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Positive Effects of Cognitive-Behavioral Therapy Targeting Severe Fatigue Following COVID-19 Are Sustained Up to 1 Year After Treatment
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Modeling COVID-19 Dynamics in Illinois under Nonpharmaceutical Interventions
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Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy
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Deep Learning with hyper-parameter tuning for COVID-19 Cough Detection
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Isolating Insecurely: A Call to Arms for the Security and Privacy Community During the Time of COVID-19
The privacy question is one that has only begun to be addressed. While on one hand, many of the staunchest privacy advocates have argued for relaxation of privacy controls in order to develop better tests, “back to work” protocols, and vaccines and other treatments, the same advocates point out that any loss of privacy for the public good should be temporary, transparent, necessary, proportionate, and follow a due process. What should solutions look like for data gathering, sharing, use, and disposal; or for protocols requiring strong individual identity verification and validation?
Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design
Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.
Characterization of the antispike IgG immune response to COVID-19 vaccines in people with a wide variety of immunodeficiencies
Research on coronavirus disease 2019 vaccination in immune-deficient/disordered people (IDP) has focused on cancer and organ transplantation populations. In a prospective cohort of 195 IDP and 35 healthy volunteers (HV), antispike immunoglobulin G (IgG) was detected in 88% of IDP after dose 2, increasing to 93% by 6 months after dose 3. Despite high seroconversion, median IgG levels for IDP never surpassed one-third that of HV. IgG binding to Omicron BA.1 was lowest among variants. Angiotensin-converting enzyme 2 pseudo-neutralization only modestly correlated with antispike IgG concentration. IgG levels were not significantly altered by receipt of different messenger RNA–based vaccines, immunomodulating treatments, and prior severe acute respiratory syndrome coronavirus 2 infections. While our data show that three doses of coronavirus disease 2019 vaccinations induce antispike IgG in most IDP, additional doses are needed to increase protection. Because of the notably reduced IgG response to Omicron BA.1, the efficacy of additional vaccinations, including bivalent vaccines, should be studied in this population.
An oral SARS-CoV-2 M[superscript pro] inhibitor clinical candidate for the treatment of COVID-19
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Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine
The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that evade immunity elicited by vaccination has placed an imperative on the development of countermeasures that provide broad protection against SARS-CoV-2 and related sarbecoviruses. Here, we identified extremely potent monoclonal antibodies (mAbs) that neutralized multiple sarbecoviruses from macaques vaccinated with AS03-adjuvanted monovalent subunit vaccines. Longitudinal analysis revealed progressive accumulation of somatic mutation in the immunoglobulin genes of antigen-specific memory B cells (MBCs) for at least 1 year after primary vaccination. Antibodies generated from these antigen-specific MBCs at 5 to 12 months after vaccination displayed greater potency and breadth relative to those identified at 1.4 months. Fifteen of the 338 (about 4.4%) antibodies isolated at 1.4 to 6 months after the primary vaccination showed potency against SARS-CoV-2 BA.1, despite the absence of serum BA.1 neutralization. 25F9 and 20A7 neutralized authentic clade 1 sarbecoviruses (SARS-CoV, WIV-1, SHC014, SARS-CoV-2 D614G, BA.1, and Pangolin-GD) and vesicular stomatitis virus–pseudotyped clade 3 sarbecoviruses (BtKY72 and PRD-0038). 20A7 and 27A12 showed potent neutralization against all SARS-CoV-2 variants and multiple Omicron sublineages, including BA.1, BA.2, BA.3, BA.4/5, BQ.1, BQ.1.1, and XBB. Crystallography studies revealed the molecular basis of broad and potent neutralization through targeting conserved sites within the RBD. Prophylactic protection of 25F9, 20A7, and 27A12 was confirmed in mice, and administration of 25F9 particularly provided complete protection against SARS-CoV-2, BA.1, SARS-CoV, and SHC014 challenge. These data underscore the extremely potent and broad activity of these mAbs against sarbecoviruses.
Enabling rapid COVID-19 small molecule drug design through scalable deep learning of generative models
We improved the quality and reduced the time to produce machine learned models for use in small molecule antiviral design. Our globally asynchronous multi-level parallel training approach strong scales to all of Sierra with up to 97.7% efficiency. We trained a novel, character-based Wasserstein autoencoder that produces a higher quality model trained on 1.613 billion compounds in 23 minutes while the previous state of the art takes a day on 1 million compounds. Reducing training time from a day to minutes shifts the model creation bottleneck from computer job turnaround time to human innovation time. Our implementation achieves 318 PFLOPs for 17.1% of half-precision peak. We will incorporate this model into our molecular design loop enabling the generation of more diverse compounds; searching for novel, candidate antiviral drugs improves and reduces the time to synthesize compounds to be tested in the lab.
COVID-19 global pandemic planning: Performance and electret charge of N95 respirators after recommended decontamination methods
Shortages of N95 respirators for use by medical personnel have driven consideration of novel conservation strategies, including decontamination for reuse and extended use. Decontamination methods listed as promising by the Centers for Disease Control and Prevention (CDC) (vaporous hydrogen peroxide (VHP), wet heat, ultraviolet irradiation (UVI)) and several methods considered for low resource environments (bleach, isopropyl alcohol and detergent/soap) were studied for two commonly used surgical N95 respirators (3M™ 1860 and 1870+ Aura™). Although N95 filtration performance depends on the electrostatically charged electret filtration layer, the impact of decontamination on this layer is largely unexplored. As such, respirator performance following decontamination was assessed based on the fit, filtration efficiency, and pressure drop, along with the relationship between (1) surface charge of the electret layer, and (2) elastic properties of the straps. Decontamination with VHP, wet heat, UVI, and bleach did not degrade fit and filtration performance or electret charge. Isopropyl alcohol and soap significantly degraded fit, filtration performance, and electret charge. Pressure drop across the respirators was unchanged. Modest degradation of N95 strap elasticity was observed in mechanical fatigue testing, a model for repeated donnings and doffings. CDC recommended decontamination methods including VHP, wet heat, and UV light did not degrade N95 respirator fit or filtration performance in these tests. Extended use of N95 respirators may degrade strap elasticity, but a loss of face seal integrity should be apparent during user seal checks. NIOSH recommends performing user seal checks after every donning to detect loss of appropriate fit. Decontamination methods which degrade electret charge such as alcohols or detergents should not be used on N95 respirators. The loss of N95 performance due to electret degradation would not be apparent to a respirator user or evident during a negative pressure user seal check.
Blood pro-thrombotic analytes and platelet activation are associated with post-acute sequelae of COVID-19
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