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cases during the study period found no community-acquired B.1.616-related COVID-19 (Flash study#5, SpF, Paris, France, unpublished data), but the low detection in standard sampling may have contributed to this result.”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