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BA.4: Recombinant of Omicron BA.1 and BA.3

BA.1, BA.3, BA.4, Coronavirus, Infection, Omicron, Recombination, South Africa, Transmission, USA

Potential BA.4 lineage with a mix of BA.1 and BA.3 mutations, 5 sequences found in South Africa and USA.

Cornelius Roemer on Github: I’m breaking this post from @c19850727 into a separate issue to allow for dedicated discussion.

Below is the original post from Sakaguchi:

Hi I came across the following 5 sequences:
Accession Virus name
EPI_ISL_8262451 hCoV-19/USA/CO-CDC-MMB12218639/2021
EPI_ISL_8439638 hCoV-19/South Africa/NICD-N23764/2021
EPI_ISL_8402519 hCoV-19/Puerto Rico/PR-CDC-S874/2021
EPI_ISL_9962725 hCoV-19/South Africa/NICD-N29342/2022
EPI_ISL_10210515 hCoV-19/South Africa/NICD-N29407/2022

They are all classified as BA.1 by Pango/Nextstrain, but with G2832A reversed. Instead, they have T670G (BA.2 and BA.3 defining ), C832T (BA.3 defining ), G4184A (BA.2 and BA.3 defining) and C4321T (BA.2 defining).
Downstream from T5386G it’s all BA.1, but with a few private mutations: G7684A, C29167T, G29734A.

Github issue page


William Haseltine at

“The simplest interpretation of the origin of BA.4 is a recombination event between BA.1 and BA.3. It is likely that BA.3 contributes the portion of the genome extending from the 5’ end halfway through the NSP3 gene of the replication complex (about 2,000 amino acids). The remainder is plausibly contributed by BA.1” article


Hong Kong: Omicron BA.2 with S:I1221T mutation designated BA.2.2




Image by Mihai Panait from Pixabay