A Simple and Fast Method to Sequence the Full-Length Spike Gene for SARS-CoV-2 Variant Identification from Patient Samples

Since the beginning of the pandemic, a race has been underway to detect SARS-CoV-2 virus infection (PCR screening, serological diagnostic kits), treat patients (drug repurposing, standard care) and develop a vaccine. After almost a year of active circulation worldwide, SARS-CoV-2 variants have appeared in different countries. Those variants include mutations in multiple regions of the genome, particularly in the spike gene. Because this surface protein is a key player in both the spread of the virus and the efficacy of vaccine strategies, the challenge is to efficiently monitor the appearance of spike mutations in the population. The present work describes a procedure based on the widely available Sanger technology to produce a full-length sequence of the spike gene from patient-derived samples

SARS-CoV-2 transmission via apical syncytia release from primary bronchial epithelia and infectivity restriction in children epithelia

The beta-coronavirus SARS-CoV-2 is at the origin of a persistent worldwide pandemic. SARS-CoV-2 infections initiate in the bronchi of the upper respiratory tract and are able to disseminate to the lower respiratory tract eventually causing acute severe respiratory syndrome with a high degree of mortality in the elderly. Here we use reconstituted primary bronchial epithelia from adult and children donors to follow the infection dynamic following infection with SARS-CoV-2. We show that in bronchial epithelia derived from adult donors, infections initiate in multi-ciliated cells. Then, infection rapidly spread within 24-48h throughout the whole epithelia. Within 3-4 days, large apical syncytia form between multi-ciliated cells and basal cells, which dissipate into the apical lumen. We show that these syncytia are a significant source of the released infectious dose. In stark contrast to these findings, bronchial epithelia reconstituted from children donors are intrinsically more resistant to virus infection and show active restriction of virus spread. This restriction is paired with accelerated release of IFN compared to adult donors. Taken together our findings reveal apical syncytia formation as an underappreciated source of infectious virus for either local dissemination or release into the environment. Furthermore, we provide direct evidence that children bronchial epithelia are more resistant to infection with SARS-CoV-2 providing experimental support for epidemiological observations that SARS-CoV-2 cases’ fatality is linked to age. Significance Statement Bronchial epithelia are the primary target for SARS-CoV-2 infections. Our work uses reconstituted bronchial epithelia from adults and children. We show that infection of adult epithelia with SARS-CoV-2 is rapid and results in the synchronized release of large clusters of infected cells and syncytia into the apical lumen contributing to the released infectious virus dose. Infection of children derived bronchial epithelia revealed an intrinsic resistance to infection and virus spread, probably as a result of a faster onset of interferon secretion. Thus, our data provide direct evidence for the epidemiological observation that children are less susceptible to SARS-CoV-2

Front Microbiol

Since 2021, 3 variants of concern (VOC) have spread to France, causing successive epidemic waves. To describe the features of Alpha, Delta and Omicron VOC circulation in the Nouvelle-Aquitaine region, France, between February 2021 and February 2022. Data from the three university hospitals (UH) of Nouvelle-Aquitaine were used to describe regional SARS-CoV-2 circulation (RT-PCR positive rates and identified VOC) as well as its consequences (total number of hospitalizations and admissions in intensive care unit). They were analyzed according to the predominant variant and compared with national data. A total of 611,106 SARS-CoV-2 RT-PCR tests were performed in the 3 Nouvelle-Aquitaine UH during the study period. The 37,750 positive samples were analyzed by variant-specific RT-PCR or whole-genome sequencing. In 2021, Alpha VOC was detected from week 5 until week 35. Delta became the most prevalent variant (77.3%) in week 26, reaching 100% in week 35. It was replaced by Omicron, which was initially detected week 48, represented 77% of positive samples in week 52 and was still predominant in February 2022. The RT-PCR positive rates were 4.3, 4.2, and 21.9% during the Alpha, Delta and Omicron waves, respectively. The ratio between intensive care unit admissions and total hospitalizations was lower during the Omicron wave than during the two previous waves due to the Alpha and Delta variants. This study highlighted the need for strong regional cooperation to achieve effective SARS-CoV-2 epidemiological surveillance, in close association with the public health authorities

Compléxité du virus de l'hépatite C dans le foie et la plasma de patients co-infectés par le virus de l'immunodéficience humaine

BORDEAUX2-BU Santé (330632101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Mise au point d'une PCR quantitative de l'herpès virus humainde type 6 au laboratoire de virologie (intérêt dans le suivi des greffes de moelle osseuse)

Human herpesvirus 6 primary infection usually happens in the first two years of life. Most of the time, it is harmless with only high fever and more rarely cutaneous rash. HHV-6 remains latent in numerous cell types and may reactivate in immunocompromised patients, especially those who undergo bone marrow or peripheral stem cell transplantation. HHV-6 infection is often associated with delayed engraftment or bone marrow suppression. It may also play a role in the outbreak or exacerbation of graft versus host disease. During this work, we developped a quantitative HHV-6 real-time PCR on the LightCycler instrument. It may efficiently help in determining HHV-6 reactivation and appreciating the effectiveness of antiviral therapy. In case of HHV-6 related symptoms, viral load quantification in blood and biopsy samples appear to be helpful to assess reactivation.TOULOUSE3-BU Santé-Centrale (315552105) / SudocSudocFranceF

Détection du parvovirus B19 par PCR en temps réél

BORDEAUX2-BU Santé (330632101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Recherche du virus d'Epstein-Barr dans le sang périphérique de patients greffés rénaux ou en attente de greffe

BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Impact de la variabilité génétique sur l'antigénicité et l'immunogénicité des glycoprotéines d'enveloppe d'isolats de HTLV-1 d'origines géographiques différentes

Les glycoprotéines d'enveloppe du rétrovirus HTLV-1 (Human T-Cell Leukemia Virus type 1), essentielles dans l'étape d'infection et très immunogènes, représentent une possible cible vaccinale. L'impact de leur variabilité génétique sur leurs fonctions est analysé par l'étude génétique et sérologique d'isolats HTLV-1 de patients d'origine géographique différente. L'analyse phylogénétique de la totalité du gène env de 62 nouveaux isolats et de souches PTLV-1 permet d'individualiser de nouveaux groupes africains. Un nouveau sous-type Maroni émerge entre les sous-types majeurs cosmopolite et d'Afrique centrale. La réactivité des sérums de patients vis-à-vis de peptides synthétiques, montre que la région 273-295 est immunodominante et comporte des épitopes linéaires et conformationnels dont certains neutralisables, identifiés par l'inhibition de la formation de syncytia. L'acide aminé H ou Y en position 290 modifie la capacité neutralisante des sérums et l'immunogénicité de l'enveloppe.The highly immunogenic HTLV-1 (Human T-Cell Leukemia Virus ttype 1) envelope glycoproteins play a critical part in the initial infection step and represent a possible vaccinal target. The ffect of their genetic variability on their functions is analysed by a genetic and serologic study of HTLV-1 isolates of patients from different geographic origin. The phylogenetic analysis of the total env gene from 62 new isolates and PTLV-1 strains allowed to identify new African groups. A new "Maroni" subtype is individualized, emerging between major cosmopolitan subtypes and subtypes from Central Africa. The reactivity of patients sera was tested against synthetic peptides. This study demonstrate that the 273-295 region is immunodominant and includes linear and conformational epitopes. Some of them induce neutralizing antibodies which inhibit syncitia formation. The amino acid H or Y in 290 position modifies the sera neutralizing activity and the envelop immunogenicity.BORDEAUX2-BU Santé (330632101) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF

Détection semi-quantitative du virus BK chez les receveurs de greffon rénal (approche préliminaire en vue de la mise en oeuvre d'une technique quantitative de routine)

BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Mise au point d'une méthode de diagnostic des infections à Adénovirus par PCR en temps réel

BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF