Drug-Repurposing Screening Identifies a Gallic Acid Binding Site on SARS-CoV-2 Non-structural Protein 7.

SARS-CoV-2 is the agent responsible for acute respiratory disease COVID-19 and the global pandemic initiated in early 2020. While the record-breaking development of vaccines has assisted the control of COVID-19, there is still a pressing global demand for antiviral drugs to halt the destructive impact of this disease. Repurposing clinically approved drugs provides an opportunity to expediate SARS-CoV-2 treatments into the clinic. In an effort to facilitate drug repurposing, an FDA-approved drug library containing 2400 compounds was screened against the SARS-CoV-2 non-structural protein 7 (nsp7) using a native mass spectrometry-based assay. Nsp7 is one of the components of the SARS-CoV-2 replication/transcription complex essential for optimal viral replication, perhaps serving to off-load RNA from nsp8. From this library, gallic acid was identified as a compound that bound tightly to nsp7, with an estimated K d of 15 µM. NMR chemical shift perturbation experiments were used to map the ligand-binding surface of gallic acid on nsp7, indicating that the compound bound to a surface pocket centered on one of the protein's four α-helices (α2). The identification of the gallic acid-binding site on nsp7 may allow development of a SARS-CoV-2 therapeutic via artificial-intelligence-based virtual docking and other strategies.

Inflammatory ocular events after inactivated COVID-19 vaccination.

To report potential vaccine-induced inflammatory ocular adverse events following inactivated COVID-19 vaccination. Retrospective study of patients with uveitis and other ocular complications following inactivated coronavirus disease 2019 (COVID-19) vaccination at a tertiary referral center between May 2021 and August 2021. Data collection consisted of demographic and clinical data. The study included 8 eyes of 5 patients (4 females, 1 male), with a mean age of 37.2 ± 12.5 years (range 28-59 years). Mean time between vaccination and ocular complications onset was 13.2 ± 11.9 days (range 3-30 days), including two patients after the first dose of the vaccine and 3 patients after the second dose. The cases reported were three anterior uveitis, one herpetic keratitis and iridocyclitis, and one posterior uveitis. Patients received treatment with local and/or systemic steroids and all the patients had good visual outcomes. Ocular inflammatory events may occur after vaccination with possible gender preponderance. However, they are rare and manageable. Overall, the efficacy and safety of vaccination should be emphasized.

Collision-Induced Affinity Selection Mass Spectrometry for Identification of Ligands.

Hyphenated mass spectrometry has been used to identify ligands binding to proteins. It involves mixing protein and compounds, separation of protein-ligand complexes from unbound compounds, dissociation of the protein-ligand complex, separation to remove protein, and injection of the supernatant into a mass spectrometer to observe the ligand. Here we report collision-induced affinity selection mass spectrometry (CIAS-MS), which allows separation and dissociation inside the instrument. The quadrupole was used to select the ligand-protein complex and allow unbound molecules to be exhausted to vacuum. Collision-induced dissociation (CID) dissociated the protein-ligand complex, and the ion guide and resonance frequency were used to selectively detect the ligand. A known SARS-CoV-2 Nsp9 ligand, oridonin, was successfully detected when it was mixed with Nsp9. We provide proof-of-concept data that the CIAS-MS method can be used to identify binding ligands for any purified protein.

Molnupiravir and Its Active Form, EIDD-1931, Show Potent Antiviral Activity against Enterovirus Infections In Vitro and In Vivo.

Enterovirus infections can cause hand, foot, and mouth disease (HFDM), aseptic meningitis, encephalitis, myocarditis, and acute flaccid myelitis, leading to death of infants and young children. However, no specific antiviral drug is currently available for the treatment of this type of infection. The Unites States and United Kingdom health authorities recently approved a new antiviral drug, molnupiravir, for the treatment of COVID-19. In this study, we reported that molnupiravir (EIDD-2801) and its active form, EIDD-1931, have broad-spectrum anti-enterovirus potential. Our data showed that EIDD-1931 could significantly reduce the production of EV-A71 progeny virus and the expression of EV-A71 viral protein at non-cytotoxic concentrations. The results of the time-of-addition assay suggest that EIDD-1931 acts at the post-entry step, which is in accordance with its antiviral mechanism. The intraperitoneal administration of EIDD-1931 and EIDD-2801 protected 1-day-old ICR suckling mice from lethal EV-A71 challenge by reducing the viral load in various tissues of the infected mice. The pharmacokinetics analysis indicated that the plasma drug concentration overwhelmed the EC50 for enteroviruses, suggesting the clinical potential of molnupiravir against enteroviruses. Thus, molnupiravir along with its active form, EIDD-1931, may be a promising drug candidate against enterovirus infections.

Binding Studies of the Prodrug HAO472 to SARS-Cov-2 Nsp9 and Variants.

SARS-CoV-2 (COVID-19) has infected over 219 million people and caused the death of over 4.55 million worldwide. In a previous screen of a natural product library against purified SARS-CoV-2 Nsp9 using a native mass spectrometry-based approach, we identified an ent-kaurane natural product, oridonin (1), with micromolar affinities. In this work, we have found that the prodrug HAO472 (2) directly binds to Nsp9, establishing replacement of the labile ester with a bioisostere as a candidate drug strategy. We further tested 1 and its clinical analogue 2 against two Nsp9 variants from human coronavirus 229E (HCoV-229E) and ferret systemic coronavirus F56 (FSCoV-F56). Both compounds showed significant binding selectivity to COVID-19 and HCoV-229E Nsp9 over FSCoV-F56 Nsp9, confirming the covalent bond with Cys73.

A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein.

The Nsp9 replicase is a conserved coronaviral protein that acts as an essential accessory component of the multi-subunit viral replication/transcription complex. Nsp9 is the predominant substrate for the essential nucleotidylation activity of Nsp12. Compounds specifically interfering with this viral activity would facilitate its study. Using a native mass-spectrometry-based approach to screen a natural product library for Nsp9 binders, we identified an ent-kaurane natural product, oridonin, capable of binding to purified SARS-CoV-2 Nsp9 with micromolar affinities. By determining the crystal structure of the Nsp9-oridonin complex, we showed that oridonin binds through a conserved site near Nsp9's C-terminal GxxxG-helix. In enzymatic assays, oridonin's binding to Nsp9 reduces its potential to act as substrate for Nsp12's Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain. We also showed using in vitro cellular assays oridonin, while cytotoxic at higher doses has broad antiviral activity, reducing viral titer following infection with either SARS-CoV-2 or, to a lesser extent, MERS-CoV. Accordingly, these preliminary findings suggest that the oridonin molecular scaffold may have the potential to be developed into an antiviral compound to inhibit the function of Nsp9 during coronaviral replication.

Progress in Traditional Chinese Medicine Against Respiratory Viruses: A Review.

Respiratory viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV)-1, SARS-CoV-2, influenza A viruses, and respiratory syncytial virus, pose a serious threat to society. Based on the guiding principles of "holism" and "syndrome differentiation and treatment", traditional Chinese medicine (TCM) has unique advantages in the treatment of respiratory virus diseases owing to the synergistic effect of multiple components and targets, which prevents drug resistance from arising. According to TCM theory, there are two main strategies in antiviral treatments, namely "dispelling evil" and "fu zheng". Dispelling evil corresponds to the direct inhibition of virus growth and fu zheng corresponds to immune regulation, inflammation control, and tissue protection in the host. In this review, current progress in using TCMs against respiratory viruses is summarized according to modern biological theories. The prospects for developing TCMs against respiratory viruses is discussed to provide a reference for the research and development of innovative TCMs with multiple components, multiple targets, and low toxicity.

Independent Risk Factors for the Dynamic Development of COVID-19: A Retrospective Study.

OBJECTIVE: To identify the risk factors for predicting the dynamic progression of COVID-19. METHODS: A total of 2321 eligible patients were included in this study from February 4 to April 15, 2020. Two illness conditions, including mild/moderate (M/M) subtype to severe/critical (S/C) and S/C to fatality, were classified. Clinical message was collected and compared, respectively. Kaplan-Meier method, Cox regression model and risk score system were used to predict disease progression in S/C COVID-19. RESULTS: A total of 112 of 1761 patients with M/M subtype were progressors (P) and 1649 non-progressors (NP). Increasing disease progression associated with higher levels of neutrophils count (HR=1.958, 95% CI=1.253-3.059, P=0.003), CK (HR=2.203, 95% CI=1.048-4.632, P=0.037), LDH (HR=3.309, 95% CI=2.083-5.256, P<0.001) and CRP (HR=2.575, 95% CI=1.638-4.049, P<0.001), and lower level of lymphocytes count (HR=1.549, 95% CI=1.018-2.355, P=0.041), as well as total lesion volume ratio greater than ≥10% (HR=2.286, 95% CI=1.451-3.601, P<0.001) on admission. In progression to fatality, 56 of the 672 S/C cases died and 616 survived. Increasing fatality associated with lower level of lymphocytes count (HR:2.060, 95% CI:1.000-4.242, P=0.050), higher levels of BUN (HR:2.715, 95% CI:1.539-4.790, P<0.001), CK-MB (HR:3.412, 95% CI:1.760-6.616, P<0.001), LDH (HR:5.578, 95% CI:2.317-13.427, P<0.001), and PT (HR:3.619, 95% CI:2.102-6.231, P<0.001). Furthermore, high risk of neutrophils count, lymphocytes count, CK, LDH, CRP, and total lesion volume ratio was powerfully correlated with the incidence of progression to S/C in patients with NS COVID-19 and high odds of lymphocytes count, BUN, CK-MB, LDH, and PT were significantly associated with death in patients with S/C COVID-19. In addition, the progression and mortality rates increased with increasing risk scores. CONCLUSION: Elevated LDH level and lymphopenia were independent predictors for COVID-19 sustainable management in classifying non-severe patients who progressed to severe condition and identifying S/C patients who deteriorated to fatal outcomes as well. Total lesion volume ratio ≥10% may provide early predictive evidence with COVID-19 patients at high risk of developing into S/C to improve prognosis.

Decrease in the chronic health effects from PM2.5 during the 13th Five-Year Plan in China: Impacts of air pollution control policies.

The Chinese government implemented a series of policies to improve air quality during the Thirteenth Five-Year Plan (13th FYP). However, the long-term health effects of the 13th FYP air pollution control policies have not been evaluated, and the outbreak of coronavirus disease 2019 (COVID-19) has brought great uncertainty regarding the evaluation of the effects. In this study, we selected 329 cities in mainland China to study the chronic health effects due to the decrease in fine particulate matter (PM2.5) during the 13th FYP. The relative risk (RR) of PM2.5 exposure was obtained from a previous study, and the total premature deaths were calculated. We also applied the grey prediction model to predict the PM2.5 concentration in each city in 2020 to evaluate the impacts of COVID-19. The results showed that the annual PM2.5 concentration was reduced from 49.7 µg/m3 in 2015 to 33.2 µg/m3 in 2020, and premature deaths were reduced from 1,186,201 (95% CI: 910,339-1,451,102) and 446,415 (in key regions, 95% CI: 343,426-544,813) in 2015 to 997,955 (95% CI: 762,167-1,226,652) and 368,786 (in key regions, 95% CI: 282,114-452,567) in 2020, respectively. A total of 188,246 (95% CI: 148,172-224,450) people avoided premature deaths due to the reduction in PM2.5 concentrations from 2015 to 2020. Although the impacts of COVID-19 in 2020 brought a significant reduction of 35.3% in February (14.2 µg/m3, p < 0.0001) and in March by 17.6% (5.8 µg/m3, p = 0.001), we found that COVID-19 showed few obvious influences on China's long-term air pollution control plans. The observed data and predicted data are very close in annual mean values and showed no statistical significance both in all cities (p = 0.98) and in key regions (p = 0.56) in 2020.

Author Correction: Near-real-time monitoring of global CO2 emissions reveals the effects of the COVID-19 pandemic.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20254-5.

Near-real-time monitoring of global CO2 emissions reveals the effects of the COVID-19 pandemic.

The COVID-19 pandemic is impacting human activities, and in turn energy use and carbon dioxide (CO2) emissions. Here we present daily estimates of country-level CO2 emissions for different sectors based on near-real-time activity data. The key result is an abrupt 8.8% decrease in global CO2 emissions (-1551 Mt CO2) in the first half of 2020 compared to the same period in 2019. The magnitude of this decrease is larger than during previous economic downturns or World War II. The timing of emissions decreases corresponds to lockdown measures in each country. By July 1st, the pandemic's effects on global emissions diminished as lockdown restrictions relaxed and some economic activities restarted, especially in China and several European countries, but substantial differences persist between countries, with continuing emission declines in the U.S. where coronavirus cases are still increasing substantially.

Positive detection of SARS-CoV-2 combined HSV1 and HHV6B virus nucleic acid in tear and conjunctival secretions of a non-conjunctivitis COVID-19 patient with obstruction of common lacrimal duct.

BACKGROUND: The current outbreak of COVID-19 has spread rapidly all over the world. Respiratory droplets and contaction with infected patients are the two major transmission routes. However, the value of tear virus nucleic acid is still not clear. We dynamic detected the SARS-CoV-2 in eye sample of one COVID-19 patient with obstruction of common lacrimal ducts. METHODS: Besides the routine examination, nasopharyngeal and eye swab were continuously measured by polymerase chain reaction assay and next-generation sequencing (NGS). Gene detection was performed for drug use guidance, and flow cytometry was performed to analyse the lymphocyte subsets. RESULTS: Nasopharyngeal swabs were positive for 22 days, but eye swabs were still continuously positive for 2 weeks after nasopharyngeal swabs turned negative. The low level of lymphocyte and the high level IL-6 lasted for almost 4 weeks, then became near normal. Next-generation sequencing (NGS) confirmed the existing of SARS-CoV-2, HSV1 and HHV6B virus nucleic acid. The gene detection for drug use guidance showed the genetic locus ABCB1 (3435T>C) rs1045642 belonged to type CC and it mean the efficiency of lopinavir-ritonavir would be significantly decreased. The flow cytometry of lymphocyte subsets showed PD-1+  CD95+ cells was accounting for 94.8% in CD3+  CD8+ T subset and for 94.8% in CD3+  TCRγδ+ T subset. CONCLUSIONS: As obstruction of common lacrimal duct, positively detection in one eye for 2 weeks more after nasopharyngeal swab became negative. More eye swabs should be collected from COVID-19 patients, especially from those immunocompromised, those with eye symptoms and those had a history of ocular diseases.