Rapid and sensitive identification of omicron by variant-specific PCR and nanopore sequencing: paradigm for diagnostics of emerging SARS-CoV-2 variants

On November 26, 2021, the World Health Organization classified B.1.1.529 as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC), named omicron. Spike-gene dropouts in conventional SARS-CoV-2 PCR systems have been reported over the last weeks as indirect diagnostic evidence for the identification of omicron. Here, we report the combination of PCRs specific for heavily mutated sites in the spike gene and nanopore-based full-length genome sequencing for the rapid and sensitive identification of the first four COVID-19 patients diagnosed in Germany to be infected with omicron on November 28, 2021. This study will assist the unambiguous laboratory-based diagnosis and global surveillance for this highly contagious VoC with an unprecedented degree of humoral immune escape. Moreover, we propose that specialized diagnostic laboratories should continuously update their assays for variant-specific PCRs in the spike gene of SARS-CoV-2 to readily detect and diagnose emerging variants of interest and VoCs. The combination with established nanopore sequencing procedures allows both the rapid confirmation by whole genome sequencing as well as the sensitive identification of newly emerging variants of this pandemic β-coronavirus in years to come.

Three exposures to the spike protein of SARS-CoV-2 by either infection or vaccination elicit superior neutralizing immunity to all variants of concern

Infection-neutralizing antibody responses after SARS-CoV-2 infection or COVID-19 vaccination are an essential component of antiviral immunity. Antibody-mediated protection is challenged by the emergence of SARS-CoV-2 variants of concern (VoCs) with immune escape properties, such as omicron (B.1.1.529) that is rapidly spreading worldwide. Here, we report neutralizing antibody dynamics in a longitudinal cohort of COVID-19 convalescent and infection-naive individuals vaccinated with mRNA BNT162b2 by quantifying anti-SARS-CoV-2-spike antibodies and determining their avidity and neutralization capacity in serum. Using live-virus neutralization assays, we show that a superior infection-neutralizing capacity against all VoCs, including omicron, developed after either two vaccinations in convalescents or after a third vaccination or breakthrough infection of twice-vaccinated, naive individuals. These three consecutive spike antigen exposures resulted in an increasing neutralization capacity per anti-spike antibody unit and were paralleled by stepwise increases in antibody avidity. We conclude that an infection-plus-vaccination-induced hybrid immunity or a triple immunization can induce high-quality antibodies with superior neutralization capacity against VoCs, including omicron.

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020

Background

In the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data.

Aim

We applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata.

Methods

We investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission.

Results

We identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions.

Conclusions

Early spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.

Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020

Containment strategies and clinical management of coronavirus disease (COVID-19) patients during the current pandemic depend on reliable diagnostic PCR assays for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we compare 11 different RT-PCR test systems used in seven diagnostic laboratories in Germany in March 2020. While most assays performed well, we identified detection problems in a commonly used assay that may have resulted in false-negative test results during the first weeks of the pandemic.

The polyomaviruses WUPyV and KIPyV: a retrospective quantitative analysis in patients undergoing hematopoietic stem cell transplantation

BACKGROUND

The polyomaviruses WUPyV and KIPyV have been detected in various sample types including feces indicating pathogenicity in the gastrointestinal (GI) system. However, quantitative viral load data from other simultaneously collected sample types are missing. As a consequence, primary replication in the GI system cannot be differentiated from swallowed virus from the respiratory tract. Here we present a retrospective quantitative longitudinal analysis in simultaneously harvested specimens from different organ sites of patients undergoing hematopoietic stem cell transplantation (HSCT). This allows the definition of sample types where deoxyribonucleic acid (DNA) detection can be expected and, as a consequence, the identification of their primary replication site.

FINDINGS

Viral DNA loads from 37 patients undergoing HSCT were quantified in respiratory tract secretions (RTS), stool and urine samples as well as in leukocytes (n = 449). Leukocyte-associated virus could not be found. WUPyV was found in feces, RTS and urine samples of an infant, while KIPyV was repeatedly detected in RTS and stool samples of 4 adult patients.RTS and stool samples were matched to determine the viral load difference showing a mean difference of 2.3 log copies/ml (p < 0.001).

CONCLUSIONS

The data collected in this study suggest that virus detection in the GI tract results from swallowed virus from the respiratory tract (RT). We conclude that shedding from the RT should be ruled out before viral DNA detection in the feces can be correlated to GI symptoms.

The Epstein-Barr virus-encoded glycoprotein gp 110 (BALF 4) can serve as a target for antibody-dependent cell-mediated cytotoxicity (ADCC)

Antibody-dependent cell-mediated cytotoxicity (ADCC) is thought to play a major role in controlling the spread of the Epstein-Barr virus (EBV) in an infected individual. Recently, the viral membrane protein gp 350/220, which is also expressed at the surface of the virus producing cell, was identified as a target for ADCC reactions. Due to its glycoprotein nature, the EBV protein gp 110 is another possible ADCC target. It is one of the most abundant proteins found during the late phase of viral replication; until now, however, researchers have not been able to localize it on the surface of EBV positive cells. By means of recombinant vaccinia viruses containing the genes for gp 350/220 and gp 110, respectively, we expressed these proteins in lymphoblastoid cells, which were then used as targets in ADCC studies with sera from EBV-positive and -negative individuals. In these experiments we were able to demonstrate the feasibility of our approach for the investigation of EBV-specific ADCC reactions and could confirm the role of gp 350/220 as an ADCC target. Furthermore, we were able to show that gp 110 can also be recognized in an ADCC reaction, proving that at least some gp 110 molecules must be expressed at the cell surface.

The BI'LF4 trans-activator of Epstein-Barr virus is modulated by type and differentiation of the host cell

We have analyzed the activity and regulated expression of a new Epstein-Barr virus (EBV) trans-activator (I'ta) encoded by left reading frame 4 (BI'LF4) of the BamHI I'fragment. The gene was detected in all genomes of established EBV strains and individual isolates, with the exception of B95-8, where the type-specific deletion of this open reading frame is tolerated in vitro. Specific trans-activation of two EBV promoters (early MS and I'ta promoter) could be shown in cotransfection assays. The I'ta product affected autoactivation but had no influence on heterologous target promoters. The I'ta promoter segment was shown to be costimulated in the process of host cell differentiation in the absence of other EBV gene products. Expression of the reading frame in bacteria identified a 48-kDa protein as a stable gene product. I'ta-specific antibodies were detected in sera from EBV-positive persons (nasopharyngeal carcinoma). When expressed with suitable eucaryotic vectors, a nuclear protein could be immunostained in transfected cells. Our experiments suggest a cell type-specific requirement for I'ta in the lytic cycle of EBV at a determined differentiation stage of the host cell.

Expression of class I major histocompatibility complex antigens in Epstein-Barr virus-carrying lymphoblastoid cell lines and Burkitt lymphoma cells

Epstein-Barr virus (EBV) carrying lymphoblastoid cell lines (LCLs) and EBV-positive Burkitt lymphoma (BL) cells were compared for their expression of class I antigens of the major histocompatibility complex. Five common BL lines, LCLs, pokeweed mitogen-stimulated blasts and resting B-cells from healthy donors, and eight pairs of BL cells and LCLs, each pair originating from one patient, were tested. Quantitative analysis was performed using a radioimmunoassay; qualitative aspects were studied by one- and two-dimensional gel electrophoresis. In general, LCLs expressed significantly higher amounts of class I antigens than BL cells, the latter showing class I densities similar to or lower than peripheral resting B-cells. From analysis of the expression of class I-specific RNA, there is some evidence that class I antigen expression is regulated on the transcriptional level. In two BL cells studied, class I expression could be enhanced by gamma-interferon, whereas the corresponding LCLs seemed to be refractory to this treatment. One- and two-dimensional gel electrophoresis showed that in some BL lines, in addition to the generally lower class I expression, distinct class I specificities were down-regulated. None of these alterations in class I expression was EBV specific; however, they may well play a role in the recognition of BL cells and LCLs by cellular immune mechanisms. Thus, down-regulation of class I antigens may contribute to the resistance of BL cells to cytotoxic T-lymphocytes, whereas their enhanced expression may improve the recognition of EBV-infected LCLs.

Distribution pattern of alpha and beta myosin in normal and diseased human ventricular myocardium

All fibers in three normal, four dilated, and two ischemic human ventricles were classified according to their myosin content using three sets of monoclonal antibodies each specific for one myosin heavy chain isoform (alpha, beta and beta'). Numerous fibers contained only beta myosin heavy chain (denoted as beta fibers), others contained either alpha and beta, or beta and beta' myosin heavy chain (denoted as alpha beta and beta beta' fibers, respectively). The percentages of alpha beta fibers were systematically determined along the walls of seven homologous regions of the ventricular myocardium. In all ventricles, there was an alpha beta-fiber transmural gradient, with less alpha beta fiber in the subendocardium than in the subepicardium. More alpha beta fibers were found in the right than in the left ventricular wall but there was no difference between the mid-portion and the apex of the free wall of each ventricle. The diseased ventricles contained a lower alpha beta fiber percentage than the normal hearts. beta beta' fibers were very rare in the normal ventricles (less than 5%) and almost inexistent in pathological hearts. The correlation between the mean alpha beta fiber percentages of the diseased hearts and their cardiac indices (r = 0.88, P less than 0.05) suggests that the small amount of alpha myosin distributed in a large number of ventricular fibers could play a role in the contractile performance of the heart. In conclusion, this study provides evidence for 1) an alpha beta fiber transmural gradient, and 2) a lower alpha myosin ratio in diseased than in normal human ventricle.

Local diversity of myosin expression in mammalian atrial muscles. Variations depending on age and thyroid state in the rat and the rabbit

Rat, rabbit, pig, and bovine atrial myocardia were investigated with anti-alpha and anti-beta myosin heavy chain monoclonal antibodies. Analysis of atrial fibers by indirect immunofluorescence and assay of myosin heavy chains in tissue micro samples by immunoaffinity chromatography revealed both heterogeneity and plasticity in the atrial myosin heavy chains, undetected by electrophoresis of native atrial myosins under nondenaturing conditions. We found both alpha- and beta-like myosin heavy chains to be expressed in rat and rabbit, as they are in pig and bovine, atrial myocardia. They were regionally distributed within atrial muscles. The beta-like myosin heavy chains were present at much lower levels in rat and rabbit atria than in pig and bovine atria. Young rat atrial myosin was composed of only alpha-like heavy chains. In the rat and the rabbit, hyperthyroidism induced a beta- to alpha-like myosin heavy chain transition, which was considerable in the right atria and complete in the left atria. In the rat, thyroidectomy induced a moderate alpha- to beta-like myosin heavy chain transition, visible in the left atria. The significance of this atrial myosin heavy chain polymorphism is discussed in relation to the existence of anatomical localizations of the two myosin variants.

An assay for pattern formation in dictyostelium discoideum using monoclonal antibodies, flow cytometry, and subsequent data analysis

An assay for determining the proportions of prespore cells in a simple multicellular organism, the slug stage of Dictyostelium discoideum, was established using a prespore-specific monoclonal antibody and a fluorescence-activated cell sorter. Appropriate techniques for data analysis were developed. The effects of slug size and age were determined. Small slugs have a lower percentage of prespore cells than large slugs. The percentage of prespore cells increases and then decreases in slugs aged between a few hours and 9 days. Pronounced effects were observed on the size of cells in aging slugs. In particular unlabelled (mostly prestalk) cells were larger than prespore cells in young slugs, but after 6 days migration they became considerably smaller than prespore cells. The fact that all unlabelled cells were coordinately shifted in size, suggests that these cells (which comprise prestalk, prestalklike, and predisc cells) are related to each other.

Evidence that positional information is used to establish the prestalk-prespore pattern in Dictyostelium discoideum aggregates

Two contrasting mechanisms have been proposed for the establishment of the prestalk-prespore pattern in the multicellular aggregate of the simple eukaryote Dictyostelium discoideum. One involves intermingled, non-position-dependent cell differentiation followed by sorting out which produces the pattern of prestalk cells in the anterior region and prespore cells posteriorly. The second mechanism involves patterning according to the position of cells within the aggregate, in which case intermingled cell types are not expected. Here we use a monoclonal antibody (MUD1), recognising a prespore cell surface antigen, to study the initial appearance of prespore cells in aggregates. Quantitative studies were made with a flow cytometer and frozen sections were used to localise the cells expressing the prespore antigen. This antigen first appeared at the onset of tip formation in the centre of aggregates in a position-dependent fashion. The prespore antigen was not detected in the tip region or in streams of cells entering the aggregate. We re-examined the evidence on which the non-position-dependent differentiation model is based. Our results support the positional model for pattern formation.

Analysis of proportion regulation in slugs of Dictyostelium discoideum using a monoclonal antibody and a FACS-IV

A quantitative assay for estimating the proportion of prespore cells in D. discoideum slugs was established by labelling disaggregated slug cells with a prespore specific monoclonal antibody and analysing the cell population with a FACS-IV. The method is validated using a wild-type strain and its stalky mutant. "Wild-type" strains have different proportions of prespore cells and it is demonstrated that slugs of some strains have an increased percentage of prespore cells when migrated in the dark compared to the light and in the presence of EGTA. The technique is rapid and will make possible genetic analysis of proportion regulation in D. discoideum.