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

Abstract

It has been 20 months since we first heard of SARS-CoV-2, the novel coronavirus detected in the Hubei province, China, in December 2019, responsible for the ongoing COVID-19 pandemic. Since then, a myriad of studies aimed at understanding and controlling SARS-CoV-2 have been published at a pace that has outshined the original effort to combat HIV during the beginning of the AIDS epidemic. This massive response started by developing strategies to not only diagnose individual SARS-CoV-2 infections but to monitor the transmission, evolution, and global spread of this new virus. We currently have hundreds of commercial diagnostic tests; however, that was not the case in early 2020, when just a handful of protocols were available, and few whole-genome SARS-CoV-2 sequences had been described. It was mid-January 2020 when several District Health Boards across New Zealand started planning the implementation of diagnostic testing for this emerging virus. Here, we describe our experience implementing a molecular test to detect SARS-CoV-2 infection, adapting the RT-qPCR assay to be used in a random-access platform (Hologic Panther Fusion® System) in a clinical laboratory, and characterizing the first whole-genome SARS-CoV-2 sequences obtained in the South Island, right at the beginning of the SARS-CoV-2 outbreak in New Zealand. We expect that this work will help us and others prepare for the unequivocal risk of similar viral outbreaks in the future.

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

“…Reference RNA for this work was prepared by the Viral Pathogenesis Laboratory, Microbiology and Immunology Department, University of Otago, using a sample obtained from an infected patient in Dunedin, NZ ( 7 ). Briefly, the positive clinical specimen was inoculated into VERO cells and incubated for 3–7 days at 37°C, with 5% CO 2 .…”

“…Early in the pandemic a number of RT-qPCR assays were designed and published that could reliably detect viral RNA from nasopharyngeal swab samples with high sensitivity and specificity. Two of these, the E-gene target ( 5 ) and N gene target ( 6 ), have proven reliable and robust and have been incorporated into processing pipelines of some centralized laboratory facilities in NZ [for example, Southern Community Laboratories (( 7 ), manuscript in preparation), and Environmental Science and Research Laboratories]. However, regardless of the target assay specifics, RT-qPCR diagnostics have the same basic and sequential steps in common: RNA extraction, reverse transcription and PCR.…”

Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic

“…Individuals infected with SARS-CoV-2 were diagnosed using a SARS-CoV-2 RT-qPCR assay implemented on the Hologic Panther Fusion ® System as described [22]. SARS-CoV-2 in cell-free supernatant was quantified using an in-house assay adapted from Corman et al [17] as previously described [22].…”

“…This simultaneous and-at times-coordinated effort, allowed for the dissemination of virus isolates to research laboratories capable of handling infectious viruses, as well as the rapid sharing of non-infectious material to clinical laboratories, public health agencies, and pharmaceutical or biotech companies. This initial work was key to developing and validating diagnostic assays [17][18][19][20][21][22], the screening of novel or re-purposed drugs as prophylactic and/or treatment strategies [23], and the design and development of numerous COVID-19 vaccine candidates [24] in every corner of the world.…”

“…We recently described our experience implementing a molecular diagnostic test on a random-access platform (Hologic Panther Fusion ® System, Marlborough, MA, USA), right on time to identify the first SARS-CoV-2 infections in New Zealand's South Island [22]. This work was initially hindered by the lack of access to key material (i.e., SARS-CoV-2 RNA), difficult to obtain during the early days of the pandemic.…”