SARS-COV-2 induces blood-brain barrier and choroid plexus barrier impairments and vascular inflammation in mice (preprint)

The coronavirus disease of 2019 (COVID-19) pandemic that has led to more than 700 million confirmed cases and near 7 million deaths. Although Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus mainly infects the respiratory system, neurological complications are widely reported in both acute infection and long-COVID cases. Despite the success of vaccines and antiviral treatments, neuroinvasiveness of SARS-CoV-2 remains as an important question, which is also centered on the mystery whether the virus is capable of breaching the barriers into the central nervous system. By studying the K18-hACE2 infection model, we observed clear evidence of microvascular damage and breakdown of the blood-brain barrier (BBB). Mechanistically, SARS-CoV-2 infection caused pericyte damage, tight junction loss, endothelial activation and vascular inflammation, which together drive microvascular injury and BBB impairment. In addition, the blood-cerebrospinal fluid barrier at the choroid plexus was also impaired after infection. Therefore, cerebrovascular and choroid plexus dysfunctions are important aspects of COVID-19 and may contribute to the neurological complications both acutely and in long COVID.

Epigenetic Memory of COVID-19 in Innate Immune Cells and Their Progenitors (preprint)

Severe coronavirus disease 2019 (COVID-19) is characterized by systemic inflammation and can result in protracted symptoms. Robust systemic inflammation may trigger persistent changes in hematopoietic cells and innate immune memory through epigenetic mechanisms. We reveal that rare circulating hematopoietic stem and progenitor cells (HSPC), enriched from human blood, match the diversity of HSPC in bone marrow, enabling investigation of hematopoiesis and HSPC epigenomics. Following COVID-19, HSPC retain epigenomic alterations that are conveyed, through differentiation, to progeny innate immune cells. Epigenomic changes vary with disease severity, persist for months to a year, and are associated with increased myeloid cell differentiation and inflammatory or antiviral programs. Epigenetic reprogramming of HSPC may underly altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.

Immunogenicity of COVID-19 mRNA Vaccines in Patients with Acute Myeloid Leukemia and Myelodysplastic Syndrome (preprint)

Immunocompromised patients are particularly susceptible to serious complications from infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Two mRNA vaccines, BNT162b2 and mRNA-1273, have been shown to have excellent clinical efficacy in immunocompetent adults, but diminished activity in immunocompromised patients. In this study, we measured anti-spike SARS-CoV-2 antibody response, avidity, and surrogate neutralizing antibody activity in Coronavirus Disease 2019 (COVID-19) vaccinated patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Anti-spike SARS-CoV-2 antibody was present in 89% of AML and 88% of MDS patients, but median antibody levels for were lower than in healthy controls (p=0.001 and p=0.04, respectively). SARS-CoV-2 antibody avidity and neutralizing antibody activity from AML patients were significantly lower than controls (p=0.028 and p=0.002, respectively). There was a trend toward higher anti-spike SARS-CoV-2 antibody levels after mRNA-1273 vaccination. Antibody avidity was greater in patients after mRNA-1273 versus BNT162b2 (p=0.01) and there was a trend toward greater neutralizing antibody activity after mRNA-1273 versus BNT162b2 vaccination.

Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery (preprint)

Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoM{phi}). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.

A Machine Learning Model Incorporating Laboratory Blood Tests Discriminates Between SARS-CoV-2 and Influenza Infections at Emergency Department Visit (preprint)

Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus are contagious respiratory pathogens with similar symptoms but require different treatment and management strategies. This study investigated whether laboratory blood tests can discriminate between SARS-CoV-2 and influenza infections at emergency department (ED) presentation. Methods 723 influenza A/B positive (2018/1/1 to 2020/3/15) and 1,281 SARS-CoV-2 positive (2020/3/11 to 2020/6/30) ED patients were retrospectively analyzed. Laboratory test results completed within 48 hours prior to reporting of virus RT-PCR results, as well as patient demographics were included to train and validate a random forest (RF) model. The dataset was randomly divided into training (2/3) and testing (1/3) sets with the same SARS-CoV-2/influenza ratio. The Shapley Additive Explanations technique was employed to visualize the impact of each laboratory test on the differentiation. Results The RF model incorporating results from 15 laboratory tests and demographic characteristics discriminated SARS-CoV-2 and influenza infections, with an area under the ROC curve value 0.90 in the independent testing set. The overall agreement with the RT-PCR results was 83% (95% CI: 80-86%). The test with the greatest impact on the differentiation was serum total calcium level. Further, the model achieved an AUC of 0.82 in a new dataset including 519 SARS-CoV-2 ED patients (2020/12/1 to 2021/2/28) and the previous 723 influenza positive patients. Serum calcium level remained the most impactful feature on the differentiation. Conclusion We identified characteristic laboratory test profiles differentiating SARS-CoV-2 and influenza infections, which may be useful for the preparedness of overlapping COVID-19 resurgence and future seasonal influenza.

More rapid, robust and sustainable antibody responses to mRNA COVID-19 vaccine in convalescent COVID-19 individuals (preprint)

Longitudinal studies are needed to evaluate the SARS-CoV-2 mRNA vaccine antibody response under "real-world" conditions. This longitudinal study investigated the quantity and quality of SARS-CoV-2 antibody response in 846 specimens from 350 subjects: comparing BNT162b2-vaccinated individuals (19 previously diagnosed with COVID-19 [RecoVax]; 49 never been diagnosed [NaiveVax]) to 122 hospitalized unvaccinated (HospNoVax) and 160 outpatient unvaccinated (OutPtNoVax) COVID-19 patients. NaiveVax experienced a delay in generating SARS-CoV-2 total antibody levels (TAb) and neutralizing antibodies (SNAb) after the 1st vaccine dose (D1), but a rapid increase in antibody levels was observed after the 2nd dose (D2). However, these never reached the robust levels observed in RecoVax. In fact, NaiveVax TAb and SNAb levels decreased 4-weeks post-D2 (p=0.003;p<0.001). For the most part, RecoVax TAb persisted throughout this study, after reaching maximal levels 2-weeks post-D2; but SNAb decreased significantly [~]6-months post-D1 (p=0.002). Although NaiveVax avidity lagged behind that of RecoVax for most of the follow-up periods, NaiveVax did reach similar avidity by [~]6-months post-D1. These data suggest that one vaccine dose elicits maximal antibody response in RecoVax and may be sufficient. Also, despite decreasing levels in TAb and SNAb overtime, long-term avidity maybe a measure worth evaluating and possibly correlating to vaccine efficacy.

SARS-CoV-2 Antibody Response in Patients Undergoing Kidney Transplantation (preprint)

Abstract The response of the immune system to COVID-19 in end stage kidney disease patients who undergo kidney transplantation has yet to be described. We report data on 72 patients who underwent SARS-CoV-2 antibody testing both before and after kidney transplantation and were followed for a median of 186 days (range 83, 277). Of the 25 patients with a positive antibody test at the time of transplant, 17 (68%) remained positive after transplantation. Patients were significantly more likely to have a persistently positive test if they reported a symptomatic COVID-19 infection prior to transplant (p=0.01). SARS-CoV-2 IgG index values were measured in a subset of kidney transplant recipients and compared to wait -listed dialysis patients. These assays demonstrated a more significant decline in IgG (58% versus 14% p = 0.008) in transplant recipients when compared to dialysis patients tested during the same time period. Additional analysis of the quality of the immune response measuring the binding of SARS-CoV-2 antibodies to the receptor-binding domain (RBD binding), the antibody neutralizing capability, and the antibody avidity demonstrated a more pronounced effect when comparing pre-transplant values to post-induction therapy/post transplant values. The attenuated IgG response seen in transplant patients compared to dialysis patients after induction therapy requires further study. These data have important implications for post-transplant management of vaccinated dialysis patients.

Serologic Response to mRNA COVID-19 Vaccination in Lymphoma Patients (preprint)

Currently available COVID-19 mRNA vaccines have demonstrated high efficacy in clinical trials.1-3 However, cancer patients, including those with hematological malignancies, were largely excluded from these trials. In this prospective, observational study we measured anti-S protein IgG titers as well as avidity in lymphoma patients (n=67) vaccinated with a COVID-19 mRNA vaccine. Serological response rates in lymphoma patients who were treatment naïve (100% in CLL, 88.9% in other, non-CLL non-Hodgkin lymphoma patients), or who were last treated more than 24 months prior to vaccination (100% in CLL, 90% in other-NHL), were similar to healthy controls (100%). Patients on active therapy, however, had a diminished response rate (40% in CLL, 21.0% in other-NHL). No patient who received anti-CD20 monoclonal antibodies (mAb) within six months of vaccination responded. Thus, the utility of testing anti-S titers should be explored in patients on active therapy or with recent anti-CD20 mAb exposure, to assess their response to vaccination. We also propose studying passive protection with S-protein mAbs as an alternative prophylactic strategy for patients who respond poorly to vaccination.

Integrative Metabolomic and Proteomic Signatures Define Clinical Outcomes in Severe COVID-19 (preprint)

The novel coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has ravaged global healthcare with previously unseen levels of morbidity and mortality. To date, methods to predict the clinical course, which ranges from the asymptomatic carrier to the critically ill patient in devastating multi-system organ failure, have yet to be identified. In this study, we performed large-scale integrative multi-omics analyses of serum obtained from COVID-19 patients with the goal of uncovering novel pathogenic complexities of this disease and identifying molecular signatures that predict clinical outcomes. We assembled a novel network of protein-metabolite interactions in COVID-19 patients through targeted metabolomic and proteomic profiling of serum samples in 330 COVID-19 patients compared to 97 non-COVID, hospitalized controls. Our network identified distinct protein-metabolite cross talk related to immune modulation, energy and nucleotide metabolism, vascular homeostasis, and collagen catabolism. Additionally, our data linked multiple proteins and metabolites to clinical indices associated with long-term mortality and morbidity, such as acute kidney injury. Finally, we developed a novel composite outcome measure for COVID-19 disease severity and created a clinical prediction model based on the metabolomics data. The model predicts severe disease with a concordance index of around 0.69, and furthermore shows high predictive power of 0.83-0.93 in two previously published, independent datasets.

COVID-19 Serology in New York State Using a Multiplex Microsphere Immunoassay (preprint)

The emergence of SARS-CoV-2, leading to COVID-19, necessitated the development of new molecular and serological tests. Here, we describe a multiplexed serological assay developed as the global pandemic moved into New York State in the spring of 2020. The original microsphere immunoassay used a target antigen from the SARS-CoV-1 virus responsible for the 2003 SARS outbreak, but evolved to incorporate multiple SARS-CoV-2 protein antigens (nucleocapsid, spike and spike domains, spike and nucleocapsid proteins from seasonal human coronaviruses). Besides being highly versatile due to multiplex capabilities, the assay was highly specific and sensitive and adaptable to measuring both total antibodies and antibody isotypes. While determining the assay performance characteristics, we were able to identify antibody production patterns (e.g., kinetics of isotypes, individual variations) for total antibodies and individual antibody classes. Overall, the results provide insights into the laboratory response to new serology needs, and how the evolution and fine-tuning of a serology assay helped contribute to a better understanding of the antibody response to SARS-CoV-2.

Naturally enhanced neutralizing breadth to SARS-CoV-2 after one year (preprint)

Over one year after its inception, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several excellent vaccines. Progress in controlling the pandemic is slowed by the emergence of variants that appear to be more transmissible and more resistant to antibodies 1,2 . Here we report on a cohort of 63 COVID-19-convalescent individuals assessed at 1.3, 6.2 and 12 months after infection, 41% of whom also received mRNA vaccines 3,4 . In the absence of vaccination antibody reactivity to the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number of RBD-specific memory B cells remain relatively stable from 6 to 12 months. Vaccination increases all components of the humoral response, and as expected, results in serum neutralizing activities against variants of concern that are comparable to or greater than neutralizing activity against the original Wuhan Hu-1 achieved by vaccination of naïve individuals 2,5-8 . The mechanism underlying these broad-based responses involves ongoing antibody somatic mutation, memory B cell clonal turnover, and development of monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations, including those found in variants of concern 4,9 . In addition, B cell clones expressing broad and potent antibodies are selectively retained in the repertoire over time and expand dramatically after vaccination. The data suggest that immunity in convalescent individuals will be very long lasting and that convalescent individuals who receive available mRNA vaccines will produce antibodies and memory B cells that should be protective against circulating SARS-CoV-2 variants.

Simulation Prediction and Control Strategy of COVID-19 Dynamic Contact Network in USA and Various States -- Based on Effective Regeneration Number and Improved Discrete SEIQDHR Model

Purpose: Based on the latest characteristics of the transmission mechanism of the COVID-19 epidemic in the United States, this article improves the classic dynamics model of the spread of infectious diseases, simulates and predicts the future trend of the COVID-19 epidemic in the United States and various states. According to the computer program of COVID-19 dynamic contact network, the results provide effective control strategies for the future epidemic prevention work of the United States. Method: The SEIR model is improved by the latest effective reproduction number of the COVID-19 epidemic in the United States, and an improved discrete SEIQDHR model is established for the spread of the COVID-19 epidemic in the United States and various states. MATLAB software is used to perform least square fitting of key parameters, and the computer simulation process of COVID-19 dynamic contact network is solved dynamically. Results: The improved discrete SEIQDHR model is reliable in the analysis of the spread of infectious diseases. The model well simulates the current dynamic contact network of the COVID-19 epidemic in the United States. The results of computer program show that mid-to-late November 2020 is the period with the largest number of new diagnoses before the end of the epidemic in the United States. In a long period of time in the future, the cumulative number of confirmed cases in the United States and states will continue to show a clear upward trend. The cumulative number of confirmed cases of the COVID-19 epidemic in the United States will reach its peak in early December 2021, which is about 37.11 million;the cumulative number of confirmed cases in Texas will reach its peak on March 15, 2021, about 3.21 million. Controlling the source of infection, blocking the route of transmission and strengthening the tracking and isolation are still effective measures to prevent and control the epidemic.

Antibody response to SARS-CoV-2 mRNA vaccines in pregnant women and their neonates (preprint)

Pregnant women were excluded from initial clinical trials for COVID-19 vaccines1-2, thus the immunologic response to vaccination in pregnancy and the transplacental transfer of maternal antibodies are just beginning to be studied4-5. Methods: Between January 28 and March 31, 2021, we studied 122 pregnant women and their neonates at time of birth. All women had received one or both doses of a messenger RNA (mRNA)-based COVID-19 vaccine. Fifty-five women received only one dose of the vaccine and 67 women received both doses of the vaccine by time of giving birth. Eighty-five women received the Pfizer-BioNTech vaccine, while 37 women received the Moderna vaccine. All women tested negative for SARS-CoV-2 infection using reverse-transcriptase PCR on nasopharyngeal swabs, and none reported any COVID-19 symptoms at the time of admission for birth. Semi-quantitative testing for antibodies against S-Receptor Binding Domain (RBD) (ET HealthCare)3 was performed on sera of maternal peripheral blood and neonatal cord blood at the time of delivery to identify antibodies mounted against the vaccine. All women tested negative for antibodies against the Nucleocapsid Protein (NP) antigen (Roche Diagnostics EUA) to ensure that the antibodies detected were not produced in response to past SARS-CoV-2 infection. Relationship between IgG antibody levels over time was studied using ANOVA with Tukey posthoc. Relationship between maternal and neonatal IgG levels was studied using Pearson correlation analysis and linear regression on log2-scaled serological values. Relationship between IgG placental transfer ratio (neonatal/maternal) vs. time was studied using Pearson correlation analysis and linear regression on log2-scaled serological values and days. Serology levels represented as log2+1. Statistical analysis was performed using R 3.6.3, RStudio 1.1.463. The study was approved by the Weill Cornell Medicine institutional review board. Results: Pregnant women vaccinated with mRNA-based COVID-19 vaccines during pregnancy and tested at time of birth had detectable immunoglobulin (Ig)G and IgM response. Eighty-seven women tested at birth produced only an IgG response, and 19 women produced both an IgM and IgG response. Sixteen women tested at birth had no detectable antibody response, and they were all within four weeks after vaccination dose 1 (Figure 1A). There was an increase over time in the number of women that mounted an antibody response, as well as the number of women that demonstrated passive immunity to their neonates (Figure 1A). All women and their neonates, except for one neonate, had detectable IgG antibodies by 4 weeks after maternal first dose of vaccination (Figure 1A). 43.6% (24/55) of neonates born to women that received only one vaccine dose had detectable IgG, while 98.5% (65/67) of neonates born to women that received both vaccine doses had detectable IgG. The IgG levels in pregnant women increased weekly from two weeks after first vaccine dose (p=0.0047;0.019), as well as between the first and second weeks after the second vaccine dose (p=2e-07) (Figure 1B). Maternal IgG levels were linearly associated with neonatal IgG levels (R=0.89, p<2.2e-16) (Figure 2A). Placental transfer ratio correlated with the weeks that elapsed since maternal second dose of vaccine (R=0.8, p=2.6e-15) (Figure 2B). Discussion: mRNA-based COVID-19 vaccines in pregnant women lead to maternal antibody production as early as 5 days after the first vaccination dose, and passive immunity to the neonate as early as 16 days after the first vaccination dose. The increasing levels of maternal IgG over time, and the increasing placental IgG transfer ratio over time suggest that timing between vaccination and birth may be an important factor to consider in the vaccination strategies of pregnant women. Further studies are needed to understand the factors that influence transplacental transfer of IgG antibody, as well as the protective nature of these antibodies.

Antibody responses to SARS-CoV-2 mRNA vaccines are detectable in saliva (preprint)

Vaccines are critical for curtailing the COVID-19 pandemic. In the USA, two highly protective mRNA vaccines are available: BNT162b2 from Pfizer/BioNTech and mRNA-1273 from Moderna. These vaccines induce antibodies to the SARS-CoV-2 S-protein, including neutralizing antibodies (NAbs) predominantly directed against the Receptor Binding Domain (RBD). Serum NAbs are induced at modest levels within ~1 week of the first dose, but their titers are strongly boosted by a second dose at 3 (BNT162b2) or 4 weeks (mRNA-1273). SARS-CoV-2 is most commonly transmitted nasally or orally and infects cells in the mucosae of the respiratory and to some extent also the gastrointestinal tract. Although serum NAbs may be a correlate of protection against COVID-19, mucosal antibodies might directly prevent or limit virus acquisition by the nasal, oral and conjunctival routes. Whether the mRNA vaccines induce mucosal immunity has not been studied. Here, we report that antibodies to the S-protein and its RBD are present in saliva samples from mRNA-vaccinated healthcare workers (HCW). Within 1-2 weeks after their second dose, 37/37 and 8/8 recipients of the Pfizer and Moderna vaccines, respectively, had S-protein IgG antibodies in their saliva, while IgA was detected in a substantial proportion. These observations may be relevant to vaccine-mediated protection from SARS-CoV-2 infection and disease.

TOP-Plus is a Versatile Biosensor Platform for Monitoring SARS-CoV-2 Antibody Durability (preprint)

BackgroundThere is a concern that low initial SARS-CoV-2 antibody titers in individuals may drop to undetectable levels within months after infection. Although this may raise concerns over long term immunity, both the antibody levels and avidity of the antibody-antigen interaction should be examined to understand the quality of the antibody response. MethodsA testing-on-a-probe "plus" panel (TOP-Plus) was developed, which included a newly developed avidity assay built into the previously described SARS-CoV-2 TOP assays that measured total antibody (TAb), surrogate neutralizing antibody (SNAb), IgM and IgG on a versatile biosensor platform. TAb and SNAb levels were compared with avidity in previously infected individuals at 1.3 and 6.2 months post-infection in paired samples from 80 COVID-19 patients. ResultsThe newly designed avidity assay in this TOP panel correlated well with a reference Bio-Layer Interferometry avidity assay (R=0.88). The imprecision of the TOP avidity assay was less than 9%. Although TAb and neutralization activity (by SNAb) decreased between 1.3 and 6.2 months post infection, the antibody avidity increased significantly (P < 0.0001). ConclusionThis highly precise and versatile TOP-Plus panel with the ability to measure SARS-CoV-2 TAb, SNAb, IgG and IgM antibody levels and avidity of individual sera on one sensor can become a valuable asset in monitoring not only SARS-CoV-2-infected patients, but also the status of individuals COVID-19 vaccination response.

Whole Genome Sequencing for Revealing the Point Mutations of SARS-CoV-2 Genome in Bangladeshi Isolates and their Structural Effects on Viral Proteins (preprint)

Coronavirus disease-19 (COVID-19) is the recent global pandemic caused by the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The virus has already killed more than one million people worldwide and billions are at risk of getting infected. As of now, there is neither any drug nor any vaccine in sight with conclusive scientific evidence that it can cure or provide protection against the illness. Since novel coronavirus is a new virus, mining its genome sequence is of crucial importance for drug/vaccine(s) development. Whole genome sequencing is a helpful tool in identifying genetic changes that occur in a virus when it spreads through the population. In this study, we performed complete genome sequencing of SARS-CoV-2 to unveil the genomic variation and indel, if present. We discovered thirteen (13) mutations in Orf1ab, S and N gene where seven (7) of them turned out to be novel mutations from our sequenced isolate. Besides, we found one (1) insertion and seven (7) deletions from the indel analysis among the 323 Bangladeshi isolates. However, the indel did not show any effect on proteins. Our energy minimization analysis showed both stabilizing and destabilizing impact on viral proteins depending on the mutation. Interestingly, all the variants were located in the binding site of the proteins. Furthermore, drug binding analysis revealed marked difference in interacting residues in mutants when compared to the wild type. Our analysis also suggested that eleven (11) mutations could exert damaging effects on their corresponding protein structures. The analysis of SARS-CoV-2 genetic variation and their impacts presented in this study might be helpful in gaining a better understanding of the pathogenesis of this deadly virus.

Machine learning analysis highlights the down-trending of the proportion of COVID-19 patients with a distinct laboratory result profile (preprint)

BackgroundNew York City (NYC) experienced an initial surge and gradual decline in the number of SARS-CoV-2 confirmed cases in 2020. A change in the pattern of laboratory test results in COVID-19 patients over this time has not been reported or correlated with patient outcome. MethodsWe performed a retrospective study of routine laboratory and SARS-CoV-2 RT-PCR test results from 5,785 patients evaluated in a NYC hospital emergency department from March to June employing machine learning analysis. ResultsA COVID-19 high-risk laboratory test result profile (COVID19-HRP), consisting of 21 routine blood tests, was identified to characterize the SARS-CoV-2 patients. Approximately half of the SARS-CoV-2 positive patients had the distinct COVID19-HRP that separated them from SARS-CoV-2 negative patients. SARS-CoV-2 patients with the COVID19-HRP had higher SARS-CoV-2 viral loads, determined by cycle-threshold values from the RT-PCR, and poorer clinical outcome compared to other positive patients without COVID19-HRP. Furthermore, the percentage of SARS-CoV-2 patients with the COVID19-HRP has significantly decreased from March/April to May/June. Notably, viral load in the SARS-CoV-2 patients declined and their laboratory profile became less distinguishable from SARS-CoV-2 negative patients in the later phase. ConclusionsOur study visualized the down-trending of the proportion of SARS-CoV-2 patients with the distinct COVID19-HRP. This analysis could become an important tool in COVID-19 population disease severity tracking and prediction. In addition, this analysis may play an important role in prioritizing high-risk patients, assisting in patient triaging and optimizing the usage of resources.

Cytokine Signatures of End Organ Injury in COVID-19 (preprint)

Increasing evidence has shown that Coronavirus disease 19 (COVID-19) severity is driven by a dysregulated immunologic response. We aimed to assess the differences in inflammatory cytokines in COVID-19 patients compared to contemporaneously hospitalized controls and then analyze the relationship between these cytokines and the development of Acute Respiratory Distress Syndrome (ARDS), Acute Kidney Injury (AKI) and mortality. In this cohort study of hospitalized patients, done between March third, 2020 and April first, 2020 at a quaternary referral center in New York City we included adult hospitalized patients with COVID-19 and negative controls. Serum specimens were obtained on the first, second, and third hospital day and cytokines were measured by Luminex. Autopsies of nine cohort patients were examined. We identified 90 COVID-19 patients and 51 controls. Analysis of 48 inflammatory cytokines revealed upregulation of macrophage induced chemokines, T-cell related interleukines and stromal cell producing cytokines in COVID-19 patients compared to the controls. Moreover, distinctive cytokine signatures predicted the development of ARDS, AKI and mortality in COVID-19 patients. Specifically, macrophage-associated cytokines predicted ARDS , T cell immunity related cytokines predicted AKI and mortality was  was associated with cytokines of activated immune pathways, of which IL-13 was universally correlated with ARDS, AKI and mortality. Histopathological examination of the autopsies showed diffuse alveolar damage with significant mononuclear inflammatory cell infiltration. Additionally, the kidneys demonstrated glomerular sclerosis, tubulointerstitial lymphocyte infiltration and cortical and medullary atrophy. These patterns of cytokine expression offer insight into the pathogenesis of COVID-19 disease, its severity, and subsequent lung and kidney injury suggesting more targeted treatment strategies. 

Testing-on-a-probe biosensors reveal association of early SARS-CoV-2 total antibodies and surrogate neutralizing antibodies with mortality in COVID-19 patients (preprint)

The association of mortality with early humoral response to SARS-CoV-2 infection within the first few days after onset of symptoms (DAOS) has not been thoroughly investigated partly due to a lack of sufficiently sensitive antibody testing methods. Here we report two sensitive and automated testing-on-a-probe (TOP) biosensor assays for SARS-CoV-2 viral specific total antibodies (TAb) and surrogate neutralizing antibodies (SNAb), which are suitable for clinical use. The TOP assays employ an RBD-coated quartz probe using a Cy5-Streptavidin-polysacharide conjugate to improved sensitivity and minimize interference. Disposable cartridge containing pre-dispensed reagents requires no liquid manipulation or fluidics during testing. The TOP-TAb assay exhibited higher sensitivity in the 0-7 DAOS window than a widely used FDA-EUA assay. The rapid (18 min) and automated TOP-SNAb correlated well with two well-established SARS-CoV-2 virus neutralization tests. The clinical utility of the TOP assays was demonstrated by evaluating early antibody responses in 120 SARS-CoV-2 RT-PCR positive adult hospitalized patients. Higher baseline TAb and SNAb positivity rates and more robust antibody responses were seen in patients who survived COVID-19 than those who died in the hospital. Survival analysis using the Cox Proportional Hazards Model showed that patients who were TAb and SNAb negative at initial hospital presentation were at a higher risk of in-hospital mortality. Furthermore, TAb and SNAb levels at presentation were inversely associated with SARS-CoV-2 viral load based on concurrent RT-PCR testing. Overall, the sensitive and automated TAb and SNAb assays allow detection of early SARS-CoV-2 antibodies which associate with mortality.