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1.
Preprint Dans Anglais | bioRxiv | ID: ppbiorxiv-452160

Résumé

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and related humans on farms. High number of farm infections (68/126) in minks and farm related personnel (>50% of farms) were detected, with limited spread to the general human population. Three of five initial introductions of SARS-CoV-2 lead to subsequent spread between mink farms until November 2020. The largest cluster acquired a mutation in the receptor binding domain of the Spike protein (position 486), evolved faster and spread more widely and longer. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combing genetic information with epidemiological information at the animal-human interface.

2.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21259212

Résumé

Worldwide exceptionally many COVID-19 clusters were observed in meat processing plants. Many contributing factors, promoting transmission, were suggested, including climate conditions in cooled production rooms favorable for environmental transmission but actual sampling studies are lacking. We aimed to assess SARS-CoV-2 contamination of air and surfaces to gain insight in potential environmental transmission in a large Dutch meat processing plant experiencing COVID-19 clusters. We performed SARS-CoV-2 screening of workers operating in cooled production rooms and intensive environmental sampling during a two-week study period in June 2020. Sampling of air (both stationary and personal), settling dust, ventilation systems, and sewage was performed. Swabs were collected from high-touch surfaces and workers hands. Screening of workers was done using oronasopharyngeal swabs. Samples were tested for presence of SARS-CoV-2 RNA by RT-qPCR. Of the 76 (predominantly asymptomatic) workers tested, 27 (35.5%) were SARS-CoV-2 RNA positive with modest to low viral loads (Ct[≥]29.7). In total, 6 out of 203 surface swabs were positive (Ct [≥]38), being swabs taken from communal touchscreens/handles. One of the 12 personal air samples and one of the 4 sewage samples were positive, RNA levels were low (Ct[≥]38). All other environmental samples tested negative. Although one-third of workers tested SARS-CoV-2 RT-PCR positive, environmental contamination was limited. Hence widespread transmission of SARS-CoV-2 via air and surfaces was considered unlikely within this plant at the time of investigation in the context of strict COVID-19 control measures in place.

3.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21252267

Résumé

Assays to measure SARS-CoV-2-specific neutralizing antibodies are important to monitor seroprevalence, to study asymptomatic infections and to reveal (intermediate) hosts. A recently developed assay, the surrogate virus-neutralization test (sVNT) is a quick and commercially available alternative to the "gold standard" virus neutralization assay using authentic virus, and does not require processing at BSL-3 level. The assay relies on the inhibition of binding of the receptor binding domain (RBD) on the spike (S) protein to human angiotensin-converting enzyme 2 (hACE2) by antibodies present in sera. As the sVNT does not require species- or isotype-specific conjugates, it can be similarly used for antibody detection in human and animal sera. In this study, we used 298 sera from PCR-confirmed COVID-19 patients and 151 sera from patients confirmed with other coronavirus or other (respiratory) infections, to evaluate the performance of the sVNT. To analyze the use of the assay in a One Health setting, we studied the presence of RBD-binding antibodies in 154 sera from nine animal species (cynomolgus and rhesus macaques, ferrets, rabbits, hamsters, cats, cattle, mink and dromedary camels). The sVNT showed a moderate to high sensitivity and a high specificity using sera from confirmed COVID-19 patients (91.3% and 100%, respectively) and animal sera (93.9% and 100%), however it lacked sensitivity to detect low titers. Significant correlations were found between the sVNT outcomes and PRNT50 and the Wantai total Ig and IgM ELISAs. While species-specific validation will be essential, our results show that the sVNT holds promise in detecting RBD-binding antibodies in multiple species.

4.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21255349

Résumé

Since its introduction in December of 2019, SARS-CoV-2, the virus that causes COVID-19 disease, has rapidly spread across the world. Whilst vaccines are being rolled out, non-pharmaceutical interventions remain the most important tools for mitigating the spread of SARS-CoV-2. Quantifying the impact of these measures as well as determining what settings are prone to instigating (super)spreading events is important for informed and safe reopening of spaces and the targeting of interventions. Mathematical models can help decipher the complex interactions that underlie virus transmission. Currently, most mathematical models developed during the COVID-19 epidemic evaluate interventions at national or subnational levels. Smaller scales of transmission, such as at the level of indoor spaces, have received less attention, despite the central role they play in both transmission and control. Models that do act on this scale use simplified descriptions of human behavior, impeding a valid quantitative analysis of the impact of interventions on transmission in indoor spaces, particularly those that aim for physical distancing. To more accurately predict the transmission of SARS-CoV-2 through a pedestrian environment, we introduce a model that links pedestrian movement and choice dynamics with SARS-CoV-2 spreading models. The objective of this paper is to investigate the spread of SARS-CoV-2 in indoor spaces as it arises from human interactions and assess the relative impact of non-pharmaceutical interventions thereon. We developed a world-wide unique combined Pedestrian Dynamics - Virus Spread model (PeDViS model), which combines insights from pedestrian modelling, epidemiology, and IT-design. In particular, an expert-driven activity assignment model is coupled with the microscopic simulation model (Nomad) and a virus spread model (QVEmod). We first describe the non-linear relationships between the risks of exposure to the virus and the duration, distance, and context of human interactions. We compared virus exposure relative to a benchmark contact (1.5meters for 15 minutes): a threshold often used by public health agencies to determine at risk contacts. We discuss circumstances under which individuals that adhere to common distancing measures may nevertheless be at risk. Specifically, we illustrate the stark increase in exposure at shorter distances, as well as longer contact durations. These risks increase when the infected individual was present in the space before the interaction occurred, as a result of buildup of virus in the environment. The latter is particularly true in poorly ventilated spaces and highlights the importance of good ventilation to prevent potential virus exposure through indirect transmission routes. Combining intervention tools that target different routes of transmission can aid in accumulating impact. We use face masks as an example, which are particularly effective at reducing virus spread that is not affected by ventilation. We then demonstrate the use of PeDViS using a simple restaurant case study, focussing on transmission between guests. In this setting the exposure risk to individuals that are not seated at the same table is limited, but guests seated at nearby tables are estimated to experience exposure risks that surpass that of the benchmark contact. These risks are larger in low ventilation scenarios. Lastly, we illustrate that the impact of intervention measures on the number of new infections heavily depends on the relative efficiency of the direct and indirect transmission routes considered. This uncertainty should be considered when assessing the risks of transmission upon different types of human interactions in indoor spaces. The PeDViS case study shows the multi-dimensionality of SARS-CoV-2 that emerges from the interplay of human behaviour and the spread of respiratory viruses in indoor spaces. A modelling strategy that incorporates this in risk assessments can be an important tool to inform policy makers and citizens. It can empower them to make better design and policy decisions pertaining to the most effective use of measures to limit the spread of SARS-CoV-2 and safely open up indoor spaces.

5.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-20195396

Résumé

Background This study aimed to assess the contribution of asymptomatic and presymptomatic residents and staff in SARS-CoV-2 transmission during a large outbreak in a Dutch nursing home. Methods Observational study in a 185-bed nursing home with two consecutive testing strategies: testing of symptomatic cases only, and weekly facility-wide testing of staff and residents regardless of symptoms. Nasopharyngeal and oropharyngeal testing with RT-PCR for SARs-CoV-2 was conducted with a standardized symptom assessment. Positive samples with a cycle threshold (CT) value below 32 were selected for sequencing. Results 185 residents and 244 staff participated. Sequencing identified one cluster. In the symptom-based test strategy period 3/39 residents were presymptomatic versus 38/74 residents in the period of weekly facility-wide testing (p-value<0.001). In total, 51/59 (91.1%) of SARS-CoV-2 positive staff was symptomatic, with no difference between both testing strategies (p-value 0.763). Loss of smell and taste, sore throat, headache or myalga was hardly reported in residents compared to staff (p-value <0.001). Median Ct-value of presymptomatic residents was 21.3, which did not differ from symptomatic (20.8) or asymptomatic (20.5) residents (p-value 0.624). Conclusions The frequency of a/presymptomatic residents compared to staff suggests that a/presymptomatic residents could be unrecognized symptomatic cases. However, symptomatic and presymptomatic/unrecognized symptomatic residents both have the same potential for viral shedding. The high prevalence symptomatic staff found in facility-wide testing suggests that staff has difficulty attributing their symptoms to possible SARS-CoV-2 infection. Weekly testing was an effective strategy for early identification of SARS-Cov-2 cases, resulting in fast isolation and mitigation of this outbreak.

6.
Preprint Dans Anglais | bioRxiv | ID: ppbiorxiv-277152

Résumé

The zoonotic origin of the SARS-CoV-2 pandemic is still unknown. Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation of outbreaks on 16 mink farms and humans living or working on these farms, using whole genome sequencing. We conclude that the virus was initially introduced from humans and has evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission. We also describe the first animal to human transmissions of SARS-CoV-2 in mink farms. One sentence summarySARS-CoV-2 transmission on mink farms.

7.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-20177857

Résumé

Understanding the coronavirus (CoV) antibody landscape in relation to disease and susceptibility is critical for modelling of steps in the next phase during the current covid-19 pandemic. In March 2020, during the first month of the epidemic in The Netherlands, we performed cross sectional studies at two time points amongst patients of the Erasmus Medical Centre in Rotterdam, to assess the presence of antibodies against seasonal human coronaviruses (OC43, 229E, NL63, HKU1), emerging zoonotic coronaviruses (SARS, MERS) and SARS-CoV-2 in nine different age groups. We observed minimal SARS-CoV-2 reactivity early March (0.7% of sera), increasing to 3.0%, four weeks later, suggesting probably undetected cases during this early phase of the epidemic. Antibody responses were mostly coronavirus species specific at young age, but possible cross-reactivity between human seasonal CoVs was observed with increasing age.

8.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-20079418

Résumé

Ten days after the first reported case of SARS-CoV-2 infection in the Netherlands, 3.9% of healthcare workers (HCWs) in nine hospitals located in the South of the Netherlands tested positive for SARS-CoV-2 RNA. The extent of nosocomial transmission that contributed to the HCW infections was unknown. We combined epidemiological data, collected by means of structured interviews of HCWs, with whole genome sequencing (WGS) of SARS-CoV-2 in clinical samples from HCWs and patients in three of nine hospitals that participated in the HCW screening, to perform an in-depth analysis of sources and modes of transmission of SARS -CoV-2 in HCWs and patients. A total of 1,796 out of 12,022 HCWs (15%) of the three participating hospitals were screened, based on clinical symptoms, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete genome sequences of 50 HCWs and 18 patients. Most sequences grouped in 3 clusters, with 2 clusters displaying local circulation within the region. The observed patterns are most consistent with multiple introductions into the hospitals through community acquired infections, and local amplification in the community. Although direct transmission in the hospitals cannot be ruled out, the data does not support widespread nosocomial transmission as source of infection in patients or healthcare workers.

9.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-20038059

Résumé

A new coronavirus, SARS-CoV-2, has recently emerged to cause a human pandemic. Whereas molecular diagnostic tests were rapidly developed, serologic assays are still lacking, yet urgently needed. Validated serologic assays are important for contact tracing, identifying the viral reservoir and epidemiological studies. Here, we developed serological assays for the detection of SARS-CoV-2 neutralizing, spike- and nucleocapsid-specific antibodies. Using serum samples from patients with PCR-confirmed infections of SARS-CoV-2, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial ELISAs. We demonstrate that most PCR-confirmed SARS-CoV-2 infected individuals seroconverted, as revealed by sensitive and specific in-house ELISAs. We found that commercial S1 IgG or IgA ELISAs were of lower specificity while sensitivity varied between the two, with IgA showing higher sensitivity. Overall, the validated assays described here can be instrumental for the detection of SARS-CoV-2-specific antibodies for diagnostic, seroepidemiological and vaccine evaluation studies.

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