Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface (preprint)

Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. Methods: We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations. Results: Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated. Conclusions: Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings. Key words: SARS-CoV-2, COVID-19, haemodialysis, renal dialysis unit, infection control, rapid sequencing, outbreak, nosocomial Key words: SARS-CoV-2, COVID-19, haemodialysis, renal dialysis unit, infection control, rapid sequencing, outbreak, nosocomial

Comparison of COVID-19 outcomes among shielded and non-shielded populations: A general population cohort study of 1.3 million (preprint)

Background Shielding (extended self-isolation) of people judged, a priori, to be at high-risk from COVID-19 has been used by some countries to protect the individuals and reduce demand on health services. It is unclear how well this strategy works in either regard. Methods A general population study was conducted using linked primary care, prescribing, laboratory, hospital and death records up to end of May 2020. Poisson regression models and population attributable fractions were used to compare COVID-19 outcomes by overall risk category, and individual risk criteria: confirmed infection, hospitalisation, intensive care unit (ICU) admission, population mortality and case-fatality. Results Of the 1.3 million population, 32,533 (2.47%) had been advised to shield, a further 347,374 (26.41%) were classified as moderate risk. Testing for COVID-19 was more common in the shielded (6.75%) and moderate (1.99%) than low (0.72%) risk categories. Referent to low-risk, the shielded group had higher risk of confirmed infection (RR 7.91, 95% 7.01-8.92), case-fatality (RR 5.19, 95% CI 4.12-6.53) and population mortality (RR 48.64, 95% 37.23-63.56). The moderate risk had intermediate risk of confirmed infection (RR 4.11, 95% CI 3.82-4.42) and population mortality (RR 26.10, 95% CI 20.89-32.60), but had comparable case-fatality (RR 5.13, 95% CI 4.24-6.21) to the shielded, and accounted for a higher proportion of deaths (PAF 75.27% vs 13.38%). Age [≥]70 years made the largest contribution to deaths (49.53%) and was associated with an 8-fold risk of infection, 7-fold case-fatality and 74-fold mortality. Conclusions Shielding has not been effective at preventing deaths in those with highest risk. To be effective as a population strategy, shielding criteria would need to be widely expanded to include other criteria, such as the elderly.