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SARS-CoV-2 Omicron B.1.1.529

SARS-CoV-2 Omicron B.1.1.529

Genomic surveillance of SARS-CoV-2 in Belgium

Report of the National Reference Laboratory (UZ Leuven & KU Leuven)

Situation update – 26 of November 2021

(report 2021_56)

Executive summary

Omicron B.1.1.529

South Africa has communicated on 25/11/2021 the emergence of a new variant of concern (will

probably be named Nu, corresponding to the pangolin lineage B.1.1.529). In this report, we discuss the

current situation in South Africa and the world, and we assess the current situation in Belgium.

We report here the first case of B.1.1.529 infection in Belgium.

Authors (National Reference Laboratory – UZ Leuven and KU Leuven):

Piet Maes, Lize Cuypers, Simon Dellicour, Guy Baele, Tom Wenseleers, Caspar Geenen, Bram Slechten,

Johan Van Weyenbergh, Els Keyaerts, Barney Potter, Sunita Janssenswillen, Elke Wollants, Marc Van

Ranst, Emmanuel André.

With the collaboration of the laboratories of UCL, ULB, UMons, UNamur, ULiège, UGent,

UZA/UAntwerpen, Jessa ZH, AZ Delta, AZ Klina, IPG, AZ St Lucas Gent, OLVZ Aalst, Briant network, ZNA,

AZ St Jan Brugge, UZ Brussel, LHUB-ULB, and UZ Leuven/KU Leuven; and Sciensano HealthData.

SARS-CoV-2 Omicron B.1.1.529

1. Situation in South Africa

2. Available genomic data worldwide

3. Genetic profile of B.1.1.529

4. High-throughput deep mutational scanning

5. Situation in Belgium

6. First case of B.1.529 in Belgium

7. Recommendations

1. Situation in South Africa

South Africa has one of the best genomic surveillance systems around the world, fueled by outstanding

scientists and a very efficient network of collaborating laboratories. The data they share with the world is

of outermost importance. Most other countries in the African continent still have very limited capacity to

accurately and quickly identify emerging public health threats, and this situation should be regarded as a

major problem at the global level.

South Africa is now experiencing the fourth wave of SARS-CoV-2 infections. The two last waves were

caused by variants of concern, namely Beta (first described in South-Africa) and Delta (first described in

India). The current wave is caused by a new variant of concern which has very recently been

characterized as B.1.1.529 or variant Nu (Figure 1). 

This resurgence of infections occurs in the context of

the summer (Southern Hemisphere) and of low baseline circulation of the Delta variant, suggesting that

the new variant might be more transmissible than the Delta variant.

Figure 1: New confirmed cases of SARS-CoV-2 per day and by a variant in South Africa.

This potentially higher transmissibility of Nu compared to Delta seems to be confirmed in a multinomial

fit analysis (Figure 2) based on the sequencing data and the data generated by the diagnostic PCR

laboratories (S gene target failure when using the TaqPath PCR). As the situation is rapidly evolving and

the disease surveillance efforts in South Africa are highly focused on the detection of this new variant

(active case finding is prioritized against baseline surveillance), the actual evolution of this variant may

be overestimated. Nevertheless, even if this unprecedented growth rate advantage (currently estimated

at 38% per day) would be lower, this new variant very probably still has the sufficient growth advantage

to become the dominant variant in South Africa and the rest of the world. In other terms, this variant

could have the potential to cause a new global wave of infections. The scale of this wave and its impact

on the health of populations will be determined by the level of vaccination (on which we can act directly)

and the still missing definitive assessment of this new variant about vaccine efficacy, the efficacy of

antiviral therapies, transmissibility, and virulence.

Figure 2: Current (dark red) and foreseen (red) share of the Nu variant in South Africa (multinomial fit),

based on the data currently available. These projections may evolve based on upcoming data, as the

current data are not yet fully representative of the situation.

In South Africa, where the majority of cases and genomic sequences are currently coming from, genome

sequencing and other genetic analysis from Tulio de Oliveria’s team found that the B.1.1.529 variant was

responsible for all of 77 of the virus samples they analyzed from Gauteng, South Africa, collected

between 12 and 20 November. Prof. de Oliveira predicts an increase of B.1.1.529 that will soon be found

in nearly 100% of genomic sequencing efforts (currently at 75%).

2. Available genomic data worldwide

Currently, 66 B.1.1.529 genomes are available on GISAID: 6 from Botswana (including the 5 earliest

available genomes), 58 from South Africa, and 2 from Hong Kong. An initial Nextstrain build, as

constructed by the Nextstrain Team (Figure 3), is available at:

Furthermore, Israel has reported the first case today, a traveler