Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations

Bhattacharjee, Maloyjo Joyraj; Bhattacharya, Anupam; Kashyap, Bhaswati; Taw, Manash Jyoti; Li, Wen-Hsiung; Mukherjee, Ashis K.; Khan, Mojibur Rohman

doi:10.1186/s12985-023-02139-3

Virology Journal

Table 1 The dN/dS ratios in the first wave of infection, the α variant, δ variants in Assam, and the omicron variant outside of Assam

From: Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations

Gene Name	Gene length (bp)	Average dN (SE)	Average dS (SE)	Average dN/dS
First wave
ORF1ab	21,290	0.0715 (0.0142)	0.0684 (0.0133)	1.045
S	3822	0.1931 (0.0416)	0.2105 (0.0485)	0.917
ORF3a	828	0.0021 (0.00001)	0.0062 (0.00001)	0.339
E	228	0 (0)	0.0216 (0.00001)	0
M	669	0 (0)	0 (0)	*
ORF6	186	0.0079 (0.0001)	0 (0)	#
ORF7a	366	0.00009 (447E-05)	0.0169 (0.0004)	0.005
ORF7b	132	0 (0)	0.0414 (1.2985E-05)	0
ORF8	366	0.0013 (0.0001)	0.0159 (0.0002)	0.082
N	1260	0.0016 (5.28E-05)	0.0053 (8.3505E-05)	0.302
Average dN/dS ratio				0.448 (0.177)
Alpha variant
ORF1ab	21,290	0.0002 (0.00004)	0.0025(0.0.0001)	0.080
S	3822	0.1681 (0.0949)	0.1646(0.0750)	1.021
ORF3a	828	0.0005 (0.0001)	0.0079(0.0002)	0.063
E	228	0 (0)	0(0)	*
M	669	0.0004 (0.0003)	0.0079(0.0001)	0.051
ORF6	186	0 (0)	0(0)	*
ORF7a	366	0 (0)	0(0)	*
ORF7b	132	0 (0)	0(0)	*
ORF8	366	0 (0)	0(0)	*
N	1260	0.0007 (0.0001)	0.0044(0.0001)	0.159
Average dN/dS ratio				0.277 (0.188)
Delta variant
ORF1ab	21,290	0.0005 (5.9083E-06)	0.0012(9.7409E-06)	0.417
S	3822	0.1732 (0.0324)	0.2372(0.0374)	0.730
ORF3a	828	0.0004 (2.4662E-05)	0.0076(9.8678E-05)	0.053
E	228	0.0062 (5.3676E-05)	0(0)	#
M	669	0.0004 (6.3839E-05)	0.0082(5.3809E-05)	0.049
ORF6	186	0.0079 (6.2997E-05)	0(0)	#
ORF7a	366	0.0014 (0.0001)	0.0144(0.0001)	0.097
ORF7b	132	0 (0)	0.0448(0.0001)	0
ORF8	366	0.0005 (0.0001)	0.0149(2.6939E-05)	0.034
N	1260	0.0009 (1.96E-05)	0.0059(5.4534E-05)	0.153
Average dN/dS ratio				0.128 (0.050)
Omicron variant
ORF1ab	21,290	0.4627 (0.0363)	0.5177(0.0417)	0.894
S	3822	0.2650 (0.0840)	0.2139(0.0595)	1.239
ORF3a	828	0.0008 (7.04E-05)	0.0084(0.0002)	0.095
E	228	0 (0)	0.0236(0.0005)	0
M	669	0.0030 (0.0001)	0.0112(0.0002)	0.268
ORF6	186	0 (0)	0(0)	*
ORF7a	366	0 (0)	0(0)	*
ORF7b	132	0.0022 (0.0004)	0.0402(0.0129)	0.055
ORF8	366	0 (0)	0(0)	*
N	1260	0.0014 (0.0001)	0.0053(0.0002)	0.264
Average dN/dS ratio				0.469 (0.197)

The cases with dS/SE < 1, where SE is the standard error, are excluded in the estimation of dN/dS and are indicated by #. *Indicates dS = dN = 0

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ISSN: 1743-422X

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