Parthenolide reveals an allosteric mode to inhibit the deISGylation activity of SARS-CoV­2 papain-like protease.

The coronavirus papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for viral polypeptide cleavage and the deISGylation of interferon-stimulated gene 15 (ISG15), which enable it to participate in virus replication and host innate immune pathways. Therefore, PLpro is considered an attractive antiviral drug target. Here, we show that parthenolide, a germacrane sesquiterpene lactone, has SARS-CoV-2 PLpro inhibitory activity. Parthenolide covalently binds to Cys-191 or Cys-194 of the PLpro protein, but not the Cys-111 at the PLpro catalytic site. Mutation of Cys-191 or Cys-194 reduces the activity of PLpro. Molecular docking studies show that parthenolide may also form hydrogen bonds with Lys-192, Thr-193, and Gln-231. Furthermore, parthenolide inhibits the deISGylation but not the deubiquitinating activity of PLpro in vitro. These results reveal that parthenolide inhibits PLpro activity by allosteric regulation.

An estimate of pediatric lives saved due to non-pharmacologic interventions during the early COVID-19 pandemic (preprint)

The net effect of the pandemic mitigation strategies on childhood mortality is not known. During the first year of the COVID-19 pandemic, mitigation policies and behaviors were widespread, and although vaccinations and effective treatments were not yet widely available, the risk of death from SARS-CoV-2 infection was low. In that first year, there was a 7% decrease in medical ("natural causes") mortality among children ages 0-9 during the first pandemic year (5% among infants <1 year and 15% among children ages 1-9) in the United States, resulting in an estimated 1,488 deaths due to medical causes averted among children ages 0-9, and 1,938 deaths averted over 24 months. The usual expected surge in winter medical deaths, particularly among children ages >1 year was absent. However, smaller increases in external ("non-natural causes") mortality were also observed during the study period, which decreased the overall number of pediatric deaths averted during both years and the pandemic period. In total, 1,468 fewer all-cause pediatric deaths than expected occurred in the United States during the first 24 months of the COVID-19 pandemic.

State-Level Excess Mortality in US Adults During the Delta and Omicron Waves of COVID-19 (preprint)

Introduction The US has continued to see excess mortality through the Delta and Omicron periods. We sought to quantify excess mortality on a state level and calculate potential deaths averted if all states matched the excess mortality rates of those with the 10 lowest excess mortality rates. Methods Observational cohort, US and state-level data. Expected monthly deaths were modeled using pre-pandemic US and state-level data (2015-2020). Mortality data was accessed from CDC public reporting. Results We find that during the Delta and Omicron waves, the US recorded over 596,000 excess deaths. 60% of the nation's total excess mortality during these periods could have been averted if all states had excess mortality rates equal to those with the 10 lowest excess mortality rates. Conclusion With large differences in excess mortality across US states in our 15-month study period, we note that a significant portion of deaths could have been averted with higher vaccination rates, policies and other behaviors.

Excess Mortality in the Vaccination Era in the United States, By State and 6-Month Period (preprint)

Introduction The US continued to record all-cause excess mortality after the rollout of vaccines. We sought to quantify excess mortality by state and compare these rates to primary series vaccination completion levels. Methods Observational cohort, US and state-level data. Expected monthly deaths were modeled using pre-pandemic US and state-level data (2015-2020). Mortality data was accessed from CDC public reporting. Results We find that in a two-year period since the rollout of vaccines, the US recorded >874,000 excess deaths. Vaccination rates and excess mortality were most strongly correlated in first two periods before the Omicron variant. Conclusion The association between vaccination and lower excess mortality rates was strongest in 2021 and early 2022, prior to high population rates of infection-acquired immunity. The findings underscore the benefits of the rapid vaccination rollout campaign and the continued need to boost at-risk populations.

Suicide deaths during the COVID-19 pandemic in the United States, by region, March 1, 2020-June 30, 2022 (preprint)

Introduction: There were concerns that suicide deaths might increase due to Covid-19 pandemic-related stressors. Previous research demonstrated that suicide deaths actually decreased in 2020 in the US. An update covering 2021-2022 with regional data is warranted. Methods: Observational cohort, US and regional data. Expected monthly deaths were modeled using pre-pandemic US and regional data (2015-2020). Mortality data was accessed from CDC public reporting. Results: We find that suicide deaths in the United States were below expected levels throughout the pandemic period (March 1, 2020-June 30,2022) with >4,100 fewer suicide deaths than would have been expected to occur during the study period. Stratifying suicide mortality by US Census Bureau region yielded statistically significant decreases from expected suicide deaths in all regions except the Midwest, (which recorded no significant change in suicide deaths during the overall pandemic period). Conclusion: Suicide mortality is down in the US since the pandemic began, through June 30, 2022. Possible explanations include an early 'coming together' effect; Later, increased access to mental health resources and a greater focus on mental health in the media may have reduced stigma and barriers in seeking necessary psychiatric care.

Two years of COVID-19: Excess mortality by age, region, gender, and race/ethnicity in the United States during the COVID-19 pandemic, March 1, 2020, through February 28, 2022 (preprint)

Introduction Excess mortality does not depend on labeling the cause of death and is an accurate representation of the pandemic population-level effects. A comprehensive evaluation of all-cause excess mortality in the United States during the first two years of the COVID-19 pandemic, stratified by age, sex, region, and race/ethnicity can provide insight into the extent and variation in harm. Methods With Centers for Disease Control and Prevention (CDC)/National Center for Health Statistics (NCHS) data from 2014-2022, we use seasonal autoregressive integrated moving averages (sARIMA) to estimate excess mortality during the pandemic, defined as the difference between the number of observed and expected deaths. We continuously correct monthly expected deaths to reflect the decreased population owing to cumulative pandemic-associated excess deaths recorded. We calculate excess mortality for the total US population, and by age, sex, US census division, and race/ethnicity. Results From March 1, 2020, through February 28, 2022, there were 1.17 million excess deaths in the United States. Overall, mortality was 20% higher than expected during the study period. Of the excess deaths, 799,477 (68%) were among residents aged 65 and older. The largest relative increase in all-cause mortality was 27% among adults ages 18-49 years. Males comprised most of the excess mortality (57%), but this predominance declined with age. A higher relative mortality occurred among non-Hispanic American Indian/Alaskan Native, non-Hispanic Black, non-Hispanic Native Hawaiian and Other Pacific Islander, Hispanic people. Excess mortality differed by region; the highest rates were in the South, including in the population ages ≥65 years. Excess mortality rose and fell contemporaneously with COVID-19 waves. Conclusion In the first two years of the pandemic, the US experienced 1.17 million excess deaths, with greater relative increases in all-cause mortality among men, in American Indian/Alaskan Native, Black and Hispanic people, and the South.

The uncoupling of all-cause excess mortality from Covid-19 cases and associated hospitalizations in late winter and spring of 2022 in a highly vaccinated state. (preprint)

Introduction: Since March 2020, all-cause excess mortality (the number of all-cause deaths exceeding the baseline number of expected deaths) has been observed in waves coinciding with Covid-19 outbreaks in the United States. We recently described high levels of excess mortality in Massachusetts during the initial 8-week Omicron wave. However, whether excess mortality continued after that period (during which an outbreak of Omicron subvariants occurred) is unknown. Methods: We applied seasonal autoregressive integrated moving averages to five years of pre-pandemic data provided by the Massachusetts Registry of Vital Records and Statistics (MRVRS) to project the weekly populations and expected deaths for the pandemic period. Observed deaths during the pandemic were also provided by MRVRS and are >99% complete for all study weeks. Results: During the 18-week Omicron subvariant period (the week ending February 27, 2022, through June 26, 2022) the incidence of all-cause excess mortality was 0.1 per 100,000-person weeks, corresponding to 148 excess deaths (95%. CI -907 to 1153), representing a 97.1% decrease from the initial Omicron period (during which all-cause excess mortality was 4.0 per 100,000-person-weeks), and a 91.9% reduction from the Delta and Delta-Omicron transition period (during which all-cause excess mortality was 1.5 per 100,000-person-weeks), despite >226,000 reported new Covid-19 cases during the subvariant/spring period. However, Covid-19-associated hospitalizations were observed during the subvariant/spring 2022 period. Conclusion: In a highly vaccinated state with a recent wave of SARS-CoV-2, all-cause excess mortality was uncoupled from new case counts, indicating the possibility of temporary protection from the most severe outcomes related to Covid-19 among high-risk individuals. However, given the possibility of waning immunity and the emerging of new variants, continued monitoring is warranted.

Huge gastric plexiform fibromyxoma presenting as pyemia by rupture of tumor: A case report.

BACKGROUND: Plexiform fibromyxoma (PF) is a rare mesenchymal tumor, with limited case reports worldwide. Common clinical symptoms are abdominal discomfort and bleeding signs, which frequently present slow-onset in reported cases. Herein, we report a case of gastric PF presenting as acute onset and with pyemia accom-panying tumor rupture. We resected the tumor as well as the distal gastric, bulbus duodeni and gallbladder for treatment in emergency surgery. Notably, before the onset of the disease, the patient received coronavirus disease 2019 (COVID-19) vaccines. CASE SUMMARY: A 26-year-old man was admitted to our hospital, due to abdominal pain and fever after having received COVID-19 vaccines. Laboratory examination indicated severe sepsis. Computed tomography scan revealed a large mass in the abdomen. Deformation of the gastrointestinal tract was seen during gastroscopy. After failure of anti-infective treatment and symptoms of shock developed, he received an emergency surgery. We found a huge and partly ruptured mass, with thick purulence. Microscopically, the mass was composed of spindle cells with clarified cytoplasm, accompanied by myxoid stroma and arborizing blood vessels. Immunohistochemistry showed the tumor cells as positive for smooth muscle actin and succinate dehydrogenase subunit B but negative for DOG-1 and CD117. Finally, the patient was diagnosed with gastric PF and discharged from the hospital. CONCLUSION: Gastric PF manifesting as tumor rupture combined with pyemia is rare. Timely surgery is critical for optimal prognosis.

Novel pectin from crude polysaccharide of Syzygium aromaticum against SARS-CoV-2 activities by targeting 3CLpro (preprint)

To date, COVID-19 is still a severe threat to public health, hence specific effective therapeutic drugs development against SARS-CoV-2 is urgent needed. 3CLpro and PLpro and RdRp are the enzymes required for the SARS-CoV-2 RNA synthesis. Therefore, binding to the enzyme may interfere the enzyme function. Before, we found that sulfated polysaccharide binding to 3CLpro might block the virus replication. Hence, we hypothesize that negative charged pectin glycan may also impede the virus replication. Here we show that 922 crude polysaccharide from Syzygium aromaticum may near completely block SARS-CoV-2 replication. The inhibition rate was 99.9% (EC50 : 0.90 muM). Interestingly, 922 can associates with 3CLpro, PLpro and RdRp. We further show that the homogeneous glycan 922211 from 922 may specifically attenuate 3CL protease activity. The IC50s of 922 and 922211 against 3CLpro are 4.73 plusmn 1.05 muM and 0.18 plusmn 0.01 muM, respectively. Monosaccharide composition analysis reveals that 922211 with molecular weight of 78.7 kDa is composed of rhamnose, galacturonic acid, galactose and arabinose in the molar ratio of 8.21 : 37.81 : 3.58 : 4.49. The structure characterization demonstrated that 922211 is a homogalacturonan linked to RG-I pectin polysaccharide. The linear homogalacturonan part in the backbone may be partly methyl esterified while RG-I type part bearing 1, 4-linked alpha-GalpA, 1, 4-linked alpha-GalpAOMe and 1, 2, 4-linked alpha-Rhap. There are four branches attached to C-1 or C4 position of Rhamnose glycosyl residues on the backbone. The branches are composed of 1, 3-linked beta-Galp, terminal (T)-linked beta-Galp, 1, 5-linked alpha-Araf, T-linked alpha-Araf, 4-linked alpha-GalpA and/or 4-linked beta-GalpA. The above results suggest that 922 and 922211 might be a potential novel leading compound for anti-SARS-CoV-2 new drug development.

Absence of Excess Mortality in a Highly Vaccinated Population During the Initial Covid-19 Delta Period. (preprint)

BackgroundAll-cause excess mortality (the number of deaths that exceed projections in any period) has been widely reported during the Covid-19 pandemic. Whether excess mortality has occurred during the Delta wave is less well understood. MethodsWe performed an observational study using data from the Massachusetts Department of Health. Five years of US Census population data and CDC mortality statistics were applied to a seasonal autoregressive integrated moving average (sARIMA) model to project the number of expected deaths for each week of the pandemic period, including the Delta period (starting in June 2021, extending through August 28th 2021, for which mortality data are >99% complete). Weekly Covid-19 cases, Covid-19-attributed deaths, and all-cause deaths are reported. County-level excess mortality during the vaccine campaign are also reported, with weekly rates of vaccination in each county that reported 100 or more all-cause deaths during any week included in the study period. ResultsAll-cause mortality was not observed after March 2021, by which time over 75% of persons over 65 years of age in Massachusetts had received a vaccination. Fewer deaths than expected (which we term deficit mortality) occurred both during the summer of 2020, the spring of 2021 and during the Delta wave (beginning June 13, 2021 when Delta isolates represented >10% of sequenced cases). After the initial wave in the spring of 2020, more Covid-19-attributed deaths were recorded that all-cause excess deaths, implying that Covid-19 was misattributed as the underlying cause, rather than a contributing cause of death in some cases. ConclusionIn a state with high vaccination rates, excess mortality has not been recorded during the Delta period. Deficit mortality has been recorded during this period.

Transcriptional Changes in CD16+ Monocytes May Contribute to the Pathogenesis of COVID-19.

The COVID-19 pandemic has caused more than three million deaths globally. The severity of the disease is characterized, in part, by a dysregulated immune response. CD16+ monocytes are innate immune cells involved in inflammatory responses to viral infections, and tissue repair, among other functions. We characterized the transcriptional changes in CD16+ monocytes from PBMC of people with COVID-19, and from healthy individuals using publicly available single cell RNA sequencing data. CD16+ monocytes from people with COVID-19 compared to those from healthy individuals expressed transcriptional changes indicative of increased cell activation, and induction of a migratory phenotype. We also analyzed COVID-19 cases based on severity of the disease and found that mild cases were characterized by upregulation of interferon response and MHC class II related genes, whereas the severe cases had dysregulated expression of mitochondrial and antigen presentation genes, and upregulated inflammatory, cell movement, and apoptotic gene signatures. These results suggest that CD16+ monocytes in people with COVID-19 contribute to a dysregulated host response characterized by decreased antigen presentation, and an elevated inflammatory response with increased monocytic infiltration into tissues. Our results show that there are transcriptomic changes in CD16+ monocytes that may impact the functions of these cells, contributing to the pathogenesis and severity of COVID-19.

Prevalence of redetectable positive SARS-CoV-2 nucleic acid in recovered COVID-19 patients: a systematic review and meta-analysis (preprint)

Background: The prevalence of positive SARS-CoV-2 nucleic acid in recovered COVID-19 patients has attracted attention. We aimed to investigate the repositive rate of SARS-CoV-2 and the clinical features of discharged COVID-19 patients. Methods: In this systematic review and meta-analysis, we searched PubMed, Embase, Web of Science, China National Knowledge Internet, Wanfang Data, China BioMedical Literature, VIP, and Google Scholar. Fixed or random-effect models were used to determine effect estimates. Results: Eleven studies were included. The pooled positive rate of viral RNA in discharged patients was 11% (95% CI 7-15; I2=90.4%). The median days from discharge to repositivity were 7 to 8 days. Coughing was the most common clinical symptom, occurring in 16% (95% CI 11-20; I2=0%) of patients at readmission. Chest CT and laboratory indicators of positive retest (PR) patients showed significant recovery trends. The prevalence of comorbidities between the PR patients and the negative retest patients were not significant (OR 0.86 [95% CI 0.38–1.95]; p=0.002; I2=76.5%). No close contacts were positive for SARS-CoV-2 RNA. Conclusion: PR patients were uncommon. The repositive result was likely due to the incomplete clearance of virus from a previous disease course. PR patients were less likely to be contagious. However, close monitoring and quarantine after discharge from the hospital are necessary. Registration: The protocol has been registered on PROSPERO, registration ID: CRD42021239650 Keywords: COVID-19, SARS-CoV-2, discharged patients, positive retest rate

Mortality from injury, overdose and suicide during the 2020 COVID-19 pandemic, March-July, 2020 (preprint)

Introduction: The COVID-19 pandemic has been associated with substantial rates of all-cause excess mortality. The contribution of external causes of death to excess mortality including drug overdose, homicide, suicide, and unintentional injuries during the initial outbreak in the United States is less well documented. Methods Using public data published by the National Center for Health Statistics on February 10, 2021, we measured monthly excess mortality (the gap between observed and expected deaths) from five external causes using national-level data published by National Center for Health Statistics; assault (homicide); intentional self-harm (suicide); accidents (unintentional injuries); and motor vehicle accidents. We used seasonal autoregressive integrated moving average (sARIMA) models developed with cause-specific monthly mortality counts and US population data from 2015-2019 and estimated the contribution of individual cause-specific mortality to all-cause excess mortality from March-July 2020. Results From March-July, 2020, 212,825 (95% CI 136,236-290,776) all-cause excess deaths occurred in the US). There were 8,540 excess drug overdoses (all intents) (95% CI 5,106 to 11,975), accounting for 4% of all excess mortality; 1,455 excess homicide deaths (95% CI 708 to 2202, accounting for 0.7% of excess mortality; 5,492 excess deaths due to unintentional accidents occurred (95% CI 85 to 10,899, accounting for 2.6% of excess mortality. Though a non-significantly 135 (95% CI -1361 to 1,630) more MVA deaths were recorded during the study period, a significant decrease in April (525; 95% CI -817 to -233) and significant increases in June-July (965; 95% CI 348 to 1,587) were observed. Suicide deaths were statistically lower than projected by 2,067 (95% CI 941-3,193 fewer deaths). Meaning Excess deaths from drug overdoses, homicide, and addicents occurred during the pandemic but represented a small fraction of all-cause excess mortality. The excess external causes of death, however, still represent thousands of lives lost. Notably, deaths from suicide were lower than expected and therefore did not contribute to excess mortality.