Table 3.

Genotyping of genome sequence variations associated with SARS-CoV-2 haplotypes in viruses isolated from Iranians (Tehran, Mashhad, Ahvaz, Shiraz) infected between December 21, 2020 and January 19, 2021 (Month 10)^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: 14)
D	4	+	.	.	+	.	+	+	.	.	.	.
L	3	+	+	.	+	+	+	+	.	.	.	.
M	2	+	+	.	+	.	+	+	.	.	.	.
Tehran samples proposed to be infected with two viruses
	No. Samples (ID)
D and H1	1 (T-30)	+	.	.	+	.	T/C	T/C	.	.	.	.
A and D	1 (T-20)	+	.	.	+	.	T/C	T/C	.	G/A	G/A	G/C
C and L	1 (T-13)	+	+	.	+	+	T/C	T/C	C/T	.	.	.
M and L	1 (T-18)	+	+	.	+	G/T	+	+	.	.	.	.
M and N	1 (T-26)	+	+	.	+	.	T/C	T/C	.	.	.	.
Samples from provinces outside of Tehran
Mashhad	4 samples	+	+	.	+
Mashhad	1 samples	+	.	.	+
Ahvaz	5 samples	+	+	.	+
Shiraz	5 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. +: variant sequence:., reference sequence, empty cell: not sequenced.