ObjectiveTo determine the rates of asymptomatic viral carriage and seroprevalence of SARS-CoV-2 antibodies in healthcare workers.DesignA cross-sectional study of asymptomatic healthcare workers undertaken on 24/25 April 2020.SettingUniversity Hospitals Birmingham NHS Foundation Trust (UHBFT), UK.Participants545 asymptomatic healthcare workers were recruited while at work. Participants were invited to participate via the UHBFT social media. Exclusion criteria included current symptoms consistent with COVID-19. No potential participants were excluded.InterventionParticipants volunteered a nasopharyngeal swab and a venous blood sample that were tested for SARS-CoV-2 RNA and anti-SARS-CoV-2 spike glycoprotein antibodies, respectively. Results were interpreted in the context of prior illnesses and the hospital departments in which participants worked.Main outcome measureProportion of participants demonstrating infection and positive SARS-CoV-2 serology.ResultsThe point prevalence of SARS-CoV-2 viral carriage was 2.4% (n=13/545). The overall seroprevalence of SARS-CoV-2 antibodies was 24.4% (n=126/516). Participants who reported prior symptomatic illness had higher seroprevalence (37.5% vs 17.1%, χ2=21.1034, p<0.0001) and quantitatively greater antibody responses than those who had remained asymptomatic. Seroprevalence was greatest among those working in housekeeping (34.5%), acute medicine (33.3%) and general internal medicine (30.3%), with lower rates observed in participants working in intensive care (14.8%). BAME (Black, Asian and minority ethnic) ethnicity was associated with a significantly increased risk of seropositivity (OR: 1.92, 95% CI 1.14 to 3.23, p=0.01). Working on the intensive care unit was associated with a significantly lower risk of seropositivity compared with working in other areas of the hospital (OR: 0.28, 95% CI 0.09 to 0.78, p=0.02).Conclusions and relevanceWe identify differences in the occupational risk of exposure to SARS-CoV-2 between hospital departments and confirm asymptomatic seroconversion occurs in healthcare workers. Further investigation of these observations is required to inform future infection control and occupational health practices.

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Clinical Microbiology and Infection xxx (xxxx) xxx Please cite this article as: Ptasinska A et al., Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations, Clinical Microbiology and Infection,

Introduction: Rapid, high throughput diagnostics are a valuable tool, allowing the detection of SARS-CoV-2 in populations, in order to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as reverse transcriptase quantitative PCR (RTqPCR), particularly throughout the first months of the pandemic. We investigated the use of LamPORE, where loop mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS CoV 2 in symptomatic and asymptomatic populations. Methods: In an asymptomatic prospective cohort; health care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self swabbed with nasopharyngeal swabs weekly for three weeks and supplied a saliva specimen daily. These samples were tested for SARS CoV 2 RNA using the Oxford Nanopore LamPORE system and a reference RTqPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza like illness from March 2020 to June 2020, were similarly tested from nasopharyngeal swabs. Results: In the asymptomatic cohort a total of 1200 participants supplied 23,427 samples (3,966 swab, 19,461 saliva) over a three-week period. The incidence of SARS CoV 2 was 0.95% using LamPORE. Diagnostic sensitivity and specificity was > 99.5% in both swab and saliva asymptomatic samples as compared to the reference RTqPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%. Conclusions: LamPORE is a highly accurate methodology for the detection of SARS CoV 2 in both the symptomatic and asymptomatic population settings and can be used as an alternative to RTqPCR.

Background:Background: Here we present the Central and South Genomic Laboratory Hub experience of verifying Optical Genome Mapping (OGM). OGM a has great potential to become the new gold standard for detecting structural and copy number variations (SVs and CNVs) identified by cytogenetic techniques for routine use in a diagnostic laboratory environment. A range of haematological referrals were analysed by OGM and results were compared with standard of care testing consisting of G-band metaphase analysis, Fluorescence in Situ Hybridisation (FISH) and SNP array analysis. The use of OGM in various research and diagnostic labs is being validated and implemented around the world.Aims: Aims: Our objective was to compare the workflows in terms of processing and analysis times and concordance of results. Methods:Methods: This next generation cytogenomic technique consists of isolating ultra-high molecular weight DNA, genome wide labelling and imaging of the molecules using the Bionano Saphyr system. This allows the acquisition of big amount of data in parallel followed by analysis using the Bionano Access software. Bionano Genomics Rare Variant Pipeline (RVP) was used for somatic variant detection. Results:Results: We show the concordance between standard of care tests and OGM in the analysed cohort and also present details of additional aberrations detected by OGM, due to its superior resolution and sensitivity compared to G-band analysis.