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.

Urinary antigen testing for respiratory infection during COVID-19: The microbiologist as a diagnostic steward

The use of antimicrobials in the management of community-acquired COVID-19 is commonplace but evidence for coinfection with common bacterial pathogens to justify their use is lacking. We undertook a retrospective review of all respiratory cultures, blood cultures and urinary antigen tests in COVID-19 patients looking for co-infection with Streptococcus pneumoniae and Legionella pneumophila, and specifically to judge the utility of urinary antigen testing. 2674 GSTT patients were included who had a positive RT-PCR test for SARS-CoV-2 performed at GSTT between 03-March-2020 and 31-Jan-2021 and who had at least one other microbiology sample for review.

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.

HIV and COVID-19 inpatient outcomes: A matched retrospective multicentre analysis

Background: Clinical outcomes for people living with HIV (PLWH) hospitalized with COVID-19 infections have shown mixed outcomes. We conducted a multicentre, UK retrospective matched cohorts' analysis. Methods: Index cases were HIV+ COVID-19 PCR+ patients hospitalized between dates 1st February - 31st May 2020. HIV-negative patients were matched to PLWH up to a 3:1 ratio across 6 sites in England, by hospital site, test date +/- 7 days, age +/- 5 years, gender, index of multiple deprivation decile (IMDD) +/- 1. The primary outcome was patients achieving ≥2-point improvement on a 7-point ordinal scale or discharge from hospital by day 28, whichever was earlier. Follow up was right-censored at day 28 for patients still in hospital. Baseline characteristics and outcomes were analysed by Coxproportional hazards regression stratified by matching clusters using multiple imputation for missing data. The model adjusted for ethnicity, clinical frailty score, body mass index, baseline hypoxia, duration of symptoms, hypertension, diabetes, malignancy, cardiac, lung and renal disease. Results: 68 PLWH and 181 HIV-negative patients were included. PLWH had an HR of 0.57 (95%CI 0.39, 0.85;p=0.005) of achieving 2-point improvement or discharge compared to HIV-negative patients. The effect size of HIV-status was attenuated (aHR 0.70;0.43, 1.17;P=0.18) after adjustment in the multivariable model (Table 1), with baseline frailty (aHR=0.79;95%CI 0.65, 0.95;p=0.011 ), malignancy (aHR=0.37;95%CI 0.17, 0.82;p=0.014) having a greater impact on the primary outcome. Proportion of deaths (19.1% vs 19.3%, p=0.266) and patients requiring ventilation (23.5% vs 17.1%, p=0.25) were similar between PLWH and HIV-negative patients. Sensitivity analyses adjusting for age and excluding missing data, remained consistent with main findings. PLWH were frailer (median clinical frailty score 3 vs 2, p=0.0069), and had higher proportion of malignancies (14.7% vs 9.9%, p=0.29) although not statistically significant. Number of non-HIV co-morbidities (2 vs 2, p=0.16) and median BMI (27.7 vs 29.4, p=0.19) were similar. The median CD4 count of PLWH was 352cells/ μL (IQR 235, 619), and 63/68 (92.3%) were taking antiretroviral therapy. Conclusion: Although PLWH were less likely to achieve improvement or discharge, after adjustment the effect of HIV-status was attenuated. Increased baseline frailty and active malignancies remain associated with poorer COVID-19 outcomes.

Perceptions of Tobacco Product-Specific COVID-19 Risk and Changes in Tobacco Use Behaviors Among Smokers, E-Cigarette Users, and Dual Users.

INTRODUCTION: Coronavirus Disease 2019 (COVID-19) is a public health crisis, but its effects on tobacco users remain ill-defined. This report aimed to assess the relationship between tobacco product-specific risk perceptions for COVID-19 and changes in tobacco use since the start of the pandemic. METHODS: A sample (n = 776) of past-30 day exclusive smokers (n = 238), exclusive e-cigarette users (n = 143), and dual users (n = 395) residing in the US and aged 18 or older were collected using Mechanical Turk from April 27 to June 8, 2020. Adjusted associations between tobacco product-specific COVID-19 risk perceptions (ie risk that smokers/vapers are at for COVID-19 relative to non-smokers/non-vapers) and changes in tobacco use since the pandemic began were assessed using partial proportional odds models. RESULTS: A majority of those who used cigarettes (63.7%) and e-cigarettes (56.1%) felt that the risk of COVID-19 was greater for users of their tobacco product than for non-users. Twenty-four percent of smokers had increased their cigarette use since the start of the pandemic and 28.0% had decreased. Similarly, 27.3% of e-cigarette users had increased their e-cigarette use since the start of the pandemic and 23.8% had decreased. Higher risk perceptions for COVID-19 were associated with reductions in tobacco use since the pandemic began for exclusive e-cigarette users and dual users. CONCLUSIONS: These findings provide the support that tobacco product-specific COVID-19 risk perceptions may be an important correlate of changes in tobacco use during the pandemic. Targeted information to inform tobacco users regarding their risks for COVID-19 is needed during this public health crisis. IMPLICATIONS: Few published studies have investigated the relationship between tobacco product-specific risk perceptions for COVID-19 and changes in tobacco product use since the pandemic began. This study enhances the current literature by providing evidence that higher tobacco product-specific risk perceptions for COVID-19 are associated with reductions in tobacco use since the pandemic began for exclusive e-cigarette users and dual users of cigarettes and e-cigarettes. Additionally, daily tobacco users may be more likely to have increased their tobacco use than non-daily users. These findings emphasize the importance of disseminating targeted health information to tobacco users regarding COVID-19 risks.