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

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.

[1]  M. Quiñones-Mateu,et al.  Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island , 2021, Viruses.

[2]  G. Evans,et al.  Chemical Synthesis of the Antiviral Nucleotide Analogue ddhCTP. , 2021, The Journal of organic chemistry.

[3]  G. Church,et al.  Ultrasensitive Measurement of Both SARS-CoV-2 RNA and Antibodies from Saliva. , 2021, Analytical chemistry.

[4]  A. Pain,et al.  A Robust, Safe, and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Wastewater Samples , 2021, Global challenges.

[5]  B. Reinius,et al.  Detection of SARS-CoV-2 using non-commercial RT-LAMP regents and raw samples. , 2020, medRxiv.

[6]  D. Federman,et al.  SARS-CoV-2 detection in setting of viral swabs scarcity: Are MRSA swabs and viral swabs equivalent? , 2020, PloS one.

[7]  H. Mao,et al.  Detecting the Coronavirus (COVID-19) , 2020, ACS sensors.

[8]  R. Tjian,et al.  Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection , 2020, RNA.

[9]  A. Vélez,et al.  Cotton-Tipped Plastic Swabs for SARS-CoV-2 RT-qPCR Diagnosis to Prevent Supply Shortages , 2020, Frontiers in Cellular and Infection Microbiology.

[10]  Victor M Corman,et al.  Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR , 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[11]  Donna M Bond,et al.  Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation , 2018, bioRxiv.

[12]  Xiujuan Zheng,et al.  A simple and efficient method for extraction of Taq DNA polymerase , 2015 .

[13]  B. Verhasselt,et al.  Quantification of Reverse Transcriptase Activity by Real-Time PCR as a Fast and Accurate Method for Titration of HIV, Lenti- and Retroviral Vectors , 2012, PloS one.

[14]  B. Srinivasan,et al.  An Improved Protection-Free One-Pot Chemical Synthesis of 2′-Deoxynucleoside-5′-Triphosphates , 2012, Nucleosides, nucleotides & nucleic acids.

[15]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[16]  L. Burton,et al.  Ribonuclease inhibitors from the livers of five mammalian species. , 2009, International journal of peptide and protein research.

[17]  S. Moore,et al.  Ribonuclease inhibitor from bovine brain. , 2009, International journal of peptide and protein research.

[18]  D. Case,et al.  O-glycoside orientation is an essential aspect of base J recognition by the kinetoplastid DNA-binding protein JBP1. , 2007, Angewandte Chemie.

[19]  R. Shapiro,et al.  Cytoplasmic ribonuclease inhibitor. , 2001, Methods in enzymology.

[20]  R. Klebe,et al.  Affinity chromatography of RNase Inhibitor , 1997, Molecular Biology Reports.

[21]  F. Pluthero.  Rapid purification of high-activity Taq DNA polymerase. , 1993, Nucleic acids research.

[22]  K. Shadan,et al.  Available online: , 2012 .

[23]  P. Murphy.  Organophosphorus reagents : a practical approach in chemistry , 2004 .

[24]  H. Williams,et al.  Facile and highly selective 5′-desilylation of multisilylated nucleosides , 2000 .