Manifestations and outcomes of intracerebral hemorrhage during COVID‐19 pandemic in China: a multicenter, longitudinal cohort study (preprint)

Background: We just right were carrying out a multicenter cohort study about ICH when COVID-19 broke out in Wuhan，and we wondered whether COVID-19 pandemic was associated with the manifestations and outcomes of intracerebral hemorrhage (ICH). Methods: : Acute ICH patients before (1/12/2018-30/11/2019) and during COVID-19(1/12/2019-30/11/2020) pandemic at 31 centers in China, were entered into the analysis. Demographic information, clinical manifestations and outcomes were collected and compared between the two groups. Results: : From December 1, 2018 to November 30, 2020, a total of 3460 patients with ICH were enrolled and eventually analyzed. Results showed that patients with ICH were more likely to be older, have higher systolic blood pressure (BP) (P<0.001), diastolic-BP (P=0.002), higher admission NIHSS score (P=0.039) and higher fasting blood glucose (P=0.003) during COVID-19 pandemic compared with before. After adjusting age, gender, COVID-19 pandemic was associated with 3-month poor outcome (OR = 1.206, 95%CI: 1.043-1.395) and 3-month mortality (OR = 1.711, 95%CI: 1.428-2.050) after ICH onset. Conclusions: : COVID-19 pandemic deteriorated the manifestations and outcomes of ICH.

Tracking the prevalence and emergence of SARS CoV2 variants of concern using a regional genomic surveillance program (preprint)

SARS-CoV-2 molecular testing coupled with whole genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOC) as well as novel variant discovery. Since the beginning of the pandemic millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of efforts of both national and regional diagnostic laboratories. Here we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the USA. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of VOC. Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories.

Utility of laboratory and immune biomarkers in predicting disease progression and mortality among patients with moderate to severe COVID-19 disease at a Philippine tertiary hospital

Purpose This study was performed to determine the clinical biomarkers and cytokines that may be associated with disease progression and in-hospital mortality in a cohort of hospitalized patients with RT-PCR confirmed moderate to severe COVID-19 infection from October 2020 to September 2021, during the first wave of COVID-19 pandemic before the advent of vaccination. Patients and methods Clinical profile was obtained from the medical records. Laboratory parameters (complete blood count [CBC], albumin, LDH, CRP, ferritin, D-dimer, and procalcitonin) and serum concentrations of cytokines (IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-18, IFN-γ, IP-10, TNF-α) were measured on Days 0-3, 4-10, 11-14 and beyond Day 14 from the onset of illness. Regression analysis was done to determine the association of the clinical laboratory biomarkers and cytokines with the primary outcomes of disease progression and mortality. ROC curves were generated to determine the predictive performance of the cytokines. Results We included 400 hospitalized patients with COVID-19 infection, 69% had severe to critical COVID-19 on admission. Disease progression occurred in 139 (35%) patients, while 18% of the total cohort died (73 out of 400). High D-dimer >1 µg/mL (RR 3.5 95%CI 1.83–6.69), elevated LDH >359.5 U/L (RR 1.85 95%CI 1.05–3.25), lymphopenia (RR 1.91 95%CI 1.14–3.19), and hypoalbuminemia (RR 2.67, 95%CI 1.05–6.78) were significantly associated with disease progression. High D-dimer (RR 3.95, 95%CI 1.62–9.61) and high LDH (RR 5.43, 95%CI 2.39–12.37) were also significantly associated with increased risk of in-hospital mortality. Nonsurvivors had significantly higher IP-10 levels at 0 to 3, 4 to 10, and 11 to 14 days from illness onset (p<0.01), IL-6 levels at 0 to 3 days of illness (p=0.03) and IL-18 levels at days 11-14 of illness (p<0.001) compared to survivors. IP-10 had the best predictive performance for disease progression at days 0-3 (AUC 0.81, 95%CI: 0.68–0.95), followed by IL-6 at 11-14 days of illness (AUC 0.67, 95%CI: 0.61–0.73). IP-10 predicted mortality at 11-14 days of illness (AUC 0.77, 95%CI: 0.70–0.84), and IL-6 beyond 14 days of illness (AUC 0.75, 95%CI: 0.68–0.82). Conclusion Elevated D-dimer, elevated LDH, lymphopenia and hypoalbuminemia are prognostic markers of disease progression. High IP-10 and IL-6 within the 14 days of illness herald disease progression. Additionally, elevated D-dimer and LDH, high IP-10, IL-6 and IL-18 were also associated with mortality. Timely utilization of these biomarkers can guide clinical monitoring and management decisions for COVID-19 patients in the Philippines.

Utility of laboratory and immune biomarkers in predicting disease progression and mortality among patients with moderate to severe COVID-19 disease at a Philippine tertiary hospital.

Purpose: This study was performed to determine the clinical biomarkers and cytokines that may be associated with disease progression and in-hospital mortality in a cohort of hospitalized patients with RT-PCR confirmed moderate to severe COVID-19 infection from October 2020 to September 2021, during the first wave of COVID-19 pandemic before the advent of vaccination. Patients and methods: Clinical profile was obtained from the medical records. Laboratory parameters (complete blood count [CBC], albumin, LDH, CRP, ferritin, D-dimer, and procalcitonin) and serum concentrations of cytokines (IL-1ß, IL-2, IL-4, IL-6, IL-8, IL-10, IL-18, IFN-γ, IP-10, TNF-α) were measured on Days 0-3, 4-10, 11-14 and beyond Day 14 from the onset of illness. Regression analysis was done to determine the association of the clinical laboratory biomarkers and cytokines with the primary outcomes of disease progression and mortality. ROC curves were generated to determine the predictive performance of the cytokines. Results: We included 400 hospitalized patients with COVID-19 infection, 69% had severe to critical COVID-19 on admission. Disease progression occurred in 139 (35%) patients, while 18% of the total cohort died (73 out of 400). High D-dimer >1 µg/mL (RR 3.5 95%CI 1.83-6.69), elevated LDH >359.5 U/L (RR 1.85 95%CI 1.05-3.25), lymphopenia (RR 1.91 95%CI 1.14-3.19), and hypoalbuminemia (RR 2.67, 95%CI 1.05-6.78) were significantly associated with disease progression. High D-dimer (RR 3.95, 95%CI 1.62-9.61) and high LDH (RR 5.43, 95%CI 2.39-12.37) were also significantly associated with increased risk of in-hospital mortality. Nonsurvivors had significantly higher IP-10 levels at 0 to 3, 4 to 10, and 11 to 14 days from illness onset (p<0.01), IL-6 levels at 0 to 3 days of illness (p=0.03) and IL-18 levels at days 11-14 of illness (p<0.001) compared to survivors. IP-10 had the best predictive performance for disease progression at days 0-3 (AUC 0.81, 95%CI: 0.68-0.95), followed by IL-6 at 11-14 days of illness (AUC 0.67, 95%CI: 0.61-0.73). IP-10 predicted mortality at 11-14 days of illness (AUC 0.77, 95%CI: 0.70-0.84), and IL-6 beyond 14 days of illness (AUC 0.75, 95%CI: 0.68-0.82). Conclusion: Elevated D-dimer, elevated LDH, lymphopenia and hypoalbuminemia are prognostic markers of disease progression. High IP-10 and IL-6 within the 14 days of illness herald disease progression. Additionally, elevated D-dimer and LDH, high IP-10, IL-6 and IL-18 were also associated with mortality. Timely utilization of these biomarkers can guide clinical monitoring and management decisions for COVID-19 patients in the Philippines.

The highly conserved stem-loop II motif is dispensable for SARS-CoV-2 (preprint)

The stem-loop II motif (s2m) is a RNA structural element that is found in the 3' untranslated region (UTR) of many RNA viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over twenty-five years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro, or growth and viral fitness in Syrian hamsters in vivo. We also compared the secondary structure of the 3' UTR of wild type and s2m deletion viruses using SHAPE-MaP and DMS-MaPseq. These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3'UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2.

Internal Risk Limits of Dealers and Corporate Bond Market Making

The Volcker metrics are confidential data reported to regulators by large banks that include banks’ internal risk limits. We examine how these limits evolved from 2017 to 2020 inside bank-affiliated corporate bond dealers as indication of capacity constraints on their market making activity. We document that dealers’ internal risk limits came closer to binding during the March 2020 market turmoil. Although dealers eased their limits to accommodate increased liquidity demand, limit adjustments were not enough to offset the increase in risk exposures. We find limit tightness is negatively associated with subsequent inventory growth at dealers’ bond trading desks, especially during the COVID-19 crisis or on days with limit changes. Overall, our results indicate the importance of internal risk limits in driving dealers’ liquidity provision in time of stress.

The highly conserved stem-loop II motif is important for the lifecycle of astroviruses but dispensable for SARS-CoV-2 (preprint)

The stem-loop II motif (s2m) is an RNA element present in viruses from divergent viral families, including astroviruses and coronaviruses, but its functional significance is unknown. We created deletions or substitutions of the s2m in astrovirus VA1 (VA1), classic human astrovirus 1 (HAstV1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For VA1, recombinant virus could not be rescued upon partial deletion of the s2m or substitutions of G-C base pairs. Compensatory substitutions that restored the G-C base-pair enabled recovery of VA1. For HAstV1, a partial deletion of the s2m resulted in decreased viral titers compared to wild-type virus, and reduced activity in a replicon system. In contrast, deletion or mutation of the SARS-CoV-2 s2m had no effect on the ability to rescue the virus, growth in vitro, or growth in Syrian hamsters. Our study demonstrates the importance of the s2m is virus-dependent.

Black swan event small-sample transfer learning (BEST-L) and its case study on electrical power prediction in COVID-19

The black swan event will usually cause a great impact on the normal operation of society. The scarcity of such events leads to a lack of relevant data and challenges in dealing with related problems. Different situations also make the traditional methods invalid. In this paper, a transfer learning framework and a convolutional neuron network are proposed to deal with the black swan small-sample events (BEST-L). Taking the COVID-19 as a typical black swan event, the BEST-L is utilized to achieve accurate mid-term load forecasting using the relationship between economy and electricity consumption. The experiment results show that the transfer learning model can effectively learn the basic knowledge about the relationship between the adopted input and output data and use a relatively small amount of data during the black swan event to improve the target areas' generalization. The approach and results can provide an effective approach to respond and react to sudden changes quickly and effectively in similar open problems.

Lessons Learned: Patient Communication During the Pandemic.

A series of mortalities among musculoskeletal tumour patients secondary to medical illnesses during the first few months of the pandemic highlighted the need to review our methods of communication with patients. Prominent among patients' concerns had been a fear of consulting at hospitals and a lack of ready access to health care. Recommendations are made for proactive consultation and patient education, identifying at-risk patients for follow-up and probing for possible co-morbidities. Telemedicine use is encouraged bearing in mind its inherent limitations. A network of physicians and pharmaceutical representatives is an added help we can offer our patients who may be isolated by community quarantine.

The Digital Analytic Patient Reviewer (DAPR) for COVID-19 Data Mart Validation (preprint)

Objective: To provide high-quality data for COVID-19 research, we validated COVID-19 clinical indicators and 22 associated computed phenotypes, which were derived by machine learning algorithms, in the Mass General Brigham (MGB) COVID-19 Data Mart. Materials and Methods: Fifteen reviewers performed a manual chart review for 150 COVID-19 positive patients in the data mart. To support rapid chart review for a wide range of target data, we offered the Digital Analytic Patient Reviewer (DAPR). DAPR is a web-based chart review tool that integrates patient notes and provides note search functionalities and a patient-specific summary view linked with relevant notes. Within DAPR, we developed a COVID-19 validation task-oriented view and information extraction logic, enabled fast access to data, and considered privacy and security issues. Results: The concepts for COVID-19 positive cohort, COVID-19 index date, COVID-19 related admission, and the admission date were shown to have high values in all evaluation metrics. For phenotypes, the overall specificities, PPVs, and NPVs were high. However, sensitivities were relatively low. Based on these results, we removed 3 phenotypes from our data mart. In the survey about using the tool, participants expressed positive attitudes towards using DAPR for chart review. They assessed the validation was easy and DAPR helped find relevant information. Some validation difficulties were also discussed. Discussion and Conclusion: DAPR's patient summary view accelerated the validation process. We are in the process of automating the workflow to use DAPR for chart reviews. Moreover, we will extend its use case to other domains.

A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope (preprint)

With the emergence of SARS-CoV-2 variants with increased transmissibility and potential resistance, antibodies and vaccines with broadly inhibitory activity are needed. Here we developed a panel of neutralizing anti-SARS-CoV-2 mAbs that bind the receptor binding domain of the spike protein at distinct epitopes and block virus attachment to cells and its receptor, human angiotensin converting enzyme-2 (hACE2). While several potently neutralizing mAbs protected K18-hACE2 transgenic mice against infection caused by historical SARS-CoV-2 strains, others induced escape variants in vivo and lost activity against emerging strains. We identified one mAb, SARS2-38, that potently neutralizes all SARS-CoV-2 variants of concern tested and protects mice against challenge by multiple SARS-CoV-2 strains. Structural analysis showed that SARS2-38 engages a conserved epitope proximal to the receptor binding motif. Thus, treatment with or induction of inhibitory antibodies that bind conserved spike epitopes may limit the loss of potency of therapies or vaccines against emerging SARS-CoV-2 variants.

In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains (preprint)

Rapidly-emerging variants jeopardize antibody-based countermeasures against SARS-CoV-2. While recent cell culture experiments have demonstrated loss of potency of several anti-spike neutralizing antibodies against SARS-CoV-2 variant strains1-3, the in vivo significance of these results remains uncertain. Here, using a panel of monoclonal antibodies (mAbs) corresponding to many in advanced clinical development by Vir Biotechnology, AbbVie, AstraZeneca, Regeneron, and Lilly we report the impact on protection in animals against authentic SARS-CoV-2 variants including WA1/2020 strains, a B.1.1.7 isolate, and chimeric strains with South African (B.1.351) or Brazilian (B.1.1.28) spike genes. Although some individual mAbs showed reduced or abrogated neutralizing activity against B.1.351 and B.1.1.28 viruses with E484K spike protein mutations in cell culture, low prophylactic doses of mAb combinations protected against infection in K18-hACE2 transgenic mice, 129S2 immunocompetent mice, and hamsters without emergence of resistance. Two exceptions were mAb LY-CoV555 monotherapy which lost all protective activity in vivo, and AbbVie 2B04/47D11, which showed partial loss of activity. When administered after infection as therapy, higher doses of mAb cocktails protected in vivo against viruses displaying a B.1.351 spike gene. Thus, many, but not all, of the antibody products with Emergency Use Authorization should retain substantial efficacy against the prevailing SARS-CoV-2 variant strains.

Municipal utilities and COVID-19: Challenges, responses, and collaboration

The COVID-19 pandemic has put pressure on essential public services. While much of the economy has been shut down, essential public services have continued. Using professional experience, publicly available information, and interviews with two municipal utility managers, we evaluate the challenges presented to municipal utility services by the COVID-19 pandemic and explore some of the responses by utilities to the pandemic. Specifically, we focus on the strategies utilities have used to keep employees safe from the virus and plans for workforce shortages. One important strategy we identify is reliance on mutual aid agreements, where utilities agree to send staff and equipment to other utilities in times of crisis. We also explore the role of a municipal utility association in coordinating response. The case of utility response to COVID-19 carries important potential implications for both public administration practice and research. (PsycInfo Database Record (c) 2021 APA, all rights reserved)

SARS-CoV-2 variants show resistance to neutralization by many monoclonal and serum-derived polyclonal antibodies (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global COVID-19 pandemic infecting more than 106 million people and causing 2.3 million deaths. The rapid deployment of antibody-based countermeasures has provided hope for curtailing disease and ending the pandemic1. However, the emergence of rapidly-spreading SARS-CoV-2 variants in the United Kingdom (B.1.1.7), South Africa (B.1.351), and elsewhere with mutations in the spike protein has raised concern for escape from neutralizing antibody responses and loss of vaccine efficacy based on preliminary data with pseudoviruses2-4. Here, using monoclonal antibodies (mAbs), animal immune sera, human convalescent sera, and human sera from recipients of the Pfizer-BioNTech (BNT162b2) mRNA vaccine, we report the impact on antibody neutralization of a panel of authentic SARS-CoV-2 variants including a B.1.1.7 isolate, a chimeric Washington strain with a South African spike gene (Wash SA-B.1.351), and isogenic recombinant variants with designed mutations or deletions at positions 69-70, 417, 484, 501, and/or 614 of the spike protein. Several highly neutralizing mAbs engaging the receptor binding domain (RBD) or N-terminal domain (NTD) lost inhibitory activity against Wash SA-B.1.351 or recombinant variants with an E484K spike mutation. Most convalescent sera and virtually all mRNA vaccine-induced immune sera tested showed markedly diminished neutralizing activity against the Wash SA-B.1.351 strain or recombinant viruses containing mutations at position 484 and 501. We also noted that cell line selection used for growth of virus stocks or neutralization assays can impact the potency of antibodies against different SARS-CoV-2 variants, which has implications for assay standardization and congruence of results across laboratories. As several antibodies binding specific regions of the RBD and NTD show loss-of-neutralization potency in vitro against emerging variants, updated mAb cocktails, targeting of highly conserved regions, enhancement of mAb potency, or adjustments to the spike sequences of vaccines may be needed to prevent loss of protection in vivo.

Biopsychosocial and Spiritual Implications of Patients with COVID-19 Dying in Isolation (preprint)

Critically ill patients with the Coronavirus disease 2019 (COVID-19) are dying in isolation without the comfort of their family or other social support in unprecedented numbers. Recently, healthcare teams at COVID-19 epicenters have been inundated with critically ill patients. Patients isolated for COVID-19 have had no contact with their family or loved ones and may have likely experienced death without closure. This situation highlights concerns about the psychological and spiritual well-being of patients with COVID-19 and their families, as they permanently part ways. While palliative care has advanced to address these patients' needs adequately, the COVID-19 pandemic presents several barriers that force healthcare teams to deprioritize these essential aspects of patient care. The severe acute respiratory syndrome (SARS) outbreak in 2003 gave us a glimpse of these challenges as these patients were also isolated in hospitals. Here, we discuss the importance of the biopsychosocial spiritual model in end-of-life care and its implications on patients dying with COVID-19. Furthermore, we outline an integrative approach to address the unique and holistic needs of critically ill patients dying with COVID-19. These include intentional and increased coordination with trained palliative care staff, early and frequent goals of care including discussion of end-of-life plans, broader use of technology to improve connectedness and shared decision making with patients’ families.

Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. (preprint)

Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly disrupt epidemic transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, yet there is no consensus as to which assay should be used for such measurements. Using an infectious molecular clone of vesicular stomatitis virus (VSV) that expresses eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We also developed a focus reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. We compared the neutralizing activities of monoclonal and polyclonal antibody preparations, as well as ACE2-Fc soluble decoy protein in both assays and find an exceptionally high degree of concordance. The two assays will help define correlates of protection for antibody-based countermeasures including therapeutic antibodies, immune {gamma}-globulin or plasma preparations, and vaccines against SARS-CoV-2. Replication-competent VSV-eGFP-SARS-CoV-2 provides a rapid assay for testing inhibitors of SARS-CoV-2 mediated entry that can be performed in 7.5 hours under reduced biosafety containment.

Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study (preprint)

OBJECTIVE: To study the neurological manifestations of patients with coronavirus disease 2019 (COVID-19). DESIGN: Retrospective case series SETTING: Three designated COVID-19 care hospitals of the Union Hospital of Huazhong University of Science and Technology in Wuhan, China. PARTICIPANTS: Two hundred fourteen hospitalized patients with laboratory confirmed diagnosis of severe acute respiratory syndrome from coronavirus 2 (SARS-CoV-2) infection. Data were collected from 16 January 2020 to 19 February 2020. MAIN OUTCOME MEASURES: Clinical data were extracted from electronic medical records and reviewed by a trained team of physicians. Neurological symptoms fall into three categories: central nervous system (CNS) symptoms or diseases (headache, dizziness, impaired consciousness, ataxia, acute cerebrovascular disease, and epilepsy), peripheral nervous system (PNS) symptoms (hypogeusia, hyposmia, hypopsia, and neuralgia), and skeletal muscular symptoms. Data of all neurological symptoms were checked by two trained neurologists. RESULTS: Of 214 patients studied, 88 (41.1%) were severe and 126 (58.9%) were non-severe patients. Compared with non-severe patients, severe patients were older (58.7 {+/-} 15.0 years vs 48.9 {+/-} 14.7 years), had more underlying disorders (42 [47.7%] vs 41 [32.5%]), especially hypertension (32 [36.4%] vs 19 [15.1%]), and showed less typical symptoms such as fever (40 [45.5%] vs 92 [73%]) and cough (30 [34.1%] vs 77 [61.1%]). Seventy-eight (36.4%) patients had neurologic manifestations. More severe patients were likely to have neurologic symptoms (40 [45.5%] vs 38 [30.2%]), such as acute cerebrovascular diseases (5 [5.7%] vs 1 [0.8%]), impaired consciousness (13 [14.8%] vs 3 [2.4%]) and skeletal muscle injury (17 [19.3%] vs 6 [4.8%]). CONCLUSION: Compared with non-severe patients with COVID-19, severe patients commonly had neurologic symptoms manifested as acute cerebrovascular diseases, consciousness impairment and skeletal muscle symptoms.