Advances in Virology

Research Article

Whole-Genome Comparison of Representatives of All Variants of SARS-CoV-2, Including Subvariant BA.2 and the GKA Clade

Table 1

Insertion/deletion pattern and its location at the whole genome of representatives of various variants of SARS-CoV-2.
NoPositionD6485-6487D11260-11268D21605-21613D21959-21967D21965-21967I21968-21971D22005-22010D22170-22172I22181-22189D22266-22274D26143-26146D27055-27067D28351-28359D29723-29748
Location at the genomeORF1ABORF1ABSpikeSpikeSpikeSpikeSpikeSpikeSpikeSpikeORF3AMANP3′UTR
Virus strain
1WH-1−−−−−−−−−−−−−−
2A-1−+−−+−−−−−−−−−
3A-2−+−−+−−−−−−−−−
4B-1−+−−−−−−−+−−−−
5B-2−+−−−−−−−−−−−−
6G-1−+−−−−−−−−−−−−
7G2−+−−−−−−−−−−−−
8D-1−−−−−−+−−−−−−−
9D2−−−−−−−−−−−+−−
10L-1−−−−−−−−−−−−−−
11L-2−−−−−−−−−−−−−−
12M-1−−−−−+−−−−+−−−
13M-2−−−−−+−−−−+−−−
14O-1−++−−−−−−−−−+−
15O-2++−+−−−++−−−+−
16BA2-1−++−−−−++−−−++
17BA2-2−++−−−−−−−−−++
18GKA-1−−−−−−−−−−−−−−
19GKA-2−−−−−−+−−−−−−−
20GH-1−−−−−−−−−−−−−−
21GH-2−−−−−−−−−−−−−−
N: no insertion/deletion; P: positive insertion/deletion; Position based on aligned sequence starting from nucleotide no. 1 of Wuhan-Hu-1; Location in the genome was based on GenBank data of Wuhan-Hu-1; Virus strains and GISAID codes WH-1 is Wuhan-Hu-1, A-1 is Alpha EPI ISL 1489174, A-2 is Alpha EPI ISL 1489173, B-1 is Beta EPI ISL 660190, B-2 is Beta EPI ISL 660613, G-1 is Gamma EPI ISL 811149, G-2 is Gamma EPI ISL 87219, D-1 is Delta EPI ISL 1544014, D-2 is Delta EPI ISL 1838642, L-1 is Lambda EPI ISL 1111127, L-2 is Lambda EPI ISL 1111341, M-1 is Mu EPI ISL 2339799, M-2 is Mu EPI ISL 2339801, O-1 is Omicron EPI ISL 9010924, O-2 is Omicron EPI ISL 9042199, BA2-1 is BA2 LSPA-3B08C6A, BA2-2 is BA2 HSLL-3B08857, GKA-1 is EPI ISL 9021856, GKA-2 is HDF-IPP08027, GH-1 is GH/490 EPI ISL 6316493, and GH-2 is GH/490 ISL 7702915.