CONTAIN: An open-source shipping container laboratory optimisedfor automated COVID-19 diagnostics

Walker, K. T.; Donora, M.; Thomas, A.; Phillips, A. J.; Ramgoolam, K.; Pilch, K. S.; Oberacker, P.; Jurkowski, T. P.; Gosman, R. M.; Fleiss, A.; Perkins, A.; MacKenzie, N.; Zuckerman, M.; Danovi, D.; Steiner, H.; Meany, T.

doi:10.1101/2020.05.20.106625

bioRxiv · 10.1101/2020.05.20.106625

CONTAIN: An open-source shipping container laboratory optimisedfor automated COVID-19 diagnostics

Walker, K. T.·Donora, M.·Thomas, A.·Phillips, A. J.·Ramgoolam, K.·Pilch, K. S.·Oberacker, P.·Jurkowski, T. P.·Gosman, R. M.·Fleiss, A.·Perkins, A.·MacKenzie, N.·Zuckerman, M.·Danovi, D.·Steiner, H.·Meany, T.

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Abstract

The COVID-19 pandemic has challenged diagnostic systems globally. Expanding testing capabilities to conduct population-wide screening for COVID-19 requires innovation in diagnostic services at both the molecular and industrial scale. No report to-date has considered the complexity of laboratory infrastructure in conjunction with the available molecular assays to offer a standardised solution to testing. Here we present CONTAIN. A modular biosafety level 2+ laboratory optimised for automated RT-qPCR COVID-19 testing based on a standard 40ft shipping container. Using open-source liquid-handling robots and RNA extraction reagents we demonstrate a reproducible workflow for RT-qPCR COVID-19 testing. With five OT2 liquid handlers, a single CONTAIN unit reaches a maximum daily testing capacity of 2400 tests/day. We validate this workflow for automated RT-qPCR testing, using both synthetic SARS-CoV-2 samples and patient samples from a local NHS hospital. Finally, we discuss the suitability of CONTAIN and its flexibility in a range of diagnostic testing scenarios including high-density urban environments and mobile response units. Visual abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/106625v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@18acad6org.highwire.dtl.DTLVardef@10ae5f1org.highwire.dtl.DTLVardef@7e34d3org.highwire.dtl.DTLVardef@1be3815_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Walker, K. T., Donora, M., Thomas, A., Phillips, A. J., Ramgoolam, K., Pilch, K. S., Oberacker, P., Jurkowski, T. P., Gosman, R. M., Fleiss, A., Perkins, A., MacKenzie, N., Zuckerman, M., Danovi, D., Steiner, H., Meany, T.. 2020-05-20. CONTAIN: An open-source shipping container laboratory optimisedfor automated COVID-19 diagnostics. https://doi.org/10.1101/2020.05.20.106625

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