KCL TEST: an open-source inspired asymptomatic SARS-CoV-2 surveillance programme in an academic institution

Objectives: To establish a SARS-CoV-2 PCR testing programme in an academic institution to analyze saliva samples collected from asymptomatic staff and students. Design: PCR to detect SARS-CoV-2 RNA in saliva self-collected by asymptomatic students and staff members from King′s College London, and their household contacts. Standards for diagnostics testing set by the DHSC (UK) were followed to develop an automated saliva PCR service for SARS-CoV-2 detection. Prospective study that run from December 2020 until July 2022. Setting: Testing took place in an academic institution including 18 different locations in London (UK). Participants: There were no selection criteria; asymptomatic participants were encouraged to test regularly (twice weekly when on campus). Main outcome measures: Number of tests, number of participants and positive rate. Results: 158,277 PCR tests were carried out on saliva, of which 2,989 were positive (1.89%), collected by 20,186 participants. Between 10-30% of campus footfall were tested. The positive rate was equivalent to that reported by the Office for National Statistics (UK), except for the period encompassing the delta variant; this wave was nearly absent in our cohort. We employed non-commercial reagents and an open source-inspired automated pipeline for sample processing. This rapidly developed service was awarded UKAS accreditation under the ISO15189 standard. Conclusions: Including academic institutions in pandemic preparedness is a critical consideration, considering the experience in developing, validating, and implementing economic and scalable testing solutions. Given the joint ventures in hospital pathology departments across the UK and the move to centralised, automated, commercial tests, focusing on academic centres that can carry out research and development to test for novel and re-emerging pathogens should be a top priority. ### Competing Interest Statement Dr Rahul Batra is the owner of IC Intelligence LTD who helped with the processing of samples for UKAS accreditation. ### Funding Statement KCL TEST was funded by Kings College London and supported by the Huo Family Foundation grant (MHM and RTMN). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: KCL TEST was initially set up as a research project under Kings College London ethics number HR-20/21-21150 and then continued as a service delivery. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Full details of methods and protocols are provided in SOP001 and SOP002. Opentrons OT-2 liquid handling robot python scripts, a blank SOP (for reference) and competency assessments for laboratory staff are also provided. We have made all our Standard Operating Procedures, scripts and LIMS available under a CC BY NC license in Open Science Framework upon request. The LIMS should be tailored to each individual set up (e.g. considering the number of robots dedicated to each task, 96 vs 384 well plate layout).