Anthony Corbett

Background: This study examined the correlation of classroom ventilation (air exchanges per hour (ACH)) and exposure to CO₂ ≥1,000 ppm with the incidence of SARS-CoV-2 over a 20-month period in a specialized school for students with intellectual and developmental disabilities (IDD). These students were at a higher risk of respiratory infection from SARS-CoV-2 due to challenges in tolerating mitigation measures (e.g. masking). One in-school measure proposed to help mitigate the risk of SARS-CoV-2 infection in schools is increased ventilation. Methods: We established a community-engaged research partnership between the University of Rochester and the Mary Cariola Center school for students with IDD. Ambient CO₂ levels were measured in 100 school rooms, and air changes per hour (ACH) were calculated. The number of SARS-CoV-2 cases for each room was collected over 20 months. Results: 97% of rooms had an estimated ACH ≤4.0, with 7% having CO₂ levels ≥2,000 ppm for up to 3 hours per school day. A statistically significant correlation was found between the time that a room had CO₂ levels ≥1,000 ppm and SARS-CoV-2 PCR tests normalized to room occupancy, accounting for 43% of the variance. No statistically significant correlation was found for room ACH and per-room SARS-CoV-2 cases. Rooms with ventilation systems using MERV-13 filters had lower SARS-CoV-2-positive PCR counts. These findings led to ongoing efforts to upgrade the ventilation systems in this community-engaged research project. Conclusions: There was a statistically significant correlation between the total time of room CO₂ concentrations ≥1,000 and SARS-CoV-2 cases in an IDD school. Merv-13 filters appear to decrease the incidence of SARS-CoV-2 infection. This research partnership identified areas for improving in-school ventilation.

Hematoxylin and Eosin staining is the standard chemical stain used on slides to be reviewed for assessment of general histopathology and the generation of a pathology report for each donor. (From Wikipedia) H&E is the combination of two histological stains: hematoxylin and eosin. The hematoxylin stains cell nuclei a purplish blue, and eosin stains the extracellular matrix and cytoplasm pink, with other structures taking on different shades, hues, and combinations of these colors. Hence a pathologist can easily differentiate between the nuclear and cytoplasmic parts of a cell, and additionally, the overall patterns of coloration from the stain show the general layout and distribution of cells and provides a general overview of a tissue sample's structure. Pattern recognition, by expert humans or by software that aids those experts in digital pathology, provides histologic information. This stain combination was first introduced in 1876 by A. Wissowzky. This protocol version accomodates removal of Phenocycler flow cell prior to H&E staining.

Background: This study examined the correlation of classroom ventilation (air exchanges per hour (ACH)) and exposure to CO ₂ ≥1,000 ppm with the incidence of SARS-CoV-2 over a 20-month period in a specialized school for students with intellectual and developmental disabilities (IDD). These students were at a higher risk of respiratory infection from SARS-CoV-2 due to challenges in tolerating mitigation measures (e.g. masking). One in-school measure proposed to help mitigate the risk of SARS-CoV-2 infection in schools is increased ventilation. Methods: We established a community-engaged research partnership between the University of Rochester and the Mary Cariola Center school for students with IDD. Ambient CO ₂ levels were measured in 100 school rooms, and air changes per hour (ACH) were calculated. The number of SARS-CoV-2 cases for each room was collected over 20 months. Results: 97% of rooms had an estimated ACH ≤ 4.0, with 7% having CO ₂ levels ≥ 2,000 ppm for up to 3 hours per school day. A statistically significant correlation was found between the time that a room had CO ₂ levels ≥1,000 ppm and SARS-CoV-2 PCR tests normalized to room occupancy, accounting for 43% of the variance. No statistically significant correlation was found for room ACH and per-room SARS-CoV-2 cases. Rooms with ventilation systems using MERV-13 filters had lower SARS-CoV-2-positive PCR counts. These findings led to ongoing efforts to upgrade the ventilation systems in this community-engaged research project. Conclusions: There was a statistically significant correlation between the total time of room CO ₂ concentrations ≥1,000 and SARS-CoV-2 cases in an IDD school. Merv-13 filters appear to decrease the incidence of SARS-CoV-2 infection. This research partnership identified areas for improving in-school ventilation.

Respiratory syncytial virus (RSV) infection results in millions of hospitalizations and thousands of deaths each year. Variations in the adaptive and innate immune response appear to be associated with RSV severity. To investigate the host response to RSV infection in infants, we performed a systems-level study of RSV pathophysiology, incorporating high-throughput measurements of the peripheral innate and adaptive immune systems and the airway epithelium and microbiota. We implemented a novel multi-omic data integration method based on multilayered principal component analysis, penalized regression, and feature weight back-propagation, which enabled us to identify cellular pathways associated with RSV severity. In both airway and immune cells, we found an association between RSV severity and activation of pathways controlling Th17 and acute phase response signaling, as well as inhibition of B cell receptor signaling. Dysregulation of both the humoral and mucosal response to RSV may play a critical role in determining illness severity.

Background: The majority of infants hospitalized with primary respiratory syncytial virus (RSV) infection have no obvious risk factors for severe disease. Objective: The aim of this study (Assessing Predictors of Infant RSV Effects and Severity, AsPIRES) was to identify factors associated with severe disease in full-term healthy infants younger than 10 months with primary RSV infection. Methods: RSV infected infants were enrolled from 3 cohorts during consecutive winters from August 2012 to April 2016 in Rochester, New York. A birth cohort was prospectively enrolled and followed through their first winter for development of RSV infection. An outpatient supplemental cohort was enrolled in the emergency department or pediatric offices, and a hospital cohort was enrolled on admission with RSV infection. RSV was diagnosed by reverse transcriptase-polymerase chain reaction. Demographic and clinical data were recorded and samples collected for assays: buccal swab (cytomegalovirus polymerase chain reaction, PCR), nasal swab (RSV qualitative PCR, complete viral gene sequence, 16S ribosomal ribonucleic acid [RNA] amplicon microbiota analysis), nasal wash (chemokine and cytokine assays), nasal brush (nasal respiratory epithelial cell gene expression using RNA sequencing [RNAseq]), and 2 to 3 ml of heparinized blood (flow cytometry, RNAseq analysis of purified cluster of differentiation [CD]4+, CD8+, B cells and natural killer cells, and RSV-specific antibody). Cord blood (RSV-specific antibody) was also collected for the birth cohort. Univariate and multivariate logistic regression will be used for analysis of data using a continuous Global Respiratory Severity Score (GRSS) as the outcome variable. Novel statistical methods will be developed for integration of the large complex datasets. Results: A total of 453 infants were enrolled into the 3 cohorts; 226 in the birth cohort, 60 in the supplemental cohort, and 78 in the hospital cohort. A total of 126 birth cohort infants remained in the study and were evaluated for 150 respiratory illnesses. Of the 60 RSV positive infants in the supplemental cohort, 42 completed the study, whereas all 78 of the RSV positive hospital cohort infants completed the study. A GRSS was calculated for each RSV-infected infant and is being used to analyze each of the complex datasets by correlation with disease severity in univariate and multivariate methods. Conclusions: The AsPIRES study will provide insights into the complex pathogenesis of RSV infection in healthy full-term infants with primary RSV infection. The analysis will allow assessment of multiple factors potentially influencing the severity of RSV infection including the level of RSV specific antibodies, the innate immune response of nasal epithelial cells, the adaptive response by various lymphocyte subsets, the resident airway microbiota, and viral factors. Results of this study will inform disease interventions such as vaccines and antiviral therapies.

BACKGROUND The majority of infants hospitalized with primary respiratory syncytial virus (RSV) infection have no obvious risk factors for severe disease. OBJECTIVE The aim of this study (Assessing Predictors of Infant RSV Effects and Severity, AsPIRES) was to identify factors associated with severe disease in full-term healthy infants younger than 10 months with primary RSV infection. METHODS RSV infected infants were enrolled from 3 cohorts during consecutive winters from August 2012 to April 2016 in Rochester, New York. A birth cohort was prospectively enrolled and followed through their first winter for development of RSV infection. An outpatient supplemental cohort was enrolled in the emergency department or pediatric offices, and a hospital cohort was enrolled on admission with RSV infection. RSV was diagnosed by reverse transcriptase-polymerase chain reaction. Demographic and clinical data were recorded and samples collected for assays: buccal swab (cytomegalovirus polymerase chain reaction, PCR), nasal swab (RSV qualitative PCR, complete viral gene sequence, 16S ribosomal ribonucleic acid [RNA] amplicon microbiota analysis), nasal wash (chemokine and cytokine assays), nasal brush (nasal respiratory epithelial cell gene expression using RNA sequencing [RNAseq]), and 2 to 3 ml of heparinized blood (flow cytometry, RNAseq analysis of purified cluster of differentiation [CD]4+, CD8+, B cells and natural killer cells, and RSV-specific antibody). Cord blood (RSV-specific antibody) was also collected for the birth cohort. Univariate and multivariate logistic regression will be used for analysis of data using a continuous Global Respiratory Severity Score (GRSS) as the outcome variable. Novel statistical methods will be developed for integration of the large complex datasets. RESULTS A total of 453 infants were enrolled into the 3 cohorts; 226 in the birth cohort, 60 in the supplemental cohort, and 78 in the hospital cohort. A total of 126 birth cohort infants remained in the study and were evaluated for 150 respiratory illnesses. Of the 60 RSV positive infants in the supplemental cohort, 42 completed the study, whereas all 78 of the RSV positive hospital cohort infants completed the study. A GRSS was calculated for each RSV-infected infant and is being used to analyze each of the complex datasets by correlation with disease severity in univariate and multivariate methods. CONCLUSIONS The AsPIRES study will provide insights into the complex pathogenesis of RSV infection in healthy full-term infants with primary RSV infection. The analysis will allow assessment of multiple factors potentially influencing the severity of RSV infection including the level of RSV specific antibodies, the innate immune response of nasal epithelial cells, the adaptive response by various lymphocyte subsets, the resident airway microbiota, and viral factors. Results of this study will inform disease interventions such as vaccines and antiviral therapies.

Lower respiratory tract infection (LRTI) commonly causes hospitalization in adults. Because bacterial diagnostic tests are not accurate, antibiotics are frequently prescribed. Peripheral blood gene expression to identify subjects with bacterial infection is a promising strategy. We evaluated whole blood profiling using RNASeq to discriminate infectious agents in adults with microbiologically defined LRTI. Hospitalized adults with LRTI symptoms were recruited. Clinical data and blood was collected, and comprehensive microbiologic testing performed. Gene expression was measured using RNASeq and qPCR. Genes discriminatory for bacterial infection were identified using the Bonferroni-corrected Wilcoxon test. Constrained logistic models to predict bacterial infection were fit using screened LASSO. We enrolled 94 subjects who were microbiologically classified; 53 as “non-bacterial” and 41 as “bacterial”. RNAseq and qPCR confirmed significant differences in mean expression for 10 genes previously identified as discriminatory for bacterial LRTI. A novel dimension reduction strategy selected three pathways (lymphocyte, α-linoleic acid metabolism, IGF regulation) including eleven genes as optimal markers for discriminating bacterial infection (naïve AUC = 0.94; nested CV-AUC = 0.86). Using these genes, we constructed a classifier for bacterial LRTI with 90% (79% CV) sensitivity and 83% (76% CV) specificity. This novel, pathway-based gene set displays promise as a method to distinguish bacterial from nonbacterial LRTI.

Key Points The persistence of a CEBPA mutation at the time of complete remission warrants germ line analysis. Not all patients harboring germ line CEBPA mutations have a family history of AML.

Respiratory syncytial virus (RSV) infection in infants has recognizable clinical signs and symptoms. However, quantification of disease severity is difficult, and published scores remain problematic. Thus, as part of a RSV pathogenesis study, we developed a global respiratory severity score (GRSS) as a research tool for evaluating infants with primary RSV infection. Previously healthy infants P < .0001). Using routine clinical variables, we developed a severity score for infants with RSV infection that should be useful as an end point for investigation of disease pathogenesis and as an outcome measure for therapeutic interventions.

Responses by resident cells are likely to play a key role in determining the severity of respiratory disease. However, sampling of the airways poses a significant challenge, particularly in infants and children. Here, we report a reliable method for obtaining nasal epithelial cell RNA from infants for genome-wide transcriptomic analysis and describe baseline expression characteristics in an asymptomatic cohort. Nasal epithelial cells were collected by brushing of the inferior turbinates and gene expression was interrogated by RNA-seq analysis. Reliable recovery of RNA occurred in the absence of adverse events. We observed high expression of epithelial cell markers and similarity to the transcriptome for intrapulmonary airway epithelial cells. We identified genes displaying low and high expression variability, both inherently and in response to environmental exposures. The greatest gene expression differences in this asymptomatic cohort were associated with the presence of known pathogenic viruses and/or bacteria. Robust bacteria-associated gene expression patterns were significantly associated with the presence of Moraxella. In summary, we have developed a reliable method for interrogating the infant airway transcriptome by sampling the nasal epithelium. Our data demonstrates both the fidelity and feasibility of our methodology and describes normal gene expression and variation within a healthy infant cohort.