Uncoupling Molecular Testing for SARS-CoV-2 From International Supply Chains

Abstract

The rapid global rise of COVID-19 from late 2019 caught major manufacturers of RT-qPCR reagents by surprise and threw into sharp focus the heavy reliance of molecular diagnostic providers on a handful of reagent suppliers. In addition, lockdown and transport bans, necessarily imposed to contain disease spread, put pressure on global supply lines with freight volumes severely restricted. These issues were acutely felt in New Zealand, an island nation located at the end of most supply lines. This led New Zealand scientists to pose the hypothetical question: in a doomsday scenario where access to COVID-19 RT-qPCR reagents became unavailable, would New Zealand possess the expertise and infrastructure to make its own reagents onshore? In this work we describe a review of New Zealand's COVID-19 test requirements, bring together local experts and resources to make all reagents for the RT-qPCR process, and create a COVID-19 diagnostic assay referred to as HomeBrew (HB) RT-qPCR from onshore synthesized components. This one-step RT-qPCR assay was evaluated using clinical samples and shown to be comparable to a commercial COVID-19 assay. Through this work we show New Zealand has both the expertise and, with sufficient lead time and forward planning, infrastructure capacity to meet reagent supply challenges if they were ever to emerge.

Extraction-Free RT-PCR Surveillance Testing and Reporting for SARS-CoV-2

“…Clinical diagnostic testing in labs with The College of American Pathologists/Clinical Laboratory Improvement Amendments (CAP/CLIA) approval was the early gold standard in testing, but its reliance on RNA extraction reagents, approved nasal swabs, and transport medium, and the need for well-trained personnel to staff the testing labs, meant that the availability of these tests early on was scarce. Other groups evaluated alternative extraction methods, the cost-effectiveness of various tests, and the use of alternative reagents to circumvent the challenges in replicating these clinical-grade tests [13][14][15]. Some groups have even suggested AI-based imaging solutions to detect COVID-19 infection due to the cost and time required to perform RT-PCR [16].…”

Improved protocol for Bst polymerase and reverse transcriptase production and application to a point-of-care diagnostics system

“…Regardless of the chosen diagnostic method, the establishment of reliable protocols to produce enzymes with high yield and activity that are not covered by patents is essential to avoid the worldwide reagent shortage problems that happened during the COVID-19 pandemic. [30][31][32] This learned lesson may be crucial to deal with future threats of new pandemics, such as other respiratory and tropical diseases caused by infectious agents. 33,34 Another important lesson learned from the pandemic is the need to decentralize test performance, allowing for both faster diagnosis and access to remotely populated areas.…”

Test accuracy of rapid diagnostic tests and reverse‐transcription polymerase chain reaction against virus isolation in cell culture for assessing SARS‐CoV‐2 infectivity: Systematic review and meta‐analysis

“…5 These requirements limit fast decision-making processes on RT-qPCR test results. 6 Furthermore, the high sensitivity of RT-qPCR assays comes with the drawback of its long tail of RNA positivity in the postacute phase of COVID-19. 1,7 As a result, the interpretation of positive RT-qPCR data is often challenging, particularly with regard to shedding of infectious viral particles, despite the possibility of semiquantification of detected viral RNA expressed as cycle threshold (Ct).…”

“…However, there are several limitations of RT‐qPCR testing, including considerable turn‐around‐time due to sample transportation to professional laboratories and testing; high demands on personnel, technical equipment and data transmission 5 . These requirements limit fast decision‐making processes on RT‐qPCR test results 6 . Furthermore, the high sensitivity of RT‐qPCR assays comes with the drawback of its long tail of RNA positivity in the postacute phase of COVID‐19 1,7 .…”