COVID-19 Prediction using Genomic Footprint of SARS-CoV-2 in Air, Surface Swab and Wastewater Samples (preprint)

ABSTRACT Importance Genomic footprints of pathogens shed by infected individuals can be traced in environmental samples. Analysis of these samples can be employed for noninvasive surveillance of infectious diseases. Objective To evaluate the efficacy of environmental surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for predicting COVID-19 cases in a college dormitory. Design Using a prospective experimental design, air, surface swabs, and wastewater samples were collected from a college dormitory from March to May 2021. Students were randomly screened for COVID-19 during the study period. SARS-CoV-2 in environmental samples was concentrated with electronegative filtration and quantified using Volcano 2 nd Generation-qPCR. Descriptive analyses were conducted to examine the associations between time-lagged SARS-CoV-2 in environmental samples and clinically diagnosed COVID-19 cases. Setting This study was conducted in a residential dormitory at the University of Miami, Coral Gables campus, FL, USA. The dormitory housed about 500 students. Participants Students from the dormitory were randomly screened, for COVID-19 for 2-3 days / week while entering or exiting the dormitory. Main Outcome Clinically diagnosed COVID-19 cases were of our main interest. We hypothesized that SARS-CoV-2 detection in environmental samples was an indicator of the presence of local COVID-19 cases in the dormitory, and SARS-CoV-2 can be detected in the environmental samples several days prior to the clinical diagnosis of COVID-19 cases. Results SARS-CoV-2 genomic footprints were detected in air, surface swab and wastewater samples on 52 (63.4%), 40 (50.0%) and 57 (68.6%) days, respectively, during the study period. On 19 (24%) of 78 days SARS-CoV-2 was detected in all three sample types. Clinically diagnosed COVID-19 cases were reported on 11 days during the study period and SARS-CoV-2 was also detected two days before the case diagnosis on all 11 (100%), 9 (81.8%) and 8 (72.7%) days in air, surface swab and wastewater samples, respectively. Conclusion Proactive environmental surveillance of SARS-CoV-2 or other pathogens in a community/public setting has potential to guide targeted measures to contain and/or mitigate infectious disease outbreaks. Key Points Question How effective is environmental surveillance of SARS-CoV-2 in public places for early detection of COVID-19 cases in a community? Findings All clinically confirmed COVID-19 cases were predicted with the aid of 2 day lagged SARS-CoV-2 in environmental samples in a college dormitory. However, the prediction efficiency varied by sample type: best prediction by air samples, followed by wastewater and surface swab samples. SARS-CoV-2 was also detected in these samples even on days without any reported cases of COVID-19, suggesting underreporting of COVID-19 cases. Meaning SARS-CoV-2 can be detected in environmental samples several days prior to clinical reporting of COVID-19 cases. Thus, proactive environmental surveillance of microbiome in public places can serve as a mean for early detection of location-time specific outbreaks of infectious diseases. It can also be used for underreporting of infectious diseases.

New Insights Into the Burden of COVID-19 Mortality for U.S. Hispanics and Blacks — When Examined by Country/Region of Origin (preprint)

Background: Florida’s diverse population composition includes persons from throughout Latin America and the Caribbean. This facilitated an insightful examination of disparities in 2020 Florida COVID-19 deaths not only among racial/ethnic populations in the aggregate (non-Hispanic White, non-Hispanic Black, Hispanic) but also at the level of country/region of origin.Methods: Age-adjusted mortality rates (AAMRs) for 2020 Florida COVID-19 deaths were calculated by race, ethnicity, and country/region of origin along with mean age at death, mean number of comorbidities, and percentage of decedents who had not completed secondary education. Regression-derived mortality rate ratios (MRRs) compared death rates for each racial/ethnic/country-of-origin population to non-Hispanic whites.Findings: The overall AAMR (per 100,000) for 18,342 Florida COVID-19 deaths in 2020 was 55.4, with a much lower AAMR for non-Hispanic Whites (39.3) than for Hispanics (86.8) or Blacks (107.6). Marked differences in AAMRs were observed for specific Black and Hispanic ethnic groups from varied countries/regions of origin. COVID-19 decedents from Mexico and Central America had the highest AAMRs (170.7 and 168.8 per 100,000, respectively), lowest age at death, lowest educational level, and fewest comorbidities. Mean comorbidities were highest for Blacks (all origins) and Cuban Hispanics.Interpretation: Florida Blacks and Hispanics experienced disproportionately high COVID-19 mortality rates throughout 2020, with notable variability based on country/region of origin. Inequities were particularly pronounced for Hispanic populations from Mexico and Central America. To better understand these heterogeneous COVID-19 mortality trends, more nuanced racial-ethnic analyses and detailed data on social determinants of health are needed.Funding Information: Supplemental funding was provided by the Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine. Research reported in this publication was also supported by the National Cancer Institute of the National Institutes of Health under Award Number P30CA240139. Declaration of Interests: The authors declare no potential conflicts of interests.

A how-to-guide to building a robust SARS-CoV-2 testing program at a university-based health system (preprint)

When South Florida became a hotspot for COVID-19 disease in March 2020, we faced an urgent need to develop test capability to detect SARS-CoV-2 infection. We assembled a transdisciplinary team of knowledgeable and dedicated physicians, scientists, technologists and administrators, who rapidly built a multi-platform, PCR- and serology-based detection program, established drive-thru facilities and drafted and implemented guidelines that enabled efficient testing of our patients and employees. This process was extremely complex, due to the limited availability of needed reagents, but outreach to our research scientists and to multiple diagnostic laboratory companies and government officials enabled us to implement both FDA authorized and laboratory developed testing (LDT)-based testing protocols. We analyzed our workforce needs and created teams of appropriately skilled and certified workers, to safely process patient samples and conduct SARS-CoV-2 testing and contact tracing. We initiated smart test ordering, interfaced all testing platforms with our electronic medical record, and went from zero testing capacity, to testing hundreds of healthcare workers and patients daily, within three weeks. We believe our experience can inform the efforts of others, when faced with a crisis situation.