Scalable and Resilient SARS-CoV-2 testing in an Academic Centre
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Abstract
The emergence of the novel coronavirus SARS-CoV-2 has led to a pandemic infecting more than two million people worldwide in less than four months, posing a major threat to healthcare systems. This is compounded by the shortage of available tests causing numerous healthcare workers to unnecessarily self-isolate. We provide a roadmap instructing how a research institute can be repurposed in the midst of this crisis, in collaboration with partner hospitals and an established diagnostic laboratory, harnessing existing expertise in virus handling, robotics, PCR, and data science to derive a rapid, high throughput diagnostic testing pipeline for detecting SARS-CoV-2 in patients with suspected COVID-19. The pipeline is used to detect SARS-CoV-2 from combined nose-throat swabs and endotracheal secretions/ bronchoalveolar lavage fluid. Notably, it relies on a series of in-house buffers for virus inactivation and the extraction of viral RNA, thereby reducing the dependency on commercial suppliers at times of global shortage. We use a commercial RT-PCR assay, from BGI, and results are reported with a bespoke online web application that integrates with the healthcare digital system. This strategy facilitates the remote reporting of thousands of samples a day with a turnaround time of under 24 hours, universally applicable to laboratories worldwide.
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SciScore for 10.1101/2020.04.19.20071373: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources This is performed by one operator on a Hamilton STAR or STARlet liquid handling platform where all individual barcodes are automatically scanned ensuring errorless sample tracking (Supplementary Method 3). STARsuggested: (STAR, RRID:SCR_015899)For Healthcare Workers (HCWs) this is particularly useful as illustrated below with the texts used at reporting: If DETECTED: Text: “Your COVID-19 test is POSITIVE; self-isolate for at least 7 days.” If NOT Detected: Text: “Your COVID-19 … SciScore for 10.1101/2020.04.19.20071373: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources This is performed by one operator on a Hamilton STAR or STARlet liquid handling platform where all individual barcodes are automatically scanned ensuring errorless sample tracking (Supplementary Method 3). STARsuggested: (STAR, RRID:SCR_015899)For Healthcare Workers (HCWs) this is particularly useful as illustrated below with the texts used at reporting: If DETECTED: Text: “Your COVID-19 test is POSITIVE; self-isolate for at least 7 days.” If NOT Detected: Text: “Your COVID-19 test is NEGATIVE; consider return to work following local Occupational Health Policy” If INVALID:Text: “Your COVID-19 test is INVALID; we recommend a REPEAT swab”. (Figure 1B and Supplementary Method 8). For Healthcaresuggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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