Table 2.

Genotyping of genome sequence variations associated with SARS-CoV-2 haplotypes in viruses isolated from Iranians infected between November 21 and December 20, 2020 (Month 9)^x.

Sequence variation		14408C>T (RdRp: p.Pro312Leu)	22189_22191delTAT (S: p.Ile210del)	22992G>A (S: p.Ser477Asn)	23403A>G (S: p.Asp614Gly)	25563G>T (ORF3a: p.Gln57His)	28688T>C (N: p.Leu139Phe)	28835T>C (N: p.Ser188Pro)	28854C>T (N: p.Ser194Leu)	28881G>A (N: p.Arg203Lys)	28882G>A (N: p.Arg203Arg)	28883G>C (N: p.Gly204Arg)
Associated haplotype*/Virus strain**		H1/G			H1/G	H1b/GH	H5	H5 linked	H1b linked	H1a/GR	H1a/GR	H1a/GR
Variation ID		V1	V2	V3	V4	V5	V6	V7	V8	V9	V10	V11
Genome type#	No. Samples in Tehran (Total: 50)
A (=H1a)	13	+		.	+	.	.	.	.	+	+	+
H1b	1 (T-35)	+		.	+	+	.	.	.	.	.	.
B (=H1b+V8)@	8	+	.	.	+	+	.	.	+	.	.	.
C (=H1b+V2+V8)@	21	+	+	.	+	+	.	.	+	.	.	.
Tehran samples proposed to be infected with viruses whose genomes are products of recombination
	No. Samples (ID)
D	1 (T-47)	+		.	+	.	+	+	.	.	.	.
E	1 (T-51)	+		.	+	.	.	.	+	.	.	.
F	1 (T-3)	+		+	+	.	.	.	.	+	+	+
G	1 (T-42)	+		+	+	+	.	.	+	.	.	.
H	1 (T-18)	+	+	+	+	+	.	.	+	.	.	.
I	1 (T-4)	+	+	.	+	+	.	.	.	.	.	.
Rasht samples proposed to be infected with two viruses and/or with viruses whose genomes are products of recombination
D	1 (R-4)	+		.	+	.	+	+	.	.	.	.
D and J	1 (R-3)	+		.	+	G/T	+	+	.	.	.	.
D and K	2 (R-1 & R-2)	C/T		.	+	.	+	+	.	.	.	.
Other samples from provinces outside of Tehran
Rasht	46 samples	+			+
Ahvaz	50 samples	+			+
Kashan	12 samples	+			+
Tabriz	12 samples	+			+
Kermanshah	12 samples	+			+
Shiraz	12 samples	+			+

^X, Summary of data presented in Table S2; *, Haplotypes described in Safari et al, (2021a); **, virus strains described in GISAID; #, each type refers to a genome with a unique combination of sequence variations; @, number of sequences with and without the variant nucleotide at position V2 extrapolated on basis of results on 12 samples in which amplicon 2 was amplified and sequenced.

+: variant sequence:., reference sequence, empty cell: not sequenced.