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

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 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 abstractCONTAIN: An open-source shipping container laboratory optimised for automated COVID-19 diagnostics

Rapid genome surveillance of SARS-CoV-2 and study of risk factors using shipping container laboratories and portable DNA sequencing technology

“…Previous work by Walker et al (2020) presented an automated, UKAS accredited (Testing Laboratory No. 22071) COVID-19 diagnostic laboratory housed within a shipping container 25 . The nanopore sequencing was conducted in an adjacent laboratory also fitted in a shipping container.…”

“…The mean Ct of age group 60-69 was higher by 1.7 for the S gene and 2.9 for the E gene compared to mean Cts of all specimens, suggesting a lower viral load in the samples of this age category. Almost half of the positive cases (49.1%) were observed in the younger age group (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29) . 3). The 30-39 had a slight effect between vaccinated and unvaccinated groups.…”

“…In September 2020, an OpenCell COVID-19 rapid testing laboratory was deployed inside a shipping container designed to diagnose the virus effectively. The laboratory carried out a reverse transcription-polymerase chain reaction (RT-qPCR) diagnostic workflow assay, which formed part of the Government of Jersey testing programme 25…”

“…In September 2020, an OpenCell COVID-19 rapid testing laboratory was deployed inside a shipping container designed to diagnose the virus effectively. The laboratory carried out a reverse transcription-polymerase chain reaction (RT-qPCR) diagnostic workflow assay, which formed part of the Government of Jersey testing programme 25 . Patient registration, swabbing, and diagnostic testing of COVID-19 (CONTAIN Jersey) had an average turnaround of 12 hours, and genome sequencing of SARS-CoV-2 took 18 hours by the MinION platform.…”

Using Robotics in Laboratories During the COVID-19 Outbreak: A Review

“…One innovative approach proposed has been for the use of modular labs in containers, an idea pioneered by OpenCell. These are fully equipped SARS-CoV-2 testing laboratories, with appropriate biosafety mechanisms (BSL2/3) and multiple robotic stations capable of 2,400 tests/day when staffed by one technician (Figure 5) [30], [31]. A unit is deployed by the airport on the Channel Island of Jersey, where its throughput fits well with capacity needs and visitor numbers.…”