Contamination of CT scanner surfaces with SARS-CoV-2 and infective potential after examination of invasively ventilated, non-invasively ventilated and non-ventilated patients with positive throat swabs: prospective investigation using real-time reverse-transcription PCR and viral cell culture

Background: During the current severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic, computed tomography (CT) has become widely used in patients with suspected or known coronavirus disease 2019 (COVID-19). This prospective observational study in 28 invasively ventilated and 18 non-invasively ventilated patients with confirmed SARS-CoV-2 contamination aims at investigating SARS-CoV-2 contamination of CT scanner surfaces and its infectiousness. Methods: Swab sampling of the CT table and gantry before and after CT examinations was performed. Additionally, the CT ventilation system air grid was wiped off after each examination. Real-time reverse-transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 RNA (ribonucleic acid) and viral cell culture were performed in the virology core lab. Results: After examination of non-invasively ventilated or non-ventilated patients, SARS-CoV-2 RNA was found in 11.1% (4/36) on patient near surfaces (CT table and gantry) and in 16.7% (3/18) on the CT air grid respectively after examination of invasively ventilated patients in 5.4% (3/56) on CT table and gantry and 7.1% (2/28) on the CT air grid. Surface contamination was more common in non-invasively ventilated or non-ventilated patients with a high viral load who were actively coughing. RT-PCR cycle threshold (Ct) was high (35.96-39.31) in all positive samples and no positive viral cell culture was found. Conclusion: Our study suggests that CT scanner surface contamination with SARS-CoV-2 is considerable and more common after examination of non-invasively ventilated or non-ventilated patients compared to invasively ventilated patients. However, no viral cell culture positivity was found, hence the infectious potential seems low

Seropositivity and flight-associated risk factors for SARS-CoV-2 infection among asylum seekers arriving in Berlin, Germany – a cross-sectional study

Introduction: Refugees and asylum seekers might be at increased risk of SARS-CoV-2 infection due to precarious living conditions during flight. Methods: Between March 24th and June 15th 2021, we conducted a cross-sectional study among adult asylum seekers arriving in Berlin. Each participant was tested for acute SARS-CoV-2 infection with a nasopharyngeal swab using reverse transcriptase PCR (rt-PCR), and for anti-SARS-CoV-2-S1 IgG antibodies using ELISA. Seropositivity, antibody avidity, and data on flight history were used to categorize individuals into two groups according to the estimated time of infection before or during flight. Sociodemographic characteristics, COVID-19 related symptoms, hygiene behaviors, and living conditions during transit were assessed using two self-report questionnaires. Results: Among 1041 participants (34·5% female, mean age 32·6 years), most frequently reported countries of origin were Moldova (20·5%), Georgia (18·9%), Syria (13·0%), Afghanistan (11·3%), and Vietnam (9·1%). Seropositivity rate was 25·1% and incidence rate of acute SARS-CoV-2 infection was 2·8%. A higher likelihood for seropositivity was observed in women (OR [95%CI]=1·64 [1·05-2·57]) but reduced by frequent hygiene behaviors (OR [95%CI]=0·75 [0·59-0·96]) or traveling by plane (OR [95%CI]=0·58 [0·35-0·96]). Other associated factors were lower educational level, accommodation in refugee shelters, traveling with children or by foot, and COVID-19 information seeking. Conclusion: Flight-associated risk factors such as accommodation in a refugee shelter and poor hygiene behaviors are associated with an elevated risk of infection, which should be addressed by public health interventions. Clinical trial registration: [https://doi.org/10.1186/ISRCTN17401860], identifier [17401860]

Global parametrization based on Ginzburg-Landau functional

International audienceQuad meshing is a fundamental preprocessing task for many applications (subdivision surfaces, boundary layer simulation). State-of-the-art quad mesh generators proceed in three steps: first a guiding cross field is computed, then a parametrization representing the quads is generated, and finally a mesh is extracted from the parameterization. In this paper we show that in the case of a periodic global parameterization two first steps answer to the same equation and inherently face the same challenges. This new insight allows us to use recent cross field generation algorithms based on Ginzburg-Landau equations to accurately solve the parametrization step. We provide practical evidence that this formulation enables us to overcome common shortcomings in parametrization computation (inaccuracy away from the boundary, singular dipole placement)

Phylogenetic Analysis Supports Horizontal Transmission as a Driving Force of the Spread of Avian Bornaviruses

Background Avian bornaviruses are a genetically diverse group of viruses initially discovered in 2008. They are known to infect several avian orders. Bornaviruses of parrots and related species (Psittaciformes) are causative agents of proventricular dilatation disease, a chronic and often fatal neurologic disease widely distributed in captive psittacine populations. Although knowledge has considerably increased in the past years, many aspects of the biology of avian bornaviruses are still undiscovered. In particular, the precise way of transmission remains unknown. Aims and Methods In order to collect further information on the epidemiology of bornavirus infections in birds we collected samples from captive and free-ranging aquatic birds (n = 738) and Passeriformes (n = 145) in Germany and tested them for the presence of bornaviruses by PCR assays covering a broad range of known bornaviruses. We detected aquatic bird bornavirus 1 (ABBV-1) in three out of 73 sampled free-ranging mute swans (Cygnus olor) and one out of 282 free-ranging Eurasian oystercatchers (Haematopus ostralegus). Canary bornavirus 1 (CnBV-1), CnBV-2 and CnBV-3 were detected in four, six and one out of 48 captive common canaries (Serinus canaria forma domestica), respectively. In addition, samples originating from 49 bornavirus-positive captive Psittaciformes were used for determination of parrot bornavirus 2 (PaBV-2) and PaBV-4 sequences. Bornavirus sequences compiled during this study were used for phylogenetic analysis together with all related sequences available in GenBank. Results of the Study Within ABBV-1, PaBV-2 and PaBV-4, identical or genetically closely related bornavirus sequences were found in parallel in various different avian species, suggesting that interspecies transmission is frequent relative to the overall transmission of these viruses. Our results argue for an important role of horizontal transmission, but do not exclude the additional possibility of vertical transmission. Furthermore we defined clearly separated sequence clusters within several avian bornaviruses, providing a basis for an improved interpretation of transmission events within and between wild bird populations and captive bird collections

Génération de maillage quadrangulaire d'un domaine du plan via les équations de Ginzburg-Landau

National audienceGénérer un maillage d'une surface est un pré-requis souvent indispensable à de nombreuses applications. Certaines (la subdivision de surfaces, la simulation de couches limites) nécessitent l'utilisation de maillage quadrangulaire. L'état de l'art procède en trois étapes. Il s'agit d'abord de calculer un champ de croix, puis de l'intégrer pour obtenir une paramétrisation et enfin d'extraire un maillage quadrangulaire à partir de la paramétrisation. Nous montrerons que les deux premières étapes réfèrent aux mêmes équations et peuvent donc être traitées de la même manière. Cette approche permet de résoudre des problèmes (imprécision loin des bords, mauvaise localisation des singularités) qui se posaient jusqu'alors

Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses

The furin cleavage site (FCS) in SARS-CoV-2 is unique within the Severe acute respiratory syndrome-related coronavirus (SrC) species. We re-assessed diverse SrC from European horseshoe bats and analyzed the spike-encoding genomic region harboring the FCS in SARS-CoV-2. We reveal molecular features in SrC such as purine richness and RNA secondary structures that resemble those required for FCS acquisition in avian influenza viruses. We discuss the potential acquisition of FCS through molecular mechanisms such as nucleotide substitution, insertion, or recombination, and show that a single nucleotide exchange in two European bat-associated SrC may suffice to enable furin cleavage. Furthermore, we show that FCS occurrence is variable in bat- and rodent-borne counterparts of human coronaviruses. Our results suggest that furin cleavage sites can be acquired in SrC via conserved molecular mechanisms known in other reservoir-bound RNA viruses and thus support a natural origin of SARS-CoV-2

COVID-19: a fatal case of acute liver failure associated with SARS-CoV-2 infection in pre-existing liver cirrhosis

Background: The detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2) is challenging, particularly in post-mortem human tissues. However, there is increasing evidence for viral SARS-CoV-2 manifestation in non-respiratory tissues. In this context, it is a current matter of debate, whether SARS-CoV-2 shows hepatotropism. Case presentation: Here, we report a case of an 88-year-old women with massive SARS-CoV-2 viremia, severe jaundice and clinical signs of an acute hepatitis, who died within a few days from an acute liver failure without showing any clinical signs of pneumonia. Autopsy revealed a severe chronic and acute liver damage with bile duct infestation by SARS-CoV-2 that was accompanied by higher expressions of angiotensin-converting enzyme-2 (ACE2), Cathepsin L and transmembrane serine protease 2 (TMPRSS2). Conclusion: Our findings indicate an enhanced biliary susceptibility to viral infection with SARS-CoV-2, that might have resulted from pre-existing severe liver damage. Furthermore, our findings emphasize the differential diagnosis of coronavirus disease 2019 (COVID-19)-associated liver failure in the clinical setting of an inexplicable jaundice

Importance of external quality assessment for SARS-CoV-2 antigen detection during the COVID-19 pandemic

Background: Antigen testing has become an essential part of fighting the ongoing COVID-19 pandemic. With the continual increase in available tests, independent and extensive comparative evaluations using data from external quality assessment (EQA) studies to evaluate test performance between different users are required.Objectives: An EQA scheme was established to assess the sensitivity of antigen tests and the potential impact of circulating SARS-CoV-2 strains on their performance.Study design: Panels were prepared for three challenges in 2021 containing inactivated SARS-CoV-2-positive samples of various genetic strains (including variants of concern, VOCs) at different concentrations, and negative samples. Data was analysed based on qualitative testing results in relation to the antigen test used. Results: Participants registered for each individual challenge in any combination. In total, 258 respondents from 27 countries worldwide were counted submitting 472 datasets. All core samples were correctly reported by 76.7 to 83.1% at participant level and by 73.5 to 83.8% at dataset level. Sensitivity differences could be shown in viral loads and SARS-CoV-2 strains/variants including the impact on performance by a B.1.1.7-like mutant strain with a deletion in the nucleoprotein gene. Lateral flow rapid antigen tests showed a higher rate of false negatives in general compared with automated point-of-care tests and laboratory ELISA/immunoassays.Conclusions: EQA schemes can provide valuable data to inform participants about weaknesses in their testing process or methods and support ongoing assay evaluations for regulatory approval or post-market surveillance