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Neuropathological complications are frequently observed in SARS‐CoV‐2 infection and brain autopsies from human subjects who died from COVID‐19 have revealed significant pathology, ...including wide‐spread neuroinflammation, hypoxic‐ischemic injury, and microhemorrhages. To begin to understand the neuropathogenesis of SARS‐CoV‐2 infection, we investigated brain from infected non‐human primates (NHP)s for pathological changes consistent with that seen among humans. Eight aged NHPs were inoculated with the 2019‐nCoV/USA‐WA1/2020 strain of SARS‐CoV‐2 via a multi‐route mucosal or aerosol challenge. Hematoxylin and eosin (H&E) and immunohistochemistry (IHC) staining was done on seven brain regions to elucidate general pathology, microhemorrhages, platelet derived thrombi, neuronal apoptosis, microglia and astrocyte morphology, hypoxia, and virus present. Similar to humans, pathology was variable but included wide‐spread neuroinflammation, nodular lesions, neuronal degeneration, and microhemorrhages. Neuronal degeneration was most often seen in the cerebellum and brainstem of infected animals. Neuronal death was confirmed through FluorJade C and cleaved (active) caspase 3 IHC, which showed foci of positivity, particularly among Purkinje cells of the cerebellum. Importantly, this was seen among infected animals that did not develop severe respiratory disease. Hypoxia inducible factor‐1α (HIF‐1α) was observed at a higher intensity around the vasculature within deep brain regions of the infected animals. Microhemorrhages were prevalent among all animals but were less frequently associated with platelet derived thrombi in the infected animals, as compared to mock‐infected controls. Sparse virus was detected in brain endothelial cells but did not associate with the severity of CNS injury. Increased HIF‐1α suggests that brain hypoxia may promote neuronal degeneration within infected brain. Wide‐spread neuroinflammation may also contribute to neuronal injury/death and neurological manifestations seen in the context of infection.
The novel coronavirus SARS‐Cov‐2 or COVID‐19 became a global pandemic and currently few medically approved curative treatments exist. SARS‐Cov‐2 acts similarly to SARS‐CoV‐1 from where it may have ...evolved. The COVID‐19 virus can survive ~3 hours in air and < 72 hours on distinct surfaces. COVID‐19 mutates by introducing sequence errors in the host’s RNA genome or by modifying proteins and enzymes. Vaccination, including booster shots, social distancing and isolation are the most generally practiced guidelines in the global management of COVID‐19. Globally the most frequently utilized pharmacologic treatments include ivermectin, hydroxychloroquine, glucocorticoids, the anti‐viral agent remdesivir, monoclonal antibodies, and convalescent plasma in combination with an antimicrobial agent such as azithromycin to minimize secondary microbial infection and nutritional supplementation (vitamins C, D3, and zinc) to enhance cellular immune responses and are included in the routine protocols of some emergency rooms. COVID‐19 viral transmission occurs via respiratory microdroplets, by inhaling COVID‐19 laden airborne particles and contact with contaminated surfaces on which these droplets have been deposited. SARS‐CoV‐2 targets ACE2 receptors in the upper and lower respiratory tracts in addition to the heart, brain, and gastrointestinal tract, and may cause thromboses in the liver, heart, and kidney.
Significant risk factors for the severity of COVID‐19 infection include advanced age and pre‐existing comorbid conditions obesity, hypertension, cardiovascular disease, diabetes, and compromised immune status, which all correlate with greater mortality. Outcome‐effecting factors include viral load, viral mutations, and pre‐existing conditions. Since its origination, genomic studies of the virus have identified numerous variants which have become regionally prevalent in different countries. Infective factors, comorbidities and viral load strongly affect outcomes; patients infected with the greatest viral load showed a higher mortality. It is opined that the number of deaths attributed to COVID‐19 may be inaccurate due to errors in diagnosing and reporting, since other similar illnesses may exhibit similar symptoms.
Future research should focus on prevention practices, comorbidities, genetic prevalence, reliable systematic and consistency in country‐by‐country testing and reporting procedures, further scrutiny regarding the efficacy of current vaccines and protocols, and the pursuit for innovative therapies for Coronaviruses and variants including biophotonics and exploration of emerging bioenergetic, nutritional, pharmacological, immunotherapeutic and vaccination‐preventive applications for eradication of COVID‐19.
Refs: 1. Cheng, RZ. (2020a). Med Drug Disc, 5, 100028; 2. Shankar, AH, & Prasad, AS. (1998). ACJN, 68(2), 447S‐463S; 3. Petrilli, CM, Jones, SA, et al. (2020); medRxiv; 4.van Doremalen, N, Bushmaker, T et al. (2020). NEJM, 382(16), 1564‐1567
Scientists continue to study SARS‐CoV‐2, the virus currently responsible for a worldwide pandemic, to determine the best methods to inactivate the virus on surfaces and reduce the risk of contact ...transmission. Its classification as a Biosafety Level (BSL) ‐3 pathogen complicates research since few facilities have the capacity for this level of containment. Human betacoronavirus OC43 (OC43) is a good surrogate for SARS‐CoV‐2 based on its genetic similarity and OC43’s BSL‐2 classification. Two industry specific surfaces were inoculated with OC43 and sampled at timepoints that reflect typical industry timelines for sanitation. The objective was to determine the stability of OC43 on typical meat facility surfaces.
OC43 was propagated on human ileocecal colorectal adenocarcinoma cells (HRT‐18, ATCC CCL‐244). Infectious virus was quantified by indirect immunofluorescence TCID50 assays on HRT‐18 cells. Stainless steel grade 316 and polyethylene (poly top) coupons were inoculated with 100 ul of 2.51 x 106 TCID50/ml virus by pipette in a grid pattern at room temperature (20ºC) in an active biosafety cabinet in triplicate for each timepoint. Coupons were rinsed with 5 ml of sterile filtered beef extract buffer (BEB7), composed of Tris base, glycine, magnesium chloride, and beef extract pH adjusted to 7.0, at 0, 1, 4, 8, and 16 hours post inoculation (hpi). The collected rinsate was aliquoted and stored at ‐80ºC until the TCID50 assays were conducted in batch. The 16 hpi stainless steel samples were created at the time of the poly top experiment. The TCID50 assays were run in duplicate for each sample and TCID50/ml was calculated and averaged for each replicate. Percent recovery of infectious virus was determined for each timepoint.
Virus was observed to have partially dried at 1 hpi and was completely dry at all following timepoints on both surfaces. Few infectious virions were lost between inoculation and 0 hpi collection from both surfaces. Mean percent recovery (MPR) of infectious OC43 from stainless steel and poly top at 0 hpi was 153% and 90%, respectively. At 1 hpi, the MPR from stainless steel was 65% while poly top was 123%. The variability of the assay explains these findings. Stainless steel and poly top had average recoveries of 60% and 25% at 4 hours, respectively. The lowest MPR for stainless steel was 17% at 8 hpi while the lowest MPR for poly top was 7% at 16 hpi. A higher MPR of 43% from stainless steel at 16 hpi reflects this timepoint being conducted on a different day.
Infectious OC43 is still detectable on common meat facility surfaces several hours after inoculation, but our current knowledge of enveloped viruses asserts that they are inviable after drying. A maximum decrease of only 1 log TCID50 between inoculation and the 16 hpi samples means that a person could potentially be infected between cleanings if it is possible to transfer dried infectious virus from a surface to a mucous membrane. However, this is a conjecture that requires further study since the infectious dose of SARS‐CoV‐2 is unknown and no experiment to determine if this contact transfer is possible has been conducted. Currently, similar experiments with SARS are underway.
The emergence of novel, zoonotic betacoronavirus, SARS‐CoV‐2, demands quantification of infectious virus rather than viral RNA to provide more accurate assessment of transmission risk for COVID‐19. ...To maximize investigator safety, similar in morphology and inactivation profile, human betacoronavirus OC43 (OC43) was used as a surrogate to refine infectious virus recovery methods for SARS‐CoV‐2, a biosafety level (BSL)‐3 pathogen. Using OC43 and SARS‐CoV‐2, we examined the ability of InnovaPrep Mano Surface Samplers (MANOs), made of hydrophobic, open‐cell polymeric foam, to recover virus from large stainless‐steel surfaces hypothesizing that they would outperform hydrophilic cellulose sponges (sponges), used for environmental sampling.
In triplicate, 1.0 x 105 TCID50 of OC43 and SARS‐CoV‐2 were applied to the inner surface of a biological safety cabinet (BSC) within the literature or vendor specified optimal surface area, 1267.36 cm2 (MANO) and 100 cm2 (sponges). The areas were sampled with eluant presoaked MANOs and sponges, and samples aliquoted and stored at ‐80ºC until batch titration by indirect immunofluorescence TCID50 assay, using human ileocecal colorectal adenocarcinoma cells (HRT‐18 CCL‐244, ATCC) for OC43 samples and crystal violet detection‐based TCID50 using African green monkey kidney epithelial cells (VeroE6 CRL‐1586, ATCC) for SARS‐CoV‐2. Tested eluants were a beef extract buffer, pH 7 (BEB7), BEB7 with 0.05% Tween‐20 (BEB7/T) and (MANOs only) phosphate buffered saline with 0.05% Tween‐20 (PBS/T), the vendor default. Additionally, an expanded surface area (0.77m2 for MANOs, 300cm2 for sponges) was tested with OC43 as described above, except with 1.0x104 TCID50 inoculum.
For OC43, recovery for MANOs with BEB7 was 2.66x105 TCID50 compared to PBS/T’s 4.40x104 TCID50. BEB7 MANOs had a higher average percent recovery (102%) than BEB7 sponges (84%). By one‐way ANOVA (α=0.05), MANO BEB7’s and BEB7/T’s average recovery percentages were significantly greater than PBS/T’s. Samples taken from the larger surface areas for both samplers were below the assay’s limits of detection for BEB7; however, OC43 eluted with BEB7/T from sponges was detectable (3.47x102 TCID50, 32% recovery). For SARS‐CoV‐2, MANO BEB7’s average recovery percentage (27%) was again shown to be significantly greater than PBS/T’s (0.38%). However, decreased recovery of infectious virus was seen across both tools and all eluants, perhaps indicating a difference between SARS‐CoV‐2 and OC43 for BEB7.
Use of BEB7 improved OC43 and SARS‐CoV‐2 recovery from optimal surface areas with MANOs. Surprisingly, when the surface area was enlarged, all samples except those from BEB7/T sponges were below the limit of detection. This might be explained by additional eluant loss on the larger surface during mechanical recovery or virus inactivation due to desiccation from BSC airflow or other environmental factors. Similar factors might explain the SARS‐CoV‐2 results. Quantification by RT‐qPCR or flow virometry, and planned experiments in BSL‐3 agricultural space, where the room is primary containment, may provide further insights.
Background
With the spread of highly infectious strains such as the Delta variant of SARS‐CoV‐2, rapid antigen testing and variant tracking are gaining more attention from infectious disease ...specialists and the general public as essentials for disease control and prevention amidst the COVID‐19 pandemic. The lateral flow based antigen tests provide fast turnaround of results within minutes, but it’s open ‐faced assay format means that the test operators are more prone to accidental exposure to pathogen‐containing samples. The viral inactivation transport media (ITMs) provide much needed protection against exposure to highly transmissive live viruses during sample collection, transport, and storage. However, the current ITMs were designed for PCR tests and share a harsh chemical formulation that denatures protein analytes, making them incompatible with antigen tests.
We developed an innovative viral transport media that is designed for a variety of tests, such as antigen testing and PCR. The new formulation can be used to safely inactivate SARS‐CoV‐2 virus while maintaining compatibility with many different formats beyond rt‐PCR.
Design
To evaluate the viral inactivation performance of the novel inactivation transport media formulation, a cytopathic effect assay was conducted using VERO E6 cells in presence of SARS‐CoV‐2 samples incubated in our novel formulation and log reduction were reported.
To assess its compatibility with different SARS‐CoV‐2 related assays, the novel formulation was used as inactivation transport media in antigen, PCR, and NGS based Swab‐Seq tests with known controls.
Results
The results for the inactivation study confirmed > 3.0 log reduction in viral titer after 30 min exposure in novel transport media formulation and demonstrated 99.5% effectiveness in SARS‐CoV‐2 inactivation. The results for the PCR and antigen test compatibility studies showed comparable and/or superior performance in detection limits for the novel formulation when compared to other sample media. The Swab‐Seq result offers preliminary support on the novel formulation’s compatibility with NGS based assays.
Conclusion
Using a novel viral transport medium, we were able to completely inactivate the SARS‐CoV‐2 virus. The new formulation was compatible with both nucleic acid and protein assays while protecting cells from infection. This viral transport media could allow more test types to be done from a single specimen, resulting in safer and reliable outcomes. Additionally, it would reduce the need for multiple samples collected from patients while supporting SARS‐CoV‐2 variant tracking via NGS.
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Introduction
Recent research suggests that endothelial activation plays a role in COVID‐19 pathogenesis by promoting a pro‐coagulative and pro‐inflammatory state. However, the mechanism ...by which the endothelium is activated in COVID‐19 is unclear.
Objective
To investigate the mechanism by which COVID‐19 activates the pulmonary endothelium.
Hypothesis
The pulmonary endothelium generates reactive oxygen species (ROS) upon exposure to the “inflammatory load” of the systemic circulation.
Methods
COVID‐19 was recreated
in vitro
and
ex vivo
, by exposing human lung endothelial cells (EC) or donor human lung slices (human precision‐cut lung slices or huPCLS) to medium supplemented with serum from COVID‐19 affected subjects. Sera were acquired from patients with COVID‐19 infection admitted to the Intensive Care Unit of the Hospital at the University of Pennsylvania. ROS (fluorescent dye, CellROX) and intercellular adhesion molecule (ICAM‐1) levels were assessed by fluorescence labeling and imaging.
Results
Both EC activation (as monitored by ROS production) and pro‐inflammatory phenotype (as assessed by ICAM‐1), were significantly higher with COVID‐19 as compared to normal subjects.
Conclusions
The endothelium is activated with COVID‐19 via ROS production; thus, the ROS produced drive a pro‐inflammatory phenotype by inducing the expression of ICAM‐1, a pivotal marker of endothelium inflammation. As ROS mediates EC activation and inflammation during COVID‐19, ROS blockade could be a therapeutic target in maintaining vascular health.
SARS‐CoV‐2 is responsible for the ongoing COVID‐19 pandemic, which causes respiratory failure and damage to multiple organ systems. Emergence of new variants of concern (VOCs), including Omicron can ...potentially render the current vaccines ineffective. However, our understanding of COVID‐19 pathophysiology and molecular basis of SARS‐CoV‐2 infection is very limited. The role of the Hippo signaling pathway, an evolutionarily conserved organogenesis circuitry, in tissue inflammation and innate immune response is beginning to be understood. Given the complexity of COVID‐19 associated cell injury and immunopathogenesis processes, we investigated this Hippo pathway dynamic in SARS‐CoV‐2 infection by utilizing COVID‐19 lung samples, transcriptome and human cell models based on pluripotent stem cell‐derived cardiomyocytes (PSC‐CMs) and human primary lung air‐liquid interface (ALI) culture. The SARS‐CoV‐2 infection resulted in stoppage of cardiomyocyte beating and extensive apoptotic cell death. Especially the infection caused activation of Hippo signaling pathway in cardiomyocytes, as shown by increased level of phosphorylated form of YAP, a downstream transcriptional co‐factor involved in tissue growth, mitochondrial biogenesis and innate immunity. Similar activation was noted in SARS‐CoV‐2 infected lung ALI epithelial cells and COVID‐19 lung autopsy samples. The shRNA‐mediated partial knockdown and pharmacological inhibitor of YAP/TAZ resulted in significantly reduced SARS‐CoV‐2 replication, whereas inhibition of Hippo pathway upstream LATS1 and MST1 kinases led to enhanced virus replication. These results indicate a direct role of Hippo signaling in SARS‐CoV‐2 mediated disease pathogenesis and this pathway can be pharmacologically targeted to treat COVID‐19.
Antibodies play an important part in combating SARS‐CoV‐2 infection whether generated by the infection or vaccination. However, the many epitopes generated by infection have not been fully ...investigated with only a few epitopes known and these being mostly limited to the S protein’s receptor binding domain (RBD) and the N‐terminal domain which limits vaccine and drug design 1‐4. The difference between epitopes generated by infection and vaccination has also not been studied. To address this, we employed a SARS‐CoV‐2 proteome microarray to screen for linear epitopes recognized by antibodies present in COVID‐19 patients and individuals vaccinated with the Pfizer‐BioNTech mRNA COVID‐19 Vaccine.
The proteome microarray consisted of S, N, and E proteins, as well as spotting peptides that were 15 amino acids in length with overlaps of 5‐amino acids, covering the entire SARS‐CoV‐2 proteome (MN908947.3) (Figure 1). Blood samples were incubated onto the arrays followed by an incubation of fluorescent secondary anti‐human antibodies. Fluorescent intensity data generated and normalized using the Z‐score method and then further analyzed for significance by parametric one‐way ANOVA with Dunnett's post hoc test (COVID‐19 cohort) and repeated measure ANOVAs with Dunnett's post hoc tests (vaccinated cohort).
The full‐length S protein showed a significant increase in COVID‐19 patients at around 20‐23 days after symptom onset and vaccinated individuals over all time points in both IgM and IgG antibodies (Figure 2A). Linear mapping of the IgM epitopes revealed a degree of overlap between infected and vaccinated individuals (22.2%; 6/27 total) with both having epitopes in the RBD and fusion peptide (FP) (Figure 2B). Structural mapping on 3D models of the S protein showed that all epitopes where on the surface of the protein and that COVID‐19 generated epitopes have a different pattern than those generated by vaccination (Figure 2C).
An Epitope identified in this study with future prospects is epitope S481‐495 from COIVD‐19 patients that partially overlapped the binding site of two neutralizing antibodies previously isolated from COVID‐19 patients, S2H135 and F2B‐2F61, and contacted amino acids that interact with ACE2 receptor6,7. One epitope of note from the vaccinated individuals is epitope S811‐825 which mapped adjacent to the fusion‐peptide proximal region. These epitopes may be helpful in future vaccine and antibody therapy development.
1 Ju, B. et al. Nature 584, 115‐119.
2 Robbiani, D. F. et al. Nature 584, 437‐442.
3 Seydoux, E. et al. bioRxiv.
4 Wu, Y. et al. Science 368, 1274‐1278.
5 Piccoli, L. et al. Cell 183, 1024‐1042 e1021.
6 Casalino, L. et al. ACS Cent Sci 6, 1722‐1734.
7 Wang, Q. et al. Cell 181, 894‐904 e899.
Parkinsonism, the clinical term for a disorder with prominent bradykinesia and variable associated extrapyramidal signs and symptoms, is accompanied by degeneration of the nigrostriatal dopaminergic ...system, with neuronal loss and reactive gliosis in the substantia nigra found at autopsy. Parkinsonism is pathologically heterogeneous, with the most common pathologic substrates related to abnormalities in the presynaptic protein α-synuclein or the microtubule binding protein tau. In idiopathic Parkinson's disease (PD), α-synuclein accumulates in neuronal perikarya (Lewy bodies) and neuronal processes (Lewy neurites). The disease process is multifocal and involves select central nervous system neurons and peripheral autonomic nervous system neurons. The particular set of neurons affected determines nonmotor clinical presentations. Multiple system atrophy (MSA) is the other major α-synucleinopathy. It is also associated with autonomic dysfunction and in some cases with cerebellar signs. The hallmark histopathologic feature of MSA is accumulation of α-synuclein within glial cytoplasmic inclusions (GCI). The most common of the Parkinsonian tauopathies is progressive supranuclear palsy (PSP), which is clinically associated with severe postural instability leading to early falls. The tau pathology of PSP also affects both neurons and glia. Given the population frequency of PD, α-synuclein pathology similar to that in PD, but not accompanied by neuronal loss, is relatively common (10% of people over 65 years of age) in neurologically normal individuals, leading to proposed staging schemes for PD progression. Although MSA-like and PSP-like pathology can be detected in neurologically normal individuals, such cases are too infrequent to permit assessment of patterns of disease progression.
Autopsies of deceased with a confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can provide important insights into the novel disease and its course. Furthermore, ...autopsies are essential for the correct statistical recording of the coronavirus disease 2019 (COVID-19) deaths. In the northern German Federal State of Hamburg, all deaths of Hamburg citizens with ante- or postmortem PCR-confirmed SARS-CoV-2 infection have been autopsied since the outbreak of the pandemic in Germany. Our evaluation provides a systematic overview of the first 80 consecutive full autopsies. A proposal for the categorisation of deaths with SARS-CoV-2 infection is presented (category 1: definite COVID-19 death; category 2: probable COVID-19 death; category 3: possible COVID-19 death with an equal alternative cause of death; category 4: SARS-CoV-2 detection with cause of death not associated to COVID-19). In six cases, SARS-CoV-2 infection was diagnosed postmortem by a positive PCR test in a nasopharyngeal or lung tissue swab. In the other 74 cases, SARS-CoV-2 infection had already been known antemortem. The deceased were aged between 52 and 96 years (average 79.2 years, median 82.4 years). In the study cohort, 34 deceased were female (38%) and 46 male (62%). Overall, 38% of the deceased were overweight or obese. All deceased, except for two women, in whom no significant pre-existing conditions were found autoptically, had relevant comorbidities (in descending order of frequency): (1) diseases of the cardiovascular system, (2) lung diseases, (3) central nervous system diseases, (4) kidney diseases, and (5) diabetes mellitus. A total of 76 cases (95%) were classified as COVID-19 deaths, corresponding to categories 1–3. Four deaths (5%) were defined as non-COVID-19 deaths with virus-independent causes of death. In eight cases, pneumonia was combined with a fulminant pulmonary artery embolism. Peripheral pulmonary artery embolisms were found in nine other cases. Overall, deep vein thrombosis has been found in 40% of the cases. This study provides the largest overview of autopsies of SARS-CoV-2-infected patients presented so far.
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