SARS-CoV-2 RNA Is Readily Detectable at Least 8 Months after Shedding in an Isolation Facility.

Environmental monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for research and public health purposes has grown exponentially throughout the coronavirus disease 2019 (COVID-19) pandemic. Monitoring wastewater for SARS-CoV-2 provides early warning signals of virus spread and information on trends in infections at a community scale. Indoor environmental monitoring (e.g., swabbing of surfaces and air filters) to identify potential outbreaks is less common, and the evidence for its utility is mixed. A significant challenge with surface and air filter monitoring in this context is the concern of "relic RNA," noninfectious RNA found in the environment that is not from recently deposited virus. Here, we report detection of SARS-CoV-2 RNA on surfaces in an isolation unit (a university dorm room) for up to 8 months after a COVID-19-positive individual vacated the space. Comparison of sequencing results from the same location over two time points indicated the presence of the entire viral genome, and sequence similarity confirmed a single source of the virus. Our findings highlight the need to develop approaches that account for relic RNA in environmental monitoring. IMPORTANCE Environmental monitoring of SARS-CoV-2 is rapidly becoming a key tool in infectious disease research and public health surveillance. Such monitoring offers a complementary and sometimes novel perspective on population-level incidence dynamics relative to that of clinical studies by potentially allowing earlier, broader, more affordable, less biased, and less invasive identification. Environmental monitoring can assist public health officials and others when deploying resources to areas of need and provides information on changes in the pandemic over time. Environmental surveillance of the genetic material of infectious agents (RNA and DNA) in wastewater became widely applied during the COVID-19 pandemic. There has been less research on other types of environmental samples, such as surfaces, which could be used to indicate that someone in a particular space was shedding virus. One challenge with surface surveillance is that the noninfectious genetic material from a pathogen (e.g., RNA from SARS-CoV-2) may be detected in the environment long after an infected individual has left the space. This study aimed to determine how long SARS-CoV-2 RNA could be detected in a room after a COVID-positive person had been housed there.

Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected With the SARS-CoV-2 Delta Variant.

We found no significant difference in cycle threshold values between vaccinated and unvaccinated persons infected with severe acute respiratory syndrome coronavirus 2 Delta, overall or stratified by symptoms. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered in settings with elevated coronavirus disease 2019 transmission.

The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?

Testing surfaces in school classrooms for the presence of SARS-CoV-2, the virus that causes COVID-19, can provide public-health information that complements clinical testing. We monitored the presence of SARS-CoV-2 RNA in five schools (96 classrooms) in Davis, California (USA) by collecting weekly surface-swab samples from classroom floors and/or portable high-efficiency particulate air (HEPA) units (n = 2,341 swabs). Twenty-two surfaces tested positive, with qPCR cycle threshold (Ct) values ranging from 36.07-38.01. Intermittent repeated positives in a single room were observed for both floor and HEPA filter samples for up to 52 days, even following regular cleaning and HEPA filter replacement after a positive result. We compared the two environmental sampling strategies by testing one floor and two HEPA filter samples in 57 classrooms at Schools D and E. HEPA filter sampling yielded 3.02% and 0.41% positivity rates per filter sample collected for Schools D and E, respectively, while floor sampling yielded 0.48% and 0% positivity rates. Our results indicate that HEPA filter swabs are more sensitive than floor swabs at detecting SARS-CoV-2 RNA in interior spaces. During the study, all schools were offered weekly free COVID-19 clinical testing through Healthy Davis Together (HDT). HDT also offered on-site clinical testing in Schools D and E, and upticks in testing participation were observed following a confirmed positive environmental sample. However, no confirmed COVID-19 cases were identified among students associated with classrooms yielding positive environmental samples. The positive samples detected in this study appeared to contain relic viral RNA from individuals infected before the monitoring program started and/or RNA transported into classrooms via fomites. High-Ct positive results from environmental swabs detected in the absence of known active infections supports this conclusion. Additional research is needed to differentiate between fresh and relic SARS-CoV-2 RNA in environmental samples and to determine what types of results should trigger interventions.

Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected with the SARS-CoV-2 Delta Variant

We found no significant difference in cycle threshold values between vaccinated and unvaccinated persons infected with SARS-CoV-2 Delta, overall or stratified by symptoms. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered in settings with elevated COVID-19 transmission.

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis.

RATIONALE: There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear. OBJECTIVES: We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis. METHODS: Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing. MEASUREMENTS AND MAIN RESULTS: Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing. CONCLUSIONS: This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs.

2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission.

With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county, and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for transmission through built environment (BE)-mediated pathways. Over the last decade, substantial research into the presence, abundance, diversity, function, and transmission of microbes in the BE has taken place and revealed common pathogen exchange pathways and mechanisms. In this paper, we synthesize this microbiology of the BE research and the known information about SARS-CoV-2 to provide actionable and achievable guidance to BE decision makers, building operators, and all indoor occupants attempting to minimize infectious disease transmission through environmentally mediated pathways. We believe this information is useful to corporate and public administrators and individuals responsible for building operations and environmental services in their decision-making process about the degree and duration of social-distancing measures during viral epidemics and pandemics.