Recherche de virus de l'hépatite C recombinants chez des patients multi-exposés

Depuis 2002, 5 virus recombinants inter-génotypiques du virus de l'hépatite C (RF_2k/1b, RF_2b/1b, RF_2i/6p, RF-2/5 et RF_2b/6w) ont été mis en évidence chez des patients toxicomanes ou hémophiles. Le génome des virus recombinants inter-génotypiques appartient au génotype 2 en 5' et à un autre génotype en 3'. Le point de recombinaison entre les 2 génotypes se situe dans la région génomique NS2-NS3. La fréquence de survenue des recombinaisons n'est pas encore évaluée car les techniques de génotypage actuellement utilisées en pratique courante, basées l'analyse d'une seule région génomique, ne permettent pas de les détecter. Nous avons recherché des souches recombinantes de VHC dans une population de 63 patients atteints d'hépatite chronique C, usagers de drogues par voie intra-veineuse ou hémophiles. La recherche a été réalisée par séquençage puis analyse phylogénétique de 2 régions génomiques différentes, l'une en 5' du génome codant pour la protéine d'enveloppe E1, et l'autre en 3' codant pour la polymérase virale NS5B. La comparaison des analyses réalisées sur les 2 extrémités du génome n'a permis de mettre en évidence ni recombinants inter-génotypiques ni cas de co-infection dans la population étudiée. En dépit d'une prévalence qui parait actuellement faible, il parait nécessaire d'étudier les virus recombinants inter-génotypiques en recherche fondamentale et clinique afin de déterminer leur mécanisme de formation, leur épidémiologie mondiale, leur prévalence et surtout leur sensibilité aux traitements actuels et du futur. Leur diffusion pourrait amener à reconsidérer l'utilisation en pratique courante des techniques de génotypage basées sur l'analyse d'une seule région du génome.CLERMONT FD-BCIU-Santé (631132104) / SudocLYON1-BU Santé (693882101) / SudocSudocFranceF

COVID‐19 systematic screening of asymptomatic haematopoietic stem cell donors: Less if often more

Abstract From COVID pandemic spread until now, many HSCT unrelated donor registries recommend as a precaution a systematic COVID‐19 testing for all donors during the precollection time. Literature is quite poor to support this systematic attitude. We report one sibling allogeneic HSCT which we proceeded despite a positive COVID test on related asymptomatic donor and summarize the all seven cases reported until now. We suggest to question this systematic COVID testing, two years after pandemic began, when there is no systematic testing on other blood products received during all the haematological malignancies treatment process

TEM-158 (CMT-9), a New Member of the CMT-Type Extended-Spectrum β-Lactamases▿

TEM-158 was found to include the substitutions previously observed for TEM-12 and TEM-35. This enzyme presented hydrolytic activity against ceftazidime and a high level of resistance against clavulanate, which can alter its detection. Its discovery highlights the need for accurate detection methods

Evaluation of real-time RT-PCR Rhino&EV/Cc r-gene® (bioMérieux) kit versions 1 and 2 for rhinovirus detection

International audienc

An accurate and reliable screening for SARS-CoV-2 in human sperm samples by RT-PCR: A requirement to evaluate the viral contamination risk during SARS-CoV-2 pandemic

International audienceStudy question:How to ensure a reliable and accurate detection of SARS-CoV-2 in seminal plasma and spermatozoa fractions of human sperm samples? Summary answer:This RT-PCR assay showed high sensibility, repeatability and reproducibility for SARS-CoV-2 detection in seminal plasma and spermatozoa fractions, with a detection limit of 17 genomes/reaction. What is known already:SARS-CoV-2 pandemic brings numerous concerns, such as the safety of gametes for patients undergoing assisted reproductive technologies, fertility preservation or sperm donation. Transient viremia and expression of SARS-CoV-2 receptors in testis and accessory glands bring the question of the presence of the virus in sperm samples. Moreover, the contamination during sperm collection may be possible. The few available studies about this issue mostly showed the absence of SARS-CoV-2 detection in semen of COVID-19 patients, except one reported study. All these studies performed SARS-CoV-2 detection with RT-PCR assays approved for naso-pharyngeal swabs, without a process specifically validated for semen fractions. Study design, size, duration:Method validation was conducted between July 2020 and January 2021. SARS-CoV-2 direct detection was performed according to the French Society of Microbiology guidelines (SFM). Repeatability (n=6), reproducibility (n=3), limit of quantification (n=2) and of detection (n=6) were evaluated in seminal plasma (SP) and spermatozoa samples isolated after density gradient centrifugation and cryopreserved. In addition, variability of the whole analytical method efficiency was evaluated in samples of men with normal (n=6) or altered sperm parameters (n=6).Participants/materials, setting, methods:Samples were surplus semen obtained from men undergoing routine semen analysis after granting informed consent. Assays were performed on SP and frozen spermatozoa fractions. After automated RNA extraction (MGISP-960, MGI-Tech®), real-time RT-PCR was performed using the one-step multiplex TaqPath COVID-19 kit (ThermoFisher®) targeting three viral regions (ORF1, nucleocapsid-N and spike-S proteins). An exogenous internal control was added before RNA extraction. Positive samples and dilution ranges were prepared with a standard (SARS-CoV-2 inactivated virus, QnosticTM Randox®). Main results and the role of chance:RT-PCR assay applied for human sperm samples has been previously validated and is routinely used for SARS-CoV-2 detection in naso-pharyngeal swabs. We evaluated the efficiency of RNA extraction and RT-PCR for SARS-CoV-2 detection in semen fractions. The qualitative and quantitative performance of the whole analytical method was validated with an accuracy profile for SP and spermatozoa fractions. Overall, for repeatability, the standard deviation (SD) of the cycle threshold (Ct) was lower than 0.40 for the strong positive sample and 0.50 for the low positive one. An exception was observed for the S target of the low positive SP samples (SD=3) which was consistent with S being the less sensitive target of the assay. For reproducibility, SD of the Ct was lower than 0.30 for the strong positive sample and 0.80 for the low positive, except for the S target of the low positive (SD=1.5). The linearity range was determined for N target, the most sensitive target of the RT-PCR assay. It layed between 5200 and 52 SARS-CoV-2 genomes/reaction. The limit of detection of the RT-PCR assay was 17 viral genomes/reaction. Equal efficiency of the assay was observed for SP and spermatozoa independently of semen parameters (normal and altered sperm parameters). Limitations, reasons for caution:Our detection method was validated for the whole process: RNA extraction (reagents and system), RT-PCR (reagents and thermocycler QuantStudio 5TM) and for both SP and frozen spermatozoa fractions. Variability might be observed with a different extraction system or a different type of biological sample.Wider implications of the findings:This validated RT-PCR assay enables accurate and reliable screening of SARS-CoV-2 in SP and spermatozoa fractions, mandatory to investigate the presence of the virus in semen samples of patients undergoing assisted reproductive techniques, fertility preservation or sperm donation, and to ensure viral safety in the cryobanking process during covid-19 pandemic

Validation of a SARS-CoV-2 RT-PCR assay: a requirement to evaluate viral contamination in human semen

International audienc

One year after ICU admission for severe community-acquired pneumonia of bacterial, viral or unidentified etiology. What are the outcomes?

IntroductionMultiplex polymerase chain reaction (mPCR) for respiratory virus testing is increasingly used in community-acquired pneumonia (CAP), however data on one-year outcome in intensive care unit (ICU) patients with reference to the causative pathogen are scarce.Materials and methodsWe performed a single-center retrospective study in 123 ICU patients who had undergone respiratory virus testing for CAP by mPCR and with known one-year survival status. Functional status including dyspnea (mMRC score), autonomy (ADL Katz score) and need for new home-care ventilatory support was assessed at a one-year post-ICU follow-up. Mortality rates and functional status were compared in patients with CAP of a bacterial, viral or unidentified etiology one year after ICU admission.ResultsThe bacterial, viral and unidentified groups included 19 (15.4%), 37 (30.1%), and 67 (54.5%) patients, respectively. In multivariate analysis, one-year mortality in the bacterial group was higher compared to the viral group (HR 2.92, 95% CI 1.71-7.28, p = 0.02) and tended to be higher compared to the unidentified etiology group (p = 0.06); but no difference was found between the viral and the unidentified etiology group (p = 0.43). In 64/83 one-year survivors with a post-ICU follow-up consultation, there were no differences in mMRC score, ADL Katz score and new home-care ventilatory support between the groups (p = 0.52, p = 0.37, p = 0.24, respectively). Severe dyspnea (mMRC score = 4 or death), severe autonomy deficiencies (ADL Katz score ≤ 2 or death), and major adverse respiratory events (new home-care ventilatory support or death) were observed in 52/104 (50.0%), 47/104 (45.2%), and 65/104 (62.5%) patients, respectively; with no difference between the bacterial, viral and unidentified group: p = 0.58, p = 0.06, p = 0.61, respectively.ConclusionsCAP of bacterial origin had a poorer outcome than CAP of viral or unidentified origin. At one-year, impairment of functional status was frequently observed, with no difference according to the etiology

Severe Pneumonia Associated with Adenovirus Type 55 Infection, France, 2014

International audienceHuman adenoviruses (HAdVs) comprise 70 recognized genotypes (as of February 15, 2016; http://hadvwg.gmu.edu/) and are frequently associated with mild and acute upper respiratory tract infections, depending on virus type and host immune status (1). HAdV type 55 (HAdV-55) has recently reemerged as a highly virulent pathogen, causing severe and sometimes fatal pneumonia among immunocompetent adults, particularly in Asia (2–4). Formerly known as HAdV-11a, HAdV-55 is a genotype resulting from recombination between HAdV-11 and HAdV-14 (5). We report 2 cases of severe pneumonia associated with HAdV-55 infection in Franc

Increase over time of antibody levels 3 months after a booster dose as an indication of better protection against Omicron infection

International audienceThe third, "booster", vaccination increases the overall immune response against SARS-CoV-2 variants. However, after the initial peak at around 3 weeks post-vaccination, anti-spike antibody levels decline. Post-booster kinetics of cellular response has been less investigated and there is no documented evidence of a true boosting effect. Furthermore, multiple studies underline the less effective immune responses against Omicron, the latest variant of concern, at both humoral and cellular levels. In this letter, we analyse humoral (anti-RBD IgG levels) and cellular (IFN-? release assay) immune response in 205 health care workers 3 weeks and 3 months after administration of an mRNA-based booster dose, either mRNA-1273 or BNT162b2. Since all subjects were SARS-CoV-2 infection-naive, we also looked at the incidence of Omicron infection between 3 and 6 months post-booster.At both timepoints, 3x mRNA-1273 vaccination had the highest overall antibody and IFN-? levels, followed by 3x BNT162b2 vaccination and heterologous mRNA-based regimens. Heterologous ChAdOx1-mRNA-based regimen had the lowest antibody levels while cellular response equal to that of 3x BNT162b2 vaccination and heterologous mRNA-based regimens. Our results show that both humoral and cellular responses waned at 3 months for all vaccination regimens. However, we identified three trajectories of dosage variation. Interestingly, the subgroup of subjects with increasing anti-RBD IgG levels over time had a lower incidence of Omicron infection. Whether increasing humoral response at 3 months post-booster is more indicative of protection than a high initial peak remains to be confirmed in a larger cohort

Comparative T and B immune responses of four different anti-COVID-19 vaccine strategies 6 months after vaccination

International audienc