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Preprint in English | medRxiv | ID: ppmedrxiv-22270799


IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. ResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. ConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.

Preprint in English | medRxiv | ID: ppmedrxiv-20215228


BackgroundDried blood spot samples (DBS) provide an alternative sample type to venous blood samples for antibody testing. DBS are used by NHS for diagnosing HCV and by PHE for large scale HIV and Hepatitis C serosurveillance; the applicability of DBS based approaches to SARS-CoV-2 antibody detection is uncertain. ObjectiveTo compare antibody detection in dried blood spot eluates using the Roche Elecsys (R) immunoassay (index test) with antibody detection in paired plasma samples, using the same assay (reference test). SettingOne Police and one Fire & Rescue facility in England. Participants195 participants within a larger sample COVID-19 serodiagnostics study of keyworkers, EDSAB-HOME. Outcome MeasuresSensitivity and specificity of DBS (the index test) relative to plasma (the reference test), at an experimental cut-off; quality of DBS sample collected; estimates of relative sensitivity of DBS vs. plasma immunoassay in a larger population. Results18/195 (9.2%) participants tested positive using plasma samples. DBS sample quality varied markedly by phlebotomist, and low sample volume significantly reduced immunoassay signals. Using a cut-off of ten median absolute deviations above the immunoassay result with negative samples, sensitivity and specificity of DBS were 89.0% (95% CI 67.2, 96.9%) and 100.0% (95% CI 97.9, 100%) respectively compared with using plasma. The limit of detection for DBS is about 30 times higher than for plasma. ConclusionDBS use for SARS-CoV-2 serology, though feasible, is insensitive relative to immunoassays on plasma. Sample quality impacts on assay performance. Alternatives, including the collection of capillary blood samples, should be considered for screening programs.

Preprint in English | medRxiv | ID: ppmedrxiv-20165043


IntroductionThe risks to surgeons of carrying out aerosol generating procedures during the COVID pandemic are unknown. To start to define these risks, in a systematic manner, we investigated the presence of SARS-CoV-2 virus in the abdominal fluid and lower genital tract of patients undergoing surgery. MethodsWe carried out a prospective cross sectional observational study of 113 patients undergoing abdominal surgery or instrumentation of the lower genital tract. We took COVID swabs from the peritoneal cavity and from the vagina from all eligible patients. Results were stratified by pre operative COVID status. ResultsIn patients who were presumed COVID negative at the time of surgery SARS-CoV-2 virus RNA was detected in 0/102 peritoneal samples and 0/98 vaginal samples. Peritoneal and vaginal swabs were also negative in one patient who had a positive nasopharyngeal swab immediately prior to surgery. ConclusionsThe presence of SARS-CoV-2 RNA in the abdominal fluid or lower genital tract of presumed negative patients is nil or extremely low. These data will inform surgeons of the risks of restarting laparoscopic surgery at a time when COVID19 is endemic in the population.