This living document is both a report of our ongoing work and a how-to guide for adapting and replicating the project. We will be updating each section as we progress, gather more data and characterise new techniques and methods.
If you want to contribute follow this link.
#ALL CONTRIBUTORS: Change ‘Editing’ to ‘Suggesting’ in the top right before contributing changes. Or, add contributions as comments.#
Below information will provide you with all the necessary information to produce a portable BSL2 container lab including H&S and standard procedures.
Definition BSL-2 -Biosafety level 2: A level of biosafety considered appropriate for agents that can cause human disease, but whose potential for transmission is limited.
Resources:
World Health Organisation: Laboratory biosafety manual
Management and operation of microbiological containment laboratories
Type: Cargo container
Size: 30ft length, 8ft width
Alternative:
Type: Portacabin
Size: 32 ft length, 10 ft width
The most affordable and time-sensitive way to purchase a converted shipping container is to reach out to a local producer with below requirements and attached technical plans.
Electrics:
Plumbing:
Air conditioning (optional):
Link to interior and fit-out inventory.
Below are suggestions. In case you are using different products please read section "Adequate materials for the fit-out of a BSL lab".
Health and Safety:
Waste bins:
Signage:
Materials requirements for interior and fit-out
List of suitable materials:
Materials NOT to use:
Wood, MDF, materials that a porous or can chip
Below showcase the layout and workflow to achieve 2400 tests in 24h.
Below spreadsheet showcases the workflow to achieve 2,400 tests in 24h. Stations will have to run in parallel to optimize the outcome. Headline showcases 24h in minutes.
A digital sample management system has been built to track samples through the testing process, analyse and log test data, and securely communicate test results to the patient and/or healthcare provider.
Samples are tracked with unique IDs linked to a printable QR code (Fig. 6). During sample handling (Station A), sample QR codes are scanned and assigned to a test run with a unique run ID. At Station C, qPCR data is uploaded into the sample management system, and test results (i.e. positive, negative or inhibitory) are automatically generated. Results are communicated using the secure FHIR (Fast Healthcare Interoperability Resources) protocol, enabling data integration with NHS or international healthcare system architectures. The system is built using Ruby-on-Rails 5.2 on Ruby 2.4, with a PostgreSQL server to persist data, and operates on a cloud platform. Technical details and resources are found on our GitHub (ref: https://github.com/UK- CoVid19/opencell-testing).
Universities seeking to resume operation while ensuring the safety of their staff and student population will require regular testing capability. For a large, multi-campus university comprising for example 10,000 staff and 30,000 students, a full-time operation of 10,000 tests per week allows every individual to be tested monthly or more frequently if we consider the majority working from home (Fig. 7). Combined with selective quarantining, this capacity would allow a university to safely resume relatively normal teaching and research practices. Commitment to supporting the health and work of the student body also gives greater peace of mind to the significant overseas student populations who currently face additional challenges in travel, healthcare and accommodation. Two dedicated CONTAIN units can meet a 10,000 test per week capacity, with their mobility enabling them to operate at multiple campuses and accommodation sites throughout the week.
Augmentation of existing healthcare infrastructure to meet the surge in demand for SARS-CoV-2 testing requires rapid deployment of suitable (BSL2+) laboratory space. CONTAIN units can be quickly transported to hospital sites and require only a car park area and utilities connection (electricity, water) to be operation-ready. The addition of a dedicated, separate facility enables a hospital to increase the scale of its testing without impacting other essential in-house laboratory work and maintains the safety of the main hospital building (Fig. 8). The flexibility of OpenCell’s CONTAIN system allows hospitals to integrate the unit with their own testing process, existing reagents, waste management system, and/or workforce. CONTAIN units can be transported overseas using standard shipping infrastructure, and additional units may be deployed or moved rapidly between hospitals to react to new outbreaks or surges.
Large cities make a good logistical case for large centralised testing facilities. In this scenario, we take advantage of the stackability of shipping containers and the modular nature of CONTAIN to envisage a multi-container testing centre [Fig. 9]. The facility, constructed of 39 containers has the potential to run up to 72,000 tests per day at full capacity, and provide office, storage and utility space for the running of the testing centre. This facility could be built rapidly and economically to serve a spike in COVID-19 cases. Once the spike of cases has passed, the facility could then be resourcefully separated back into individual containers and distributed around the country to act as local testing facilities and follow local outbreaks.
Below will cover the necessary health and safety procedures you will have to set in place.
It is the responsibility of all personnel to ensure the safe and correct disposal of all wastes produced in the course of their work. It is essential that the appropriate disposal procedures given below are strictly adhered to.
Waste disposal streams
The types of waste generated within the laboratory can be categorised as:
Sharps waste consists of all contaminated and non-contaminated items capable of piercing the skin and includes lancets, needles, scalpels, sutures and contaminated disposable glassware. Be careful when handling sharps and resultant waste and dispose of in designated sharps bins. Never use the sharps bin for the disposal of any other type of waste. Waste needs to be autoclaved before picked up by medical/biological waste collectors.
Container to use: Sharps Bin
Wasteflow: Sharps bin -> Autoclave -> Pick-Up biological waste service -> Landfill
Clinical waste includes all other contaminated material (e.g. swabs, examination
gloves, specula,, etc.) and yellow clinical waste bags are available for the
disposal of this type of waste. Do not dispose of general waste in these bags as it leads
to an unnecessary increase in waste disposal costs. Waste needs to be autoclaved before picked up by medical/biological waste collectors.
Container to use: Biohazard cardboard container
Colour code for bin and bag: Yellow
Wasteflow: Sharps bin -> Autoclave -> Pick-Up biological waste service -> Landfill
General waste
Examples of general waste are packaging from consumables and paper towels and general waste bins are available for this type of waste. Under no circumstances should any sharps or clinical waste be disposed of in the general waste bin.
Container to use: Standard bin
Colour code for bin and bag: black
Wasteflow: Pick-Up standard waste service -> Landfill
Liquid waste
All liquid waste must be stored in leakproof containers with a screw- top or other secure lid and labelled appropriately with content. Snap caps, mis-sized caps, parafilm and other loose-fitting lids are not acceptable.
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In Station A, samples are unpacked and logged with a barcode scanner. Then 240 μL of each lysed sample is pipetted into a 2 mL 96 well deep well plate. Once a plate has been filled with 92 samples, the sample plate is passed to Station B.
Below equipment is for a single container lab Station A capable of running 2400 tests in 24h.
Link to equipment inventory list.
Using Bomb Bio magnetic beads (link to page and protocol, plus original RNA extraction protocol we modified and validated first)
If viral samples have been inactivated with a lysis buffer in station A this work can be safely undertaken at containment level 2. At 21 ± 2 °C (70 ± 4 °F) and 60 ± 10 % humidity.
Below equipment is for a single container lab Station A capable of running 2400 tests in 24h.
Link to equipment inventory list.
Reagent setup [2x 96 deep well plates]
Set up OT2
1. Connect via laptop (wifi or ethernet)
If first run, calibrate deck
2. Load automation protocol code
3. Follow calibration instructions for each piece of equipment (see diagram below).
[2x 96 deep well plates with reagents (slot 8) and EtOH (slot 6)]
[6x 96 filter tip racks 200ul (slots 2-5 inclusive, 7, 11)] #NB MAY NEED EXTRA RACK IN 10
[1x 96 well plate (slot 1)]
[MagDeck (slot 9)]
[Samples in 96 deep well (slot 9)]
Calibration can also be done using a “dummy” set of tips and plates which are reused for each calibration. This lowers the risk of contaminating fresh plastics.
4. When calibrated, virtual deck should appear as above.
5. Remove plasticware and clean OT2 deck and pippet with RNAseZap. (if using a dummy set for the calibration step replace the OT2 with the intended plasticware after cleaning)
6. Run protocol.
7. When finished, remove 96 well PCR plate (slot 1), which contains RNA extracted from samples. Move to Station C. If samples will not go through station C immediately, plate should be sealed and stored at -20℃ for short term storage or -80 for long term storage.
Visit https://github.com/UK-CoVid19/OpentronDev for up to date protocols.
In Station C, we have designed an automated protocol for adding one-step RT-qPCR master mixes to the extracted RNA samples and plating each reaction into the final qPCR plate for RT- qPCR . We based our RT-qPCR reaction around the uniplex SARS-CoV-2 assay from the CDC14. We used the N1 and the RNaseP primer-probe mixes in our assay. As we use a uniplex assay, it is necessary to run two RT-qPCR reactions for each sample, one for the N1 target and one for the RNaseP target, which acts as an extraction and sampling control. Both reactions for each sample were conducted on the same plate, however, to conduct RT-qPCR reactions for a full 92 samples, requires setting up two PCR plates for each sample plate.
Below equipment is for a single container lab Station A capable of running 2400 tests in 24h.
Link to equipment inventory list.
Below will provide an overview of the used RT-qPCR testing method from swab to result.
The Testing system consists of 3 main processes:
Workflow Overview
There are 4 main ingredients that go into a swab system
Sourcing these kits | There are two main options
Taking a sample workflow
Outputs | There will be two outputs