Associations between SARS-CoV-2 Infection or COVID-19 Vaccination and Human Milk Composition: A Multi-Omics Approach (preprint)

The risk of contracting SARS-CoV-2 via human milk-feeding is virtually non-existent. Adverse effects of COVID-19 vaccination for lactating individuals are not different from the general population, and no evidence has been found that their infants exhibit adverse effects. Yet, there remains substantial hesitation among this population globally regarding the safety of these vaccines. Herein we aimed to determine if compositional changes in milk occur following infection or vaccination, including any evidence of vaccine components. Using an extensive multi-omics approach, we found that compared to unvaccinated individuals SARS-CoV-2 infection was associated with significant compositional differences in 67 proteins, 385 lipids, and 13 metabolites. In contrast, COVID-19 vaccination was not associated with any changes in lipids or metabolites, although it was associated with changes in 13 or fewer proteins. Compositional changes in milk differed by vaccine. Changes following vaccination were greatest after 1-6 hours for the mRNA-based Moderna vaccine (8 changed proteins), 3 days for the mRNA-based Pfizer (4 changed proteins), and adenovirus-based Johnson and Johnson (13 changed proteins) vaccines. Proteins that changed after both natural infection and Johnson and Johnson vaccine were associated mainly with systemic inflammatory responses. In addition, no vaccine components were detected in any milk sample. Together, our data provide evidence of only minimal changes in milk composition due to COVID-19 vaccination, with much greater changes after natural SARS-CoV-2 infection.

Transforming Clinical Research to Meet Health Challenges.

This Viewpoint discusses specific areas of improvement in the National Institutes of Health's funding of and research criteria for clinical trials to be inclusive, transparent, and broad reaching.

Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections

The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics and correlative analysis of an immunologically naïve SARS-CoV-2 clinical cohort from blood plasma of uninfected controls, mild, and severe infections. Consistent with previous observations, severe patient populations showed an elevation of pulmonary surfactant levels. Intriguingly, mild patients showed a statistically significant elevation in the carnosine dipeptidase modifying enzyme (CNDP1). Mild and severe patient populations showed a strong elevation in the metabolite L-cystine (oxidized form of the amino acid cysteine) and enzymes with roles in glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both mild and severe populations, and NET formation was higher in severe vs. mild samples. Our correlative analysis suggests a potential protective role for CNDP1 in suppressing PSPB release from the pulmonary space whereas NET formation correlates with increased PSPB levels and disease severity. In our discussion we put forward a possible model where NET formation drives pulmonary occlusions and CNDP1 promotes antioxidation, pleiotropic immune responses, and vasodilation by accelerating histamine synthesis.

Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections.

The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics and correlative analysis of an immunologically naïve SARS-CoV-2 clinical cohort from blood plasma of uninfected controls, mild, and severe infections. Consistent with previous observations, severe patient populations showed an elevation of pulmonary surfactant levels. Intriguingly, mild patients showed a statistically significant elevation in the carnosine dipeptidase modifying enzyme (CNDP1). Mild and severe patient populations showed a strong elevation in the metabolite L-cystine (oxidized form of the amino acid cysteine) and enzymes with roles in glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both mild and severe populations, and NET formation was higher in severe vs. mild samples. Our correlative analysis suggests a potential protective role for CNDP1 in suppressing PSPB release from the pulmonary space whereas NET formation correlates with increased PSPB levels and disease severity. In our discussion we put forward a possible model where NET formation drives pulmonary occlusions and CNDP1 promotes antioxidation, pleiotropic immune responses, and vasodilation by accelerating histamine synthesis.

Longitudinal antibody response kinetics following SARS-CoV-2 messenger RNA vaccination in pregnant and nonpregnant persons.

BACKGROUND: For some vaccine-preventable diseases, the immunologic response to vaccination is altered by a pregnant state. The effect of pregnancy on SARS-CoV-2 vaccine response remains unclear. OBJECTIVE: We sought to characterize the peak and longitudinal anti-S immunoglobulin G, immunoglobulin M, and immunoglobulin A responses to messenger RNA-based SARS-CoV-2 vaccination in pregnant persons and compare them with those in nonpregnant, reproductive-aged persons. STUDY DESIGN: We conducted 2 parallel prospective cohort studies among pregnant and nonpregnant persons who received SARS-CoV-2 messenger RNA vaccinations. Blood was collected at the time of first and second vaccine doses, 2 weeks post second dosage, and with serial longitudinal follow-up up to 41.7 weeks post vaccination initiation. Anti-S immunoglobulin M, immunoglobulin G, and immunoglobulin A were analyzed by enzyme-linked immunosorbent assay. We excluded those with previous evidence of SARS-CoV-2 infection by history or presence of antinucleocapsid antibodies. In addition, for this study, we did not include individuals who received a third or booster vaccine dosage during the study period. We also excluded pregnant persons who were not fully vaccinated (14 days post receipt of the second vaccine dosage) by time of delivery and nonpregnant persons who became pregnant through the course of the study. We studied the effect of gestational age at vaccination on the anti-S response using Spearman correlation. We compared the peak anti-S antibody responses between pregnant and nonpregnant persons using a Mann-Whitney U test. We visualized and studied the longitudinal anti-S antibody response using locally weighted scatterplot smoothing, Mann-Whitney U test, and mixed analysis of variance test. RESULTS: Data from 53 pregnant and 21 nonpregnant persons were included in this analysis. The median (interquartile range) age of the pregnant and nonpregnant participants was 35.0 (33.3-37.8) years and 36.0 (33.0-41.0) years, respectively. Six (11.3%) participants initiated vaccination in the first trimester, 23 (43.3%) in the second trimester, and 24 (45.3%) in the third trimester, with a median gestational age at delivery of 39.6 (39.0-40.0) weeks. The median (interquartile range) follow-up time from vaccine initiation to the last blood sample collected was 25.9 (11.9) weeks and 28.9 (12.9) weeks in the pregnant and nonpregnant cohort, respectively. Among pregnant persons, anti-S immunoglobulin G, immunoglobulin A, and immunoglobulin M responses were not associated with gestational age at vaccine initiation (all P>.05). The anti-S immunoglobulin G response at 2 weeks post second dosage was not statistically different between pregnant and nonpregnant persons (P>.05). However, the anti-S immunoglobulin M and immunoglobulin A responses at 2 weeks post second dosage were significantly higher in nonpregnant persons (P<.001 for both). The anti-S immunoglobulin G and immunoglobulin M levels 6 to 8 months after vaccine initiation fell to comparable proportions of the peak 2 weeks post second dosage antibody levels between pregnant and nonpregnant persons (immunoglobulin G P=.77; immunoglobulin M P=.51). In contrast, immunoglobulin A levels 6 to 8 months after vaccine initiation fell to statistically significantly higher proportions of peak 2 weeks post second dosage antibody levels in pregnant compared with nonpregnant persons (P=.002). Maternal anti-S immunoglobulin G levels were strongly correlated with umbilical cord anti-S immunoglobulin G levels (R=0.8, P<.001). CONCLUSION: The anti-S immunoglobulin A, immunoglobulin M, and immunoglobulin G response to SARS-CoV-2 vaccination in pregnancy is independent of gestational age of vaccine initiation. Maintenance of the immunoglobulin G response is comparable between pregnant and nonpregnant persons. The differential peak response of immunoglobulin M and immunoglobulin A and the differential decline of anti-S immunoglobulin A between pregnant and nonpregnant persons requires further investigation.

Lost time: COVID-19 indemnity claim reporting and results in the Wisconsin workers' compensation system from March 12 to December 31, 2020.

BACKGROUND: The COVID-19 pandemic introduced a new compensable infectious disease to workplaces. METHODS: This was a descriptive analysis of Wisconsin COVID workers' compensation (WC) claims between March 12 and December 31, 2020. The impact of the presumption law (March 12 to June 10, 2020) was also evaluated. RESULTS: Less than 1% of working-age residents with COVID-19 filed a claim. COVID-19 WC claim rates (per 100,000 FTE) were notably low for frontline industry sectors such as Retail Trade (n = 115), Manufacturing (n = 88), and Wholesale Trade (n = 31). Healthcare workers (764 claims per 100,000 FTE) comprised 73.2% of COVID-19 claims. Most claims (52.8%) were denied and the proportion of denied claims increased significantly after the presumption period for both first responders and other occupations. CONCLUSION: The presumption law made benefits accessible primarily to first responders. Further changes to WC systems are needed to offset the individual and collective costs of infectious diseases.

SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8+ T-cells.

Efforts to cure HIV have focused on reactivating latent proviruses to enable elimination by CD8+ cytotoxic T-cells. Clinical studies of latency reversing agents (LRA) in antiretroviral therapy (ART)-treated individuals have shown increases in HIV transcription, but without reductions in virologic measures, or evidence that HIV-specific CD8+ T-cells were productively engaged. Here, we show that the SARS-CoV-2 mRNA vaccine BNT162b2 activates the RIG-I/TLR - TNF - NFκb axis, resulting in transcription of HIV proviruses with minimal perturbations of T-cell activation and host transcription. T-cells specific for the early gene-product HIV-Nef uniquely increased in frequency and acquired effector function (granzyme-B) in ART-treated individuals following SARS-CoV-2 mRNA vaccination. These parameters of CD8+ T-cell induction correlated with significant decreases in cell-associated HIV mRNA, suggesting killing or suppression of cells transcribing HIV. Thus, we report the observation of an intervention-induced reduction in a measure of HIV persistence, accompanied by precise immune correlates, in ART-suppressed individuals. However, we did not observe significant depletions of intact proviruses, underscoring challenges to achieving (or measuring) HIV reservoir reductions. Overall, our results support prioritizing the measurement of granzyme-B-producing Nef-specific responses in latency reversal studies and add impetus to developing HIV-targeted mRNA therapeutic vaccines that leverage built-in LRA activity.

Serious bradycardia and remdesivir for coronavirus 2019 (COVID-19): A new safety concern

Introduction: In recent clinical trials some cardiac arrhythmias were reported with use of remdesivir for COVID-19. To address this safety concern, we investigated whether use of remdesivir for COVID-19 is associated with an increased risk of bradycardia. Material and methods: Using VigiBase®, the World Health Organization Global Individual Case Safety Reports database, we compared the cases of bradycardia reported in COVID-19 patients exposed to remdesivir with those reported in COVID-19 patients exposed to hydroxychloroquine, lopinavir/ritonavir, tocilizumab or glucocorticoids. All reports of patients with COVID-19 registered up to the 23 September 2020 were included. We conducted disproportionality analyses allowing the estimation of reporting odds ratios (RORs) with 95% CI. Results: We found 302 cardiac effects including 94 bradycardia (31%) among the 2603 reports with remdesivir prescribed in COVID-19 patients. Most of the 94 reports were serious (75, 80%), and in 16 reports (17%) evolution was fatal. Compared with hydroxychloroquine, lopinavir/ritonavir, tocilizumab or glucocorticoids, the use of remdesivir was associated with an increased risk of reporting bradycardia (ROR 1.65;95% CI 1.23-2.22). Consistent results were observed in other sensitivity analyses. Discussion/Conclusion: This post-marketing study in a real-world setting suggests that the use of remdesivir is significantly associated with an increased risk of reporting bradycardia and serious bradycardia when compared with the use of with hydroxychloroquine, lopinavir/ritonavir, tocilizumab or glucocorticoids. This result is in line with the pharmacodynamic properties of remdesivir.

What gets resident physicians stressed and how would they prefer to be supported? A best-worst scaling study.

INTRODUCTION: Physician burnout has severe consequences on clinician well-being. Residents face numerous work-stressors that can contribute to burnout; however, given specialty variation in work-stress, it is difficult to identify systemic stressors and implement effective burnout interventions on an institutional level. Assessing resident preferences by specialty for common wellness interventions could also contribute to improved efficacy. METHODS: This cross-sectional study used best-worst scaling (BWS), a type of discrete choice modelling, to explore how 267 residents across nine specialties (anaesthesiology, emergency medicine, internal medicine, neurology, obstetrics and gynaecology, pathology, psychiatry, radiology and surgery) prioritised 16 work-stressors and 4 wellness interventions at a large academic medical centre during the COVID-19 pandemic (December 2020). RESULTS: Top-ranked stressors were work-life integration and electronic health record documentation. Therapy (63%, selected as 'would realistically consider intervention') and coaching (58%) were the most preferred wellness supports in comparison to group-based peer support (20%) and individual peer support (22%). Pathology, psychiatry and OBGYN specialties were most willing to consider all intervention options, with emergency medicine and internal medicine specialties least willing to consider intervention options. CONCLUSION: BWS can identify relative differences in surveyed stressors, allowing for the generation of specialty-specific stressor rankings and preferences for specific wellness interventions that can be used to drive institution-wide changes to improve clinician wellness. BWS surveys are a potential methodology for clinician wellness programmes to gather specific information on preferences to determine best practices for resident wellness.

Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection.

Mass spectrometry (MS)-based, integrated proteomics, metabolomics, and lipidomics (collectively, multi-omics) studies provide a very detailed snapshot of virus-induced changes to the host following infection and can lead to the identification of novel prophylactic and therapeutic targets for preventing or lessening disease severity. Multi-omics studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of biosafety level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins, and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of the three separate analytes, and their subsequent informatics pipelines.

Serious bradycardia and remdesivir for coronavirus 2019 (COVID-19): a new safety concerns

OBJECTIVES: In recent clinical trials some cardiac arrhythmias were reported with use of remdesivir for COVID-19. To address this safety concern, we investigated whether use of remdesivir for COVID-19 is associated with an increased risk of bradycardia. METHODS: Using VigiBase R, the World Health Organization Global Individual Case Safety Reports database, we compared the cases of bradycardia reported in COVID-19 patients exposed to remdesivir with those reported in COVID-19 patients exposed to hydroxychloroquine, lopinavir/ritonavir, tocilizumab or glucocorticoids. All reports of patients with COVID-19 registered up to the 23 September 2020 were included. We conducted disproportionality analyses allowing the estimation of reporting odds ratios (RORs) with 95% CI. RESULTS: We found 302 cardiac effects including 94 bradycardia (31%) among the 2603 reports with remdesivir prescribed in COVID-19 patients. Most of the 94 reports were serious (75, 80%), and in 16 reports (17%) evolution was fatal. Compared with hydroxychloroquine, lopinavir/ritonavir, tocilizumab or glucocorticoids, the use of remdesivir was associated with an increased risk of reporting bradycardia (ROR 1.65;95% CI 1.23-2.22). Consistent results were observed in other sensitivity analyses. DISCUSSION: This post-marketing study in a real-world setting suggests that the use of remdesivir is significantly associated with an increased risk of reporting bradycardia and serious bradycardia when compared with the use of with hydroxychloroquine, lopinavir/ritonavir, tocilizumab or glucocorticoids. This result is in line with the pharmacodynamic properties of remdesivir.

All Hands on Deck: Local Public Health Agencies Leveraging the Incident Command System During Crises.

The COVID-19 pandemic has stretched limited public health resources beyond measures, particularly at the local level. What started as an interesting report of pneumonia of unknown etiology in late December 2019 in Wuhan, China, bloomed into an international crisis by mid-January 2020. However, it was not until late January, when the first case was reported in the United States, that a new reality took shape for US public health agencies. After all, severe acute respiratory syndrome never made it to this country, and the only 2 cases of Middle East respiratory syndrome here were imported and never spread. Local public health agencies are notoriously short-staffed and underfunded. Therefore, when a crisis looms, personnel from a multitude of areas within the agencies are called upon to help out. Under its innovative and forward-thinking leadership, the St. Louis County Department of Health internally implemented the Incident Command System, a component of the National Incident Management System. While reassignment of individuals to new responsibilities under a new and temporary reporting structure did not always go perfectly, Incident Command System kept its promise to be adaptable to a fast-evolving situation, to clearly outline needed areas of responsibility, and to provide scaffolding that kept the Department of Health functional in chaotic times. It was able to be implemented quickly within hours of the first confirmed COVID-19 case in St. Louis County and enhanced the quality and timeliness of the public health response. This experience is being shared to provide a model of how organizations with limited personnel can use the Incident Command System to reorganize and meet unexpected challenges with increased success.

Validity of In-Home Teleneuropsychological Testing in the Wake of COVID-19.

OBJECTIVE: Teleneuropsychology (TNP) has been shown to be a valid assessment method compared with in-person neuropsychological evaluations. Interest in delivering TNP directly to patients' homes has arisen in response to the coronavirus disease 2019 (COVID-19) pandemic. However, prior research has typically involved patients tested in clinical settings, and the validity of in-home TNP testing has not yet been established. The present study aims to explore the validity and clinical utility of in-home TNP testing in a mixed clinical sample in the wake of COVID-19. METHODS: Test profiles for 111 in-home TNP patients were retrospectively compared with 120 patients who completed in-person evaluations. The TNP test battery consisted of tests measuring attention/processing speed, verbal memory, naming, verbal fluency, and visuoconstruction. TNP scores of cognitively normal (CN) patients were compared with patients with neurocognitive disorders (NCD), and score profiles were examined among suspected diagnostic groups of Alzheimer's disease (AD), Parkinson's disease (PD), and vascular disease (VaD). RESULTS: TNP test scores did not significantly differ from in-person testing across all tests except the Hopkins Verbal Learning Test-Revised Discrimination Index. Within the TNP group, significant differences between the CN and NCD groups were found for all tests, and the memory and semantic fluency tests yielded large effect sizes (d ≥ 0.8). Score profiles among the AD, PD, and VaD groups were explored. CONCLUSIONS: These findings support the validity of in-home TNP testing compared with in-person neuropsychological testing. Practice considerations, limitations, and future directions are discussed.

COVID-19 in Hospitalized Adults With HIV.

BACKGROUND: The spread of SARS-CoV-2 and the COVID-19 pandemic have caused significant morbidity and mortality worldwide. The clinical characteristics and outcomes of hospitalized patients with SARS-CoV-2 and HIV co-infection remain uncertain. METHODS: We conducted a matched retrospective cohort study of adults hospitalized with a COVID-19 illness in New York City between March 3, 2020, and May 15, 2020. We matched 30 people with HIV (PWH) with 90 control group patients without HIV based on age, sex, and race/ethnicity. Using electronic health record data, we compared demographic characteristics, clinical characteristics, and clinical outcomes between PWH and control patients. RESULTS: In our study, the median age (interquartile range) was 60.5 (56.6-70.0) years, 20% were female, 30% were black, 27% were white, and 24% were of Hispanic/Latino/ethnicity. There were no significant differences between PWH and control patients in presenting symptoms, duration of symptoms before hospitalization, laboratory markers, or radiographic findings on chest x-ray. More patients without HIV required a higher level of supplemental oxygen on presentation than PWH. There were no differences in the need for invasive mechanical ventilation during hospitalization, length of stay, or in-hospital mortality. CONCLUSIONS: The clinical manifestations and outcomes of COVID-19 among patients with SARS-CoV-2 and HIV co-infection were not significantly different than patients without HIV co-infection. However, PWH were hospitalized with less severe hypoxemia, a finding that warrants further investigation.

Heart disease mortality during the early pandemic period in the United States. (preprint)

Importance: The coronavirus disease 2019 (COVID-19) outbreak has been associated with decreases in acute myocardial infarction diagnoses (AMI) and admissions in the United States. Whether this affected heart disease deaths is unknown. Objective: To determine whether changes in heart disease deaths occurred during the early pandemic period in the US, we analyzed areas without large COVID-19 outbreaks. This isolated the effect of decreased healthcare-seeking behavior during the early outbreak. Design, Setting, and Participants: We performed an observational study of heart disease-specific mortality using National Center for Health Statistics data (NCHS). Weekly provisional counts were disaggregated by jurisdiction of occurrence during 2019 and 2020 for all-cause deaths, COVID-19 deaths, and heart disease deaths. For the primary analysis, jurisdictions were included if; 1) There was no all-cause excess mortality during the early pandemic period (weeks 14-17, 2020); 2) The completeness of that data was estimated by NCHS to be >97% as of July 22, 2020, and; 3) Decreases in emergency department (ED) visits occurred during the study period. We compared heart disease death rates during the early pandemic period with corresponding weeks in 2019 and a pre-pandemic control period of 2020 as a sensitivity analysis. Incident rate and rate ratios were calculated. Exposure: The US COVID-19 outbreak. Main Outcomes and Measures: Incidence of heart disease deaths. Results: Twelve states met the primary inclusion criteria, capturing 747,375,188 person-weeks for the early pandemic period and 740,987,984 person-weeks for the 2019 control period. The mean incidence rate (per 100,000 person-weeks) for heart disease in states without excess deaths during the early pandemic period was 3.95 (95% CI 3.83 to 4.06) versus 4.19 (95% CI 4.14 to 4.23) during the corresponding period in 2019. The incident rate ratio (2020/2019) was 0.91 (95% CI 0.87 to 0.97). No state recorded an increase from either the corresponding period in 2019 or the 2020 pre-pandemic control period. Two states recorded fewer heart disease deaths. Conclusions and Relevance: This observational study found a decrease in heart disease deaths during the early US outbreak in regions without significant COVID-19 burdens, despite decreases in ED utilization. Long term follow-up data are needed.