Table 1.

Sequence profiles from the analysis of separate aliquots of the same primary sample and of the viral isolates. Only mutations above 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. Conversely, in the viral isolates the ORF1ab portion is Delta-like (italics), the rest of the genome is Omicron-like (bold). This mutational pattern is consistent with a single viral population, deriving from the recombination of two separate lineages.

	Sequence 1			Sequence 2			Plaque assay
gene	protein	depth	var fraction %	protein	depth	var fraction (%)	gene	protein	depth	var fraction (%)	gene	protein	depth	var fraction (%)	gene	protein	depth	var fraction (%)
ORF1ab				Ile695Val	1702	73.6	ORF1ab	Ile695Val	1515	99.7	Spike	Ala67Val	2995	99.8	ORF3a	Thr64=	2786	99.8
	Phe924=	2101	99.7	Phe924=	1777	99.3		Phe924=	1871	99.5		His69_Val70del	3001	99.9	E gene	Thr9Ile	1556	100
				Pro2046Leu	1017	71.5		Gly934Val	1856	99.5		Thr95Ile	3931	99.9	M gene	Asp3Gly	2015	99.9
				Pro2287Ser	2874	74.1		Asn1076=	1771	99.9		Gly142_Tyr145delinsAsp	4445	99.9		Gln19Glu	2013	99.9
				Ala2529Val	1633	74.3		Ala1306Ser	3610	99.9		Asn211_Leu212delinsIle	1308	100		Ala63Thr	2158	99.9
	Thr3255Ile	1690	100	Thr3255Ile	1616	99.8		Tyr1873=	1737	99.8		Arg214_Asp215insGluProGlu	1305	97.5	ORF6	Arg20=	459	99.1
				Ala3645=	3997	72.2		Pro2046Leu	1217	99.4		Gly339Asp	2524	99.8	ORF7b	Leu18=	3204	99.8
				Thr3646Ala	3997	72.2		Pro2287Ser	4221	99.6		Ser371Pro	134	100	N gene	Pro13Leu	5706	99.9
	Leu3674_Gly3676del	744	100	Leu3674_Gly3676del	525	100		Ala2529Val	2973	99.7		Ser371Phe	134	100		Glu31_Ser33del	2189	99.7
	Val3689=	746	100	Val3689=	1199	99.7		Asp2907=	2428	99.6		Ser373Pro	134	100		Arg203Lys	1771	99.8
	Pro4715Leu	2651	99.7	Pro4715Leu	2368	99.9		Val2930Leu	522	99.2		Ser375Phe	134	100		Arg203=	1771	99.9
	Gly5063Ser	6005	73.2	Gly5063Ser	5473	75.3		Thr3255Ile	2100	99.9		Lys417Asn	584	100		Gly204Arg	1771	99.9
	Pro5401Leu	5085	74.3	Pro5401Leu	6446	76.2		Ala3645=	8379	99.8		Asn440Lys	4132	99.9
				Ala6319Val	471	71.5		Thr3646Ala	8379	99.8		Gly446Ser	4131	99.9
Spike	Ala67Val	1323	73.5					Val3689=	2176	99.9		Thr547Lys	2721	99.7
	His69_Val70del	1323	73.3					Pro4715Leu	2930	99.8		Asp614Gly	5187	99.9
	Thr95Ile	2156	99.9	Thr95Ile	2304	99.9		Gly5063Ser	5078	99.9		His655Tyr	4796	99.8
	Gly142_Tyr145delinsAsp	1211	100	Gly142_Tyr145delinsAsp	1181	100		Pro5401Leu	9979	99.9		Asn679Lys	3369	100
	Glu156_Arg158delinsGly	334	98.2	Glu156_Arg158delinsGly	252	100		Ala6319Val	2302	100		Pro681His	3368	99.8
	Leu452Arg	159	100	Leu452Arg	106	100						Ala701Val	231	99.6
	Thr478Lys	314	100	Thr478Lys	210	100						Asn764Lys	1232	99.5
	Asp614Gly	2780	99.9	Asp614Gly	3559	100						Asp796Tyr	408	100
	Asp950Asn	651	79.7	Asp950Asn	1003	90.1						Asn856Lys	3903	99.2
												Gln954His	1544	99.8
												Asn969Lys	872	100
												Leu981Phe	884	99.5
												Asp1146=	1428	99.7

ORF, open reading frame.