tetano
Editor, Senior Moderator
Clin Microbiol Infect
. 2021 Oct 7;S1198-743X(21)00565-6.
doi: 10.1016/j.cmi.2021.09.035. Online ahead of print.
A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality: an observational study
Pierre Fillâtre[SUP] 1 [/SUP], Marie-José Dufour[SUP] 2 [/SUP], Sylvie Behillil[SUP] 3 [/SUP], Remi Vatan[SUP] 4 [/SUP], Pascale Reusse[SUP] 5 [/SUP], Alice Gabellec[SUP] 5 [/SUP], Nicolas Velmans[SUP] 6 [/SUP], Catherine Montagne[SUP] 7 [/SUP], Sophie Geffroy Du Coudret[SUP] 8 [/SUP], Edith Droumaguet[SUP] 9 [/SUP], Véronique Merour[SUP] 10 [/SUP], Vincent Enouf[SUP] 11 [/SUP], Rodolphe Buzele[SUP] 12 [/SUP], Marion Valence[SUP] 12 [/SUP], Elena Guillotel[SUP] 13 [/SUP], Bertrand Gagniere[SUP] 14 [/SUP], Artem Baidaliuk[SUP] 15 [/SUP], Anna Zhukova[SUP] 16 [/SUP], Mathieu Tourdjman[SUP] 17 [/SUP], Vincent Thibault[SUP] 18 [/SUP], Claire Grolhier[SUP] 18 [/SUP], Charlotte Pronier[SUP] 18 [/SUP], François-Xavier Lescure[SUP] 19 [/SUP], Etienne Simon-Loriere[SUP] 15 [/SUP], Dominique Costagliola[SUP] 20 [/SUP], Sylvie Van Der Werf[SUP] 3 [/SUP], Pierre Tattevin[SUP] 21 [/SUP], Nicolas Massart[SUP] 22 [/SUP]
Affiliations
Abstract
Objectives: In early January 2021, an outbreak of nosocomial cases of COVID-19 emerged in Western France, with RT-PCR tests repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole genome sequencing (WGS) revealed a new variant, currently defining a novel SARS-CoV-2 lineage: B.1.616. In March, WHO classified this variant as 'under investigation' (VUI). We analyzed the characteristics and outcomes of COVID-19 cases related to this new variant.
Methods: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled inpatients with either: i) positive SARS-CoV-2 RT-PCR on a respiratory sample; ii) seroconversion with anti-SARS-CoV-2 IgG/IgM; iii) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as either: i) B.1.616; ii) variant of concern (VOC); iii) unknown.
Results: From January 1[SUP]st[/SUP] to March 24[SUP]th[/SUP], 2021, 114 patients fulfilled inclusion criteria: B.1.616 (n=39), VOC (n=32), and unknown (n=43). B.1.616-related cases were older than VOC-related cases (81 years interquartile range [IQR] [73-88], vs 73 years IQR [67-82], P<0.05) and their first RT-PCR tests were rarely positive (6/39, 15% vs 31/32, 97%, P<0.05). B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.0 95% CI [1.5-10.9]), and increased lethality: 28-day mortality 18/39 (46%) for B.1.616, vs. 5/32 (16%) for VOC, P=0.006.
Conclusion: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, poorly detected by RT-PCR on nasopharyngeal samples, with high lethality.
Keywords: COVID-19 / Epidemiology; Coronavirus infections; SARS-CoV-2 variants; Severity of illness index / Virology.
. 2021 Oct 7;S1198-743X(21)00565-6.
doi: 10.1016/j.cmi.2021.09.035. Online ahead of print.
A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality: an observational study
Pierre Fillâtre[SUP] 1 [/SUP], Marie-José Dufour[SUP] 2 [/SUP], Sylvie Behillil[SUP] 3 [/SUP], Remi Vatan[SUP] 4 [/SUP], Pascale Reusse[SUP] 5 [/SUP], Alice Gabellec[SUP] 5 [/SUP], Nicolas Velmans[SUP] 6 [/SUP], Catherine Montagne[SUP] 7 [/SUP], Sophie Geffroy Du Coudret[SUP] 8 [/SUP], Edith Droumaguet[SUP] 9 [/SUP], Véronique Merour[SUP] 10 [/SUP], Vincent Enouf[SUP] 11 [/SUP], Rodolphe Buzele[SUP] 12 [/SUP], Marion Valence[SUP] 12 [/SUP], Elena Guillotel[SUP] 13 [/SUP], Bertrand Gagniere[SUP] 14 [/SUP], Artem Baidaliuk[SUP] 15 [/SUP], Anna Zhukova[SUP] 16 [/SUP], Mathieu Tourdjman[SUP] 17 [/SUP], Vincent Thibault[SUP] 18 [/SUP], Claire Grolhier[SUP] 18 [/SUP], Charlotte Pronier[SUP] 18 [/SUP], François-Xavier Lescure[SUP] 19 [/SUP], Etienne Simon-Loriere[SUP] 15 [/SUP], Dominique Costagliola[SUP] 20 [/SUP], Sylvie Van Der Werf[SUP] 3 [/SUP], Pierre Tattevin[SUP] 21 [/SUP], Nicolas Massart[SUP] 22 [/SUP]
Affiliations
- PMID: 34627988
- DOI: 10.1016/j.cmi.2021.09.035
Abstract
Objectives: In early January 2021, an outbreak of nosocomial cases of COVID-19 emerged in Western France, with RT-PCR tests repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole genome sequencing (WGS) revealed a new variant, currently defining a novel SARS-CoV-2 lineage: B.1.616. In March, WHO classified this variant as 'under investigation' (VUI). We analyzed the characteristics and outcomes of COVID-19 cases related to this new variant.
Methods: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled inpatients with either: i) positive SARS-CoV-2 RT-PCR on a respiratory sample; ii) seroconversion with anti-SARS-CoV-2 IgG/IgM; iii) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as either: i) B.1.616; ii) variant of concern (VOC); iii) unknown.
Results: From January 1[SUP]st[/SUP] to March 24[SUP]th[/SUP], 2021, 114 patients fulfilled inclusion criteria: B.1.616 (n=39), VOC (n=32), and unknown (n=43). B.1.616-related cases were older than VOC-related cases (81 years interquartile range [IQR] [73-88], vs 73 years IQR [67-82], P<0.05) and their first RT-PCR tests were rarely positive (6/39, 15% vs 31/32, 97%, P<0.05). B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.0 95% CI [1.5-10.9]), and increased lethality: 28-day mortality 18/39 (46%) for B.1.616, vs. 5/32 (16%) for VOC, P=0.006.
Conclusion: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, poorly detected by RT-PCR on nasopharyngeal samples, with high lethality.
Keywords: COVID-19 / Epidemiology; Coronavirus infections; SARS-CoV-2 variants; Severity of illness index / Virology.