Pyridostigmine reduces mortality of patients with severe SARS-CoV-2 infection: A phase 2/3 randomized controlled trial.

BACKGROUND: Respiratory failure in severe coronavirus disease 2019 (COVID-19) is associated with a severe inflammatory response. Acetylcholine (ACh) reduces systemic inflammation in experimental bacterial and viral infections. Pyridostigmine increases the half-life of endogenous ACh, potentially reducing systemic inflammation. We aimed to determine if pyridostigmine decreases a composite outcome of invasive mechanical ventilation (IMV) and death in adult patients with severe COVID-19. METHODS: We performed a double-blinded, placebo-controlled, phase 2/3 randomized controlled trial of oral pyridostigmine (60 mg/day) or placebo as add-on therapy in adult patients admitted due to confirmed severe COVID-19 not requiring IMV at enrollment. The primary outcome was a composite of IMV or death by day 28. Secondary outcomes included reduction of inflammatory markers and circulating cytokines, and 90-day mortality. Adverse events (AEs) related to study treatment were documented and described. RESULTS: We recruited 188 participants (94 per group); 112 (59.6%) were men; the median (IQR) age was 52 (44-64) years. The study was terminated early due to a significant reduction in the primary outcome in the treatment arm and increased difficulty with recruitment. The primary outcome occurred in 22 (23.4%) participants in the placebo group vs. 11 (11.7%) in the pyridostigmine group (hazard ratio, 0.47, 95% confidence interval 0.24-0.9; P = 0.03). This effect was driven by a reduction in mortality (19 vs. 8 deaths, respectively). CONCLUSION: Our data indicate that adding pyridostigmine to standard care reduces mortality among patients hospitalized for severe COVID-19.

SARS-CoV-2 protein encoded by ORF8 contains a histone mimic that disrupts chromatin regulation (preprint)

SARS-CoV-2 emerged in China at the end of 2019 and caused the global pandemic of COVID-19, a disease with high morbidity and mortality. While our understanding of this novel virus is rapidly increasing, gaps remain in our understanding of how SARS-CoV-2 can effectively suppress host cell antiviral responses. Recent work on other viruses has demonstrated a novel mechanism through which viral proteins can mimic critical regions of human histone proteins. Histone proteins are responsible for governing genome accessibility and their precise regulation is critical for a cell’s ability to control transcription and respond to viral threats. Here, we show that the protein encoded by ORF8 (Orf8) in SARS-CoV-2 functions as a histone mimic of two critical histone 3 sites containing an ARKS motif. Orf8 expression in cells disrupts multiple critical histone post-translational modifications (PTMs) while Orf8 lacking this histone mimic motif does not. Orf8 binds to numerous histone-associated proteins and to DNA, and is itself acetylated within the histone mimic site. Importantly, SARS-CoV-2 infection of multiple susceptible cell types causes the same global changes of histone post-translational modifications that are disrupted by Orf8 expression; these include induced pluripotent stem cell-derived alveolar type 2 cells (iAT2) and cardiomyocytes (iCM) and postmortem patient lung tissue. These findings demonstrate a novel function for the poorly understood SARS-CoV-2 ORF8 encoded protein and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Notably, this work provides a potential mechanism for emerging findings from human patients indicating that ORF8 deletion results in less severe illness and describes a potentially druggable pathway that may contribute to the virulence of SARS-CoV-2.

A k-mer based approach for virus classification identifies coronavirus infections and viral associations in human and plant microbiomes (preprint)

Background Viruses are underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken (a parallelized version of Kraken), a metagenomic/transcriptomic classifier. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, especially samples without virus-induced pathophysiology, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain tissue. In the Populus study, we identified genotype and compartment-specific viral signatures, while in the Autism study we identified a significant increase in abundance of eight viral sequences in post mortem brains. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we utilize the NCBI databases to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples to validate the potential usefulness of classifying viruses. Conclusion Viruses represent an essential component of the microbiome. The ability to classify viruses represents the compulsory first step in better understanding their role in the microbiome. Our viral classification method allows for a more complete identification of viral sequences than previous methods. This will improve identification of associations between viruses and their hosts as well as viruses and other microbiome members and can be used with any tool that utilizes a taxonomy for classification (such as Kraken).

Comparison of Fear of COVID-19 in Medical and Nonmedical Personnel in a Public Hospital in Mexico: A Brief Report. (preprint)

The world is social distancing and compulsory confinement has caused stress, psychological instability, stigmatization, fear, and discrimination in the general population. In this cross-sectional survey study, we administered the Fear of COVID-19 Scale (FCV-19S) to hospital medical and nonmedical personnel. A total of 1,216 participants were surveyed from May 25 to May 29 of 2020. We asked all the staff for their participation in the study and physical copies of the survey were distributed to the staff willing to participate. All surveys were answered anonymously. We found that the global FCV-19S mean score was 16.4 ± 6.1, with a significant difference between women and men’s scores. Medical students presented higher scores than experienced medical personnel. Additionally, the medical and nursing personnel presented a higher level of fear than hospital staff who did not work directly with COVID-19 patients. Our findings suggest that greater knowledge of medicine or infectious diseases could decrease the overall psychological impact of the pandemic disease.

Fear of COVID-19 Scale for Hospital Staff in Regional Hospitals in Mexico: A Survey Study (preprint)

The presence of COVID-19 has had psychological consequences among health personnel; these include fear, anxiety, and depression. In the current study, we used the Fear of COVID-19 Scale (FCV-19S) to assess the response to fear within health staff in Mexico. This was a cross-sectional survey study in which we administered the FCV-19S to hospital staff. A total of 2,860 participants—1,641 female and 1,218 male personnel from three hospitals—were included in the study. We found a global FCV-19S mean score of 19.3 ± 6.9, with a significant difference in scores for women and men. There was a high correlation between items 3, 5, 6, and 7, suggesting that these items could indicate the physiological responses to fear, and a high correlation between items 1, 2, and 4, suggesting these items could represent the emotional responses to fear. Our survey shows a significantly higher level of fear in nursing and administrative personnel, which may be explained by the nursing staff being in close contact with infected patients and the administrative staff lacking understanding of the possible implications of the infection, compared with non-clinical hospital personnel. The FCV-19S showed validity and reliability in our population to assess fear in response to COVID-19. Our results are consistent with those of other researchers.