe	170	65	*ORF6*	Arg20=	334	51
	Thr3255Ile	100	1616		Lys417Asn	508	50
	Pro3395His	27	2849		Leu452Arg	106	100	*ORF7a*	Thr120Ile	2315	54
	Ala3645=	72	3997		Thr478Lys	210	100
	Thr3646Ala	72	3997		Thr547Lys	3698	41	*ORF7b*	Leu18=	3123	52
	Leu3674_Gly3676del	100	525		Asp614Gly	3559	100	*ORF7b*	Thr120Ile	811	30
	Val3689=	100	1199		His655Tyr	5317	45
	Ile3758Val	39	2381		Asn679Lys	2604	45	*N gene*	Pro13Leu	8973	46
	Val4310=	32	4634		Pro681Arg^a	1438	55		Asp63Gly	1574	50
	Pro4715Leu	100	2368		Pro681His^a	1161	45		Arg203Met^a	1711	55
	Asn4992=	29	2079		Asn764Lys	1804	52		Arg203Lys^a	1378	45
	Gly5063Ser	75	5473		Asn856Lys	4261	65		Gly204Arg	3096	45
	Pro5401Leu	76	6446		Asp950Asn	1003	90		Gly215Cys	10837	57
	Ile5967Val	28	2662		Asn969Lys	933	53		Asp377Tyr	5012	48
	Ala6319Val	72	470		Leu981Phe	938	53
					Asp1146=	1276	65

^⁎

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.