Variant tracking by PCR at HUG


Rue Gabrielle-Perret-Gentil 4
1205 Geneva

Isabella Eckerle
Isabella Eckerle
Physician in charge of the Centre
Laurent Kaiser
Laurent Kaiser
Head of division

S-gene dropout PCR monitoring of different variants

Since the start of the pandemic, a deletion that results in failure to amplify the S-gene target, referred to as "S-gene dropout", in a PCR test (TaqPath RT-PCR) has been useful for tracking the spread of different variants . This deletion is currently not found in the currently dominant XBB variants, but is found in the BA.2.86 variant. As a result, this PCR was used as a proxy to monitor the prevalence of BA.2.86 relative to the XBB variants. Similarly, the S-gene dropout was useful to monitor the replacement of BA.2 by BA.5 as can be seen below (graphs under +INFOS), the percentage of PCR tests with "S-gene dropout" increased rapidly from May 2022 onwards, until it replaced BA.2. 

In view of the appearance of BA.2.86 the virology laboratory currently systematically performs additional PCR tests for S-gene dropout. Variants are monitored by sequencing as part of the national SARS-CoV-2 sequencing program.

346T mutation follow-up

The R:346T mutation has been described as an escape mutation to the monoclonal antibody cilgavimab, which is given concomitantly with tixagevimab and known as Evusheld®. It results in reduced or no in vitro neutralization by cilgavimab. It involves a mutation in the spike protein at amino acid 346: arginine (R) is replaced by the amino acid threonine (T).  Since tixagevimab already shows reduced or no neutralization against circulating variants, this mutation means that Evusheld® will be less effective or even lose its effectiveness against currently circulating variants.  

Until January 2023, a PCR (TIB Molbiol) was performed once a week to estimate the prevalence of this mutation. This mutation is now present in almost all currently circulating variants.

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Last update : 25/01/2024