We designed an observational study to assess the clinical profile and outcome of patients infected with the SARS-CoV-2, before and during the spread of the UK-variant. Patients admitted in the Emergency department (ED), in the Infectious Diseases department (IDD) and the ICU at Nice University Hospital (Cote d’Azur University UCA), France, were part of this study. Data were extracted from the hospital electronic database (n°410) of patient’s record, registered on clinicaltrial.gov NCT04779021, also from the hospital Virology Lab and the Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275 CNRS/UNS (for sewage samples analysis).
In the way to quickly characterize the clinical consequences of the spread of these new variants, we designed a three-step approach.
First step: Spread of the UK-variant in our area and among hospitalized patients. Data of the sequencing of SARS-CoV-2 identified from the sewage collector of the city of Nice (overall gathering) in December and January, and PCR screening from all positive samples analyzed at the hospital Virology Lab from newly admitted and diagnosed patients (starting late January 2021).
Second step: Concomitant epidemiology and clinical characteristics at hospital admission of COVID-19 overtime, by an evaluation over a three-month period, from December 1st 2020 to February 22nd 2021, of all patients admitted in the ED for COVID-19. Demographic data, clinical severity as recorded by the NEWS-2 scoring system and the follow-up (ward admission versus ambulatory follow-up). Patients coming from Elderly Care facilities clusters or transferred from another hospital with a SARS-CoV-2 positive PCR were not included in the study.
Third step: Clinical severity and follow-up of hospitalized patients for a SARS-CoV-2 pneumonia, in the IDD or ICU over three fortnights:
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before the spread of the UK-variant in our area,i.e. from December 7th to 21st 2020 (Bef-F),
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the two fortnights after starting a PCR screening from all positive samples analyzed at the hospital Virology Lab from newly admitted and diagnosed patients (late January 2021), i.e. from January 24th to February 7th and from February 8th to 22nd, 2021 respectively Aft1-F and Aft2-F)
Demographic data, clinical signs and severity were recorded by the NEWS-2 (ED), SAPS-2 and SOFA scores (ICU), CT-Scan findings and the follow-up were recorded and analyzed.
We assessed the UK-variant spread in sewage through the Nice wastewater plant, which treats the sewage for a population of 390,000 inhabitants. The daily incoming volume varied from 97,000 m3 (in December 15th, 2020) to 128,000 (January 21st, 2021), due to rain at the end of January. Sequencing followed the protocol of the Artic consortium (https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye), data being analyzed with their pipeline (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html). For each position associated with 20I/501Y.V1 lineage (https://cov-lineages.org/pangolin_tutorial.html) the fraction of 20I/501Y.V1 lineage reads relative to the total number of reads is assessed.
The virological assessment of positive PCR for SARS-CoV-2 variants at the Virology Lab was done as follow : SARS-CoV-2 positive samples were screened for the presence of the 20I/501Y.V1 lineage using either TaqPath COVID-19 RT‐PCR (ThermoFisher, Illkirch-Graffenstaden, France) or ViroBOAR Spike 1.0 RT-PCR (Eurofins Biomnis, Lyon, France) kits, following manufacturer’s instructions. Identification of the 20I/501Y.V1 variant was further verified by sequencing by sequencing a random set of samples in which the reliability of the RT-PCR screening tests was checked.. Briefly, Spike protein regions covering ∆69/70 and ∆144 deletions, as well as the N501Y substitution, were amplified through RT-PCR, and amplicons were sequenced by the Sanger method.
Patients who were hospitalized with an identification of the UK-variant at the Virology Lab (see upper) were paired (1:2) with patients hospitalized during the three first weeks of December (variant-free period), on age and gender. News-2 score, time 1st symptoms-ED admission and further hospital orientation (ICU versus medical ward) were the main evaluated criteria.
Data were expressed as mean ± standard deviation SD. Comparisons are done using Chi-2, Fisher exact-test for categorical variables and Student-t test, Kruskall Wallis test and Man Whitney U-test for continuous variables comparisons, if required. All data were analyzed using SPSS software®.