Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals.

BACKGROUND: The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals. AIM: To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice. METHODS: A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT. FINDINGS: The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks. CONCLUSION: Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.

Real-world deployment of point-of-care SARSCoV-2 testing in the emergency department admission pathway can support the safe, accurate and rapid diagnosis of COVID-19

Aims/Objectives/Background Patients admitted to hospital via the emergency department (ED) need to be separated by SARS-CoV-2 infection status to prevent transmission. Using clinical criteria alone is not feasible due to the range of symptoms and asymptomatic spread. Turnaround time of laboratory PCR assays (~6-24 hrs) hinders patient movement through the hospital with pressure on side-rooms pending results and exposure risk if unsuspected cases are moved into bays. Lateral flow devices (LFD) can provide a rapid diagnosis and aid patient movement. This implementation study aimed to assess the accuracy and safety of LFDs within an ED during a highprevalence period. Methods/Design Two rapid point-of-care tests (POCT) were introduced during December 2020: Cobas®-Liat® system (Roche Diagnostics) is a 20-minute assay comparable to laboratory PCR (in-house validation), and LFDs. Symptomatic patients with a positive LFD were cohorted on a 'red' ward. Asymptomatic patients with a negative result were allocated an 'amber' ward, pending lab PCR. Where there were discrepancies between results and symptoms;a Liat® was performed. The LFDs were validated by PCR swabs to determine true positive and false negative (FN) rates and to minimise fallout via contact tracing. The PCR cycle threshold (CT) values were recorded to evaluate the LFD sensitivity and specificity. Results were collected between December 2020-March 2021. Results/Conclusions Comparing LFD with PCR results, the sensitivity and specificity were 70.7% and 99.1%. LFD FNs had higher CT values (25), indicating the beginning or end of infection - unlikely infectious. One period of false positives during lower prevalence revealed a faulty batch. During the study period 90% of patients left the ED with a virological diagnosis. We conclude that POCT can aid the diagnosis of COVID- 19 in the ED when combined with existing laboratory-based PCR algorithms. We demonstrate a safe and effective use of POCT in the ED which could be replicated across other centres.

Real-world deployment of lateral flow SARS-CoV-2 antigen detection in the emergency department to provide rapid, accurate and safe diagnosis of COVID-19.

BACKGROUND: Point-of-care (POC) SARS-CoV-2 lateral-flow antigen detection (LFD) testing in the emergency department (ED) could inform rapid infection control decisions but requirements for safe deployment have not been fully defined. METHODS: Review of LFD test results, laboratory and POC-RT-PCR results and ED-performance metrics during a two-week high SARS-CoV-2 prevalence period followed by several months of falling prevalence. AIM: Determine whether LFD testing can be safely deployed in ED to provide an effective universal SARS-CoV-2 testing capability. FINDINGS: 93% (345/371) of COVID-19 patients left ED with a virological diagnosis during the 2-week universal LFD evaluation period compared to 77% with targeted POC-RT-PCR deployment alone, on background of approximately one-third having an NHS Track and Trace RT-PCR test-result at presentation. LFD sensitivity and specificity was 70.7% and 99.1% respectively providing a PPV of 97.7% and NPV of 86.4% with disease prevalence of 34.7%. ED discharge-delays (breaches) attributable to COVID-19 fell to 33/3532 (0.94%) compared with the preceding POC-RT-PCR period (107/4114 (2.6%); p=<0.0001). Importantly, LFD testing identified 1 or 2 clinically-unsuspected COVID-19 patients/day. Three clinically-confirmed LFD false positive patients were appropriately triaged based on LFD action-card flowchart, and only 5 of 95 false-negative LFD results were inappropriately admitted to non-COVID-19 areas where no onward-transmission was identified. LFD testing was restricted to asymptomatic patients when disease prevalence fell below 5% and detected 1-3 cases/week. CONCLUSION: Universal SARS-CoV-2 LFD testing can be safely and effectively deployed in ED alongside POC-RT-PCR testing during periods of high and low disease prevalence.