Using Discarded Facial Tissues to Monitor and Diagnose Viral Respiratory Infections.

Molecular biology amplification enables sensitive detection of most respiratory viruses through nasopharyngeal swabbing. We developed an innovative approach to detect viral genomes on used facial tissues. In 2 communities of children, used tissues were collected once weekly for 1 year. Pooled analysis of tissues enabled detection of successive virus circulation in 4 age groups over time and forecasted by several weeks the circulation of influenza in the general population. At the individual level, in a proof-of-concept study of 30 volunteers with influenza-like signs/symptoms, we identified common respiratory viruses. The signals for SARS-CoV-2 obtained in parallel from 15 facial tissues and swab samples were similar and often higher for the tissues (11/15). Individual analysis of tissues offers a noninvasive, sensitive, and affordable alternative to self-sampling without a medical care requirement. Pooled analyses may be used to detect virus spread in specific communities, predict seasonal epidemics, and alert the population to viral infections.

Facteurs de risque de contamination professionnelle des soignants par le SARS-CoV-2 : enquête par TDR et sérologies au CHU de Rennes

Introduction Depuis décembre 2019, et l’apparition de l’épidémie par SARS-CoV-2, de nombreux soignants ont été contaminés par ce virus au cours de leur exercice professionnel. La transmission du virus peut en effet se faire par voie cutanée, par voie respiratoire, en particulier par les gouttelettes émises par les malades lors de toux, et enfin par aérosol. Toutefois, les circonstances exactes ne sont pas connues avec précision, alors même que ces éléments sont indispensables à la prévention. L’objectif de cette étude est de rechercher l’existence de gestes professionnels à risque associés à une plus grande prévalence de contamination par ce virus. Méthodes Entre le 29 mai et le 10 juillet 2020, l’ensemble du personnel du CHU de Rennes a été convié à participer à une enquête séro-épidémiologique. Dix équipes de 3 personnes sont ainsi passées systématiquement dans tous les services du CHU à plusieurs reprises. Tous les personnels volontaires ont rempli un questionnaire standardisé sur la présence de symptômes compatibles avec la COVID-19 et leurs activités durant l’épidémie (février à juin 2020). Ils bénéficiaient dans le même temps d’un test rapide (TDR) de Ng Biotech®, approuvé par le CNR. Un échantillon de sujets tirés au sort selon leurs activités dans un service ayant accueilli ou non des patients COVID-19 positifs a rempli un questionnaire complémentaire sur les gestes réalisés ainsi que l’utilisation d’équipements de protection individuelle (masques, gants, charlottes, blouses, …). Les sujets ayant eu une RT-PCR durant l’épidémie ont également été inclus dans cet échantillon. Les TDR positifs ont fait l’objet d’une confirmation sérologique par au moins un test ELISA sur la base du volontariat. Résultats Plus de 7000 personnels du CHU ont participé au dépistage, dont 3500 à l’étude ancillaire. Le taux de positivité du TDR ou de la sérologie est de 3,78 %. L’analyse préliminaire montre que le risque d’un TDR ou d’une sérologie positive associé à la prise en charge d’un patient COVID-19 positif est de 1,15 (0,74–1,78), de 2,00 (1,33–3,01) lors du contact avec un professionnel lui-même positif et de 2,06 (1,31–3,26) lors de la présence dans la vie personnelle d’un sujet identifié comme COVID-19 certain ou possible. En analyse univariée, certains gestes paraissent plus à risque de contamination chez les soignants (examen clinique, ophtalmologique, respiratoire). Les résultats plus complets seront présentés au Congrès. Conclusion Le risque de contamination professionnelle par le SARS-CoV-2 semble être surtout lié aux contacts entre professionnels, à l’environnement privé et à certains gestes professionnels. Le respect des mesures de prévention doit être systématisé dans toutes les circonstances professionnelles, y compris hors soins.

Delay between COVID-19 complete vaccination and SARS-CoV-2 infection among healthcare workers.

OBJECTIVES: Healthcare workers (HCWs), at increased risk of coronavirus disease 2019 (COVID-19) were among the primary targets for vaccination, which became mandatory for them on September 15th, 2021 in France. In November they were confronted to the fifth COVID-19 wave despite excellent vaccine coverage. We aimed to estimate the incidence of SARS-CoV-2 infection after complete vaccination among HCWs with different vaccination schemes, and its determinants. METHODS: We enrolled all HCWs in the university hospital of Rennes, France who had received complete vaccination (two doses of COVID-19 vaccine). The delay from last vaccination dose to SARS-CoV-2 infection was computed.Fitted mixed Cox survival model with a random effect applied to exposure risk periods to account for epidemic variation was used to estimate the determinants of SARS-CoV-2 infection after complete vaccination. RESULTS: Of the 6674 (82%) HCWs who received complete vaccination (36% BNT162b2, 29% mRNA-1273, and 34% mixed with ChAdOx1 nCoV-19) and were prospectively followed-up for a median of 7.0 [6.3-8.0] months, 160 (2.4%) tested positive for SARS-CoV-2 by RT-PCR. Incidence density of SARS-CoV-2 infection after complete vaccination was 3.39 [2.89-3.96] infections per 1000 person-month. Median time from vaccine completion to SARS-CoV-2 infection was 5.5 [3.2-6.6] months. Using fitted mixed Cox regression with the delay as a time-dependent variable and random effect applied to exposure risk periods, age (P < 0.001) was independently associated with the incidence of SARS-CoV-2 infection. Vaccine schemes were not associated with SARS-CoV-2 infection (P = 0.068). A period effect was significantly associated with the incidence of SARS-CoV-2 infection (P < 0.001). CONCLUSIONS: In this real-world study, incidence of SARS-CoV-2 infection increases with time in fully vaccinated HCWs with no differences according to the vaccination scheme. The short delay between complete vaccination and incident SARS-CoV-2 infection highlights the need for sustained barrier measures even in fully vaccinated HCWs.

Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020.

BackgroundThe COVID-19 pandemic has led to an unprecedented daily use of RT-PCR tests. These tests are interpreted qualitatively for diagnosis, and the relevance of the test result intensity, i.e. the number of quantification cycles (Cq), is debated because of strong potential biases.AimWe explored the possibility to use Cq values from SARS-CoV-2 screening tests to better understand the spread of an epidemic and to better understand the biology of the infection.MethodsWe used linear regression models to analyse a large database of 793,479 Cq values from tests performed on more than 2 million samples between 21 January and 30 November 2020, i.e. the first two pandemic waves. We performed time series analysis using autoregressive integrated moving average (ARIMA) models to estimate whether Cq data information improves short-term predictions of epidemiological dynamics.ResultsAlthough we found that the Cq values varied depending on the testing laboratory or the assay used, we detected strong significant trends associated with patient age, number of days after symptoms onset or the state of the epidemic (the temporal reproduction number) at the time of the test. Furthermore, knowing the quartiles of the Cq distribution greatly reduced the error in predicting the temporal reproduction number of the COVID-19 epidemic.ConclusionOur results suggest that Cq values of screening tests performed in the general population generate testable hypotheses and help improve short-term predictions for epidemic surveillance.

Risk factors for SARS-CoV-2 infection among health care workers.

BACKGROUND: Health care workers (HCWs) are on the front line for COVID-19. Better knowledge of risk factors for SARS-CoV-2 infection is crucial for their protection. We aimed to identify these risk factors with a focus on care activities. METHODS: We conducted a seroprevalence survey among HCWs in a French referral hospital. Data on COVID-19 exposures, care activities, and protective equipment were collected on a standardized questionnaire. Multivariate logistic regressions were used to assess risk factors for SARS-CoV-2 IgG adjusted on potential confounding. FINDINGS: Among the 3,234 HCWs enrolled, the prevalence of SARS-CoV-2 IgG was 3.8%. Risk factors included contact with relatives or HCWs with COVID-19 (odds ratio [OR] 2.20 [1.40-3.45] and 2.16 [1.46-3.18], respectively), but not contact with COVID-19 patients. In multivariate analyses, suboptimal use of protective equipment during nasopharyngeal sampling (OR 3.46 [1.15-10.40]), mobilisation of patients in bed (OR 3.30 [1.51-7.25]), clinical examination (OR 2.51 [1.16-5.43]), and eye examination (OR 2.90 [1.01-8.35]) were associated with SARS-CoV-2 infection. Patients washing and dressing and aerosol-generating procedures were additional risk factors, with or without appropriate use of protective equipment (OR 1.37 [1.04-1.81] and 1.74 [1.05-2.88]). CONCLUSIONS: Risk factors for SARS-CoV-2 infection among HCWs are (1) contact with relatives or HCWs with COVID-19, (2) close or prolonged contact with patients, (3) aerosol-generating procedures. Enhanced protective measures during the two latter care-activities may be warranted.

Effectiveness of mRNA-BNT162b2, mRNA-1273, and ChAdOx1 nCoV-19 vaccines against COVID-19 in healthcare workers: an observational study using surveillance data.

OBJECTIVES: Healthcare workers (HCWs) at increased risk of coronavirus disease 2019 (COVID-19) were among the primary targets for vaccine campaigns. We aimed to estimate the protective efficacy of the first three COVID-19 vaccines available in Western Europe. METHODS: We merged two prospective databases that systematically recorded, in our institution: (a) HCWs positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by RT-PCR on nasopharyngeal samples, and (b) HCWs who received at least one dose of COVID-19 vaccine. We excluded HCWs with SARS-CoV-2 infection during the 6 months prior to the study. HCWs were categorized as non-vaccinated if they received no vaccine and until the first injection +13 days, partially vaccinated from the first injection +14 days to the second injection +13 days, and fully vaccinated thereafter. RESULTS: Of the 8165 HCWs employed in our institution, 360 (4.4%) tested positive for SARS-CoV-2 by RT-PCR during the study period (4th January to 17th May 2021). Incidence was 9.1% (8.2-10.0) in non-vaccinated HCWs, 1.2% (0.7-1.9) after one dose of ChAdOx1 nCoV-19, 1.4% (0.6-2.3) and 0.5% (0.1-1.0) after one and two doses of mRNA BNT162b2, 0.7% (0.1-1.9) and 0% after one and two doses of mRNA-1273 (p < 0.0001). Vaccine effectiveness (Cox model) was estimated at, respectively, 86.2% (76.5-91.0), 38.2% (6.3-59.2), and 49.2% (19.1-68.1) 14 days after the first dose for ChAdOx1 nCoV-19, mRNA-1273, and mRNA-BNT162b2, and 100% (ND) and 94.6% (61.0-99.2) 14 days after the second dose for mRNA-1273 and mRNA-BNT162b2. CONCLUSIONS: In this real-world study, the observed effectiveness of COVID-19 vaccines in HCWs was in line with the efficacy reported in pivotal randomized trials.

A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study.

OBJECTIVES: In early January 2021 an outbreak of nosocomial cases of coronavirus disease 2019 (COVID-19) emerged in Western France; RT-PCR tests were repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole-genome sequencing (WGS) revealed a new variant, currently defining a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.616. In March, the WHO classified this as a 'variant under investigation' (VUI). We analysed the characteristics and outcomes of COVID-19 cases related to this new variant. METHODS: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled those inpatients with: (a) positive SARS-CoV-2 RT-PCR on a respiratory sample, (b) seroconversion with anti-SARS-CoV-2 IgG/IgM, or (c) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as B.1.616, a variant of concern (VOC), or unknown. RESULTS: From 1st January to 24th March 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n = 39), VOC (n = 32), and unknown (n = 43). B.1.616-related cases were older than VOC-related cases (81 years, interquartile range (IQR) 73-88 versus 73 years, IQR 67-82, p < 0.05) and their first RT-PCR tests were rarely positive (6/39, 15% versus 31/32, 97%, p < 0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.0, 95%CI 1.5-10.9) and increased lethality (28-day mortality 18/39 (46%) for B.1.616 versus 5/32 (16%) for VOC, p = 0.006). CONCLUSION: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, which is poorly detected by RT-PCR on nasopharyngeal samples and is associated with high lethality.

SARS-CoV-2 integral membrane proteins shape the serological responses of patients with COVID-19.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has elicited a unique mobilization of the scientific community to develop efficient tools to understand and combat the infection. Like other coronavirae, SARS-CoV-2 hijacks host cell secretory machinery to produce viral proteins that compose the nascent virions; including spike (S), envelope (E), and membrane (M) proteins, the most exposed transmembrane proteins to the host immune system. As antibody response is part of the anti-viral immune arsenal, we investigate the immunogenic potential of S, E, and M using a human cell-based system to mimic membrane insertion and N-glycosylation. Both S and M elicit specific Ig production in patients with SARS-CoV-2. Patients with moderate and severe diseases exhibit elevated Ig responses. Finally, reduced Ig binding was observed with spike G614 compared to D614 variant. Altogether, our assay points toward an unexpected immune response against M and represents a powerful tool to test humoral responses against actively evolving SARS-CoV-2 variants and vaccine effectiveness.

Chilblains during lockdown are associated with household exposure to SARS-CoV-2: a multicentre case-control study.

OBJECTIVES: During the COVID-19 pandemic, numerous cases of chilblains have been reported. However, in most cases, RT-PCR or serology did not confirm SARS-CoV-2 infection. Hypotheses have been raised about an interferon-mediated immunological response to SARS-CoV-2, leading to effective clearance of the SARS-CoV-2 without the involvement of humoral immunity. Our objective was to explore the association between chilblains and exposure to SARS-CoV-2. METHODS: In this multicentre case-control study, cases were the 102 individuals referred to five referral hospitals for chilblains occurring during the first lockdown (March to May 2020). Controls were recruited from healthy volunteers' files held by the same hospitals. All members of their households were included, resulting in 77 case households (262 individuals) and 74 control households (230 individuals). Household exposure to SARS-CoV-2 during the first lockdown was categorized as high, intermediate or low, using a pre-established algorithm based on individual data on symptoms, high-risk contacts, activities outside the home and RT-PCR testing. Participants were offered a SARS-CoV-2 serological test. RESULTS: After adjustment for age, the association between chilblains and viral exposure was estimated at OR 3.3, 95% CI (1.4-7.3) for an intermediate household exposure, and 6.9 (2.5-19.5) for a high household exposure to SARS-CoV-2. Out of 57 case households tested, six (11%) had positive serology for SARS-CoV-2, whereas all control households tested (n = 50) were seronegative (p = 0.03). The effect of potential misclassification on exposure has been assessed in a bias analysis. DISCUSSION: This case-control study demonstrates the association between chilblains occurring during the lockdown and household exposure to SARS-CoV-2.

European multicenter evaluation of Xpert® Xpress SARS-CoV-2/Flu/RSV test.

Rapid diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are paramount for reducing the spread of the current pandemic. During additional seasonal epidemics with influenza A/B and respiratory syncytial virus (RSV), the clinical signs and symptoms cannot be distinguished easily from SARS-CoV-2. Therefore, a new assay combining four targets in the form of the new Xpert Xpress SARS-CoV-2/Flu/RSV assay was evaluated. The assay was compared to the Xpert Xpress SARS-CoV-2, Xpert Xpress Flu/RSV, Seegene Flu/RSV, influenza A/B r-gene® and RSV/hMPV r-gene®. A total of 295 nasopharyngeal and throat swabs were tested at four institutes throughout Europe including 72 samples positive for SARS-CoV-2, 65 for influenza A, 47 for influenza B, and 77 for RSV. The sensitivity of the new assay was above 95% for all targets, with the highest for SARS-CoV-2 (97.2%). The overall correlation of SARS-CoV-2 Ct values between Xpert Xpress SARS-CoV-2 assay and Xpert Xpress SARS-CoV-2/Flu/RSV assay was high. The agreement between Ct values above 30 showed the multiplex giving higher Ct values for SARS-CoV-2 on average than the singleplex assay. In conclusion, the new assay is a rapid and reliable alternative with less hands-on time for the detection of not one, but four upper respiratory tract pathogens that may circulate at the same time.

Cross-validation of ELISA and a portable surface plasmon resonance instrument for IgG antibody serology with SARS-CoV-2 positive individuals.

We report on the development of surface plasmon resonance (SPR) sensors and matching ELISAs for the detection of nucleocapsid and spike antibodies specific against the novel coronavirus 2019 (SARS-CoV-2) in human serum, plasma and dried blood spots (DBS). When exposed to SARS-CoV-2 or a vaccine against SARS-CoV-2, the immune system responds by expressing antibodies at levels that can be detected and monitored to identify the fraction of the population potentially immunized against SARS-CoV-2 and support efforts to deploy a vaccine strategically. A SPR sensor coated with a peptide monolayer and functionalized with various sources of SARS-CoV-2 recombinant proteins expressed in different cell lines detected human anti-SARS-CoV-2 IgG antibodies in clinical samples. Nucleocapsid expressed in different cell lines did not significantly change the sensitivity of the assays, whereas the use of a CHO cell line to express spike ectodomain led to excellent performance. This bioassay was performed on a portable SPR instrument capable of measuring 4 biological samples within 30 minutes of sample/sensor contact and the chip could be regenerated at least 9 times. Multi-site validation was then performed with in-house and commercial ELISA, which revealed excellent cross-correlations with Pearson's coefficients exceeding 0.85 in all cases, for measurements in DBS and plasma. This strategy paves the way to point-of-care and rapid testing for antibodies in the context of viral infection and vaccine efficacy monitoring.

Successful heart transplantation for COVID-19-associated post-infectious fulminant myocarditis.

Various clinical presentations of the 2019 coronavirus disease (COVID-19) have been described, including post-infectious acute and fulminant myocarditis. Here, we describe the case of a young patient admitted for COVID-19-associated post-infectious fulminant myocarditis. Despite optimal pharmacologic management, haemodynamic status worsened requiring support by veno-arterial extracorporeal membrane oxygenation. Emergent heart transplantation was required at Day 11 given the absence of cardiac function improvement. The diagnosis of post-infectious COVID-19-associated myocarditis was made from both pathologic examination of the explanted heart and positive SARS-CoV-2 serology.

Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values (preprint)

The SARS-CoV-2 pandemic has led to an unprecedented daily use of molecular RT-PCR tests. These tests are interpreted qualitatively for diagnosis, and the relevance of the test result intensity, i.e. the number of amplification cycles (Ct), is debated because of strong potential biases. We analyze a national database of tests performed on more than 2 million individuals between January and November 2020. Although we find Ct values to vary depending on the testing laboratory or the assay used, we detect strong significant trends with patient age, number of days after symptoms onset, or the state of the epidemic (the temporal reproduction number) at the time of the test. These results suggest that Ct values can be used to improve short-term predictions for epidemic surveillance.

Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort.

The characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral kinetics in hospitalized patients and its association with mortality is unknown. We analyzed death and nasopharyngeal viral kinetics in 655 hospitalized patients from the prospective French COVID cohort. The model predicted a median peak viral load that coincided with symptom onset. Patients with age ≥65 y had a smaller loss rate of infected cells, leading to a delayed median time to viral clearance occurring 16 d after symptom onset as compared to 13 d in younger patients (P < 10-4). In multivariate analysis, the risk factors associated with mortality were age ≥65 y, male gender, and presence of chronic pulmonary disease (hazard ratio [HR] > 2.0). Using a joint model, viral dynamics after hospital admission was an independent predictor of mortality (HR = 1.31, P < 10-3). Finally, we used our model to simulate the effects of effective pharmacological interventions on time to viral clearance and mortality. A treatment able to reduce viral production by 90% upon hospital admission would shorten the time to viral clearance by 2.0 and 2.9 d in patients of age <65 y and ≥65 y, respectively. Assuming that the association between viral dynamics and mortality would remain similar to that observed in our population, this could translate into a reduction of mortality from 19 to 14% in patients of age ≥65 y with risk factors. Our results show that viral dynamics is associated with mortality in hospitalized patients. Strategies aiming to reduce viral load could have an effect on mortality rate in this population.

A lateral flow immunoassay test performance in SARS-CoV-2 seroprevalence surveys: a validation study among healthcare workers.

The objective of this study was to evaluate the validity and reliability of NG-Test® when used as a finger-prick test on healthcare workers and to compare it to the ELISA Wantai Immunoassay. Fifty-one healthcare workers who were RT-PCR SARS-CoV-2 positive and 59 who were RT-PCR SARS-CoV-2 negative accepted to participate in this study. They were subjected to an NG-Test® finger-prick test and collection of a blood sample on the same day. A second NG-Test® on another finger was performed for the first 30 cases and controls and read blinded to the first. Sera obtained from blood samples were used to perform the Wantai SARS-CoV-2 ELISA. The interobserver agreement for the NG-Test® test was perfect (kappa coefficient = 100% [98%-100%]). The sensitivity of NG-Test® was estimated to be 85% [71.9%-92.3%] and the specificity 98.3% [95.0%-100.0%]) for both IgG and IgM. The percentage of agreement between the Wantai immunoassay and NG-Test® was 92.73% for IgG (Kappa = 0.85 [0.75-0.95]) and 65.45% (Kappa = 0.42 [0.26-0.58]) for IgM. Our study highlights the need to validate rapid immunoassay tests under real-life conditions. If NG-Test® is used in seroprevalence surveys, we recommend that its diagnostic performance be taken into consideration to obtain a reliable estimation.

COVID-19 in Patient with Sarcoidosis Receiving Long-Term Hydroxychloroquine Treatment, France, 2020.

Because of in vitro studies, hydroxychloroquine has been evaluated as a preexposure or postexposure prophylaxis for coronavirus disease (COVID-19) and as a possible COVID-19 curative treatment. We report a case of COVID-19 in a patient with sarcoidosis who was receiving long-term hydroxychloroquine treatment and contracted COVID-19 despite adequate plasma concentrations.