How have mathematical models contributed to understanding the transmission and control of SARS-CoV-2 in healthcare settings? A systematic search and review (preprint)

Background: Since the onset of the COVID-19 pandemic, mathematical models have been widely used to inform public health recommendations regarding COVID-19 control in healthcare settings. Objectives: To systematically review SARS-CoV-2 transmission models in healthcare settings, and summarise their contributions to understanding nosocomial COVID-19. Methods: Systematic search and review. Data sources: Published articles indexed in PubMed. Study eligibility criteria: Modelling studies describing dynamic inter-individual transmission of SARS-CoV-2 in healthcare settings, published by mid-February 2022. Participants and interventions: Any population and intervention described by included models. Assessment of risk of bias: Not appropriate for modelling studies. Methods of data synthesis: Structured narrative review. Results: Models have mostly focused on acute care and long-term care facilities in high-income countries. Models have quantified outbreak risk across different types of individuals and facilities, showing great variation across settings and pandemic periods. Regarding surveillance, routine testing - rather than symptom-based testing - was highlighted as essential for COVID-19 prevention due to high rates of silent transmission. Surveillance impacts were found to depend critically on testing frequency, diagnostic sensitivity, and turn-around time. Healthcare re-organization was also found to have large epidemiological impacts: beyond obvious benefits of isolating cases and limiting inter-individual contact, more complex strategies such as staggered staff scheduling and immune-based cohorting reduced infection risk. Finally, vaccination impact, while highly effective for limiting COVID-19 burden, varied substantially depending on assumed mechanistic impacts on infection acquisition, symptom onset and transmission. Studies were inconsistent regarding which individuals to prioritize for interventions, probably due to the high diversity of settings and populations investigated. Conclusions: Modelling results form an extensive evidence base that may inform control strategies for future waves of SARS-CoV-2 and other viral respiratory pathogens. We propose new avenues for future models of healthcare-associated outbreaks, with the aim of enhancing their efficiency and contributions to decision-making.

Modelling the association between neutralizing antibody levels and SARS-CoV-2 viral dynamics : implications to define correlates of protection against infection (preprint)

Background While anti-SARS-CoV-2 antibody kinetics have been well described in large populations of vaccinated individuals, we still poorly understand how they evolve during a natural infection and how this impacts viral clearance. Methods For that purpose, we analyzed the kinetics of both viral load and neutralizing antibody levels in a prospective cohort of individuals during acute infection by Alpha variant. Results Using a mathematical model, we show that the progressive increase in neutralizing antibodies leads to a shortening of the half-life of both infected cells and infectious viral particles. We estimated that the neutralizing activity reached 90% of its maximal level within 8 days after symptoms onset and could reduce the half-life of both infected cells and infectious virus by a 6-fold factor, thus playing a key role to achieve rapid viral clearance. Using this model, we conducted a simulation study to predict in a more general context the protection conferred by the existence of pre-existing neutralization, due to either vaccination or prior infection. We predicted that a neutralizing activity, as measured by ED50 >103, could reduce by 50% the risk of having viral load detectable by standard PCR assays and by 99% the risk of having viral load above the threshold of cultivable virus. Conclusions This threshold value for the neutralizing activity could be used to identify individuals with poor protection against disease acquisition.

SARS-CoV-2 Exposures of Healthcare Workers from Primary Care, Long-Term Care Facilities and Hospitals: A Nationwide Matched Case-Control Study (preprint)

ABSTRACT Objectives Healthcare workers (HCWs) are at higher risk of contracting coronavirus disease-19 (COVID-19) than the general population. This study assessed the roles of various exposures and personal protective equipment (PPE) use on that risk for HCWs working in primary care, long-term-care facilities (LTCFs) or hospitals. Methods We conducted a matched case-control (1:1) study (10 April–9 July 2021). Cases (HCWs with confirmed COVID-19) and controls (HCWs without any COVID-19-positive test or symptoms) recruited by email were invited to complete an online questionnaire on their exposures and PPE use. Questions covered the 10 days preceding symptom onset for cases (or testing if asymptomatic) or inclusion for controls. Results A total of 4152 matched cases and controls were included. The multivariable conditional logistic regression analysis retained exposure to an infected person outside work (adjusted odds ratio, 19.9 [95% confidence intervaI, 12.4–31.9]), an infected colleague (2.26 [1.53–3.33]) or COVID-19 patients (2.37 [1.66–3.40]), as independent predictors of COVID-19 in HCWs, while partial or complete immunization was protective. Eye protection (0.57 [0.37–0.87]) and wearing a gown (0.58 [0.34–0.97]) during COVID-19 patient care were protective, while wearing an apron slightly increased the risk of infection (1.47 [1.00–2.18]). N95-respirator protection was comparable to that of surgical masks. Results were consistent across healthcare-facility categories. Conclusions HCWs were more likely to get COVID-19 in their personal sphere than during occupational activities. Our results suggest that eye protection for HCWs during patient care should be actively promoted.

Prevention of Sars-Cov-2 Transmission During a Large, Live, Indoor Gathering: The Noninferiority Randomised-Controlled Spring Trial (preprint)

Background: Mass indoor gatherings were banned in early 2020 to prevent SARS-CoV-2 spread. We aimed to assess, under controlled conditions, whether systematic antigen-screening within 3 days, medical mask-wearing and optimized ventilation could prevent SARS-CoV-2 spread during a large, indoor gathering without physical distancing.Methods: The non-inferiority, prospective, open-label, randomized (2:1)-controlled SPRING trial was conducted on May 29, 2021 in Paris, France. Participants, 18–45 years old, had no comorbidities, COVID-19 symptoms and recent case contact, and a negative rapid antigen diagnostic test within 3 days before the concert. Participants were randomly allocated to the experimental arm (attendees) or to the control arm (non-attendees). The primary outcome measure was the number of SARS-CoV-2–positive RT-PCR on self-collected saliva 7 days (D7) post-gathering. An artificial intelligence tool analyzing anonymised, continuous video-capture data evaluated participants’ mask-wearing compliance. This trial is registered with ClinicalTrials.gov, NCT04872075.Findings: Among 6678 randomized participants (median age 28 years; 59% women), 88% of each group complied with follow-up requirements. The D7 RT-PCR was positive for eight of the 3917 attendees (observed incidence, 0.20%; 95% Confidence Interval [CI], 0.09 to 0.40) and 3 of the 1,947 non-attendees (0.15%; 0.03 to 0.45) (absolute difference, 95%CI, –0.26% to +0.28%), findings that met the non-inferiority criterion (margin <0.35%) for the primary endpoint. Global facemask-wearing compliance (i.e., covering nose and mouth) was estimated at 91.4% (95%CI, 87.7 to 95.4).Interpretation: Participation in a large, indoor, live gathering without physical distancing was not associated with increased SARS-CoV-2–transmission risk, provided a comprehensive preventive intervention was implemented.Trial Registration: This study was registered on ClinicalTrials.gov (NCT04872075).Funding: French Ministry of HealthDeclaration of Interest: All authors declare no competing interestsEthical Approval: The trial protocol was approved by the Scientific Ethics Committee of the Sud-Ouest and Outremer Regions of France and the French Data-Protection Agency

Evaluation of saliva molecular point of care for detection of SARS-CoV-2 in ambulatory care (preprint)

Background: Rapid identification of SARS-Cov-2 infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. Methods We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV™) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Results Overall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97% respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference test, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. Conclusion The detection of SARS-CoV-2 from crude saliva samples with a RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing. Registration number : NCT04578509

Evaluation of saliva molecular point of care for detection of SARS-CoV-2 in ambulatory care (preprint)

BackgroundRapid identification of SARS-Cov-2 infected individuals is a cornerstone in strategies for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. Objectives and methodsWe conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) specifically designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR (reference test), to saliva RT-PCR and to nasopharyngeal antigen testing. ResultsOverall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% (95%CI: 26-44) and 97% (95%CI: 96-98) respectively. The performance was similar in symptomatic and asymptomatic participants. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p=0.028). Considering six alternate criteria for reference test, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. ConclusionIn the ambulatory setting, the detection of SARS-CoV-2 from crude saliva samples with the RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing. Registration numberNCT04578509 Funding SourcesFrench Ministry of Health and the Assistance Publique-Hopitaux de Paris Foundation.

Accuracy of antigen and nucleic acid amplification testing on saliva and naopharyngeal samples for detection of SARS-CoV-2 in ambulatory care (preprint)

Background Nasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the current standard diagnostic test for of coronavirus disease 2019 (COVID-19). However, the NAAT technique is lengthy and nasopharyngeal sampling requires trained personnel. Saliva NAAT represents an interesting alternative but diagnostic performances vary widely between studies. Objective To assess the diagnostic accuracy of a nasopharyngeal point-of-care antigen (Ag) test and of saliva NAAT for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), as compared to nasopharyngeal NAAT. Design Prospective participant enrollment from 19 October through 18 December 2020. Setting Two community COVID-19 screening centers in Paris, France. Participants 1452 ambulatory children and adults referred for SARS-CoV-2 testing. Interventions NAAT on a saliva sample (performed with three different protocols for pre-processing, amplification and detection of SARS-CoV-2) and Ag testing on a nasopharyngeal sample. Measurements Performance of saliva NAAT and nasopharyngeal Ag testing. Results Overall, 129/1443 (9%) participants tested positive on nasopharyngeal NAAT (102/564 [18%] in symptomatic and 27/879 [3%] in asymptomatic participants). Sensitivity was of 94% (95% CI, 86% to 98%), 23% (CI, 14% to 35%), 94% (CI, 88% to 97%) and 96% (CI, 91% to 99%) for the nasopharyngeal Ag test and the three different protocols of saliva NAAT, respectively. Estimates of specificity were above 95% for all methods. Diagnostic accuracy was similar in symptomatic and asymptomatic individuals. Limitations Few children (n=122, 8%) were included. Conclusion In the ambulatory setting, diagnostic accuracy of nasopharyngeal Ag testing and of saliva NAAT seems similar to that of nasopharyngeal NAAT, subject to strict compliance with specific pre-processing and amplification protocols. Registration number NCT04578509 Funding Sources French Ministry of Health and the Assistance Publique-Hôpitaux de Paris Foundation.

Serological reconstruction of COVID-19 epidemics through analysis of antibody kinetics to SARS-CoV-2 proteins (preprint)

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. Waning antibody levels lead to reduced sensitivity of serological diagnostic tests over time. This undermines the utility of serological surveillance as the SARS-CoV-2 pandemic progresses into its second year. Here we develop a multiplex serological test for measuring antibodies of three isotypes (IgG, IgM, IgA) to five SARS-CoV-2 antigens (Spike (S), receptor binding domain (RBD), Nucleocapsid (N), Spike subunit 2, Membrane-Envelope fusion) and the Spike proteins of four seasonal coronaviruses. We measure antibody responses in several cohorts of French and Irish hospitalized patients and healthcare workers followed for up to eleven months after symptom onset. The data are analysed with a mathematical model of antibody kinetics to quantify the duration of antibody responses accounting for inter-individual variation. One year after symptoms, we estimate that 36% (95% range: 11%, 94%) of anti-S IgG remains, 31% (9%, 89%) anti-RBD IgG remains, and 7% (1%, 31%) anti-N IgG remains. Antibodies of the IgM isotype waned more rapidly, with 9% (2%, 32%) anti-RBD IgM remaining after one year. Antibodies of the IgA isotype also waned rapidly, with 10% (3%, 38%) anti-RBD IgA remaining after one year. Quantitative measurements of antibody responses were used to train machine learning algorithms for classification of previous infection and estimation of time since infection. The resulting diagnostic test classified previous infections with 99% specificity and 98% (95% confidence interval: 94%, 99%) sensitivity, with no evidence for declining sensitivity over the time scale considered. The diagnostic test also provided accurate classification of time since infection into intervals of 0 - 3 months, 3 - 6 months, and 6 - 12 months. Finally, we present a computational method for serological reconstruction of past SARS-CoV-2 transmission using the data from this test when applied to samples from a single cross-sectional sero-prevalence survey.

Distinct systemic and mucosal immune responses to SARS-CoV-2 (preprint)

Coordinated local mucosal and systemic immune responses following SARS-CoV-2 infection protect against COVID-19 pathologies or fail leading to severe clinical outcomes. To understand this process, we performed an integrated analysis of SARS-CoV-2 spike-specific antibodies, cytokines, viral load and 16S bacterial communities in paired nasopharyngeal swabs and plasma samples from a cohort of clinically distinct COVID-19 patients during acute infection. Plasma viral load was associated with systemic inflammatory cytokines that were elevated in severe COVID-19, and also with spike-specific neutralizing antibodies. In contrast, nasopharyngeal viral load correlated with SARS-CoV-2 humoral responses but inversely with interferon responses, the latter associating with protective microbial communities. Potential pathogenic microrganisms, often implicated in secondary respiratory infections, were associated with mucosal inflammation and elevated in severe COVID-19. Our results demonstrate distinct tissue compartmentalization of SARS-CoV-2 immune responses and highlight a role for the nasopharyngeal microbiome in regulating local and systemic immunity that determines COVID-19 clinical outcomes.

Dysregulated primary hemostasis in critically ill COVID-19 patients (preprint)

Background: Microvascular thrombosis, as well as arterial and venous thrombotic events, have been largely described during severe Coronavirus disease 19 (COVID-19). Therapeutic anticoagulation has been proposed in critical patients, however mechanisms underlying hemostasis dysregulation remain unclear. Methods: We explored two independent cross-sectional cohorts to identify soluble markers and gene-expression signatures that discriminated COVID-19 severity and outcomes. Results: We found that elevated soluble (s) P-selectin at admission was associated with disease severity. Elevated sP-selectin was predictive of intubation and death (ROC AUC = 0.67, p = 0.028 and AUC = 0.74, p = 0.0047, respectively). An optimal cutoff value of 150 NC (normalized concentration) was predictive of intubation with 66% negative predictive value (NPV) and 61% positive predictive value (PPV), and of death with 90% NPV and 55% PPV. Next, an unbiased gene set enrichment analysis revealed that critically ill patients had increased expression of genes related to primary hemostasis. Hierarchical clustering identified ITG2AB, GP1BB, PPBP and SELPLG to be upregulated in a grade-dependent manner. ROC curve analysis for the prediction of mechanical ventilation was significant for SELPLG and PPBP (AUC = 0.8, p = 0.046 for both markers). An optimal cutoff value for PBPP was predictive of mechanical ventilation with 100% NPV and 45% PPV, and for SELPLG was predictive of mechanical ventilation with 100% NPV and 50% PPV.Conclusion: We provide evidence that platelets contribute to disease severity with the identification of sP-selectin as a biomarker for poor outcome. Transcriptional analysis identified PPBP and SELPLG RNA count as biomarkers for mechanical ventilation. These findings provide rationale for novel therapeutic approaches with antiplatelet agents.

Transmission routes of SARS-CoV-2 among healthcare workers of a French university hospital in Paris, France: a case-control study (preprint)

In this case-control study on 564 healthcare workers of a university hospital in Paris (France), contacts without protection with COVID-19 patients or with colleagues were associated with infection with SARS-CoV-2, while working in a COVID-dedicated unit, using public transportation and having children kept in childcare facilities were not.

Airborne contamination of COVID-19 in hospitals: a scoping review of the current evidence. (preprint)

Introduction A controversy remains worldwide regarding the transmission routes of SARS-CoV-2 in hospital settings. We reviewed the current evidence on the air contamination with SARS-CoV-2 in hospital settings, and the factors associated to the contamination including the viral load and the particles size. Methods The MEDLINE, Embase, Web of Science databases were systematically interrogated for original English-language articles detailing COVID-19 air contamination in hospital settings between 1 December 2019 and 21 July 2020. This study was conducted in accordance with the PRISMA-ScR guidelines. The positivity rate of SARS-CoV-2 viral RNA and culture were described and compared according to the setting, clinical context, air ventilation system, and distance from patient. The SARS-CoV-2 RNA concentrations in copies per m3 of air were pooled and their distribution were described by hospital areas. Particle sizes and SARS-CoV-2 RNA concentrations in copies or TCID50 per m3 were analysed after categorization of sizes in <1 micrometers, 1-4 micrometers, and >4 micrometers. Results Among 2,034 records identified, 17 articles were included in the review. Overall, 27.5% (68/247) of air sampled from close patients environment were positive for SARS-CoV-2 RNA, without difference according to the setting (ICU: 27/97, 27.8%; non-ICU: 41/150, 27.3%; p=0.93), the distance from patients (<1 meter: 1/64, 1.5%; 1-5 meters: 4/67, 6%; p=0.4). In other areas, the positivity rate was 23.8% (5/21) in toilets, 9.5% (20/221) in clinical areas, 12.4% (15/121) in staff areas, and 34.1% (14/41) in public areas. A total of 78 viral cultures were performed in three studies, and 3 (4%) were positive, all from close patients environment. The median SARS-CoV-2 RNA concentrations varied from 1.103 copies per m3 (IQR: 0.4.103-9.103) in clinical areas to 9.7.103 (5.1.103-14.3.103) in the air of toilets or bathrooms. The protective equipment removal and patients rooms had high concentrations/titre of SARS-CoV-2 with aerosol size distributions that showed peaks in the <1 micrometers region, and staff offices in the >4 micrometers region. Conclusion In hospital, the air near and away from COVID-19 patients is frequently contaminated with SARS-CoV-2 RNA, with however, rare proofs of their viability. High viral loads found in toilet/bathrooms, staff and public hallways suggests to carefully consider these areas.

Comparing dynamics and determinants of SARS-CoV-2 transmissions among health care workers of adult and pediatric settings in central Paris (preprint)

Background: From the start of the pandemic, health-care workers (HCW) have paid a heavy toll to the coronavirus disease-19 (COVID-19) outbreak. Objectives: To describe the dynamics and determinants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in HCW. Design: Prospective observational study conducted from February 24th until April 10th, 2020. Setting: Comparison of a 1,500-bed adult and a 600-bed pediatric setting of a tertiary-care university hospital located in central Paris. Participants: All symptomatic HCW screened for SARS-CoV-2 on a nasopharyngeal swab. Measurements: HCW screened positive were prospectively questioned on their profession, symptoms, occupational and non-occupational exposures to SARS-CoV-2. Results: Among 1344 symptomatic HCW tested, 373 were positive (28%) and 336 (90%) corresponding questionnaires were completed. Three hospitalizations and no death were reported. Most HCW (70%) had patient-facing occupational activities (22% in COVID-19 dedicated units). The total number of HCW cases peaked on March 23rd, then decreased slowly, concomitantly with a continuous increase of compliance to preventive measures (including universal medical masking and personal protective equipment (PPE) for direct care to COVID-19 patients). Attack rates were of 3.2% and 2.3% in the adult and pediatric setting, respectively (p=0.0022). In the adult setting, HCW more frequently reported exposure to COVID-19 patients without PPE (25% versus 15%, p=0.046). Report of contacts with children attending out-of-home care facilities dramatically decreased over the study period. Limitations: Lack of COVID-19 negative controls and recall bias. Conclusion: Universal masking, reinforcement of hand hygiene, and PPE with medical masks for patients' care allowed protection of HCW and containment of the outbreak. Residual transmissions were related to persistent exposures with undiagnosed patients or colleagues and not to contacts with children attending out-of-home care facilities.

Plasma concentration and safety of lopinavir/ritonavir in patients with Covid-19: a retrospective cohort study (preprint)

Background: There is an urgent need of active treatment for coronavirus disease 2019 (Covid-19). Although efficacy have not been proven, lopinavir/ritonavir 400 mg/100 mg twice daily has been proposed as a treatment of moderate to severe Covid-19. Previously published cohorts showed Covid-19 is associated with major inflammation. To date, no data are available regarding lopinavir/ritonavir plasma concentration and its safety in Covid-19 patients. Methods: Real-world Covid-19 experience based on a retrospective cohort study Results: On the cohort of 31 patients treated by lopinavir/ritonavir for Covid-19, we observed very high lopinavir plasma concentrations, increased of 4.6-fold (IQR 2.9-6.4), with regards to average plasma concentrations in HIV treatment. All except two patients were above the upper limit of the concentration ranges of HIV treatment. In this cohort, about one over four to five patients prematurely stopped lopinavir/ritonavir therapy due to a moderate adverse drug reaction, mainly hepatic and gastrointestinal disorders. Conclusion: Patients with Covid-19 pneumonitis treated with lopinavir/ritonavir have plasma concentrations dramatically higher than expected. Owing to that high plasma concentration may be required for antiviral activity against SARS-CoV-2, it appears that lopinavir dosage should not be reduced in the absence of adverse effect. About 80% of the patients well tolerated lopinavir/ritonavir therapy under these plasma concentrations. However, cautious is necessary as drug repurposing can be associated with a new drug safety profile.

Serological signatures of SARS-CoV-2 infection: Implications for antibody-based diagnostics (preprint)

Background Infection with SARS-CoV-2 induces an antibody response targeting multiple antigens that changes over time. This complexity presents challenges and opportunities for serological diagnostics. Methods A multiplex serological assay was developed to measure IgG and IgM antibody responses to seven SARS-CoV-2 spike or nucleoprotein antigens, two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and three non-coronavirus antigens. Antibodies were measured in serum samples from patients in French hospitals with RT-qPCR confirmed SARS-CoV-2 infection (n = 259), and negative control serum samples collected before the start of the SARS-CoV-2 epidemic (n = 335). A random forests algorithm was trained with the multiplex data to classify individuals with previous SARS-CoV-2 infection. A mathematical model of antibody kinetics informed by prior information from other coronaviruses was used to estimate time-varying antibody responses and assess the potential sensitivity and classification performance of serological diagnostics during the first year following symptom onset. A statistical estimator is presented that can provide estimates of seroprevalence in very low transmission settings. Results IgG antibody responses to trimeric Spike protein identified individuals with previous RT-qPCR confirmed SARS-CoV-2 infection with 91.6% sensitivity (95% confidence interval (CI); 87.5%, 94.5%) and 99.1% specificity (95% CI; 97.4%, 99.7%). Using a serological signature of IgG and IgM to multiple antigens, it was possible to identify infected individuals with 98.8% sensitivity (95% CI; 96.5%, 99.6%) and 99.3% specificity (95% CI; 97.6%, 99.8%). Informed by prior data from other coronaviruses, we estimate that one year following infection a monoplex assay with optimal anti-Stri IgG cutoff has 88.7% sensitivity (95% CI: 63.4%, 97.4%), and that a multiplex assay can increase sensitivity to 96.4% (95% CI: 80.9%, 100.0%). When applied to population-level serological surveys, statistical analysis of multiplex data allows estimation of seroprevalence levels less than 1%, below the false positivity rate of many other assays. Conclusion Serological signatures based on antibody responses to multiple antigens can provide accurate and robust serological classification of individuals with previous SARS-CoV-2 infection. This provides potential solutions to two pressing challenges for SARS-CoV-2 serological surveillance: classifying individuals who were infected greater than six months ago, and measuring seroprevalence in serological surveys in very low transmission settings.

Impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients (preprint)

Background: Coronavirus disease 2019 (Covid-19) is a major global threat that has already caused more than 100,000 deaths worldwide. It is characterized by distinct patterns of disease progression implying a diverse host immune response. However, the immunological features and molecular mechanisms involved in Covid-19 severity remain so far poorly known. Methods: We performed an integrated immune analysis that included in-depth phenotypical profiling of immune cells, whole-blood transcriptomic and cytokine quantification on a cohort of fifty Covid19 patients with a spectrum of disease severity. All patient were tested 8 to 12 days following first symptoms and in absence of anti-inflammatory therapy. Results: A unique phenotype in severe and critically ill patients was identified. It consists in a profoundly impaired interferon (IFN) type I response characterized by a low interferon production and activity, with consequent downregulation of interferon-stimulated genes. This was associated with a persistent blood virus load and an exacerbated inflammatory response that was partially driven by the transcriptional factor NF{kappa}B. It was also characterized by increased tumor necrosis factor (TNF)- and interleukin (IL)-6 production and signaling as well as increased innate immune chemokines. Conclusion: We propose that type-I IFN deficiency in the blood is a hallmark of severe Covid-19 and could identify and define a high-risk population. Our study provides a rationale for testing IFN administration combined with adapted anti-inflammatory therapy targeting IL-6 or TNF- in most severe patients. These data also raise concern for utilization of drugs that interfere with the IFN pathway.