End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments

Parker, Ceth W.; Singh, Nitin Kumar; Tighe, Scott; Blachowicz, Adriana; Wood, Jason M.; Seuylemezian, Arman; Vaishampayan, Parag; Urbaniak, Camilla; Hendrickson, Ryan C.; Laaguiby, Pheobe; Clark, Kevin; Clement, Brian; O’Hara, Niamh B.; Couto-Rodriguez, Mara; Bezdan, Daniela; Mason, Chris; Venkateswaran, Kasthuri

doi:10.1101/2020.08.16.20172668

Cited by 5 publications

(6 citation statements)

References 46 publications

(52 reference statements)

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“…2). The mean recovery efficiencies ranged from 28 to 42% across the three surfaces, values similar to those reported in a previous study of SARS-CoV-2 surface swabbing 19 .…”

Section: Discussionsupporting

confidence: 86%

SARS-CoV-2 Detection from the Built Environment and Wastewater and Its Use for Hospital Surveillance

Hinz

Liu

Doukhanine

et al. 2021

Preprint

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Background. SARS-CoV-2 causes significant morbidity and mortality in health care settings. Our understanding of the distribution of this virus in the built healthcare environment and wastewater, and relationship to disease burden, is limited. Methods. We performed a prospective multi-center study of environmental sampling of SARS-CoV-2 from hospital surfaces and wastewater and evaluated their relationships with regional and hospital COVID-19 burden. We developed and validated a qPCR-based approach to surface sampling, and swab samples were collected weekly from different locations and surfaces across two tertiary care hospital campuses for a 10-week period during the pandemic, along with wastewater samples. Results. Over a 10-week period, 963 swab samples were collected and analyzed. We found 61 (6%) of swabs were positive for SARS-CoV-2, with the majority of these (n=51) originating from floor samples. Wards that actively managed patients with COVID-19 had the highest frequency of positive samples (p<0.01). Detection frequency in built environment swabs was significantly associated with active cases in the hospital throughout the study (p<0.025). Wastewater viral signal changes appeared to predate change in case burden. Conclusions. Environment sampling for SARS-CoV-2, in particular from floors, may offer a unique and resolved approach to surveillance of COVID-19.

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“…2). The mean recovery efficiencies ranged from 28 to 42% across the three surfaces, values similar to those reported in a previous study of SARS-CoV-2 surface swabbing 19 .…”

Section: Discussionsupporting

confidence: 86%

SARS-CoV-2 Detection from the Built Environment and Wastewater and Its Use for Hospital Surveillance

Hinz

Liu

Doukhanine

et al. 2021

Preprint

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“…As the standard real samples, NATtrol™ SARS-CoV-2 stock that contains an intact virus in the specific matrix is widely used ( Parker et al, 2020 ; Pickering et al, 2021 ), and the matrix of NATtrol™ samples was made to contain antioxidants, buffer salts, preservatives, antibiotics, and matrix stabilizing fillers such as sugars, proteins that mimic the composition of clinical sample ( Chan et al, 2016 ; Eboigbodin et al, 2016 ; Favaro et al, 2021 ). And then, the assay results were compared with a commercially available rapid test kit.…”

Section: Resultsmentioning

confidence: 99%

Capacitive biosensor based on vertically paired electrodes for the detection of SARS-CoV-2

Park

Lee

Song

et al. 2022

Biosensors and Bioelectronics

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Vertically paired electrodes (VPEs) with multiple electrode pairs were developed for the enhancement of capacitive measurements by optimizing the electrode gap and number of electrode pairs. The electrode was fabricated using a conductive polymer layer of PEDOT:PSS instead of Ag and Pt metal electrodes to increase the VPE fabrication yield because the PEDOT:PSS layer could be effectively etched using a reactive dry etching process. In this study, sensitivity enhancement was realized by decreasing the electrode gap and increasing the number of VPE electrode pairs. Such an increase in sensitivity according to the electrode gap and the number of electrode pairs was estimated using a model analyte for an immunoassay. Additionally, a computer simulation was performed using VPEs with different electrode gaps and numbers of VPE electrode pairs. Finally, VPEs with multiple electrode pairs were applied for SARS-CoV-2 nucleoprotein (NP) detection. The capacitive biosensor based on the VPE with immobilized anti-SARS-CoV-2 NP was applied for the specific detection of SARS-CoV-2 in viral cultures. Using viral cultures of SARS-CoV-2, SARS-CoV, MERS-CoV, and CoV-strain 229E, the limit of detection (LOD) was estimated to satisfy the cutoff value (dilution factor of 1/800) for the medical diagnosis of COVID-19, and the assay results from the capacitive biosensor were compared with commercial rapid kit based on a lateral flow immunoassay.

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“…In addition to assessing exclusivity (that primers bind only to the pathogen or target region of interest), it is also necessary to evaluate their inclusivity by comparing them against known variations in the targeted region (Corman et al 2020, Sapoval et al 2020. This is particularly (and increasingly) important as new variants of the virus emerge (https://www.gisaid.org/; https://nextstrain.org) to ensure newly arising viral variants are still detectable with these primer sets, including for low-input samples (Parker et al 2020). From an inclusivity perspective, LAMP is, in general, quite tolerant of small changes to the target sequence, although the converse is that it is more difficult to create specificity for single-nucleotide polymorphisms (SNPs) or variants at the level of primer selection (see "Topic C").…”

Section: In Silico Primer Design and Selectionmentioning

confidence: 99%

“…An exception to this is sequencing using nanopores, which can take as little as 1 hour when samples are not multiplexed at high numbers (James et al 2020). For example, Parker et al (2020) describe purifying the amplified LAMP DNA using a traditional column-based method and synthesizing a single, rapid nanopore library with RAD004 or a multiplex, rapid library with RBK004. This technique is similar to RT-LAMP sequencing devised by Dao Thi et al (2020) that multiplexes many RT-LAMP samples after an intermediate PCR step.…”

Section: Ngs For Lampmentioning

confidence: 99%

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

Moore

Cahill²,

Aidelberg

et al. 2021

J Biomol Tech

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As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.

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End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments

Cited by 5 publications

References 46 publications

SARS-CoV-2 Detection from the Built Environment and Wastewater and Its Use for Hospital Surveillance

SARS-CoV-2 Detection from the Built Environment and Wastewater and Its Use for Hospital Surveillance

Capacitive biosensor based on vertically paired electrodes for the detection of SARS-CoV-2

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

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