key: cord-0974598-lup6mgq5
authors: Bal, A.; Destras, G.; Gaymard, A.; Regue, H.; Semanas, Q.; d'Aubarde, C.; Billaud, G.; Laurent, F.; Gonzales, C.; Valette, M.; Lina, B.; Morfin, F.; Josset, L.
title: Screening of the H69 and V70 deletions in the SARS-CoV-2 spike protein with a RT-PCR diagnosis assay reveals low prevalence in Lyon, France
date: 2020-11-13
journal: nan
DOI: 10.1101/2020.11.10.20228528
sha: 346d82e09d54b2271418d17039abd55f2bea6e0d
doc_id: 974598
cord_uid: lup6mgq5

The H69 and V70 deletions in SARS-CoV-2 spike protein have been detected in mink and human infections. We found that these deletions resulted in a false negative result for the spike target of a commercial RT-PCR assay. From August 3rd to November 1st, 39/6964 (0.56%) of positive tests performed in Lyon, France, displayed a S negative profile suggesting a limited circulation of the deleted variant. This RT-PCR assay could be useful to address the risk of the mink variant spreading.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted November 13, 2020. ; https://doi.org/10.1101/2020.11.10.20228528 doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.

2 Abstract 30 The H69 and V70 deletions in SARS-CoV-2 spike protein have been detected in mink and 31 human infections. We found that these deletions resulted in a false negative result for the spike 32 target of a commercial RT-PCR assay. From August 3 rd to November 1 st , 39/6964 (0.56%) of is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted November 13, 2020. ; https://doi.org/10.1101/2020.11.10.20228528 doi: medRxiv preprint 3 A SARS-CoV-2 variant detected both in minks and humans in Denmark has raised concerns 37 about mutations associated with potential reduced susceptibility to neutralizing antibodies [1, is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted November 13, 2020. ; https://doi.org/10.1101/2020.11.10.20228528 doi: medRxiv preprint H69del and V70del screening with RT-PCR kit 62 In order to assess the use of TaqPath RT-PCR kit for the screening of the H69del and V70del, is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted November 13, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted November 13, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted November 13, 2020. We would like to thank all microbiologist, clinicians, laboratory technicians who contributed 138 to this investigation. We thank the authors, the originating and submitting laboratories for their 139 sequence and metadata shared through GISAID on which this research is based. We gratefully is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted November 13, 2020. ; https://doi.org/10.1101/2020.11.10.20228528 doi: medRxiv preprint

ECDC to assess risk associated with spread of SARS-CoV-2 in mink farms. European 148 Centre for Disease Prevention and Control

events/ecdc-assess-risk-associated-spread-sars-cov-2-mink-farms

CoV-GLUE: A Web Application for Tracking 153 SARS-CoV-2 Genomic Variation

Emerging genetic 155 diversity among clinical isolates of SARS-CoV-2: Lessons for today

Emergence of 158 genomic diversity and recurrent mutations in SARS-CoV-2

Human neutralizing antibodies elicited by 161 SARS-CoV-2 infection

Genomic 163 diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-164

GISAID -Mutations in spike putatively linked to outbreak in Danish mink farms

SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

The N-terminal 172 domain of spike glycoprotein mediates SARS-CoV-2 infection by associating with L-SIGN 173 and DC-SIGN

A neutralizing human antibody 175 binds to the N-terminal domain of the Spike protein of SARS-CoV-2

It is made available under a perpetuity.is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted November 13, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted November 13, 2020. ; https://doi.org/10.1101/2020.11.10.20228528 doi: medRxiv preprint