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Background SARS-CoV-2 emerged in 2019 and has become a major global pathogen. Its emergence is notable due to its impacts on individuals residing within long term care facilities (LTCFs) such as rehabilitation centers and nursing homes. LTCF residents tend to possess several risk factors for more severe SARS-CoV-2 outcomes, including advanced age and multiple comorbidities. Indeed, residents of LTCFs represent approximately 40% of SARS-CoV- 2 deaths in the United States. Methods To assess the prevalence and incidence of SARS-CoV-2 among LTCF workers, determine the extent of asymptomatic SARS-CoV-2 infection, and provide information on the genomic epidemiology of the virus within these unique care settings, we collected nasopharyngeal swabs from workers for 8-11 weeks at six Colorado LTCFs, determined the presence and level of viral RNA and infectious virus within these samples, and sequenced 54 nearly complete genomes. Findings Our data reveal a strikingly high degree of asymptomatic/mildly symptomatic infection, a strong correlation between viral RNA and infectious virus, prolonged infections and persistent RNA in a subset of individuals, and declining incidence over time. Interpretation Our data suggest that asymptomatic SARS-CoV-2 infected individuals contribute to virus persistence and transmission within the workplace, due to high levels of virus. Genetic epidemiology revealed that SARS-CoV-2 likely spreads between staff within an LTCF. Funding Colorado State University Colleges of Health and Human Sciences, Veterinary Medicine and Biomedical Sciences, Natural Sciences, and Walter Scott, Jr. College of Engineering, the Columbine Health Systems Center for Healthy Aging, and the National Institute of Allergy and Infectious Diseases. Research in Context Evidence before this study We searched PubMed and Google Scholar on April 15, 2020 for manuscripts published in 2020 with the key words “SARS-CoV-2 OR COVID-19 AND Long- Term Care Facility AND Surveillance OR Screening. We did not restrict our search to the English language. Our search retrieved two reports of original research. The relevant publications described transmission and course of infection among residents in LTCFs. Of particular relevance was that large quantities of SARS-CoV-2 viral RNA could be detected in asymptomatic, presymptomatic and symptomatic residents, providing early evidence of the heterogeneity of infection characteristics among residents at LTCFs. A significant number of LTCF residents were presymptomatic with symptoms emerging 7 days after initial detection of viral RNA, indicating a longer than expected latency period. Therefore, symptomatic screening for early detection and resultant mitigation response was likely to be ineffective in preventing transmission among residents of LTCFs. There were no reports involving longitudinal surveillance testing of LTCF staff. Added value of this study While prior studies reported results of facility-wide (residents and staff) testing for SARS-CoV-2 and describe transmission dynamics among residents of LTCFs, no prior data was available describing the longitudinal characteristics of SARS-CoV-2 dynamics among staff working at LTCFs during a time period where “shelter-in-place” public guidance was in effect. During this time period, LTCF residents were largely isolated, however staff (those with both direct care and those without direct contact) were permitted to leave and return to work daily. We were therefore interested in this broad staff cohort specifically because they represent a significant and ongoing potential source of transmission within LTCFs. RT-qPCR testing for SARS-CoV-2 was performed weekly on 544 staff in six LTCFs over an 8-11-week period. Symptom data were collected and site-specific prevalence at study onset and incidence rate over time were calculated to explore the influence of identifying and removing asymptomatic SARS-CoV-2-infected individuals from the workplace. Implications of all the available evidence Our results document a surprising degree of asymptomatic/mildly symptomatic infection among apparently healthy staff, and extreme variation in SARS-CoV-2 prevalence and incidence among staff between different facilities. Plaque assay revealed a strong relationship between vRNA and infectious virus in nasopharyngeal swab material, indicating the asymptomatic or mildly symptomatic individuals are infectious. Moreover, phylogenetic analysis of SARS-CoV-2 sequences collected from LTCF staff suggest that the predominant transmission pattern is between staff members within facilities, and that individual unrelated community import events are less common. Finally, decreasing prevalence over time within facilities where longitudinal surveillance testing was performed suggests that identifying and isolating positive staff may serve as part of an effective mitigation program to prevent or curtail transmission among staff within LTCFs.

Wild birds are the primary source of genetic diversity for influenza A viruses that eventually emerge in poultry and humans. Much progress has been made in the descriptive ecology of avian influenza viruses (AIVs), but contributions are less evident from quantitative studies (e.g., those including disease dynamic models). Transmission between host species, individuals and flocks has not been measured with sufficient accuracy to allow robust quantitative evaluation of alternate control protocols. We focused on the United States of America (USA) as a case study for determining the state of our quantitative knowledge of potential AIV emergence processes from wild hosts to poultry. We identified priorities for quantitative research that would build on existing tools for responding to AIV in poultry and concluded that the following knowledge gaps can be addressed with current empirical data: (1) quantification of the spatio-temporal relationships between AIV prevalence in wild hosts and poultry populations, (2) understanding how the structure of different poultry sectors impacts within-flock transmission, (3) determining mechanisms and rates of between-farm spread, and (4) validating current policy-decision tools with data. The modeling studies we recommend will improve our mechanistic understanding of potential AIV transmission patterns in USA poultry, leading to improved measures of accuracy and reduced uncertainty when evaluating alternative control strategies.