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Genomic Surveillance

Executive summary

Genomic surveillance in Belgium is based on whole genome sequencing (WGS) of a selection of
representative samples, complemented with targeted active surveillance initiatives and targeted
molecular markers aiming to early detect and precisely monitor the epidemiological evolution of
variants of concern (VOCs). Currently, 5.050 sequences of samples collected in Belgium are available
on GISAID in open access. During week 3 of 2021, Belgium achieved a coverage of 3,5% of all positive
sequences being sequenced.
During the last 2 weeks (week 5 and 6), 146 samples have been sequenced as part of the baseline
surveillance, among which 48 (33%) were 501Y.V1 and 8 (5%) were 501Y.V2.
Since week 52 of 2020, Belgium has experienced multiple introductions of VOCs followed by sustained
local transmissions. As a consequence of a higher transmissibility of these variants, we observe a
progressive shift in viral populations, with 501Y.V1 expected to represent the majority of circulating
strains by early March. Together with the rollout of vaccination, genomic surveillance will monitor the
eventual positive selection of VOCs harbouring immune escape mutations such as S:E484K.
During the last 2 weeks, the progressive phenomenon of viral population replacement by more
transmissible strains did not alter the overall stability of the epidemic in Belgium. This is probably due
to a combination of active public health response and limited number of social interactions in the
population. The risk of disruption of this equilibrium remains, as the proportion of more transmissible
viruses will continue rising, but this risk can be mitigated by a combination of active outbreak control
interventions, maintained efforts to reduce transmission in the population and rapid roll-out of