Experts Have Confirmed Omicron Has 4 New ‘Sub-Variants’

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Omicron is changing as it infects more and more people. Scientists in South Africa and Botswana who are working with the World Health Organization have picked up these subtly different versions of omicron and are currently analysing their samples (WHO, 2022).

What is a ‘sub-variant’ of omicron?

They are Omicron viruses with a new combination of mutations, which are not yet classified as new variants (NICD, 2022). There are dozens of mutations that distinguish Omicron BA.1 (the original variant) from BA.2 (Callaway, 2022). These mutations are particularly at key portions of the virus’s spike protein (Callaway, 2022).

How many omicron sub-variants have been identified?

The Omicron variant has been divided into three ‘sublineages‘, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3). New research released by the WHO suggests there may even be versions BA.4 and BA.5 which have so far been identified in four people in Botswana and 23 in South Africa. Outside Africa, the BA.4 and the BA.5 have been confirmed in Belgium, Denmark, Germany and the United Kingdom (WHO, 2022).

What is known about the omicron sub-variants?

Original Omicron (BA.1): has high transmissibility and infectivity compared to the Delta variant, but the hospitalization rates are lower, and it has a less severe progression (Mohapatra et al., 2022).

(BA.2): has a high transmissibility and may have high severity (Mohapatra et al., 2022). However, there is presently no evidence on the severity of the BA.2 sub-lineage as per data provided by the FDA (Dhawan & Choudhary, 2022).

(BA.3): spreads slowly and causes fewer cases, may be due to the loss of six mutations that were part of the original BA.1 Omicron variant (Mohapatra et al., 2022).

(BA.4 & BA.5): it is still too early to definitively know if there are any new symptoms associated with these lineages (NICD, 2022). What we do know is that BA.4 and BA.5 have identical spike proteins, most comparable to BA.2 (Tegally et al., 2022). Whilst the Bayesian phylogenetic methods employed in Tegally et al., ( 2022) suggest that BA.4 and BA.5 are independent sub-variants that originated around the same time as BA.1 and BA.3, other studies methods suggest they could have descended from BA.2.

Why are scientists worried about the new Omicron sub-variants?

Scientists have a number of reasons to be wary of the rapidly spreading sub-variants. However, the biggest concern currently seems be around the ability of BA.2 to lower the protective ability of vaccines and natural protection offered by past infections (WHO, 2022).

Scientists in Israel have identified a handful of cases in which people who had recovered from BA.1 became infected with BA.2. (Callaway, 2022). But more research needs to be done to fully understand this issue.


Is BA.2 in South Africa?

Yes, according to an article released by the WHO, BA.2 is currently circulating in South Africa along with 3 other sub-variants (WHO, 2022).

Which Version Of Omicron is the most Common?

Our study partner The National Institute For Communicable Diseases Of South Africa, which worked with us on the Cough Check study, has said that:

Omicron has been the dominant variant in South African since it emerged in November 2021. In the beginning of the omicron wave, BA.1 (the original omicron) was the dominant lineage, and remained dominant through January 2022 (NICD, 2022).

Omicron BA.2 started increasing in the proportion of the South African population it infected in December 2021 and was dominant by February 2022 (NICD, 2022).

Omicron BA.3 never became dominant, but has been continually detected a low levels (see NICD press release, 2022; NICD, 2022).

BA.4 and BA.5 have increased in prevalence in SA, and as of 29 April 2022 to the 4th of May when this statement was released by the NICD, together make up the majority of genomes found amongst COVID patients tested in South Africa (NICD, 2022).

BA.4 and/or BA.5 have been confirmed in seven provinces in South Africa (Eastern Cape, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, North West and Western Cape) in samples collected between 1 January 2022 and 20 April 2022 (Tegally et al., 2022).

In Gauteng and KwaZulu-Natal, BA.4 and BA.5 have rapidly replaced BA.2, and are responsible for approximately 60-75% of sequenced cases by the week starting 18 April 2022 (Tegally et al., 2022).

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