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: https://nextstrain.org/ncov/gisaid/africa.
Furthermore, Israel has reported the first case today, a traveler