The VOI 20C / H655Y (lineage B.1.616) initially detected in Lannion, in Brittany, was classified as variant to follow on 03/14/2021. Among the mutations and deletions carried by this VOI, several are found in one or more VOCs and VOIs, and could lead to increased transmissibility (H655Y in particular), post-vaccination or post-infection immune escape or even lower efficacy monoclonal antibody treatments (Y144- deletion, D215G and V483A mutations).
However, according to analyzes carried out by the CNR using sera from vaccinated subjects, infected subjects, or antibodies monoclonal, the data available at this stage do not show significant escape of the variant 20C / 655Y on neutralization. As of 05/04/2021, 42 confirmed cases of infection with the 20C / 655Y variant have been reported in France, including 39 in Brittany and 3 in other regions in people linked to the zone of circulation of the virus in Brittany (made up of several urban communities around Lannion, Guingamp, Saint- Brieuc, Paimpol). Eighteen deaths (43%) were reported, mostly in the elderly (age median 84 years) or with co-morbidities.
The high lethality associated with this variant is probably related to a bias in the identification of cases in which this variant was detected, most often from deep samples (generally more serious), but additional investigations are carried out to characterize the impact of this variant in terms of severity. The majority of confirmed cases are related to transmission chains in healthcare establishments in this geographical area (CH de Guingamp, de Lannion, de Paimpol).
We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, characterized by poor detection by RT-PCR tests on nasopharyngeal samples despite typical clinical, radiological, and biological features of COVID-19. We also noted high case fatality rate in our sampled population. This work also highlights the difficulties to manage nosocomial cases when the gold-standard test fails to confirm the diagnosis. With constantly emerging new variants, one should remain attentive to any unusual clinical situation that could be linked to such emergence.
In our study, among patients with a positive RT-PCR assay in the B.1.616 group, the sensitivity of one, two, three, and four tests on nasopharyngeal samples were, respectively, 5/34 (15%), 13/34 (38%), 14/34 (45%), and 17/34 (55%). RT-PCR tests on sputum, or broncho-alveolar lavage (BAL), were positive in 8/34 (24%) B.1.616-related COVID-19 cases with previous negative nasopharyngeal RT-PCR tests.
As samples from the lower respiratory tract are more difficult to obtain in frail patients, the real extent of the B.1.616-related COVID-19 outbreak in our institution has probably been underestimated. A large surveillance study, with sequencing of a representative sample of 15% of all RT-PCR-positive COVID-19 cases during the study period found no community-acquired B.1.616-related COVID-19 (Flash study#5, SpF, Paris, France, unpublished data), but the low detection in standard sampling may have contributed to this result.”
MedrXiv preprint – A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality