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Table 1 Observed variations within the four SARS-CoV-2 isolates reported in this study

From: Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2

Genomic position: Variation Variation Type Associated genomic region Protein: amino acid change Frequency in the four isolates used in this study Frequency in the other Bangladeshi isolates Frequency in the isolates from rest of the world
1: ATTAAAGGTTTA>- Intergenic variant 5′UTR 1
1: ATTAAAGGTTTATA>- Intergenic variant 5′UTR 1
2: T>TA Intergenic variant 5′UTR 1 0 0
2: T>TTTCAAAGATCAAGTCA Intergenic variant 5′UTR 1 0 0
4: A>T Intergenic variant 5′UTR 1 0 58
7: G>C Intergenic variant 5′UTR 1 0 16
9: T>TTTTCGC Intergenic variant 5′UTR 1 0 0
12: A>T Intergenic variant 5′UTR 1 0 22
13: T>C Intergenic variant 5′UTR 1 0 36
280: C>T Synonymous variant orf1ab 5 V 1 0 5
601: C>T Synonymous variant orf1ab 112G 1 1 6
8782: C>T Synonymous variant orf1ab 2839S 4 1 3012
10,323: A>G Missense variant orf1ab 3353 K>R 1 5 154
10,329: A>G Missense variant orf1ab 3355D>G 3 1 1
10,870: G>T Synonymous variant orf1ab 3535L 1 0 27
12,119: C>T Missense variant orf1ab 3952P>S 1 0 8
15,324: C>T Synonymous variant orf1ab 5020 N 3 5 818
19,414: G>A Missense variant orf1ab 6384 V>I 1 0 0
22,468: G>T Synonymous variant S 302 T 4 1 99
23,320: C>T Synonymous variant S 586D 1 0 2
25,505: A>T Missense variant ORF3a 38Q>L 1 0 2
28,087: C>T Missense variant ORF8 65A>V 1 0 23
28,144: T>C Missense variant ORF8 84L>S 4 1 3050
28,878: G>A Missense variant N 202S>N 4 1 253
29,392: G>T Missense variant N 373 K>N 2 2 6
29,742: G>A Downstream gene variant 3′UTR 4 1 21
29,856: T>A Intergenic variant 3′UTR 1 0 6
29,858: T>A Intergenic variant 3′UTR 1 0 5
29,864: GAATGACAAAAAAAAAAAAAAAAAAAAA>G Intergenic variant 3′UTR 1 0 0
29,864: GAATGACAAAAAAAAAAAAAAAAAAAAAAA>T Intergenic variant 3′UTR 1 0 0
29,870: CAAAAAAAAAAAAAAAAAAAAAAAAAAA>C Intergenic variant 3′UTR 1 1
29,870: C>G Intergenic variant 3′UTR 1 0 3
29,872: A>T Intergenic variant 3′UTR 1 0 12
29,873: A>C Intergenic variant 3′UTR 1 0 3
29,874: A>G Intergenic variant 3′UTR 1 0 12
29,875: A>G Intergenic variant 3′UTR 1 1 5
29,878: A>T Intergenic variant 3′UTR 1 0 3
29,880: A>G Intergenic variant 3′UTR 1 2 5
29,882: A>G Intergenic variant 3′UTR 1 0 13
29,883: A>T Intergenic variant 3′UTR 1 0 8
29,884: A>C Intergenic variant 3′UTR 1 0 10
29,885: A>G Intergenic variant 3′UTR 1 1 11
29,886: A>T Intergenic variant 3′UTR 1 1 5
29,887: A>G Intergenic variant 3′UTR 1 0 11
29,888: A>T Intergenic variant 3′UTR 1 1 4
29,890: A>G Intergenic variant 3′UTR 1 1 6
29,891: A>G Intergenic variant 3′UTR 1 0 15
29,892: A>G Intergenic variant 3′UTR 1 0 13
29,893: A>G Intergenic variant 3′UTR 1 0 15
29,895: A>T Intergenic variant 3′UTR 2 0 6
29,896: A>G Intergenic variant 3′UTR 1 0 7
29,896: A>C Intergenic variant 3′UTR 1 0 3
29,897: A>G Intergenic variant 3′UTR 2 0 4
29,898: A>G Intergenic variant 3′UTR 2 0 6
29,898: A>T Intergenic variant 3′UTR 1 0 5
29,900: A>G Intergenic variant 3′UTR 1 0 10
29,901: AAA>A Intergenic variant 3′UTR 1 0
29,901: A>G Intergenic variant 3′UTR 2 0 5
29,903: A>GCCGTCGT Intergenic variant 3′UTR 1 0
29,903: A>GCGTCGTGT Intergenic variant 3′UTR 1 0