Evaluation of extraction and amplification assays for the detection of SARS-CoV-2 at Auckland Hospital laboratory during the COVID-19 outbreak in New Zealand

Basu, Indira; Nagappan, Ramesh; Fox-Lewis, Shivani; Muttaiyah, Sharmini; McAuliffe, Gary

doi:10.1016/j.jviromet.2020.114042

Cited by 8 publications

(7 citation statements)

References 2 publications

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“…It was during the week of 13 March 2020, when our newly implemented SARS-CoV-2 assay was ready in the clinical laboratory, that the first few cases of COVID-19 were identified in the South Island, New Zealand: the ideal debut and test for our assay. At the time, clinical laboratories across the country were using other LDTs to diagnose SARS-CoV-2 infections [30,31]. We showed that our assay performed similarly to the other contemporary molecular diagnostic tests, correctly identifying (or not) infections by SARS-CoV-2.…”

Section: Discussionmentioning

confidence: 69%

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

Lawley

Grant

Harfoot

et al. 2021

Viruses

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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.

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Section: Discussionmentioning

confidence: 69%

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

Lawley

Grant

Harfoot

et al. 2021

Viruses

View full text Add to dashboard Cite

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“…PPE was in short supply across the globe, affecting the availability of this critical safety equipment in many countries, including New Zealand. The country was able to organize an good response to the COVID-19 pandemic, starting with a series of public health-measures [48,49], establishing molecular diagnostic assays [2][3][4], monitoring the SARS-CoV-2 variants in the region [6,50], and isolating the virus circulating in New Zealand [51]. However, New Zealand experienced the same PPE shortages as numerous other countries, and the NZ Office of the Auditor-General reported gaps in planning of PPE procurement and distribution, with insufficient national stock reserves (https: //oag.parliament.nz/, accessed on 26 October 2021).…”

Section: Discussionmentioning

confidence: 99%

“…SARS-CoV-2 was first identified in Aotearoa/New Zealand (henceforth referred to as New Zealand) in February 2020 [1]. A combination of public-health measures including a swift lockdown [1], establishment of diagnostic capabilities [2][3][4], and research programs [5,6], together with an exemplary response from the community, allowed the country to control the initial virus outbreak [1,5,7]. Even to date, in the middle of surges of SARS-CoV-2 delta and omicron variants worldwide, New Zealand is one of the countries with the lowest number of confirmed COVID-19 cases per capita (https://nzcoviddashboard.esr.cri.nz/#!/international, accessed on 26 November 2021).…”

Section: Introductionmentioning

confidence: 99%

Ultraviolet-C Irradiation, Heat, and Storage as Potential Methods of Inactivating SARS-CoV-2 and Bacterial Pathogens on Filtering Facepiece Respirators

et al. 2022

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The arrival of SARS-CoV-2 to Aotearoa/New Zealand in February 2020 triggered a massive response at multiple levels. Procurement and sustainability of medical supplies to hospitals and clinics during the then upcoming COVID-19 pandemic was one of the top priorities. Continuing access to new personal protective equipment (PPE) was not guaranteed; thus, disinfecting and reusing PPE was considered as a potential alternative. Here, we describe part of a local program intended to test and implement a system to disinfect PPE for potential reuse in New Zealand. We used filtering facepiece respirator (FFR) coupons inoculated with SARS-CoV-2 or clinically relevant multidrug-resistant pathogens (Acinetobacter baumannii Ab5075, methicillin-resistant Staphylococcus aureus USA300 LAC and cystic-fibrosis isolate Pseudomonas aeruginosa LESB58), to evaluate the potential use of ultraviolet-C germicidal irradiation (UV-C) or dry heat treatment to disinfect PPE. An applied UV-C dose of 1000 mJ/cm2 was sufficient to completely inactivate high doses of SARS-CoV-2; however, irregularities in the FFR coupons hindered the efficacy of UV-C to fully inactivate the virus, even at higher UV-C doses (2000 mJ/cm2). Conversely, incubating contaminated FFR coupons at 65 °C for 30 min or 70 °C for 15 min, was sufficient to block SARS-CoV-2 replication, even in the presence of mucin or a soil load (mimicking salivary or respiratory secretions, respectively). Dry heat (90 min at 75 °C to 80 °C) effectively killed 106 planktonic bacteria; however, even extending the incubation time up to two hours at 80 °C did not completely kill bacteria when grown in colony biofilms. Importantly, we also showed that FFR material can harbor replication-competent SARS-CoV-2 for up to 35 days at room temperature in the presence of a soil load. We are currently using these findings to optimize and establish a robust process for decontaminating, reusing, and reducing wastage of PPE in New Zealand.

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“…In the past 3 years, most devices, but especially small and less expensive ones, had been featured in at least one published application where they have been used to create an automated platform or improve existing ones. Analytik Jena's CyBio Felix [29] and Eppendorf's epMotion [30] were used to perform RNA extraction from patient samples in clinical settings. Other devices were employed to perform more complex applications related to SARS-CoV-2 virus than those highlighted above.…”

Section: Specific Applications Of Lhdmentioning

confidence: 99%

Automated liquid-handling operations for robust, resilient, and efficient bio-based laboratory practices

Torres‐Acosta

Lye

Dikicioglu

2022

Preprint

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Increase in the adoption of liquid handling devices (LHD) can facilitate experimental activities. Initially adopted by businesses and industry-based laboratories, the practice has also moved to academic environments, where a wide range of non-standard/non-typical experiments can be performed. Current protocols or laboratory analyses require researchers to transfer liquids for the purpose of dilution, mixing, or inoculation, among other operations. LHD can render laboratories more efficient by performing more experiments per unit of time, by making operations robust and resilient against external factors and unforeseen events such as the COVID-19 pandemic, and by remote operation. The present work reviews literature that reported the adoption and utilisation of LHD available in the market and presents examples of their practical use. Applications demonstrate the critical role of automation in research development and its ability to reduce human intervention in the experimental workflow. Ultimately, this work will provide guidance to academic researchers to determine which LHD can fulfil their needs and how to exploit their use in both conventional and non-conventional applications. Furthermore, the breadth of applications and the scarcity of academic institutions involved in research and development that utilise these devices highlights an important area of opportunity for shift in technology to maximize research outcomes.

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Evaluation of extraction and amplification assays for the detection of SARS-CoV-2 at Auckland Hospital laboratory during the COVID-19 outbreak in New Zealand

Cited by 8 publications

References 2 publications

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

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

Ultraviolet-C Irradiation, Heat, and Storage as Potential Methods of Inactivating SARS-CoV-2 and Bacterial Pathogens on Filtering Facepiece Respirators

Automated liquid-handling operations for robust, resilient, and efficient bio-based laboratory practices

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