How much should we sequence? An analysis of the Swiss SARS- CoV-2 surveillance effort (preprint)

Background During the SARS-CoV-2 pandemic, many countries directed substantial resources towards genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. Aim We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic dataset from Switzerland, comprising more than 143k sequences. Methods We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. Results The impact of downsampling on VOC detection is disparate for the three VOC lineages , but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. Conclusion A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage dependent - something that is unknown at the time of sequencing - and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.

Antibody response and intra-host viral evolution after plasma therapy in COVID-19 patients pre-exposed or not to B-cell depleting agents (preprint)

Background: Administration of plasma therapy may contribute to viral control and survival of COVID-19 patients receiving B-cell depleting agents that hinder the endogenous humoral response. However, little is known on the impact of anti-CD20 pre-exposition and the use of different sources of plasma (convalescent versus vaccinated) on the kinetics of SARS-CoV-2-specific antibodies and viral evolution after plasma therapy. Methods: Eligible COVID-19 patients (n = 36), half of them after anti-CD20 targeted therapy, were treated with therapeutic plasma from convalescent (n = 17) or mRNA-vaccinated (n = 19) donors. Each plasma-transfused patient was thoroughly monitored over time by anti-S IgG quantification and whole-genome SARS-CoV-2 sequencing. Results: The majority of anti-CD20 pre-exposed patients (15/18) showed progressive declines of anti-S protein IgG titers following plasma therapy, indicating that they mostly relied on the passive transfer of anti-SARS-CoV-2 antibodies. Such antibody kinetics correlated with prolonged infection before virus clearance, contrasting with the endogenous humoral response predominantly present in patients who had not received B-cell depleting agents (15/18). No relevant differences were observed between patients treated with plasma from convalescent and/or vaccinated donors. Finally, 4/30 genotyped patients showed increased intra-host viral evolution and 3/30 included 1 to 4 spike mutations, potentially associated to immune escape. Conclusions: Convalescent and/or vaccinated plasma therapy may provide anti-SARS-CoV-2 antibodies and clinical benefit to B-cell depleted COVID-19 patients. Only a limited number of patients acquired viral mutations prior to clinical recovery, yet our study further emphasizes the need for long-term surveillance for intra-host variant evolution, to guide best therapeutic strategies.

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data (preprint)

Genome sequences allow quantification of changes in case introductions from abroad and local transmission dynamics. We sequenced 11,357 SARS-CoV-2 genomes from Switzerland in 2020 - the 6th largest effort globally. Using these data, we estimated introductions and their persistence throughout 2020. By contrasting estimates with null models, we estimate at least 83% of introductions were adverted during Switzerland's border closures. Further, transmission chain persistence roughly doubled after the partial lockdown was lifted. Then, using a novel phylodynamic method, we suggest transmission in newly introduced outbreaks slowed 36 - 64% upon outbreak detection in summer 2020, but not in fall. This could indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.

The dark side of SARS-CoV-2 rapid antigen testing: screening asymptomatic patients. (preprint)

Most of the reports describing SARS-CoV-2 rapid antigen tests (RATs) performances derive from COVID-19 symptomatic subjects in outpatient settings during periods of highest incidence of infections and high rates of hospital admissions. Here we investigated the role of RATs in an Emergency Department, as a screening tool before admission for COVID-19 asymptomatic patients. Each patient was screened with two simultaneous nasopharyngeal swabs: one immediately analyzed at the bedside using RAT and the other sent to the laboratory for RT-PCR analysis. A total of 116 patients were screened at hospital admission in a 250-bed community hospital in Morges (EHC), Switzerland. With a disease prevalence of 6% based on RT-PCR results, RAT detected only two out of seven RT-PCR positive patients (sensitivity 28.6%) and delivered two false positive results (specificity 98.2%), thus resulting not fiable enough to be used as a screening method in this clinical scenario.

Sensitivity of rapid antigen testing and RT-PCR performed on nasopharyngeal swabs versus saliva samples in COVID-19 hospitalized patients: results of a prospective comparative trial (RESTART). (preprint)

Objectives: Saliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen testing (RAT) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples. Methods: We conducted a prospective observational study among COVID-19 hospitalized patients between 10th December 2020 and 1st February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia(R) COVID-19 Ag (Precision Biosensor, Korea) and Standard Q(R) COVID-19 Rapid Antigen Test (Roche-Switzerland). Results: A total of 58 paired NP-saliva specimens were collected. Thirty-two of 58 (55%) patients were hospitalized in the intensive care unit and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively whereas the specificity of these RT-PCRs assays were of 100%. NP RAT exhibited much lower diagnostic performances with sensitivities of 35% and 41% for the Standard Q(R) and Exdia(R) assays respectively, when a wet-swab approach was used (i.e. when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4 and 8%) when applied to salivary swabs. Conclusions: Nasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RAT are not appropriate for hospitalized patients.

An automated Dashboard to improve laboratory COVID-19 diagnostics management (preprint)

Background: In response to the CoVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. Thanks to our automated molecular diagnostic platform, more than 140 000 SARS-CoV-2 RT-PCR tests were achieved over 12 months, with peaks higher than 1 500 daily tests. A dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management. Methods: RT-PCR data extraction of four respiratory viruses - SARS-CoV-2, influenza A and B and RSV - from our laboratory information system (LIS), was automated. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny). Information is updated every 4 hours. Results: The dashboard is organized into three main parts. The Filter page presents all the KPIs, divided into five sections: i) general and gender-related indicators, ii) number of tests and positivity rate, iii) cycle threshold and viral load, iv) test durations, and v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, or a requester for instance. The Comparison page allows a custom charting of all the available variables, which represents more than 182 combinations. The Data page gives the user access to the raw data in table format, with the possibility of filtering, allowing for a deeper analysis and data download in Excel format. Conclusions: The dashboard, that gives a rapid access to a huge number of up-to-date information, represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management. The dashboard represent an added value for diagnosric laboratories during a pandemic, where rapid and efficient adaptation is mandatory.

Performance of RT-PCR on saliva specimens compared to nasopharyngeal swabs for the detection of SARS-CoV-2 in children: A prospective comparative clinical trial (preprint)

BackgroundSaliva RT-PCR is an attractive alternative for the detection of SARS-CoV-2 in adults with much less known in children. MethodsChildren and adolescents with symptoms suggestive of COVID-19 were prospectively enrolled in a comparative clinical trial of saliva and nasopharyngeal (NP) RT-PCR between November and December 2020. Detection rates and sensitivities of saliva and NP RT-PCR were compared. Participants with discordant NP and saliva RT-PCR results including viral load (VL) were also analyzed. ResultOut of 405 patients enrolled, 397 patients had two tests performed. Mean age was 12.7 years (range 1.2-17.9). Detection rates were 22.9% (95%CI 18.8-27.1%) by saliva RT-PCR, 25.4% (21.2-29.7%) by NP RT-PCR, and 26.7% (22.4-31.1%) by any test. The sensitivity of saliva was 85.2% (78.2-92.1%) when using NP as the gold standard; in contrast, when saliva was considered the gold standard, the sensitivity of NP was 94.5% (89.8-99.2%).For a NP RT-PCR VL threshold of [≥]103 and [≥]104 copies/ml, sensitivity of saliva increases to 88.7% and 95.2% respectively. Sensitivity of saliva and NP swabs was respectively 89.5% and 95.3% in patient with symptoms less than 4 days (p=0.249) and 70.0% and 95.0% in those with symptoms [≥] 4 to 7 days (p=0.096). The 15 patients who had an isolated positive NP RT-PCR were significantly younger (p=0.034), had a lower NP VL (median 5.6x103 vs 3.9x107, p<0.001), and were not able to drool saliva at the end of the sampling (p=0.002). VLs were significantly lower with saliva PCR than with NP RT-PCR (median 8.7 cp/ml x104; IQR 1.2x104-5.2x105; vs median 4.0x107cp/ml; IQR 8.6x105-1.x108; p<0.001). ConclusionSaliva PCR shows diagnostic performances close to NP RT-PCR for SARS-CoV2 detection in most symptomatic outpatient children and adolescents.

Size and duration of COVID-19 clusters go along with a high SARS-CoV-2 viral load : a spatio-temporal investigation in Vaud state, Switzerland (preprint)

To understand the geographical and temporal spread of SARS-CoV-2 during the first wave of infection documented in the canton of Vaud, Switzerland, we analysed clusters of positive cases using the precise place of residence of 33651 individuals tested (RT-PCR) between January 10 and June 30, 2020. We identified both space-time (SaTScan) and transmission (MST-DBSCAN) clusters; we estimated their duration, their transmission behavior (emergence, growth, reduction, etc.) and relative risk. For each cluster, we computed the within number of individuals, their median age and viral load. Among 1684 space-time clusters identified, 457 (27.1%) were significant (p [≤] 0.05), i.e. harboring a higher relative risk of infection, as compared to other regions. They lasted a median of 11 days (IQR 7-13) and included a median of 12 individuals per cluster (IQR 5-20). The majority of significant clusters (n=260; 56.9 %) had at least one person with an extremely high viral load (above 1 billion copies/ml). Those clusters were considerably larger (median of 17 infected individuals, p < 0.001) than clusters with subjects showing a viral load lower than 1 million copies/ml (median of 3 infected individuals). The highest viral loads were found in clusters with the lowest average age, while clusters with the highest average age had low to middle viral load. Interestingly, in 20 significant clusters the viral load of three first cases were all below 100000 copies/ml suggesting that subjects with less than 100000 copies/ml may still have been contagious. Noteworthy, the dynamics of transmission clusters made it possible to identify three diffusion zones, which mainly differentiated rural from urban areas, the latter being more prone to last and spread in a new nearby clusters. The use of geographic information is key for public health decision makers to mitigate the spread of the virus. This study suggests that early localization of clusters help implementing targeted protective measures limiting the spread of the SARS-CoV-2 virus.

ImplemeNting SARS-CoV-2 Rapid antigen testing in the Emergency wArd of a Swiss univErsity hospital: the INCREASE study (preprint)

BackgroundWhile facing a second wave in SARS-CoV-2 pandemic, in November 2020 the Swiss Federal Office of Public Health (FOPH) authorized the use of rapid antigen tests (RATs) in addition to the gold-standard reverse transcription-polymerase chain reaction (RT-PCR). MethodsWe implemented the use of RAT in the emergency ward of our university hospital for rapid patients triaging and compared performances of four different antigen tests. All results were compared to SARS-CoV-2 specific RT-PCR (reference standard). ResultsTriaging patients using RAT in association with RT-PCR allowed us to isolate promptly positive patients and to save resources, in a context of rapid RT-PCR reagents shortage. Among 532 patients with valid results, overall sensitivities were 48.3% for One Step Exdia and 41.2% for Standard Q(R), Panbio-and BD Veritor. All four antigen tests exhibited specificity above 99%. Sensitivity increased up to 74.6%, 66.2%, 66.2% and 64.8% for One Step Exdia, Standard Q, Panbio, and BD Veritor respectively, when considering viral loads above 105copies/ml, up to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/ml and 100% (for all tests) when considering viral loads above 107 copies/ml. Sensitivity was significantly higher for patients presenting with symptoms onset within 4 days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with evolution of symptoms for more than 4 days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Sensitivities of all RAT assays were of only 33% among hospitalized patients without COVID-19 symptoms. ConclusionRAT might represent a useful epidemiological resource in selected clinical settings as a complementary tool to the molecular tests for rapid patients triaging, but the lower sensitivity compared to RT-PCR, especially in late presenters and subjects without COVID-19 symptoms, must be taken into account in order to correctly use RAT for triaging.

Prevalence of SARS-CoV-2 in Household Members and Other Close Contacts of COVID-19 Cases: A Serologic Study in Canton of Vaud, Switzerland (preprint)

Background: Understanding community-based SARS-CoV-2 transmission is crucial to inform public health decisions. Research on SARS-CoV-2 transmission within households and other close settings using serological testing is scarce.Methods: We invited COVID-19 cases diagnosed between February 27 and April 1, 2020 in canton of Vaud, Switzerland, to participate, along with household members and other close contacts. Anti-SARS-CoV-2 IgG antibodies were measured using a Luminex immunoassay. We estimated factors associated with serological status using generalized estimating equations.Findings: Overall, 219 COVID-19 index cases, 302 household members, and 69 other close contacts participated between May 4 and June 27, 2020. More than half of household members (57·2%, 95%CI 49·7-64·3) had developed a serologic response to SARS-CoV-2, while 19·0% (95%CI 10·0-33·2) of other close contacts were seropositive. After adjusting for individual and household characteristics, infection risk was higher in household members aged 65 or more than in younger adults (aOR 3·63, 95%CI 1·05-12·60), and in those not strictly adhering to simple hygiene rules like hand washing (aOR 1·80, 95%CI 1·02-3·17). The risk was lower when more than 5 people outside home were met during the semi-confinement, compared to none (aOR 0·35, 95%CI 0·16-0·74). The individual risk of household members to be seropositive was lower in large households (22% less per each additional person).Interpretation: We find that, during semi-confinement, household members of a COVID-19 case were at very high risk of getting infected, 3 times more than close contacts outside home. This highlights the need to provide clear messages on specific protective measures applicable at home. For elderly couples, who were especially at risk, providing them external support for daily basic activities is essential.Funding: Center for Primary Care and Public Health (Unisanté), Canton of Vaud, Leenaards Foundation, Fondation pour l'Université de Lausanne. SerocoViD is part of Corona Immunitas coordinated by SSPH+.Declaration of Interests: We declare no competing interests.Ethics Approval Statement: The Cantonal Ethics Committee of Vaud, Switzerland (ID 2020-00887) approved the protocol.

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples (preprint)

BackgroundSARS-CoV-2 genotyping has been instrumental to monitor virus evolution and transmission during the pandemic. The reliability of the information extracted from the genotyping efforts depends on a number of aspects, including the quality of the input material, applied technology and potential laboratory-specific biases. These variables must be monitored to ensure genotype reliability. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in studies of viral spread and evolution. ResultsWe used clinical samples and synthetic viral genomes to evaluate the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination using an amplicon-based approach. We found that at least 1000 viral genomes are necessary to confidently detect variants in the genome at frequencies of 10% or higher. The broad applicability of our recommendations was validated in >200 clinical samples from six independent laboratories. The genotypes of clinical isolates with viral load above the recommended threshold cluster by sampling location and period. Our analysis also supports the rise in frequency of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was favoured by travelling during the summer 2020. ConclusionsWe present much-needed recommendations for reliable determination of SARS-CoV-2 genome sequence and demonstrate their broad applicability in a large cohort of clinical samples.

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19 (preprint)

Antibodies are becoming a frontline therapy for SARS-CoV-2, but the risk of viral evolutionary escape remains unclear. Here we map how all mutations to SARS-CoV-2's receptor-binding domain (RBD) affect binding by the antibodies in Regeneron's REGN-COV2 cocktail and Eli Lilly's LY-CoV016. These complete maps uncover a single amino-acid mutation that fully escapes the REGN-COV2 cocktail, which consists of two antibodies targeting distinct structural epitopes. The maps also identify viral mutations that are selected in a persistently infected patient treated with REGN-COV2, as well as in lab viral escape selections. Finally, the maps reveal that mutations escaping each individual antibody are already present in circulating SARS-CoV-2 strains. Overall, these complete escape maps enable immediate interpretation of the consequences of mutations observed during viral surveillance.

Differential effects of antiseptic mouth rinses on SARS-CoV-2 infectivity in vitro (preprint)

SARS-CoV-2 is detectable in saliva from asymptomatic individuals, suggesting the potential necessity for the use of mouth rinses to suppress viral load to reduce virus spread. Published studies on anti-SARS-CoV-2 activities of antiseptics determined by virus-induced cytotoxic effects cannot exclude antiseptic-associated cytotoxicity. Here, we determined the effect of commercially available mouth rinses and antiseptic povidone-iodine on the infectivity of pseudotyped SARS-CoV-2 virus. We first determined the effect of mouth rinses on cell viability to ensure that antiviral activity was not a consequence of mouth rinse-induced cytotoxicity. Colgate Peroxyl (hydrogen peroxide) exhibited the most cytotoxicity, followed by povidone-iodine-10% solution, chlorhexidine gluconate-0.12% (CHG), and Listerine (essential oils and alcohol). Analysis of the anti-viral activity of mouth rinses at non-cytotoxic concentrations showed that 1.5% (v/v) diluted CHG was a potent inhibitor when present in cells during infection, but the potency was reduced when CHG was removed after viral attachment, suggesting that the prolonged effect of mouth rinses on cells impacts the anti-viral activity. To minimalize mouth rinse-associated cytotoxicity, we pelleted treated-viruses to remove most of the mouth rinse prior to infection of cells. Colgate Peroxyl or povidone-iodine at 5% (v/v) completely blocked the viral infectivity. Listerine or CHG at 5% (v/v) had a moderate suppressive effect on the virus, and 50% (v/v) Listerine or CHG blocked the viral infectivity completely. Prolonged incubation of virus with mouth rinses was not required to block viral infectivity. Our results indicate that mouth rinses can significantly reduce virus infectivity, suggesting their potential use to reduce SARS-CoV-2 spread.

Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2 (preprint)

Severe acute respiratory syndrome (SARS) and novel coronavirus disease (COVID-19) are caused by two closely related beta-coronaviruses, SARS-CoV and SARS-CoV-2, respectively. The envelopes surrounding these viruses are decorated with spike proteins, whose receptor binding domains (RBDs) initiate invasion by binding to the human angiotensin-converting enzyme 2 (ACE2). Subtle changes at the interface with ACE2 seem to be responsible for the enhanced affinity for the receptor of the SARS-CoV-2 RBD compared to SARS-CoV RBD. Here, we use Elastic Network Models (ENMs) to study the response of the viral RBDs and ACE2 upon dissassembly of the complexes. We identify a dominant detachment mode, in which the RBD rotates away from the surface of ACE2, while the receptor undergoes a conformational transition which stretches the active-site cleft. Using the Structural Perturbation Method, we determine the network of residues, referred to as the Allostery Wiring Diagram (AWD), which drives the large-scale motion activated by the detachment of the complex. The AWD for SARS-CoV and SARS-CoV-2 are remarkably similar, showing a network that spans the interface of the complex and reaches the active site of ACE2, thus establishing an allosteric connection between RBD binding and receptor catalytic function. Informed in part by the AWD, we used Molecular Dynamics simulations to probe the effect of interfacial mutations in which SARS-CoV-2 residues are replaced by their SARS-CoV counterparts. We focused on a conserved glycine (G502 in SARS-CoV-2, G488 in SARS-CoV) because it belongs to a region that initiates the dissociation of the complex along the dominant detachment mode, and is prominent in the AWD. Molecular Dynamics simulations of SARS-CoV-2 wild-type and G502P mutant show that the affinity for the human receptor of the mutant is drastically diminished. Our results suggest that in addition to residues that are in direct contact with the interface those involved in long range allosteric communication are also a determinant of the stability of the RBD-ACE2 complex.

Neutrophil and monocyte dysfunctional effector response towards bacterial challenge in critically-ill COVID-19 patients (preprint)

COVID-19 displays diverse disease severities and symptoms. Elevated inflammation mediated by hypercytokinemia induces a detrimental dysregulation of immune cells. However, there is limited understanding of how SARS-CoV-2 pathogenesis impedes innate immune signaling and function against secondary bacterial infections. We assessed the influence of COVID-19 hypercytokinemia on the functional responses of neutrophils and monocytes upon bacterial challenges from acute and corresponding recovery COVID-19 ICU patients. We show that severe hypercytokinemia in COVID-19 patients correlated with bacterial superinfections. Neutrophils and monocytes from acute COVID-19 patients showed severely impaired microbicidal capacity, reflected by abrogated ROS and MPO production as well as reduced NETs upon bacterial challenges. We observed a distinct pattern of cell surface receptor expression on both neutrophils and monocytes leading to a suppressive autocrine and paracrine signaling during bacterial challenges. Our data provide insights into the innate immune status of COVID-19 patients mediated by their hypercytokinemia and its transient effect on immune dysregulation upon subsequent bacterial infections

Prevalence of SARS-CoV-2 in household members and other close contacts of COVID-19 cases: a serologic study in canton of Vaud, Switzerland (preprint)

BackgroundUnderstanding community-based SARS-CoV-2 transmission is crucial to inform public health decisions. Research on SARS-CoV-2 transmission within households and other close settings using serological testing is scarce. MethodsWe invited COVID-19 cases diagnosed between February 27 and April 1, 2020 in canton of Vaud, Switzerland, to participate, along with household members and other close contacts. Anti-SARS-CoV-2 IgG antibodies were measured using a Luminex immunoassay. We estimated factors associated with serological status using generalized estimating equations. FindingsOverall, 219 COVID-19 index cases, 302 household members, and 69 other close contacts participated between May 4 and June 27, 2020. More than half of household members (57{middle dot}2%, 95%CI 49{middle dot}7-64{middle dot}3) had developed a serologic response to SARS-CoV-2, while 19{middle dot}0% (95%CI 10{middle dot}0-33{middle dot}2) of other close contacts were seropositive. After adjusting for individual and household characteristics, infection risk was higher in household members aged 65 or more than in younger adults (aOR 3{middle dot}63, 95%CI 1{middle dot}05-12{middle dot}60), and in those not strictly adhering to simple hygiene rules like hand washing (aOR 1{middle dot}80, 95%CI 1{middle dot}02-3{middle dot}17). The risk was lower when more than 5 people outside home were met during the semi-confinement, compared to none (aOR 0{middle dot}35, 95%CI 0{middle dot}16-0{middle dot}74). The individual risk of household members to be seropositive was lower in large households (22% less per each additional person). InterpretationWe find that, during semi-confinement, household members of a COVID-19 case were at very high risk of getting infected, 3 times more than close contacts outside home. This highlights the need to provide clear messages on specific protective measures applicable at home. For elderly couples, who were especially at risk, providing them external support for daily basic activities is essential. FundingCenter for Primary Care and Public Health (Unisante), Canton of Vaud, Leenaards Foundation, Fondation pour lUniversite de Lausanne. SerocoViD is part of Corona Immunitas coordinated by SSPH+.

Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: a prospective comparative clinical trial (preprint)

Background Nasopharyngeal antigen Rapid Diagnostic Tests (RDTs) and saliva RT-PCR have shown variable performance to detect SARS-CoV-2. Methods In October 2020, we conducted a prospective trial involving patients presenting at testing centers with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR. Results Out of 949 patients enrolled, 928 patients had all three tests. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) >=106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively. Sensitivity of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients and 96.5% (93.6-98.3%) for those with VL>=106. Sensitivity of STANDARD-Q;, Panbio and COVID-VIRO; Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL>=106, sensitivities were 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%) and >=4 days (85.7%) after symptoms onset (p=0.6). Sensitivities of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR. Conclusions The high performance of RDTs allows rapid identification of COVID cases with immediate isolation of the vast majority of contagious individuals. RDT could be a game changer in primary care practices, and even more so in resource-constrained settings. PCR on saliva can replace NP PCR.

CSF of SARS-CoV-2 patients with neurological syndromes reveals hints to understand pathophysiology (preprint)

Objective: Coronavirus disease (COVID-19) has been associated with a large variety of neurological disorders. However the mechanisms underlying these neurological complications remain elusive. In this study we aimed at determining whether neurological symptoms were caused by SARS-CoV-2 direct infection of by pro-inflammatory mediators. Methods: We checked for SARS-CoV-2 RNA by RT-qPCR, SARS-CoV-2-specific antibodies and for 48 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluids (CSF) +/- sera of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological control patients (inflammatory [IND], non inflammatory [NIND], multiple sclerosis [MS]). Results: We found SARS-CoV-2 RNA and antibodies specific for this virus in the CSF of 0/17 and 8/16 COVID-19 patients, respectively. The presence of SARS-CoV-2 antibodies was explained by a rupture of the blood brain barrier (passive transfer) in 6/16 (38%). An intrathecal synthesis of SARS-CoV2-specific antibodies was present in 2/16 patients. Of the four categories of tested patients, the CSF of IND exhibited the highest level of chemokines (CCL4, CCL5, CXCL8, CXCL10, CXCL12, and CXCL13), followed by the CSF of MS patients (CXCL12, and CXCL13). There was no significant difference between COVID-19 and NIND patients, even if some chemokines (CCL4, CCL5, CXCL8, andCXCL10) tended to be higher in the former. Interestingly, among COVD-19 patients, the CSF of those with a severe disease (encephalitis/encephalopathy) contained higher levels CXCL8 and CXCL10 than those with other neurological presentations. Interpretation: Our results do not show obvious SARS-CoV-2 infection of the central nervous system, but point to a mild inflammatory reaction reflecting an astrocytic reaction. Methods: We checked for SARS-CoV-2 mRNA by qPCR, SARS-CoV-2-specific antibodies and for 49 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluid (CSF) +/- serum of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological controls (inflammatory, non inflammatory, multiple sclerosis). Results: We found SARS-CoV-2 mRNA and antibodies specific for this virus in the CSF of 0/17 and 8/16 COVID-19 patients, respectively. The presence of SARS-CoV-2 antibodies was explained by a rupture of the blood brain barrier (passive transfer) in 6/16 (37,5%), but an intrathecal synthesis of SARS-CoV2-specific antibodies was present in 2/17.As compared to SARS-CoV-2-negative NIND patients, the CSF of IND patients exhibited the highest level of chemokines (CCL4, CCL5, CXCL8, CXCL10, CXCL12, and CXCL13), followed the CSF of MS patients (CXCL12, and CXCL13). There was no difference between COVID-19 patients with neurological diseases compared to NIND even if some chemokines (CCL4, CCL5, CXCL8, andCXCL10) tended to be higher than NIND. Interestingly, among COVD-19 patients, the CSF of those with a severe disease (encephalitis/encephalopathy) contained higher levels CXCL8 and CXCL10 than those with other neurological presentations. Interpretation: Our results confirm the absence of obvious SARS-CoV-2 infection of the central nervous system and point to a mild inflammatory reaction reflecting an astrocytic reaction.

Computer-aided medical microbiology monitoring tool: a strategy to adapt to the SARS-CoV-2 epidemic and that highlights RT-PCR consistency (preprint)

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on the SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR, with up to 1,007 tests per day. To maintain a rapid turnaround time to support patient management and public health authorities' decisions, we moved from a case-by-case validation of RT-PCR to an automated validation and immediate transmission of the results to clinicians. To maintain high quality and to track possible aberrant results, we developed a quality-monitoring tool based on a homemade algorithm coded in R. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results corresponding to 30,198 patients. Patients tested several times led to 4,939 pairwise comparisons; 88% concordant and 12% discrepant. Among the 573 discrepancies, 428 were automatically solved by the algorithm. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to "Clinical evolution", 27.9% to "Preanalytical" problems, and 25.3% to "Stochastic". Finally, 11 discrepant results could not be explained, including 8 received from external partners for which clinical data were not available. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable TAT. This work highlighted the high RT-PCR consistency for the detection of SARS-CoV-2 and the importance of automated processes to handle a huge number of samples while preserving quality.