Evidence of a Sjogrens disease-like phenotype following COVID-19 (preprint)

Objectives: Sjogrens Disease (SjD) is a chronic and systemic autoimmune disease characterized by lymphocytic infiltration and the development of dry eyes and dry mouth resulting from the secretory dysfunction of the exocrine glands. SARS-CoV-2 may trigger the development or progression of autoimmune diseases, as evidenced by increased autoantibodies in patients and the presentation of cardinal symptoms of SjD. The objective of the study was to determine whether SARS-CoV-2 induces the signature clinical symptoms of SjD. Methods: The ACE2-transgenic mice were infected with SARS-CoV-2. SJD profiling was conducted. COVID-19 patient sera were examined for autoantibodies. Clinical evaluations of convalescent COVID-19 subjects, including minor salivary gland (MSG) biopsies, were collected. Lastly, monoclonal antibodies generated from single B cells of patients were interrogated for ACE2/spike inhibition and nuclear antigens. Results: Mice infected with the virus showed a decreased saliva flow rate, elevated antinuclear antibodies (ANAs) with anti-SSB/La, and lymphocyte infiltration in the lacrimal and salivary glands. Sera of COVID-19 patients showed an increase in ANA, anti-SSA/Ro52, and anti-SSB/La. The male patients showed elevated levels of anti-SSA/Ro52 compared to female patients, and female patients had more diverse ANA patterns. Minor salivary gland biopsies of convalescent COVID-19 subjects showed focal lymphocytic infiltrates in four of six subjects, and 2 of 6 subjects had focus scores >2. Lastly, we found monoclonal antibodies produced in recovered patients can both block ACE2/spike interaction and recognize nuclear antigens. Conclusion: Overall, our study shows a direct association between SARS-CoV-2 and SjD. Hallmark features of SjD salivary glands were histologically indistinguishable from convalescent COVID-19 subjects. The results potentially implicate that SARS-CoV-2 could be an environmental trigger for SjD.

Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population (preprint)

COVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. The widespread clinical symptoms encompass a large group of asymptomatic COVID-19 patients, raising a crucial question regarding genetic susceptibility, e.g., whether individual differences in immunity play a role in patient symptomatology and how much human leukocyte antigen (HLA) contributes to this. To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. We identified two loci on chromosomes 5q32 and 11p12, which reach the significance threshold of suggestive association (p<1x10-5 threshold adjusted for multiple trait testing) and are associated with the COVID-19 susceptibility in the European ancestry (index rs17448496: odds ratio [OR] = 0.173; 95% confidence interval [CI], 0.08-0.36 for G allele; p=5.15x 10-5 and index rs768632395: OR = 0.166; 95% CI, 0.07-0.35 for A allele; p= 4.25x10-6, respectively), which were associated with two genes, PPP2R2B at 5q32, and LRRC4C at 11p12, respectively. To explore the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases. Using In-silico binding predictions to map the binding of risk/protective HLA to the viral structural proteins, we found the differential presentation of viral peptides in both ancestries. Lastly, extrapolation of the identified HLA from the cohort to the worldwide population revealed notable correlations. The study uncovers possible differences in susceptibility to COVID-19 in different ancestral origins in the genetic background, which may provide new insights into the pathogenesis and clinical treatment of the disease.

Identification of risk and protective human leukocyte antigens in COVID-19 using genotyping and structural modeling (preprint)

COVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. Since innate and adaptive immune responses are elicited in COVID-19 patients, we genotyped 94 Florida patients with confirmed COVID-19 and 89 healthy controls. We identified an HLA gene, HLA-DPA1, in which specific alleles were associated with the risk of SARS-CoV-2 positivity and COVID-19 disease. HLA-DPA1*01:03 was associated with reduced incidence of SARS-CoV-2 positivity, whereas HLA-DPA1*03:01 was associated with increased risk of SARS-CoV-2 positivity. These data suggest a model in which COVID-19 severity is influenced by immunodominant peptides derived from SARS-CoV-2 preferentially presented by specific HLA-DP molecules to either protective (for asymptomatic COVID-19) or pathogenic T cells (in severe COVID-19). Although this study is limited to comparing SARS-CoV-2 positive and negative subjects, these data suggest that HLA typing of COVID-19 patients stratified for disease severity may be informative for identifying biomarkers and disease mechanisms in high-risk individuals.

Emergence of porcine delta-coronavirus pathogenic infections among children in Haiti through independent zoonoses and convergent evolution (preprint)

Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, coronavirus emergence in our species has been associated with zoonotic transmissions from animal reservoirs 1,2 , underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae – Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus , – human infections reported to date have been limited to alpha- and betacoronaviruses 3 . We identify, for the first time, porcine deltacoronavirus (PDCoV) strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the nsp15 and the spike glycoprotein genes by convergent evolution. In particular, structural analysis predicts that one of the changes in the Spike S1 subunit, which contains the receptor-binding domain, may affect protein’s flexibility and binding to the host cell receptor. Our findings not only underscore the ability of deltacoronaviruses to adapt and potentially lead to human-to-human transmission, but also raise questions about the role of such transmissions in development of pre-existing immunity to other coronaviruses, such as SARS-CoV-2.

The Influence of Selection Bias on Identifying an Association between Allergy Medication Use and SARS-CoV-2 Infection (preprint)

Background: Medications to prevent and treat SARS-CoV-2 infection are needed to complement emerging vaccinations. Recent in vitro studies suggested that certain allergy medications could prevent SARS-CoV-2 infection so we sought to characterize this relationship using existing electronic health record (EHR) data.Methods: We analyzed associations of three allergy medications (cetirizine, diphenhydramine or hydroxyzine) with testing negative for SARS-CoV-2 infection, and measuring also the potential effect of selection bias on these associations. We used EHR data from 230,376 patients (18 years+) who visited outpatient clinicians in a single, large academic center at least once but were never hospitalized (10/1/2020-6/1/2020). Main exposures included EHR documentation of three allergy medications and allergy, with intermediate outcome of receipt of a SARS-CoV-2 test, and the primary outcome as testing negative. Findings: Testing rates varied by sex, age, race/ethnicity and insurance type. Higher age categories and public insurance were associated with a higher adjusted odds of a negative test, while being Black or Hispanic was significantly associated with test positivity. Allergy diagnosis and use of any of three allergy medications were each associated with a higher likelihood of receiving a test (e.g. diphenhydramine - Odds Ratio (OR) 2.99, 95% Confidence Interval (CI) 2.73, 3.28; cetirizine 1.75 (95% CI 1.60, 1.92)). Among those who were tested, only use of diphenhydramine was associated with a negative SARS-CoV-2 test (adjusted OR = 2.23, 95% CI 1.10, 4.55). However, further analyses revealed that selection bias was likely responsible for the apparent protective effect of diphenhydramine.Interpretation: While EHR-based observational studies can inform a need for interventional trials, this study highlights their limitations. The finding that diphenhydramine was associated with a higher odds of testing negative for SARS-CoV-2 must be interpreted with caution due to selection bias.Funding: The Children’s Miracle Network of the University of Florida partially funded this study.Declaration of Interests: Dr. Rasmussen has served on advisory committees for the Teva Pregnancy Registry and Solriamfetol Pregnancy Registry and has consulted for F. Hoffmann-La Roche AG as a litigation expert. Dr. Ostrov has a patent pending for compounds to prevent and treat COVID-19 and methods of using the same. All other authors have nothing to declare. Ethics Approval Statement: We received human subjects approval from the University of Florida Institutional Review Board.