A5035255464- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Respiratory viral infections research
- Viral gastroenteritis research and epidemiology
- Animal Virus Infections Studies
- COVID-19 epidemiological studies
- Bacteriophages and microbial interactions
- Long-Term Effects of COVID-19
- Influenza Virus Research Studies
- Evolution and Genetic Dynamics
- Bacillus and Francisella bacterial research
- CRISPR and Genetic Engineering
- COVID-19 Impact on Reproduction
- Pneumonia and Respiratory Infections
- Plant Virus Research Studies
- Nosocomial Infections in ICU
- Virus-based gene therapy research
- Immune responses and vaccinations
- CAR-T cell therapy research
- Maternal and fetal healthcare
- Antibiotic Resistance in Bacteria
- Viral Infections and Outbreaks Research
- vaccines and immunoinformatics approaches
- Monoclonal and Polyclonal Antibodies Research
Hospices Civils de Lyon
2019-2025
Université Claude Bernard Lyon 1
2019-2025
École Normale Supérieure de Lyon
2019-2025
Inserm
2019-2025
Centre National de la Recherche Scientifique
2019-2025
Virologie et Pathologies Humaines
2020-2023
Centre International de Recherche en Infectiologie
2019-2023
Hôpital de la Croix-Rousse
2020-2023
Laboratoire National de Référence
2022
Hôpital Albert-Chenevier
2021
We report the strategy leading to first detection of variant concern 202012/01 (VOC) in France (21 December 2020). First, spike (S) deletion H69–V70 (ΔH69/ΔV70), identified certain SARS-CoV-2 variants including VOC, is screened for. This associated with a S-gene target failure (SGTF) three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. approach revealed mutations co-occurring ΔH69/ΔV70 S:N501Y VOC.
Abstract Since the beginning of COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with use very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare performance four NGS-based approaches for WGS. Twenty-four clinical respiratory samples a large scale Ct values (from 10.7 to 33.9) were sequenced Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including...
Background Early detection and characterisation of SARS-CoV-2 variants have been continue to be essential for assessing their public health impact. In August 2023, Santé publique France implemented enhanced surveillance BA.2.86 sub-lineage JN.1 because genetic divergence from other increased prevalence. Aim To detail how combining epidemiological laboratory data sources, targeted investigations modelling enabled comprehensive JN.1. Methods Data were collected using a standardised...
Improving timeliness of pathogen identification is crucial to allow early adaptation antibiotic therapy and improve prognosis in patients with pneumonia. We evaluated the relevance a new syndromic rapid multiplex PCR test (rm-PCR) on respiratory samples guide empirical antimicrobial adult community-acquired pneumonia (CAP), hospital-acquired (HAP), ventilator-acquired (VAP).This retrospective multicenter study was conducted four French university hospitals. Respiratory were obtained from...
A reliable diagnostic assay is crucial to early detect new COVID-19 cases and limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Since the onset of pandemic, World Health Organization has published several molecular approaches developed by referral laboratories, including Charité (Germany), HKU (Hong Kong), China CDC (China), US (United States), Institut Pasteur, Paris (France). We aimed compare sensitivity specificity these different RT-PCR assays using...
The emergence of SARS-CoV-2 variant 20I/501Y.V1 (VOC-202012/1 or GR/501Y.V1) is concerning given its increased transmissibility. We reanalysed 11,916 PCR-positive tests (41% all positive tests) performed on 7-8 January 2021 in France. prevalence was 3.3% among nationwide and 6.9% the Paris region. Analysing recent rise 20I/501Y.V1, we estimate that, French context, 52-69% more transmissible than previously circulating lineages, depending modelling assumptions.
We aimed to investigate the first Omicron cases detected in France order assess case characteristics and provide supporting information on possible impact of this variant healthcare system. A standardized questionnaire was used collect from confirmed probable cases. Median age 468 investigated 35 years, 376 were symptomatic (89%); 64% vaccinated with two doses 7% had received three doses. Loss smell taste reported by 8.3% 9% cases, respectively. Seven hospitalized, those unvaccinated...
High viral load in upper respiratory tract specimens observed for Delta cases might contribute to its increased infectivity compared the other variant. However, it is not yet documented if Omicron variant's enhanced also related a higher load. Our aim was determine spread loads variant.Nasopharyngeal swabs, 129 (Omicron) and 85 (Delta), from Health Care Workers were collected during December 2021 at University Hospital of Lyon, France. Cycle threshold (Ct) RdRp target cobas® 6800 SARS-CoV-2...
Abstract From December 2021-February 2022, an intense and unprecedented co-circulation of SARS-CoV-2 variants with high genetic diversity raised the question possible co-infections between how to detect them. Using 11 mixes Delta:Omicron isolates at different ratios, we evaluated performance 4 sets primers used for whole-genome sequencing developed unbiased bioinformatics method detection involving genetically distinct lineages. Applied on 21,387 samples collected 6, 2021 February 27, 2022...
To describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France 7 immunocompetent epidemiologically unrelated patients.
During routine molecular surveillance of SARS-CoV-2 performed at the National Reference Center Respiratory Viruses (Lyon, France) (n = 229 sequences collected February–April 2020), two frameshifting deletions were detected in open reading frame 6, same position (27267). While a 26-nucleotide deletion variant (D26) was only found one nasopharyngeal sample March 2020, 34-nucleotide (D34) within single geriatric hospital unit 5/9 patients and health care worker April 2020. Phylogeny analysis...
ABSTRACT Respiratory viruses represent a significant public health threat. There is the need for robust and coordinated surveillance to guide global responses. Established in 2012, Global Influenza Hospital Surveillance Network (GIHSN) addresses this by collecting clinical virological data on persons with acute respiratory illnesses across network of hospitals worldwide. GIHSN utilizes standardized patient enrolment collection protocol its study sites. It leverages pre‐existing national...
Abstract We report a novel severe acute respiratory syndrome coronavirus 2 variant derived from clade 19B (HMN.19B or Henri Mondor variant). This is characterized by the presence of 18 amino acid substitutions, including 7–8 substitutions in spike protein and deletions. These variants actively circulate different regions France.
Abstract Background: Targeted-sequencing sequencing methods, such as 16S-rRNA profiling, viral metagenomics, and human mRNA are mainly used for the exploration of microbiome, yet their combination can be expensive time-consuming. Metatranscriptomics snapshots entire active microbiome trough bulk RNA in one test, but lacks adequate comparisons with targeted-sequencing approaches. Results: We compared metatranscriptomics targeted methods bacterial, viral, components, using 20 nasopharyngeal...
Abstract We report the implementation of a two-step strategy for identification SARS-CoV-2 variants carrying spike deletion H69-V70 (ΔH69/ΔV70). This resulted in S-gene target failure (SGTF) three-target RT-PCR assay (TaqPath kit). Whole genome sequencing performed on 37 samples with SGTF revealed several receptor-binding domain mutations co-occurring ΔH69/ΔV70. More importantly, this enabled first detection variant concern 202012/01 France December 21 th 2020. Since September (S)...
Abstract High viral load in upper respiratory tract specimens observed for Delta cases may contributed to its increased infectivity compared the Alpha variant. Herein, we showed that RT-PCR Ct values Health Care Workers sampled within five days after symptom onset were significantly higher Omicron than (+2.84 Ct, p=0.008). This result comfort studies showing transmissibility of is related other mechanisms virus excretion.
Abstract The sensitivity of SARS-CoV-2 RT-PCR tests developed by Charité (Germany), HKU (Hong-Kong), China CDC (China), US (United-States), and Institut Pasteur, Paris (France) was assessed on cell culture supernatants clinical samples. Although all assays performed well for detection, RdRp Pasteur (IP2, IP4), N CDC, N1 were found to be the most sensitive.