Plasma proteome of Long-COVID patients indicates HIF-mediated vasculo-proliferative disease with impact on brain and heart function.

AIMS: Long-COVID occurs after SARS-CoV-2 infection and results in diverse, prolonged symptoms. The present study aimed to unveil potential mechanisms, and to inform prognosis and treatment. METHODS: Plasma proteome from Long-COVID outpatients was analyzed in comparison to matched acutely ill COVID-19 (mild and severe) inpatients and healthy control subjects. The expression of 3072 protein biomarkers was determined with proximity extension assays and then deconvoluted with multiple bioinformatics tools into both cell types and signaling mechanisms, as well as organ specificity. RESULTS: Compared to age- and sex-matched acutely ill COVID-19 inpatients and healthy control subjects, Long-COVID outpatients showed natural killer cell redistribution with a dominant resting phenotype, as opposed to active, and neutrophils that formed extracellular traps. This potential resetting of cell phenotypes was reflected in prospective vascular events mediated by both angiopoietin-1 (ANGPT1) and vascular-endothelial growth factor-A (VEGFA). Several markers (ANGPT1, VEGFA, CCR7, CD56, citrullinated histone 3, elastase) were validated by serological methods in additional patient cohorts. Signaling of transforming growth factor-ß1 with probable connections to elevated EP/p300 suggested vascular inflammation and tumor necrosis factor-α driven pathways. In addition, a vascular proliferative state associated with hypoxia inducible factor 1 pathway suggested progression from acute COVID-19 to Long-COVID. The vasculo-proliferative process predicted in Long-COVID might contribute to changes in the organ-specific proteome reflective of neurologic and cardiometabolic dysfunction. CONCLUSIONS: Taken together, our findings point to a vasculo-proliferative process in Long-COVID that is likely initiated either prior hypoxia (localized or systemic) and/or stimulatory factors (i.e., cytokines, chemokines, growth factors, angiotensin, etc). Analyses of the plasma proteome, used as a surrogate for cellular signaling, unveiled potential organ-specific prognostic biomarkers and therapeutic targets.

Telehealth among substance using justice-involved persons on community supervision: Benefits, challenges, and suggestions for future use.

OBJECTIVE: The purpose of this study was to understand the uses of telehealth with justice-involved adults under community supervision with substance use problems, including their experiences during the pandemic. METHODS: Structured interviews were administered among 17 justice-involved adults under community supervision about their experiences with telehealth services to treat substance use disorders. Thematic coding was used for the analysis. RESULTS: We identified 5 primary themes: (1) knowledge about and experiences with telehealth services during the pandemic; (2) telehealth services available; (3) service changes during the pandemic; and (4) individual motivations around treatment-seeking behavior. CONCLUSION: Overall, our findings reveal that many individuals on probation or parole appreciate having access to telehealth and found that modality convenient for counseling services. Findings shed light on participants' understanding of telehealth, their experiences in using the modality, and how this modality may serve their needs in other ways. External and internal barriers to accessing telehealth are also discussed.

Organ and cell-specific biomarkers of Long-COVID identified with targeted proteomics and machine learning.

BACKGROUND: Survivors of acute COVID-19 often suffer prolonged, diffuse symptoms post-infection, referred to as "Long-COVID". A lack of Long-COVID biomarkers and pathophysiological mechanisms limits effective diagnosis, treatment and disease surveillance. We performed targeted proteomics and machine learning analyses to identify novel blood biomarkers of Long-COVID. METHODS: A case-control study comparing the expression of 2925 unique blood proteins in Long-COVID outpatients versus COVID-19 inpatients and healthy control subjects. Targeted proteomics was accomplished with proximity extension assays, and machine learning was used to identify the most important proteins for identifying Long-COVID patients. Organ system and cell type expression patterns were identified with Natural Language Processing (NLP) of the UniProt Knowledgebase. RESULTS: Machine learning analysis identified 119 relevant proteins for differentiating Long-COVID outpatients (Bonferonni corrected P < 0.01). Protein combinations were narrowed down to two optimal models, with nine and five proteins each, and with both having excellent sensitivity and specificity for Long-COVID status (AUC = 1.00, F1 = 1.00). NLP expression analysis highlighted the diffuse organ system involvement in Long-COVID, as well as the involved cell types, including leukocytes and platelets, as key components associated with Long-COVID. CONCLUSIONS: Proteomic analysis of plasma from Long-COVID patients identified 119 highly relevant proteins and two optimal models with nine and five proteins, respectively. The identified proteins reflected widespread organ and cell type expression. Optimal protein models, as well as individual proteins, hold the potential for accurate diagnosis of Long-COVID and targeted therapeutics.

Evaluating the generalisability of neural rumour verification models

Research on automated social media rumour verification, the task of identifying the veracity of questionable information circulating on social media, has yielded neural models achieving high performance, with accuracy scores that often exceed 90%. However, none of these studies focus on the real-world generalisability of the proposed approaches, that is whether the models perform well on datasets other than those on which they were initially trained and tested. In this work we aim to fill this gap by assessing the generalisability of top performing neural rumour verification models covering a range of different architectures from the perspectives of both topic and temporal robustness. For a more complete evaluation of generalisability, we collect and release COVID-RV, a novel dataset of Twitter conversations revolving around COVID-19 rumours. Unlike other existing COVID-19 datasets, our COVID-RV contains conversations around rumours that follow the format of prominent rumour verification benchmarks, while being different from them in terms of topic and time scale, thus allowing better assessment of the temporal robustness of the models. We evaluate model performance on COVID-RV and three popular rumour verification datasets to understand limitations and advantages of different model architectures, training datasets and evaluation scenarios. We find a dramatic drop in performance when testing models on a different dataset from that used for training. Further, we evaluate the ability of models to generalise in a few-shot learning setup, as well as when word embeddings are updated with the vocabulary of a new, unseen rumour. Drawing upon our experiments we discuss challenges and make recommendations for future research directions in addressing this important problem. © 2022 The Author(s)

Cross-immunity against SARS-COV-2 variants of concern in naturally infected critically ill COVID-19 patients.

Critically ill patients infected with SARS-CoV-2 display adaptive immunity, but it is unknown if they develop cross-reactivity to variants of concern (VOCs). We profiled cross-immunity against SARS-CoV-2 VOCs in naturally infected, non-vaccinated, critically ill COVID-19 patients. Wave-1 patients (wild-type infection) were similar in demographics to Wave-3 patients (wild-type/alpha infection), but Wave-3 patients had higher illness severity. Wave-1 patients developed increasing neutralizing antibodies to all variants, as did patients during Wave-3. Wave-3 patients, when compared to Wave-1, developed more robust antibody responses, particularly for wild-type, alpha, beta and delta variants. Within Wave-3, neutralizing antibodies were significantly less to beta and gamma VOCs, as compared to wild-type, alpha and delta. Patients previously diagnosed with cancer or chronic obstructive pulmonary disease had significantly fewer neutralizing antibodies. Naturally infected ICU patients developed adaptive responses to all VOCs, with greater responses in those patients more likely to be infected with the alpha variant, versus wild-type.

Plasma Proteome of Long-covid Patients Indicates Hypoxia-mediated Vasculo-proliferative Disease With Impact on Brain and Heart Function (preprint)

Aims Long-COVID occurs after SARS-CoV-2 infection and results in diverse, prolonged symptoms. The present study aims to determine the underlying mechanisms, and to inform prognosis and treatment.Methods Plasma proteome from Long-COVID outpatients was analyzed in comparison to acutely ill COVID-19 (mild and severe) inpatients and healthy control subjects. The expression of approximately 3000 protein biomarkers was determined with proximity extension assays and then deconvoluted with multiple bioinformatics tools into both cell types and signaling mechanisms, as well as organ specificity.Results Compared to age- and sex-matched acutely ill COVID-19 inpatients and healthy control subjects, Long-COVID outpatients showed natural killer cells with a resting phenotype, as opposed to active, and neutrophils that formed extracellular traps. This resetting of cell phenotypes was reflected in vascular events mediated by both angiopoietin-1 (ANGPT1) and vascular-endothelial growth factor-A (VEGFA). Levels of ANGPT1 and VEGFA were validated by serological methods in different patient cohorts. Silent signaling of transforming growth factor-β1 with elevated EP300 favored not only vascular inflammation, but also tumor necrosis factor-α driven pathways. In addition, a vascular proliferative state associated with hypoxia inducible factor 1 pathway was predicted that progressed from COVID-19 to Long-COVID. The vasculo-proliferative process identified in Long-COVID was associated with significant changes in the organ-specific proteome reflective of neurological and cardiometabolic dysfunction.Conclusions Taken together, our study uncovered a vasculo-proliferative process in Long-COVID initiated by prior hypoxia, and identified potential organ-specific prognostic biomarkers and therapeutic targets.

Atypical jobs in psychology: Interview of Dr. Donna Rasin-Waters.

This article provides an overview of Dr. Donna Rasin-Waters' career path and experiences providing telehealth at the Brooklyn Campus of the Veterans Affairs New York Harbor Healthcare Systems. Dr. Rasin-Waters, a psychologist and neuropsychologist with a specialty in geropsychology, began working toward the provision of evidence-based therapy via telehealth for Veterans in 2010. She believed that, in addition to rural communities, telehealth held utility for Veterans in densely populated areas, particularly for elderly adults with limited means for transportation. Since the COVID-19 pandemic, Dr. Rasin-Waters has seen a rapid boom in the use of telehealth for a variety of clinical activities with Veterans. This has further brought to light promising implications for the provision of remote mental health services, as well as important telehealth training and cultural considerations for clinicians. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Telehealth visits for contraception during the covid-19 pandemic: A national survey

To examine demographic, socioeconomic, and regional differences between in-person and telehealth contraception visits and telehealth visit quality in the US during the COVID-19 pandemic. In July 2020 and January 2021, we surveyed reproductive-aged women about experiences seeking contraception. We created a COVID-19 hardship score assessing pandemic-related job, income, and housing loss and a telehealth quality score assessing telehealth visit convenience, communication, and privacy. We used chi-square tests and multivariable logistic regression to examine relationships between baseline variables and in-person vs. telehealth visits and telehealth quality scores. Among 2,028 respondents who answered questions about contraception visits, 1,490 (73.4%) reported any visit, of which 530 (35.6%) were telehealth. In adjusted analyses, respondents identifying as Hispanic/Latina and mixed race/other (adjusted OR (aOR), 0.59 and 0.36, respectively), from the South, Midwest, or Northeast (aOR, 0.63, 0.64, 0.52, respectively), without insurance (aOR 0.63), and with greater COVID-19 hardship (aOR 0.52) had significantly lower odds of attending any visit (all p<0.05). Among respondents with any visit for contraception, respondents from the Midwest and South had significantly lower odds of having a telehealth versus in-person visit (aOR 0.63 and 0.54 respectively, p<0.01). Hispanic/Latina respondents and those in the Northeast had significantly lower odds of reporting high telehealth quality (≥75th percentile) (aOR 0.53 and 0.65, respectively, p<0.05). Disparities in telehealth usage for contraception among people identifying as Hispanic/Latina and people in the South and Midwest, and in telehealth quality among Hispanic/Latina people. Further research should focus on patients' desires around telehealth and increasing access to telehealthcare. [ FROM AUTHOR]

Elevated vascular transformation blood biomarkers in Long-COVID indicate angiogenesis as a key pathophysiological mechanism.

BACKGROUND: Long-COVID is characterized by prolonged, diffuse symptoms months after acute COVID-19. Accurate diagnosis and targeted therapies for Long-COVID are lacking. We investigated vascular transformation biomarkers in Long-COVID patients. METHODS: A case-control study utilizing Long-COVID patients, one to six months (median 98.5 days) post-infection, with multiplex immunoassay measurement of sixteen blood biomarkers of vascular transformation, including ANG-1, P-SEL, MMP-1, VE-Cad, Syn-1, Endoglin, PECAM-1, VEGF-A, ICAM-1, VLA-4, E-SEL, thrombomodulin, VEGF-R2, VEGF-R3, VCAM-1 and VEGF-D. RESULTS: Fourteen vasculature transformation blood biomarkers were significantly elevated in Long-COVID outpatients, versus acutely ill COVID-19 inpatients and healthy controls subjects (P < 0.05). A unique two biomarker profile consisting of ANG-1/P-SEL was developed with machine learning, providing a classification accuracy for Long-COVID status of 96%. Individually, ANG-1 and P-SEL had excellent sensitivity and specificity for Long-COVID status (AUC = 1.00, P < 0.0001; validated in a secondary cohort). Specific to Long-COVID, ANG-1 levels were associated with female sex and a lack of disease interventions at follow-up (P < 0.05). CONCLUSIONS: Long-COVID patients suffer prolonged, diffuse symptoms and poorer health. Vascular transformation blood biomarkers were significantly elevated in Long-COVID, with angiogenesis markers (ANG-1/P-SEL) providing classification accuracy of 96%. Vascular transformation blood biomarkers hold potential for diagnostics, and modulators of angiogenesis may have therapeutic efficacy.

DUPLICATE FIT TESTING AS A SAFETY NETTING STRATEGY FOR PATIENTS AT RISK OF COLORECTAL CANCER

Introduction Faecal immunochemical testing (FIT) has been shown to have an acceptable positive predictive value (PPV) and negative predictive value (NPV) for the detection of colorectal cancer (CRC). NHS-E/NICE COVID pandemic guidance recommends that patients with a FIT < 10μgHb/g do not need urgent colonic imaging but can be 'safety-netted' if not anaemic. Nonetheless concerns remain, that based on a FIT test alone up to 10% of patients with CRC might be missed by this approach, possibly due to the inherent risks of sampling error. The AIM of this study was to determine if the NPV and PPV of FIT could be improved by a strategy of duplicate FIT testing. Methods An observational cohort study of duplicate FIT testing of all patients referred on a Lower GI TWW pathway across 4 NHS provider trusts in the Lancashire and South Cumbria Cancer alliance from Jan2019-Feb 2021. FIT samples were analysed at a single centre using OC-sensor with a cut off > 10 0μgHb/g of faeces taken as a positive. CRC diagnoses were ascertained from local hospital records and cross referenced with the Somerset Cancer Registry. Results 28,622 of 30,105 (95%) referred patients (median [range] age 66y [16-103], 56% female) submitted duplicate FIT tests. 317/28,622 (1.1%) were diagnosed with CRC, of whom 22/317 (59%) were men. Of 18,952/28622 (66%) with two negative FIT tests, CRC was subsequently diagnosed in 7 patients (0.04%) with anaemia (n=7) and right sided tumours (n=6). In contrast, a single FIT strategy would have missed 22 patients of whom only 7 (32%) were anaemic. Interestingly duplicate FIT testing also improved the PPV, which increased from 0.3% if both tests were >10 - 100 0μgHb/g to a PPV of 14% if both tests were >100 0μgHb/g of faeces Conclusions A strategy of duplicate testing improves the NPV and PPV of FIT and should be considered as a mitigation to reducing missed cancer diagnosis. In patients at risk of CRC with no anaemia, duplicate FIT testing effectively rules out CRC and allows patients to be safely managed in primary care.

Patients with severe COVID-19 do not have elevated autoantibodies against common diagnostic autoantigens.

OBJECTIVES: Infection by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen of coronavirus disease 2019 (COVID-19) presents occasionally with an aberrant autoinflammatory response, including the presence of elevated circulating autoantibodies in some individuals. Whether the development of autoantibodies against self-antigens affects COVID-19 outcomes remains unclear. To better understand the prognostic role of autoantibodies in COVID-19, we quantified autoantibodies against 23 markers that are used for diagnosis of autoimmune disease. To this end, we used serum samples from patients with severe [intensive care unit (ICU)] and moderate (ward) COVID-19, across two to six consecutive time points, and compared autoantibody levels to uninfected healthy and ICU controls. METHODS: Acute and post-acute serum (from 1 to 26 ICU days) was collected from 18 ICU COVID-19-positive patients at three to six time points; 18 ICU COVID-19-negative patients (sampled on ICU day 1 and 3); 21 ward COVID-19-positive patients (sampled on hospital day 1 and 3); and from 59 healthy uninfected controls deriving from two cohorts. Levels of IgG autoantibodies against 23 autoantigens, commonly used for autoimmune disease diagnosis, were measured in serum samples using MSD® U-PLEX electrochemiluminescence technology (MSD division Meso Scale Discovery®), and results were compared between groups. RESULTS: There were no significant elevations of autoantibodies for any of the markers tested in patients with severe COVID-19. CONCLUSIONS: Sample collections at longer time points should be considered in future studies, for assessing the possible development of autoantibody responses following infection with SARS-CoV-2.

Escherichia coli recombinant expression of SARS-CoV-2 protein fragments.

We have developed a method for the inexpensive, high-level expression of antigenic protein fragments of SARS-CoV-2 proteins in Escherichia coli. Our approach uses the thermophilic family 9 carbohydrate-binding module (CBM9) as an N-terminal carrier protein and affinity tag. The CBM9 module was joined to SARS-CoV-2 protein fragments via a flexible proline-threonine linker, which proved to be resistant to E. coli proteases. Two CBM9-spike protein fragment fusion proteins and one CBM9-nucleocapsid fragment fusion protein largely resisted protease degradation, while most of the CBM9 fusion proteins were degraded at some site in the SARS-CoV-2 protein fragment. All of the fusion proteins were highly expressed in E. coli and the CBM9-ID-H1 fusion protein was shown to yield 122 mg/L of purified product. Three purified CBM9-SARS-CoV-2 fusion proteins were tested and found to bind antibodies directed to the appropriate SARS-CoV-2 antigenic regions. The largest intact CBM9 fusion protein, CBM9-ID-H1, incorporates spike protein amino acids 540-588, which is a conserved region overlapping and C-terminal to the receptor binding domain that is widely recognized by human convalescent sera and contains a putative protective epitope.

Leveraging COVID-19 vaccination to enhance hcv testing in priority populations

Background: Intersecting priority populations are disproportionately affected by HCV and COVID-19;including people who use drugs, those with mental health issues, and those who are homeless/street-involved. COVID-19 vaccine clinics present an opportunity for co-localization of HCV testing by leveraging resources and infrastructure that promote COVID-19 vaccination among these populations. Methods: HHCV Ab point-of-care testing (POCT) was offered at two COVID-19 vaccination sites: the Centre for Addiction and Mental Health (CAMH) in Toronto, ON and the Ontario Addiction Treatment Centre (OATC) in North Bay, ON. Vaccine recipients (VRs) were staff, community members, or patients (CAMH);or patients and household members (OATC). HCV outreach workers approached VRs for testing, which was promoted by clinic staff. At OATC, VRs received a $5 coffee card incentive to undergo testing. At both sites, Ab POCT was done by fingerprick (OraQuick) during or after a 15-minute post-vaccine observation period. Results were provided after 5 minutes based on prior data showing this approach detects all viremic individuals (VIRCAN 5-Minute Rule). Dried blood spot (DBS) samples were collected by fingerprick for HCV RNA testing following Ab+ results. Results: CAMH - 2759 individuals received vaccine over 12 days (mean 230/day, range 102-350). 621 (23%) underwent Ab POCT (mean 52/day, range 16-106). The mean age was 46 yrs (range 12-87) and 307 (49%) were male. Staff constituted 55% of tested VRs with a positivity rate of 0% compared to 2.2% in patients/community members. Of 6 Ab+ individuals, 5 DBS samples were collected and 2 were RNA+. One Ab+ individual was counseled by phone to follow up for RNA testing due to a late Ab+ result (20'). OATC - 150 individuals received vaccine over 9 days (mean 17/day, range 11-33). 27 (18%) were recruited for Ab POCT (mean 3/day, range 0-10). The mean age was 37 yrs (range 25-56) and 14 (52%) were male. Seven individuals were known to be Ab+ and DBS samples were collected from each, of which 4 were RNA+. The remaining 20 individuals were all Ab- by POCT. Outreach and linkage to care is ongoing at both sites. Conclusion: Co-localization of HCV testing with COVID-19 vaccination enables reaching and re-engaging populations with a tenuous link to the healthcare system. HCV Ab POCT with the VIRCAN 5-Minute Rule followed by DBS sample collection is a quick, low-barrier approach that enables high throughput and ensures complete diagnosis of HCV.

Escherichia coli recombinant expression of SARS-CoV-2 protein fragments. (preprint)

We have developed a method for the inexpensive, high-level expression of antigenic protein fragments of SARS-CoV-2 proteins in Escherichia coli. Our approach used the thermophilic carbohydrate binding domain 9 (CBM9) module as an N-terminal carrier protein and affinity tag. The CBM9 module was joined to SARS-CoV-2 protein fragments via a flexible proline-threonine rich linker, which proved to be resistant to E. coli proteases. Two CBM9-spike protein fragment fusion proteins and one CBM9-nucleocapsid fragment fusion protein largely resisted protease degradation, while most of the CBM9-fusion proteins were degraded at some site in the SARS-CoV-2 protein fragment. All fusion proteins were expressed in E. coli at about 0.1 g/L, and could be purified with a single affinity binding step using inexpensive cellulose powder. Three purified CBM9-SARS-CoV-2 fusion proteins were tested and found to bind antibody directed to the appropriate SARS-CoV-2 antigenic region. The largest CBM9 fusion protein incorporates a spike protein self-folding domain, and includes amino acids 540-588 of the spike protein. This conserved region is immediately C-terminal to the receptor binding domain, is widely recognized by human convalescent sera, and contains a putative protective epitope.