An ecological study of COVID-19 outcomes among Florida counties (preprint)

BackgroundDuring the COVID-19 pandemic, Florida reported some of the highest number of cases and deaths in the US; however, county-level variation in COVID-19 outcomes has not been comprehensively investigated. The present ecological study aimed to assess corelates of COVID-19 outcomes among Florida counties that explain variation in case rates, mortality rates, and case fatality rates (CFR) across pandemic waves. MethodWe obtained county-level administrative data and COVID-19 case reports from public repositories. We tested spatial autocorrelation to assess geographic clustering in COVID-19 outcomes: case rate, mortality rate, and CFR. Stepwise linear regression was employed to test the association between case, death, and CFR and 18 demographic, socioeconomic, and health-related county-level predictors. ResultsWe found mortality rate and CFR were significantly higher in rural counties compared to urban counties, among which significant differences in vaccination coverage was also observed. Multivariate analysis found that the percentage of the population aged over 65 years, the percentage of the obese people, and the percentage of rural population were significant predictors of COVID-19 case rate. Median age, vaccination coverage, percentage of people who smoke, and percentage of the population with diabetes were significant influencing factors for CFR. Importantly, vaccination coverage was significantly associated with a reduction in case rate (R = - 0.26, p = 0.03) and mortality (R = -0.51, p < 0.001). Last, we found that spatial dependencies play a role in explaining variations in COVID-19 CFR among Florida counties. ConclusionOur findings emphasize the need for targeted, equitable public health strategies to reduce disparities and enhance population resilience during public health crises. We further inform future spatial-epidemiological analyses and present actionable data for policies related to preparedness and response to current and future epidemics in Florida and elsewhere.

Environmental Surface Monitoring as a Noninvasive Method for SARS-CoV-2 Surveillance in Community Settings: Lessons from a University Campus Study (preprint)

Environmental testing of high-touch objects is a potential noninvasive approach for monitoring population-level trends of SARS-CoV-2 and other respiratory viruses within a defined setting. We aimed to determine the association between SARS-CoV-2 contamination on high-touch environmental surfaces, community level case incidence, and university student health data. Environmental swabs were collected from January 2022 to November 2022 from high-touch objects and surfaces from five locations on a large university campus in Florida, USA. RT-qPCR was used to detect and quantify viral RNA, and a subset of positive samples was analyzed by viral genome sequencing to identify circulating lineages. During the study period, we detected SARS-CoV-2 viral RNA on 90.7% of 162 tested samples. Levels of environmental viral RNA correlated with trends in community-level activity and case reports from the student health center. A significant positive correlation was observed between the estimated viral gene copy number in environmental samples and the weekly confirmed cases at the university. Viral sequencing data from environmental samples identified lineages contemporaneously circulating in the local community and state based on genomic surveillance data. Further, we detected emerging variants in environmental samples prior to their identification by clinical genomic surveillance. Our results demonstrate the utility of viral monitoring on high-touch environmental surfaces for SARS-CoV-2 surveillance at a community level. In communities with delayed or limited testing facilities, immediate environmental surface testing may considerably inform epidemic dynamics.

Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2 (preprint)

Viral genomic surveillance has been integral in the global response to the SARS-CoV-2 pandemic. Surveillance efforts rely on the availability of representative clinical specimens from ongoing testing activities. However, testing practices have recently shifted due to the widespread availability and use of rapid antigen tests, which could lead to gaps in future monitoring efforts. As such, genomic surveillance strategies must adapt to include laboratory workflows that are robust to sample type. To that end, we compare the results of RT-qPCR and viral genome sequencing using samples from positive BinaxNOW COVID-19 Antigen Card swabs (N=555) to those obtained from previously collected nasopharyngeal (NP) swabs used for nucleic acid amplification testing (N=135). We show that swabs obtained from antigen cards are comparable in performance to clinical excess samples from NP swabs, providing a viable alternative. This validation permits the reliable expansion of viral genomic surveillance to cases identified in the clinic or home setting where rapid antigen tests are used.

Early emergence phase of SARS-CoV-2 Delta variant in Florida (preprint)

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2020. The highly contagious B.1.617.2 (Delta) Variant of Concern (VOC) was first identified in October 2020 in India and subsequently disseminated worldwide, later becoming the dominant lineage in the U.S. Despite considerable genomic analysis of SARS-CoV-2 in the U.S., several gaps in the understanding of the local dynamics during early introductions remain, which when elucidated could translate the results of viral genomic epidemiology to actionable mitigation efforts. Here, we explore the early emergence of the Delta variant in Florida, U.S. using phylogenetic analysis of representative Florida and globally sampled genomes. We find multiple independent introductions into Florida primarily from North America and Europe, with a minority originating from Asia. These introductions lead to three distinct clades that demonstrated varying relative rates of transmission and possessed five distinct substitutions that were 3-21 times more prevalent in the Florida sample as compared to the global sample. Our results underscore the benefits of routine viral genomic surveillance to monitor epidemic spread and support the need for more comprehensive genomic epidemiology studies of emerging variants. In addition, we provide a model of epidemic spread of newly emerging VOCs that can inform future public health responses.

Differential effect of corticosteroid treatment on Influenza, SARS, MERS, and SARS-CoV-2 patients: A meta-analysis and systematic review (preprint)

BackgroundCorticosteroid has been used to manage inflammation caused by many diseases including respiratory viral infections. Many articles are available to support the good and bad side of this steroid use but remain inconclusive. To find some evidence about the safety of the drug, we investigated the effect of corticosteroids on the mortality of patients with respiratory viral infections including SARS-CoV-2, SARS, MERS, and Influenza. MethodWe searched articles in PubMed, Scopus, Cochrane, Medline, Google Scholar, and Web of Science records using keywords "corticosteroid" or "viral infection" or "patients" or "control study". Mortality was the primary outcome. ResultOur selected 24 studies involving 16633 patients were pooled in our meta-analysis. Corticosteroid use and overall mortality were not significantly associated (P=0.176), but in subgroup analysis, corticosteroid use was significantly associated with lower mortality in the case of SARS (P=0.003) but was not significantly associated with mortality for Influenza (H1N1) (P=0.260) and SARS-CoV-2 (P=0.554). Further analysis using study types of SARS-CoV-2, we found that corticosteroid use was not significantly associated with mortality in the case of retrospective cohort studies (P=0.256) but was significantly associated with lower mortality in the case of randomized control trials (P=0.005). Our findings uncover how the outcome of particular drug treatment for different diseases with comparable pathogenesis may not be similar and, RCTs are sometimes required for robust outcome data. ConclusionAt the beginning of the COVID-19 pandemic, data of corticosteroid use from other viral infections along with COVID-19 observational and retrospective cohort studies created confusion of its effect, but randomized control trials showed that corticosteroid can be used to treat COVID-19 patients.