Influence of SARS-CoV-2 surveillance outputs produced by the UK health security agency (UKHSA) outbreak surveillance team on decision-making by local stakeholders.

BACKGROUND: The UK Health Security Agency (UKHSA) COVID-19 Outbreak Surveillance Team (OST) was established in June 2020 to provide Local Authorities (LAs) in England with surveillance intelligence to aid their response to the SARS-CoV-2 epidemic. Reports were produced using standardised metrics in an automated format. Here we evaluate how the SARS-CoV-2 surveillance reports influenced decision making, how resources evolved and how they could be refined to meet the requirements of stakeholders in the future. METHODS: Public health professionals (n = 2,400) involved in the COVID-19 response from the 316 English LAs were invited to take part in an online survey. The questionnaire covered five themes: (i) report use; (ii) influence of surveillance outputs on local intervention strategies; (iii) timeliness; (iv) current and future data requirements; and (v) content development. RESULTS: Of the 366 respondents to the survey, most worked in public health, data science, epidemiology, or business intelligence. Over 70% of respondents used the LA Report and Regional Situational Awareness Report daily or weekly. The information had been used by 88% to inform decision making within their organisations and 68% considered that intervention strategies had been instituted as a result of these decisions. Examples of changes instigated included targeted communications, pharmaceutical and non-pharmaceutical interventions, and the timing of interventions. Most responders considered that the surveillance content had reacted well to evolving demands. The majority (89%) said that their information requirements would be met if the surveillance reports were incorporated into the COVID-19 Situational Awareness Explorer Portal. Additional information suggested by stakeholders included vaccination and hospitalisation data as well as information on underlying health conditions, infection during pregnancy, school absence and wastewater testing. CONCLUSIONS: The OST surveillance reports were a valuable information resource used by local stakeholders in their response to the SARS-CoV-2 epidemic. Control measures that affect disease epidemiology and monitoring requirements need to be considered in the continuous maintenance of surveillance outputs. We identified areas for further development and, since the evaluation, information on repeat infections and vaccination data have been included in the surveillance reports. Furthermore, timeliness of publications has been improved by updating the data flow pathways.

Transmission history of SARS-CoV-2 in humans and white-tailed deer.

The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human-animal interface.

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer.

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ∼75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive "One Health" approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.