DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.

BACKGROUND: The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. RESULTS: Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. CONCLUSIONS: DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com .

Congenital orbital teratoma: A clinicopathologic case report.

PURPOSE: Orbital teratoma can be removed in order to preserve the bulb. OBSERVATIONS: Case report of a newborn with an orbital tumor. After spontaneous birth, a massive bulbus protrusion on the left side was observed. Magnetic Resonance Imaging (MRI) diagnosis showed an intraorbital cystic lesion containing solid parts and displacing the bulbus oculi. Suspecting a teratoma, primarily a cystic puncture was performed on the first day of life. On the 3rd day of life, cystic lesion was completely resected while preserving the bulbus. Histologically a mature cystic teratoma was observed. CONCLUSION AND IMPORTANCE: This case shows how important prenatal diagnostics is in order to plan the necessary birth preparations in advance and that a bulbus-preserving surgery in orbital teratoma is possible. In the absence of yolk-salk tumor it is associated with a good prognosis.

Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study.

AIMS OF THE STUDY: Wastewater-based epidemiology has contributed significantly to the comprehension of the dynamics of the current COVID-19 pandemic. Its additional value in monitoring SARS-CoV-2 circulation in the population and identifying newly arising variants independently of diagnostic testing is now undisputed. As a proof of concept, we report here correlations between SARS-CoV-2 detection in wastewater and the officially recorded COVID-19 case numbers, as well as the validity of such surveillance to detect emerging variants, exemplified by the detection of the B.1.1.529 variant Omicron in Basel, Switzerland. METHODS: From July 1 to December 31, 2021, wastewater samples were collected six times a week from the inflow of the local wastewater treatment plant that receives wastewater from the catchment area of the city of Basel, Switzerland, comprising 273,075 inhabitants. The number of SARS-CoV-2 RNA copies was determined by reverse transcriptase-quantitative PCR. Spearman's rank correlation coefficients were calculated to determine correlations with the median seven-day incidence of genome copies per litre of wastewater and official case data. To explore delayed correlation effects between the seven-day median number of genome copies/litre wastewater and the median seven-day incidence of SARS-CoV-2 cases, time-lagged Spearman's rank correlation coefficients were calculated for up to 14 days. RNA extracts from daily wastewater samples were used to genotype circulating SARS-CoV-2 variants by next-generation sequencing. RESULTS: The number of daily cases and the median seven-day incidence of SARS-CoV-2 infections in the catchment area showed a high correlation with SARS-CoV-2 measurements in wastewater samples. All correlations between the seven-day median number of genome copies/litre wastewater and the time-lagged median seven-day incidence of SARS-CoV-2 cases were significant (p<0.001) for the investigated lag of up to 14 days. Correlation coefficients declined constantly from the maximum of 0.9395 on day 1 to the minimum of 0.8016 on day 14. The B.1.1.529 variant Omicron was detected in wastewater samples collected on November 21, 2021, before its official acknowledgement in a clinical sample by health authorities. CONCLUSIONS: In this proof-of-concept study, wastewater-based epidemiology proved a reliable and sensitive surveillance approach, complementing routine clinical testing for mapping COVID-19 pandemic dynamics and observing newly circulating SARS-CoV-2 variants.

SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display.

Characterization of COVID-19 antibodies has largely focused on memory B cells; however, it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in resolving SARS-CoV-2 infection. Little is known about the specificity of plasma cells, largely because plasma cells lack surface antibody expression, thereby complicating their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and mammalian display to interrogate the specificity of plasma cells from 16 convalescent patients. Single-cell sequencing allows us to profile antibody repertoire features and identify expanded clonal lineages. Mammalian display screening is used to reveal that 43 antibodies (of 132 candidates) derived from expanded plasma cell lineages are specific to SARS-CoV-2 antigens, including antibodies with high affinity to the SARS-CoV-2 receptor-binding domain (RBD) that exhibit potent neutralization and broad binding to the RBD of SARS-CoV-2 variants (of concern/interest).

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients.

COVID-19 disease outcome is highly dependent on adaptive immunity from T and B lymphocytes, which play a critical role in the control, clearance and long-term protection against SARS-CoV-2. To date, there is limited knowledge on the composition of the T and B cell immune receptor repertoires [T cell receptors (TCRs) and B cell receptors (BCRs)] and transcriptomes in convalescent COVID-19 patients of different age groups. Here, we utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. We discovered highly expanded T and B cells in multiple patients, with the most expanded clonotypes coming from the effector CD8+ T cell population. Highly expanded CD8+ and CD4+ T cell clones show elevated markers of cytotoxicity (CD8: PRF1, GZMH, GNLY; CD4: GZMA), whereas clonally expanded B cells show markers of transition into the plasma cell state and activation across patients. By comparing young and old convalescent COVID-19 patients (mean ages = 31 and 66.8 years, respectively), we found that clonally expanded B cells in young patients were predominantly of the IgA isotype and their BCRs had incurred higher levels of somatic hypermutation than elderly patients. In conclusion, our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.

Reproductive number of the COVID-19 epidemic in Switzerland with a focus on the Cantons of Basel-Stadt and Basel-Landschaft.

The reproductive number in Switzerland was between 1.5 and 2 during the first third of March, and has consistently decreased to around 1. After the announcement of the latest strict measure on 20 March 2020, namely that gatherings of more than five people in public spaces are prohibited, the reproductive number dropped significantly below 1; the authors of this study estimate the reproductive number to be between 0.6 and 0.8 in the first third of April.

Retrobulbar haematoma in the era of anticoagulants.

AIM: The present retrospective study aimed to evaluate the frequency and distribution of retrobulbar haematoma (RBH) among 26 patients (12 male/14 female) who had suffered maxillofacial trauma/surgery, with special focus on anticoagulants, causes of accidents, treatment, and outcome. METHODS: Patient ages ranged from 8 to 94 years, with a mean of 65 years. Among all patients, 43% had received anticoagulant therapy at admission; 92.3% had a previous history of maxillofacial trauma. RESULTS: The most frequent cause of RBH were falls (65.4%), and three patients experienced RBH postoperatively after treatment using polydioxanone foil. Postoperatively (after RBH relief), 33.3% of the patients reported persistent complete visual loss; of these patients, 29% had received anticoagulation therapy, and the oral anticoagulant intake was not documented in further 29% of the patients. CONCLUSION: Awareness of this pathologic process is crucial for preventing permanent loss of vision via early diagnosis and adequate therapy. With increasing age, patients are more likely to receive an anticoagulant, which leads to a higher risk of RBH. Because falling was the most frequent cause of RBH in our patient population and increases in frequency with increasing age, fall prevention is crucial.

Evaluation of Two 3D Printers for Guided Implant Surgery.

PURPOSE: To compare the suitability of a fused filament fabrication (FFF) consumer 3D printer with a professional digital light processing (DLP) printer for the production of surgical templates for guided oral implant surgery. MATERIALS AND METHODS: Eight virtual templates were printed with two different 3D printers. These were optically scanned and the incongruences between virtual and printed templates were determined after alignment of the surface scans and the virtual data. Minimum, maximum, and mean incongruences were determined, and a t test between both groups was performed to determine statistically significant differences in accuracy. RESULTS: Templates printed with the professional DLP printer showed statistically significantly less incongruence (P = .001) than those fabricated by the consumer FFF 3D printer. CONCLUSION: The accuracy of manufactured templates is strongly dependent on the printing device and method. At this time, the tested consumer 3D FFF printer is not suitable for the fabrication of templates for implant guided surgery. Minimum requirements regarding printers' features and 3D-printed templates need to be assessed in future studies.

Progenitor cell therapy for sacral pressure sore: a pilot study with a novel human chronic wound model.

INTRODUCTION: Chronic wounds are a major health-care issue, but research is limited by the complexity and heterogeneity in terms of wound etiology as well as patient-related factors. A suitable animal model that replicates the situation in humans is not available. Therefore, the aim of the present work is to present a standardized human wound model and the data of a pilot study of topically applied progenitor cells in a sacral pressure sore. METHODS: Three patients underwent cell harvest from the iliac crest at the time of the initial debridement. Forty-eight hours after bone marrow harvest and debridement, the CD34+ selected cell suspension was injected into the wound. With the aid of a laser scanner, three-dimensional analyses of wound morphometry were performed until the defect was reconstructed with a local flap 3 weeks after debridement. RESULTS: Decreases in volume to 60%±6% of baseline on the sham side and to 52%±3% of baseline on the cell side were measured. Histologic work-up revealed no signs of metaplastic, dysplastic, or neoplastic proliferation/differentiation after progenitor cell treatment. CD34+ cells were detected in the biopsies of day 0. CONCLUSIONS: The pressure sore wound model allows investigation of the initial 3 weeks after cell-based therapy. Objective outcome analysis in terms of wound volume and histology can be performed without, or with, minimal additional morbidity, and the anatomy of the sacral area allows a control and study side in the same patient. Therefore, this model can serve as a standard for wound-healing studies. TRIAL REGISTRATION: ClinicalTrials.gov NCT00535548.