The Association Between Stool Shedding of SARS-Cov-2, Microbiome Diversity and Intestinal Inflammation

Introduction: The transmission of the etiologic virus of COVID-19 (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) is thought to occur mainly via respiratory droplets even though limited evidence has shown the virus can be found in feces and involve the gastrointestinal (GI) tract. Within the group with a (+) NPT, those patient with detectable SARS-CoV-2 in the stool were younger but no differences were seen in demographic, symptoms, or fecal calprotectin levels (Table). Differences in characteristics among COVID-19 patients with and without detectable fecal SARS-CoV-2 viral loads (+) NS test 1 (n=54) (-) NPT1 (n=45) P value Age [Mean in years (SD)] 37 (10) 40 (13) 0.30 Female gender [n (%)] 41 (75.9) 38 (82.6) 0.41 Race [n (%)]  Caucasian  Black  Asian  Unknown 31 (56.4) 18 (32.7) 1 (1.8) 5 (9.1) 29 (63.0) 16 (34.8) 1 (2.2) None 0.22 Hispanic ethnicity [n (%)] 3 (5.6) 1 (2.2) 0.39 Detectable stool SARS-Cov-2 [n (%)] 39 (70.9) 1 (2.2) < 0.0001* Body Mass Index [Mean in Kg/m2 (SD)] 31.5 (8.4) 28.0 (6.8) 0.1 Oxygen saturation [Mean in % (SD)] 98.1 (1.5) 97.8 (1.9) 0.49 Respiratory rate [Mean in RPM (SD)] 18 (2.7) 19 (2.5) 0.22 Fecal calprotectin [Median in μg/mg(IQR)] 30 (30-83) 30 (30-34) 0.92 Symptoms at presentation Fevers [n (%)] 14 (25.5) 11 (23.9) 0.86 Fatigue [n (%)] 34 (61.8) 22 (47.8) 0.16 Cough [n (%)] 32 (58.2) 22 (47.8) 0.30 Anorexia [n (%)] 1 (1.8) 1 (2.2) 0.9 Pharyngalgia [n (%)] 25 (45.5) 21 (45.7) 0.98 Myalgias [n (%)] 33 (60.0) 17 (37.0) 0.02* Anosmia [n (%)] 12 (21.8) 3 (6.5) 0.03* Dysgeusia [n (%)] 13 (23.6) 3 (6.5) 0.019* Any gastrointestinal Symptoms [n (%)] 32 (58.2) 23 (50.0) 0.41 Diarrhea [n (%)] 15 (27.3) 11 (23.9) 0.7 Abdominal pain [n (%)] 2 (3.6) 6 (13.0) 0.08 Nausea [n (%)] 15 (27.3) 17 (37.0) 0.3 Blood in the stool [n (%)] None 1 (4.4) 0.12 1 Nasopharyngeal test * Statistically significant

Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Asymptomatic Infections in 2 Large Academic Health Systems in Wisconsin.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) asymptomatic infections may play a critical role in disease transmission. We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at 2 hospital systems in 2 counties in Wisconsin. The SARS-CoV-2 prevalence was 1% or lower at both systems despite the higher incidence of coronavirus disease 2019 (COVID-19) in Milwaukee County.

Cytotoxic CD8-positive T-lymphocyte infiltration in the lungs as a histological pattern of SARS-CoV-2 pneumonitis.

Despite millions of PCR confirmed cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, the long-term pathophysiological changes induced by this infection in the lungs and their relationship with possible immune triggers remain incompletely understood. Acute respiratory distress syndrome and subsequent respiratory failure are the most common causes of mortality in hospitalised patients. Severe lung tissue destruction can be due to an overactive immune system that far exceeds the harm that would have been caused by direct virus replication. This study extends our previous investigation and presents detailed histopathological findings on cryotransbronchial biopsy in patients with persistent (range 31-182 days) pneumonitis and severe interstitial inflammatory infiltration in the lungs due to SARS-CoV-2 infection. We describe a novel lung injury pattern associated with SARS-CoV-2 pneumonitis, which manifests as a marked interstitial CD8-positive T-cell lymphocytic infiltration. These findings provide a better understanding of the changes in the lungs that ensue due to SARS-CoV-2 infection.

Point-of-care COVID-19 testing in the emergency department: current status and future prospects.

INTRODUCTION: This expert review outlines current and future point-of-care technologies for the diagnosis of the SARS-CoV-2 virus, which is responsible for causing coronavirus disease COVID-19 in the emergency department. COVID-19 first emerged in late 2019 and is responsible for a range of presentations from minor upper respiratory tract symptoms to severe pneumonia and multisystem organ failure. Among the technologies available include the gold standard of molecular point-of-care tests as well as antigen detection tests. AREAS COVERED: We discuss point-of-care molecular tests including multiplex, targeted, and single plex panels as well as various antigen testing methodologies in terms of availability and performance characteristics. In addition, we focus on current testing best practices and considerations for point-of-care testing in the emergency department based on a search of the literature available in PubMed to date and a review of FDA and CDC guidance. EXPERT OPINION: While there have been many advances in SARS-CoV-2 point-of-care testing, there remain challenges to implementation in the emergency department setting. A paradigm shift is needed to improve diagnosis and clinical outcomes.

Cytotoxic CD8 positive T-lymphocyte infiltration in the lungs as a histological pattern of SARS-CoV-2 pneumonitis

Despite millions of PCR confirmed cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, the long-term pathophysiological changes induced by this infection in the lungs and their relationship with possible immune triggers remain incompletely understood. Acute respiratory distress syndrome and subsequent respiratory failure are the most common cause of mortality in hospitalised patients. Severe lung tissue destruction can be due to an overactivity immune system that far exceeds the harm that would have been caused by direct virus replication. This study extends our previous investigation and presents detailed histopathological findings on cryotransbronchial biopsy in patients with persistent (range 31–182 days) pneumonitis and severe interstitial inflammatory infiltration in the lungs due to SARS-CoV-2 infection. We describe a novel lung injury pattern associated with SARS-CoV-2 pneumonitis, which manifests as a marked interstitial CD8 positive T-cell lymphocytic infiltration. These findings provide a better understanding of the changes in the lungs that ensue due to SARS-CoV-2 infection.

Evaluation of a High-Definition PCR Assay for the Detection of SARS-CoV-2 in Extracted and Nonextracted Respiratory Specimens Collected in Various Transport Media.

OBJECTIVES: We conducted an analytic and clinical comparison of a novel high-definition polymerase chain reaction PCR (HDPCR) assay to traditional real-time PCR (RT-PCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper respiratory specimens. METHODS: Analytic performance of RT-PCR, HDPCR, and extraction-free HDPCR was established through replicate testing of a serially diluted clinical specimen containing SARS-CoV-2. A clinical comparison of all 3 assays was conducted using 351 prospectively collected upper respiratory swab specimens obtained from symptomatic and asymptomatic individuals collected in various transport media. RESULTS: RT-PCR and HDPCR assays using extracted nucleic acid demonstrated similar analytic limits of detection (LoD) and clinical performance, with 100% positive and negative agreement. Extraction-free HDPCR demonstrated a 1.5 to 2.0 log10 increase in LoD based on cycle threshold values. However, clinical performance of extraction-free HDPCR remained high, demonstrating 97.8% positive and 99.6% negative agreement with RT-PCR. An overall increase in "invalid" and "presumptive" results was observed when using the extraction-free method, but this was highly variable based on transport medium used. CONCLUSIONS: HDPCR performs similar to RT-PCR for the detection of SARS-CoV-2. The use of an extraction-free HDPCR protocol maintained high clinical performance despite reduced analytic LoD, with the benefit of reduced hands-on time and cost of reagents associated with nucleic acid extraction.

Air contamination of households versus hospital inpatient rooms occupied by severe acute respiratory coronavirus virus 2 (SARS-CoV-2)-positive patients.

The household setting has some of the highest coronavirus disease 2019 (COVID-19) secondary-attack rates. We compared the air contamination in hospital rooms versus households of COVID-19 patients. Inpatient air samples were only positive at 0.3 m from patients. Household air samples were positive even without a COVID-19 patient in the proximity to the air sampler.

Racial Disparities in Incidence and Outcomes Among Patients With COVID-19.

Importance: Initial public health data show that Black race may be a risk factor for worse outcomes of coronavirus disease 2019 (COVID-19). Objective: To characterize the association of race with incidence and outcomes of COVID-19, while controlling for age, sex, socioeconomic status, and comorbidities. Design, Setting, and Participants: This cross-sectional study included 2595 consecutive adults tested for COVID-19 from March 12 to March 31, 2020, at Froedtert Health and Medical College of Wisconsin (Milwaukee), the largest academic system in Wisconsin, with 879 inpatient beds (of which 128 are intensive care unit beds). Exposures: Race (Black vs White, Native Hawaiian or Pacific Islander, Native American or Alaska Native, Asian, or unknown). Main Outcomes and Measures: Main outcomes included COVID-19 positivity, hospitalization, intensive care unit admission, mechanical ventilation, and death. Additional independent variables measured and tested included socioeconomic status, sex, and comorbidities. Reverse transcription polymerase chain reaction assay was used to test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Results: A total of 2595 patients were included. The mean (SD) age was 53.8 (17.5) years, 978 (37.7%) were men, and 785 (30.2%) were African American patients. Of the 369 patients (14.2%) who tested positive for COVID-19, 170 (46.1%) were men, 148 (40.1%) were aged 60 years or older, and 218 (59.1%) were African American individuals. Positive tests were associated with Black race (odds ratio [OR], 5.37; 95% CI, 3.94-7.29; P = .001), male sex (OR, 1.55; 95% CI, 1.21-2.00; P = .001), and age 60 years or older (OR, 2.04; 95% CI, 1.53-2.73; P = .001). Zip code of residence explained 79% of the overall variance in COVID-19 positivity in the cohort (ρ = 0.79; 95% CI, 0.58-0.91). Adjusting for zip code of residence, Black race (OR, 1.85; 95% CI, 1.00-3.65; P = .04) and poverty (OR, 3.84; 95% CI, 1.20-12.30; P = .02) were associated with hospitalization. Poverty (OR, 3.58; 95% CI, 1.08-11.80; P = .04) but not Black race (OR, 1.52; 95% CI, 0.75-3.07; P = .24) was associated with intensive care unit admission. Overall, 20 (17.2%) deaths associated with COVID-19 were reported. Shortness of breath at presentation (OR, 10.67; 95% CI, 1.52-25.54; P = .02), higher body mass index (OR per unit of body mass index, 1.19; 95% CI, 1.05-1.35; P = .006), and age 60 years or older (OR, 22.79; 95% CI, 3.38-53.81; P = .001) were associated with an increased likelihood of death. Conclusions and Relevance: In this cross-sectional study of adults tested for COVID-19 in a large midwestern academic health system, COVID-19 positivity was associated with Black race. Among patients with COVID-19, both race and poverty were associated with higher risk of hospitalization, but only poverty was associated with higher risk of intensive care unit admission. These findings can be helpful in targeting mitigation strategies for racial disparities in the incidence and outcomes of COVID-19.

Distribution of SARS-CoV-2 PCR Cycle Threshold Values Provide Practical Insight Into Overall and Target-Specific Sensitivity Among Symptomatic Patients.

OBJECTIVES: We examined the distribution of reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values obtained from symptomatic patients being evaluated for coronavirus disease 2019 (COVID-19) to determine the proportion of specimens containing a viral load near the assay limit of detection (LoD) to gain practical insight to the risk of false-negative results. We also examined the relationship between CT value and patient age to determine any age-dependent difference in viral load or test sensitivity. METHODS: We collected CT values obtained from the cobas severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay corresponding to 1,213 combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals that were reported as positive or presumptive positive for SARS-CoV-2. CT values were stratified by SARS-CoV target and patient age group. RESULTS: In total, 93.3% to 98.4% of specimens demonstrated CT values greater than 3× the assay LoD, at which point false-negative results would not be expected. The mean of CT values between age groups was statistically equivalent with the exception of patients in age group 80 to 89 years, which demonstrated slightly lower CTs. CONCLUSIONS: Based on the distribution of observed CT values, including the small proportion of specimens with values near the assay LoD, there is a low risk of false-negative RT-PCR results in combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals.