Changes in emergency department utilization in vulnerable populations after COVID-19 shelter in place orders (preprint)

Purpose: To compare emergency department (ED) utilization and admission rates for patients with a history of mental health (MH), substance use disorder (SUD) and social determinants of health (SDOH) before and after implementing COVID-19's shelter-inplace (SIP) orders. Methods: This was a retrospective, multicenter study leveraging electronic medical record data from 20 EDs across a large Midwest integrated healthcare system from 5/2/2019 to 12/31/2019 (pre-SIP) and from 5/2/2020 to 12/31/2020 (post-SIP). Diagnoses were documented in the patient's medical records. Poisson and logistic regression models were used to evaluate ED utilization and admission rate changes. Results: 871,020 total ED encounters from 487,028 unique patients were captured. 2,572 (0.53%) patients had a documented Z code for SDOH. Patients with previously diagnosed MH or SUDs were more likely to seek ED care after the SIP orders were implemented (RR: 1.20, 95% CI: 1.18 - 1.22, p<0.001), as were patients with SDOH (RR: 2.37, 95% CI: 2.19 - 2.55, p<0.001). Patients with both previously diagnosed MH or SUD and a documented SDOH had even higher ED utilization (RR: 3.31, 95% CI: 2.83 - 3.88, p<0.001) than those with either condition alone. Patients with MH and SUDs (OR: 0.89, 95% CI: 0.86 - 0.92, p<0.001) or SDOH (OR: 0.67, 95% CI: 0.54, 0.83, p<0.001) were less likely to be admitted post-SIP orders while patients with a history of diseases of physiologic systems were more likely to be admitted. Conclusions: Vulnerable populations with a history of MH, SUD, and SDOH experienced increased ED utilization but a lower rate of hospital admissions after the implementation of SIP orders. The findings highlight the importance of addressing these needs to mitigate the impact of public health crises on these populations.

The experiences and impact of the COVID-19 pandemic on Young Carers: practice implications and planning for future health emergencies (preprint)

Background: Young Carers faced significant challenges brought on by the COVID-19 pandemic. We explored the impact of the pandemic and associated restrictions on mental health, wellbeing and access to support in Young Carers in the United Kingdom (UK) to understand how to improve services, as well as support this population in future health emergencies. Method: We conducted 22 qualitative semi-structured interviews from May to November 2021, with 14 Young Carers and 8 staff working in organisations that supported them. Interviews took place remotely over video or telephone call, discussing topics such as experiences of the pandemic on their health, wellbeing and caring responsibilities. We used reflexive thematic analysis to analyse interview transcripts. Results: We identified 4 overarching themes pertaining to the impact of the pandemic and associated restrictions on mental health, wellbeing, and access to support in Young Carers in the UK: 1) challenges to following the guidelines, 2) changes to and loss of routine, 3) changes in provision of informal and formal support and 4) better understanding of inner resilience and goals. Many participants struggled with their mental health and wellbeing as a result of pandemic related restrictions, impacting on support structures for themselves, as well as the individual cared for. However, positive impacts pertained to additional support from local authority and third sector organisations. Conclusions: Our findings highlight some of the changes that affected Young Carers during the COVID-19 pandemic. The impact of changes to routine and a reduction in pre-pandemic support were the greatest concerns reported by participants in this study. The additional support provided by local authority and third sector organisations during social restrictions suggests such organisations could play a greater role in supporting this population going forward, and that schools and Governments may wish to put in additional strategies and provisions to protect this population in the future.

Early antiviral CD4 and CD8 T cell responses are associated with upper respiratory tract clearance of SARS-CoV-2 (preprint)

T cells are involved in protective immunity against numerous viral infections. Limited data have been available regarding roles of human T cell responses controlling SARS-CoV-2 viral clearance in primary COVID-19. Here, we examined longitudinal SARS-CoV-2 upper respiratory tract viral RNA levels and early adaptive immune responses from 95 unvaccinated individuals with acute COVID-19. Acute SARS-CoV-2-specific CD4 and CD8 T cell responses were evaluated in addition to antibody responses. Most individuals with acute COVID-19 developed rapid SARS-CoV-2-specific T cell responses during infection, and both early CD4 T cell and CD8 T cell responses correlated with reduced upper respiratory tract SARS-CoV-2 viral RNA, independent of neutralizing antibody titers. Overall, our findings indicate a distinct protective role for SARS-CoV-2-specific T cells during acute COVID-19.

A deep learning framework for predicting the neutralizing activity of COVID-19 therapeutics and vaccines against evolving SARS-CoV-2 variants (preprint)

Understanding how viral variants evade neutralization is crucial for improving antibody-based treatments, especially with rapidly evolving viruses like SARS-CoV-2. Yet, conventional assays are limited in the face of rapid viral evolution, relying on a narrow set of viral isolates, and falling short in capturing the full spectrum of variants. To address this, we have developed a deep learning approach to predict changes in neutralizing antibody activity of COVID-19 therapeutics and vaccines against emerging viral variants. First, we trained a variational autoencoder (VAE) using all 67,885 unique SARS-CoV-2 spike protein sequences from the NCBI virus (up to October 31, 2022) database to encode spike protein variants into a latent space. Using this VAE and a curated dataset of 7,069 in vitro assay data points from the NCATS OpenData Portal, we trained a neural network regression model to predict fold changes in neutralizing activity of 40 COVID-19 therapeutics and vaccines against spike protein sequence variants, relative to their neutralizing activity against the ancestral strain (Wuhan-Hu-1). Our model also employs Bayesian inference to quantify prediction uncertainty, providing more nuanced and informative estimates. To validate the model\'s predictive capacity, we assessed its performance on a test set of in vitro assay data collected up to eight months after the data included in the model training (N = 980). The model accurately predicted fold changes in neutralizing activity for this prospective dataset, with an R2 of 0.77. Expanding our methodology to include all available data from NCBI virus and NCATS OpenData Portal up to date, we assessed predicted changes in activity for current COVID-19 monoclonal antibodies and vaccines against newly identified SARS-CoV-2 lineages. Our predictions suggest that current therapeutic and vaccine-induced antibodies will have significantly reduced activity against newer XBB descendants, notably EG.5, FL.1.5.1, and XBB.1.16. Using the model, we were able to primarily attribute the observed predicted loss in activity to the F456L spike mutation found in EG.5 and FL.1.5.1 sequences. Conversely, mRNA-bivalent vaccines are predicted to be less susceptible to the recent BA.2.86 variant compared to new XBB descendants. These findings align closely with recent research, underscoring the potential of deep learning in shaping therapeutic and vaccine strategies for emerging viral variants.

Reduced Monocyte Proportions and Responsiveness in Convalescent COVID-19 Patients (preprint)

The clinical manifestations of acute severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection and COVID-19 suggest a dysregulation of the host immune response that leads to inflammation, thrombosis, and organ dysfunction. It is less clear whether these dysregulated processes persist during the convalescent phase of disease or during long COVID. We investigated the effects of SARS-CoV-2 infection on the proportions of classical, intermediate, and non-classical monocytes, their activation status, and their functional properties in convalescent COVID-19 patients and uninfected control subjects. We found that the percentage of total monocytes was decreased in convalescent COVID-19 patients compared to uninfected controls. This was due to decreased intermediate and non-classical monocytes. Classical monocytes from convalescent COVID-19 patients demonstrated a decrease in activation markers, such as CD56, in response to stimulation with bacterial lipopolysaccharide (LPS). In addition, classical monocytes from convalescent COVID-19 patients showed decreased expression of CD142 (tissue factor), which can initiate the extrinsic coagulation cascade, in response to LPS stimulation. Finally, we found that monocytes from convalescent COVID-19 patients produced less TNF- and IL-6 in response to LPS stimulation, than those from uninfected controls. In conclusion, SARS-CoV-2 infection exhibits a clear effect on the relative proportions of monocyte subsets, the activation status of classical monocytes, and proinflammatory cytokine production that persists during the convalescent phase of disease.

Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens (preprint)

The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 subunit. S2, in contrast, is the most evolutionarily conserved region of the spike and can elicit broadly neutralizing and protective antibodies. Yet, the usage of S2 as an alternative vaccine strategy is hampered by its general instability. Here, we use a simulation-driven approach to design highly stable S2-only antigens retaining a closed prefusion conformation. Weighted ensemble simulations provide mechanistic characterization of the S2 trimer opening, informing the design of tryptophan substitutions that impart kinetic and thermodynamic stabilization. Alchemical free energy perturbation calculations and a corroborating set of experiments confirm that V991W and T998W in the central helices of S2 stabilize the trimer in the closed prefusion conformation, producing an antigen with increased protein expression, superior thermostability, and preserved immunogenicity against sarbecoviruses.

Cross-platform comparison of highly-sensitive immunoassays for inflammatory markers in a COVID-19 cohort (preprint)

A variety of commercial platforms are available for the simultaneous detection of multiple cytokines and associated proteins, often employing antibody pairs to capture and detect target proteins. In this study, we comprehensively evaluated the performance of three distinct platforms: the fluorescent bead-based Luminex assay, the proximity extension-based Olink assay, and a novel proximity ligation assay platform known as Alamar NULISAseq. These assessments were conducted on serum samples from the NIH IMPACC study, with a focus on three essential performance metrics: detectability, correlation, and differential expression. Our results reveal several key findings. Firstly, the Alamar platform demonstrated the highest overall detectability, followed by Olink and then Luminex. Secondly, the correlation of protein measurements between the Alamar and Olink platforms tended to be stronger than the correlation of either of these platforms with Luminex. Thirdly, we observed that detectability differences across the platforms often translated to differences in differential expression findings, although high detectability did not guarantee the ability to identify meaningful biological differences. Our study provides valuable insights into the comparative performance of these assays, enhancing our understanding of their strengths and limitations when assessing complex biological samples, as exemplified by the sera from this COVID-19 cohort.

Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are robust to differential shedding (preprint)

The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting and assessing the spread of SARS-CoV-2 variants in communities and for estimating important epidemiological parameters such as the growth advantage of the variant. However, despite demonstrated successes, epidemiological data derived from wastewater suffers from potential biases. Of particular concern are differential shedding profiles that different variants of concern exhibit, because they can shift the relationship between viral loads in wastewater and prevalence estimates derived from clinical cases. Using mathematical modeling, simulations, and Swiss surveillance data, we demonstrate that this bias does not affect estimation of the growth advantage of the variant and has only a limited and transient impact on estimates of the effective reproduction number. Thus, population-level epidemiological parameters derived from wastewater maintain their advantages over traditional clinical-derived estimates, even in the presence of differential shedding among variants.

The Influence Of Covid-19 On Patient Mobilization And Injury Attributes In The ICU: A Retrospective Analysis Of A Level II Trauma Center (preprint)

The objectives of this study were to determine the effect of COVID-19 on physical therapy (PT) mobilization of traumatically-injured patients and to determine if mobilization affected patient course in the ICU. This retrospective study included patients who were admitted to the ICU of a level II trauma center. The patients were divided into two groups, i.e., those admitted before (n=378) and after (n=499) April 1, 2020 when Georgia's COVID-19 Shelter-in-place order was mandated. The two groups were contrasted on nominal and ratio variables using Chi-square and Student's t-tests. A secondary analysis focused specifically on the after COVID patients examined the extent to which mobilization (n=328) or lack of mobilization (n=171) influenced ICU outcomes (e.g., mortality, readmission). The two groups were contrasted on nominal and ratio variables using Chi-square and Student's -tests. The after COVID patients had higher injury severity as a greater proportion was classified as severely injured (i.e., >15 on Injury Severity Score) compared to the before COVID patients. After COVID patients also had greater cumulative number of comorbidities and experienced greater complications in the ICU. Despite this, there was no difference between patients in receiving a PT consultation or day-to-mobilization. Within the after COVID cohort, those that were mobilized were older, a higher proportion were female, they had greater Glasgow Coma Scale scores, had longer total hospital days, and a lesser mortality rate. Despite shifting patient injury attributes post-COVID-19, a communicable disease, mobilization care remained consistent and effective.

'We are not the virus - Experiences of racism among East & Southeast Asian heritage young people in London during the height of the COVID-19 pandemic (preprint)

The spread of COVID-19 was accompanied by news reports of surging racism, xenophobia, and hate crime all over the Global North targeting individuals of East and Southeast Asian (ESEA) descent. However, little empirical research has documented the impacts of COVID-19 on child and adolescent ESEAs. We describe and analyse the mental health experiences of young ESEA Londoners during the height of the COVID-19 pandemic. We purposively recruited 23 young people (aged 9-20) of ESEA heritage through social media and existing ESEA networks and analysed transcripts using thematic analysis. Participants experienced distress from being exposed to multiple forms of racism ranging from strangers on the street avoiding or harassing them to classmates at school or university making racist jokes, comments or banter. Participants worried about hate crimes reported in news media and experienced anxiety from seeing pervasive racist content in online social media. Some participants responded by physically isolating themselves at home for long periods, whilst others chose to participate in activism, providing a sense of agency. Action by parents and school authorities was reported to help prevent further bullying, but respondents did not always feel able to approach these for help. Our findings put into focus the strain on young ESEA Londoners mental health caused by COVID-related racism and jar against simplified depictions of metropolitan places, such as London, as centres of cosmopolitanism and tolerance. To promote the emotional wellbeing of young ESEAs, future policy should facilitate action by schools and universities against anti-ESEA racism and support ESEA community-building efforts to enhance resilience in the face of racism.

Changes in sleep duration during the long-lasting COVID-19 pandemic: individual and regional disparities (preprint)

The adequate quality and quantity of sleep are related to maintaining the immune system and mental well-being; therefore, it is necessary to evaluate sleep duration during COVID-19. This study aimed to investigate the changes in sleep duration during the long-lasting COVID-19 period (2020 and 2021) in South Korea, and to examine the individual and regional disparities. The study population comprised 1,143,460 adults aged [≥]19 years who participated in the 2017-2021 Korea Community Health Survey excluding those who did not respond to the daily sleep duration questionnaire. For statistical analysis, we first conducted a multiple regression model for 229 districts to estimate the district-specific changes in sleep duration. We then applied a meta-analysis to pool the 229 estimates and a meta-regression to examine the association between changes in sleep duration and regional characteristics. The sleep duration increased by 9.66 (95% CI: 8.53, 10.80) min in 2020 and 3.66 (95% CI: 2.09, 5.22) min in 2021 compared to the pre-pandemic period (2017-2019). The increase was more prominent in males, younger adults, employed individuals, and those with a high socioeconomic status compared to the general population. Communities with a higher proportion of apartments, lower normalized difference vegetation index in summer, and lower practice rate of moderate exercise were associated with a higher increase in sleep duration during the pandemic. The sleep duration increased during the COVID-19 pandemic, and the increase decreased as the COVID-19 lasted longer. The findings of our study highlight that preventive measures to manage sleep health during a pandemic should be framed in consideration of individual and regional characteristics.

Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA (preprint)

While SARS-CoV-2 vaccines have shown strong efficacy, their suboptimal uptake combined with the continued emergence of new viral variants raises concerns about the ongoing and future public health impact of COVID-19. We investigated viral and host factors, including vaccination status, that were associated with SARS-CoV-2 disease severity in a setting with low vaccination rates. We analyzed clinical and demographic data from 1,957 individuals in the state of Georgia, USA, coupled with viral genome sequencing from 1,185 samples. We found no difference in disease severity between individuals infected with Delta and Omicron variants among the participants in this study, after controlling for other factors, and we found no specific mutations associated with disease severity. Compared to those who were unvaccinated, vaccinated individuals experienced less severe SARS-CoV-2 disease, and the effect was similar for both variants. Vaccination within 270 days before infection was associated with decreased odds of moderate and severe outcomes, with the strongest association observed at 91-270 days post-vaccination. Older age and underlying health conditions, especially immunosuppression and renal disease, were associated with increased disease severity. Overall, this study provides insights into the impact of vaccination status, variants/mutations, and clinical factors on disease severity in SARS-CoV-2 infection when vaccination rates are low. Understanding these associations will help refine and reinforce messaging around the crucial importance of vaccination in mitigating the severity of SARS-CoV-2 disease.

Fc-dependent functional activity of ChAdOx1-S and CoronaVac vaccine-induced antibodies to the SARS-CoV-2 spike protein (preprint)

Ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and COVID-19 disease severity is influenced by immunity acquired by natural exposure and/or vaccination, whereby most vaccines are formulated on the Ancestral strain. However, population-level immunity is complicated by the emergence of variants of concern (VOCs), such as Omicron that is the dominant variant currently in circulation. Antibody Fc-dependent effector functions are being increasingly recognised as important mediators in immunity, especially against VOCs. However, induction of these functions in populations with diverse infection and/or vaccination histories, remains poorly defined. Here, we evaluated Fc-dependent functional antibodies following vaccination with two widely used vaccines: AstraZeneca (AZ; ChAdOx1-S) and Sinovac (SV). We quantified Fc{gamma}R-binding and C1q-fixing antibodies against Ancestral and variant spike (S) proteins in Brazilian adults vaccinated with AZ or SV (n=222), some of which were previously exposed to SARS-CoV-2. AZ induced greater Fc{gamma}R-binding responses to Ancestral S than the SV vaccine. Previously exposed individuals had significantly greater vaccine-induced responses compared to their naive counterparts, with notably high C1q-fixation levels, irrespective of vaccine type. Fc{gamma}R-binding was highest among AZ vaccinated individuals with a prior exposure, and these responses were well retained against the Omicron S protein. Overall, these findings contribute to our understanding of vaccine-induced immunity and its effectiveness against evolving variants.

Plasma-based antigen persistence in the post-acute phase of SARS-CoV-2 infection (preprint)

BACKGROUND: Although RNA viruses like SARS-CoV-2 are generally thought to be transient, the persistence of viral components beyond the acute phase can be driven by a variety of virologic and immunologic factors. Recent studies have suggested that SARS-CoV-2 antigens may persist following COVID-19 but were limited by a lack of comparison to a large number of true negative control samples. METHODS: Using single molecule array (Simoa) assays for SARS-CoV-2 spike, S1, and nucleocapsid antigen in plasma from 171 pandemic-era individuals in the post-acute phase of SARS-CoV-2 infection and 250 pre-pandemic control samples, we compared prevalence of antigen detection. We used logistic regression models and prevalence ratios (PRs) to assess the relationship between demographic and disease factors and antigen persistence. RESULTS: Compared to the proportion of antigen positivity in the pre-pandemic controls (2%), detection of any SARS-CoV-2 antigen was more frequent across all post-acute COVID-19 time bins (3-6 months: 12.6%, p<0.001; 6-10 months, 10.7%, p=0.0002; 10-14 months, 7.5%, p=0.017). These differences were driven by spike protein for up to 14 months and nucleocapsid in the first 6 months after infection. The co-occurrence of multiple antigens at a single timepoint was uncommon. Hospitalization for acute COVID-19 (versus not hospitalized) and worse self-reported health during acute COVID-19 among those not hospitalized (versus more benign illness) were associated with higher prevalence of post-acute antigen detection (PR 1.86, p=0.03; PR 3.5, p=0.07, respectively) in the pandemic era. CONCLUSIONS: Our findings provide strong evidence that SARS-CoV-2 antigens can persist beyond the period of acute illness. The observation that more than 10% of plasma samples for over a year following initial SARS-CoV-2 infection contain detectable viral antigen, which are potentially immunogenic, has significant implications given the sheer number of people infected with SARS-CoV-2 to date. More work will be needed to determine whether these antigens have a causal role in post-acute sequelae of SARS-CoV-2 infection (PASC).

COVID-19 vaccination-induced antibody responses and waning by age and comorbidity status in a large population-based prospective cohort study (preprint)

Background Information on the magnitude and duration of antibody levels after COVID-19 vaccination in different groups may be useful for prioritizing of additional vaccinations. Methods Serum samples were collected every six months in a prospective cohort study among adults in the Netherlands. Geometric mean concentrations (GMCs) of antibodies against the receptor binding domain of the SARS-CoV-2 spike protein were calculated after the primary series, first, and second booster vaccinations. Effects of age (18-59 vs 60-85 years) and medical risk conditions on GMC 2-6 weeks and 21-25 weeks after each vaccination, and on waning during 3-25 weeks after each vaccination, were estimated by linear regression. Results We included 20,816, 16,820 and 5,879 samples collected after primary, first and second booster vaccination, respectively. GMCs at 2-6 and 21-25 weeks after primary series were lower in participants with older age or medical risk conditions. After the first booster, older age was associated with lower GMC at 2-6 weeks, higher GMC at 21-25 weeks, and slower waning. GMCs or waning after the first and second boosters (only 60-85) were not associated with medical risk conditions. Conclusions Since antibody differences by age and medical risk groups have become small with increasing number of doses, other factors such as disease severity rather than antibody levels are useful for prioritization of additional vaccinations.

Projections of the incidence of COVID-19 in Japan and the potential impact of a Fall 2023 COVID-19 Vaccine (preprint)

Background: The study objective was to estimate the incidence of COVID-19 infection, hospitalization, and deaths in Japan from September 2023 to August 2024 and potential impact of a Fall 2023 COVID-19 vaccine for adults 18 years and older on these outcomes. Methods: A previously developed Susceptible Exposed Infected Recovered model for the United States (US) was adapted to Japan. The numbers of symptomatic infections, COVID-19 related hospitalizations, and deaths were calculated. Given differences in vaccination coverage, masking practices and social mixing patterns between the US and Japan, all inputs were updated to reflect the Japanese context. Vaccine effectiveness (VE) values are hypothetical, but predicted based on existing VE values of bivalent BA.4/BA.5 boosters against BA.4/BA.5 in Japan, from the VERSUS test-negative case-control study. Sensitivity analyses were performed. Results: The base case model predicts overall that there will be approximately 35.2 million symptomatic COVID-19 infections, 690,000 hospitalizations, and 62,000 deaths in Japan between September 2023 and August 2024. If an updated COVID-19 vaccine is offered to all adults aged 18 years and older in Fall 2023, the model predicts that 7.3 million infections, 275,000 hospitalizations and 26,000 deaths will be prevented. If vaccines are only given to those aged 65 years and older, only 2.9 million infections, 180,000 hospitalizations and 19,000 deaths will be prevented. Sensitivity analysis results suggest that hospitalizations and deaths prevented are most sensitive to initial vaccine effectiveness (VE) against infection and hospitalizations, and the waning rate associated with VE against infection. Symptomatic infections prevented was most sensitive to initial VE against infection and VE waning. Conclusions: Results suggest that a Fall 2023 COVID-19 vaccine would reduce total numbers of COVID-19 related infections, hospitalizations, and deaths.

Inferring community transmission of SARS-CoV-2 in the United Kingdom using the ONS COVID-19 Infection Survey (preprint)

Key epidemiological parameters, including the effective reproduction number, R(t), and the instantaneous growth rate, r(t), generated from an ensemble of models, have been informing public health policy throughout the COVID-19 pandemic in the four nations of the United Kingdom of Great Britain and Northern Ireland (UK). However, estimation of these quantities became challenging with the scaling down of surveillance systems as part of the transition from the 'emergency' to 'endemic' phase of the pandemic. The Office for National Statistics (ONS) COVID-19 Infection Survey (CIS) provided an opportunity to continue estimating these parameters in the absence of other data streams. We used a penalised spline model fitted to the ONS CIS test positivity estimates to produce a smoothed estimate of the prevalence of SARS-CoV-2 positivity over time. The resulting fitted curve was used to estimate the 'ONS-based' R(t) and r(t) across the four nations of the UK. Estimates produced under this model are compared to government-published estimates with particular consideration given to the contribution that this single data stream can offer in the estimation of these parameters. Depending on the nation and parameter, we found that up to 77% of the variance in the government-published estimates can be explained by the ONS-based estimates, demonstrating the value of this singular data stream to track the epidemic in each of the four nations. We additionally find that the ONS-based estimates uncover epidemic trends earlier than the corresponding government-published estimates. Our work shows that the ONS CIS can be used to generate the key COVID-19 epidemics across the four UK nations. This is not intended as an alternative to ensemble modelling, rather it is intended as a potential solution to the aforementioned challenge faced by public health officials in the UK in early 2022.

A 50-gene high-risk profile predictive of COVID-19 and Idiopathic Pulmonary Fibrosis mortality originates from a molecular imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease (preprint)

Background: We aim to study the source of circulating immune cells expressing a 50-gene signature predictive of COVID-19 and IPF mortality. Methods: Whole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 231 subjects with COVID-19, post-COVID-19-ILD, IPF and controls. We measured the 50-gene signature (nCounter, Nanostring), interleukin 6 (IL6), interferon gamma;-induced protein (IP10), secreted phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-beta) by Luminex. PCR was used to validate COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Controller (10X Genomics). For analysis we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger, Seurat, Propeller, Kaplan-Meier curves, CoxPH models, Two-way ANOVA, T-test, and Fisher exact. Results: We identified three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19 with significant differences in IL6, IP10, SPP1 and TGF{beta}-1. scRNA-seq identified Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+ and high levels of the 7-gene signature (7Gene-M-MDSC) in COVID-19. These cells were not observed in post-COVID-19-ILD or IPF. The 43-gene signature was mostly expressed in CD4 T and CD8 T cell subsets. Increased expression of the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19-ILD. The expression of these genes remained low in IPF. Conclusion: A 50-gene, high-risk profile in COVID-19 is characterized by a genomic imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease.

SARS-CoV-2 induces acute neurological signs while Calcitonin Gene-Related Peptide (CGRP) signaling blockade reduces interleukin 6 (IL-6) release and weight loss in mouse models (preprint)

COVID-19 can result in neurological symptoms such as fever, headache, dizziness, and nausea. We evaluated whether the Calcitonin Gene-Related Peptide (CGRP) receptor antagonist, olcegepant, used in migraine treatment could mitigate acute neuroinflammatory and neurological responses to SARS-COV-2 infection. We infected wildtype C57BL/6J and 129/SvEv mice, and a 129 CGRP-null mouse line with a mouse-adapted SARS-CoV-2 virus, and evaluated the effect of CGRP receptor antagonism on the outcome of that infection. We determined that CGRP receptor antagonism provided protection from permanent weight loss in older (>12 m) C57BL/6J and 129 SvEv mice. We also observed acute fever and motion-induced dizziness in all older mice, regardless of treatment. However, in both wildtype mouse lines, CGRP antagonism reduced acute interleukin 6 (IL-6) levels by half, with virtually no IL-6 release in mice lacking CGRP. These findings suggest that blockage of CGRP signaling protects against acute IL-6 release and subsequent inflammatory events after SARS-CoV-2 infection.

Heterotypic responses against nsp12/nsp13 from prior SARS-CoV-2 infection associates with lower subsequent endemic coronavirus incidence (preprint)

Immune responses from prior SARS-CoV-2 infection and COVID-19 vaccination do not prevent re-infections and may not protect against future novel coronaviruses (CoVs). We examined the incidence of and immune differences against human endemic CoVs (eCoV) as a proxy for response against future emerging CoVs. Assessment was among those with known SARS-CoV-2 infection, COVID-19 vaccination but no documented SARS-CoV-2 infection, or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not COVID-19 vaccination alone, protects against subsequent symptomatic eCoV infection. CD8+ T cell responses to the non-structural eCoV proteins, nsp12 and nsp13, were significantly higher in individuals with previous SARS-CoV-2 infection as compared to the other groups. The three groups had similar cellular responses against the eCoV spike and nucleocapsid, and those with prior spike exposure had lower eCoV-directed neutralizing antibodies. Incorporation of non-structural viral antigens in a future pan-CoV vaccine may improve protection against future heterologous CoV infections.