Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses

Barksdale, Stephanie M.; Barclay, Robert A.; Smith, Natalie; Fernandes, Justin; Goldfarb, Daniel; Barbero, Robbie; Jones-Roe, Tara; Besse, Katherine; Dunlap, Ross; Kelly, Ross E. A.; Miao, Shida; Ruhunusiri, Chamodya; Munns, A. R. I.; Mosavi, Sayed; Munns, Denton; Sanson, Laura; Sahoo, Saswata; Swahn, Olivia; Hull, Killian; White, David O.; Kolb, Kevin; Noroozi, Fatemeh; Seelam, Joshna; Patnaik, Anurag; Lepene, Benjamin

doi:10.1101/2021.12.08.471814

Cited by 3 publications

(5 citation statements)

References 32 publications

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“…This capability has been demonstrated with Nanotrap particles used in a coinfection scenario with HIV and Rift Valley Fever Virus in bovine serum [12] . Since the COVID-19 pandemic began, Nanotrap particles have been used to detect SARS-CoV-2 [14, 15] and other respiratory viruses [16, 17] in wastewater. For example, Anderson et al [17] demonstrated that Nanotrap particles can be used for simultaneous concentration and detection of SARS-CoV-2, influenza, and Respiratory Syncytial Virus in wastewater.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Simple and Convenient Methods for SARS-CoV-2 Detection in Wastewater in high and Low Resource Settings

Liu

Guo

Cavallo

et al. 2023

Preprint

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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA monitoring in wastewater has become an important tool for COVID-19 surveillance. Although many viral concentration methods such as membrane filtration and skim milk are reported, these methods generally require large volumes of wastewater, expensive lab equipment, and laborious processes. We utilized a Nanotrap&R Microbiome A Particles (Nanotrap particle) method for virus concentration in wastewater. The method was evaluated across six parameters: pH, temperature, incubation time, wastewater volumes, RNA extraction methods, and two virus concentration approaches vs. a one-step method. The method was further evaluated with the addition of the Nanotrap Enhancement Reagent 1 (ER1) by comparing the automated vs. a manual Nanotrap particle method. RT-qPCR targeting the nucleocapsid protein was used for detection and quantification of SARS-CoV-2 RNA. Different pH, temperature, incubation time, wastewater volumes, and RNA extraction methods did not result in reduced SARS-CoV-2 detection in wastewater samples. The two-step concentration method showed significantly better results (P<0.01) than the one-step method. Adding ER1 to wastewater prior to viral concentration using the Nanotrap particles significantly improved PCR Ct results (P<0.0001) in 10 mL grab samples processed by automated Nanotrap particle method or 10 mL and 40 mL samples processed by manual Nanotrap particle method. SARS-CoV-2 detection in 10 mL grab samples with ER1 and the automated method showed significantly better (P=0.0008) results than 150 mL grab samples using the membrane filtration method. SARS-CoV-2 detection in 10 mL swab samples with ER1 via the automated method was also significantly better than without ER1 (P<0.0001) and the skim milk method in 250 mL Moore swab samples (P=0.012). These results suggest that Nanotrap methods could substitute the traditional membrane filtration and skim milk methods for viral concentration without compromising on the assay sensitivity. The manual method can be used in resource-limited areas, and the high-throughput platform is appropriate for large-scale COVID-19 wastewater-based surveillance.

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Section: Introductionmentioning

confidence: 99%

Evaluation of Simple and Convenient Methods for SARS-CoV-2 Detection in Wastewater in high and Low Resource Settings

Liu

Guo

Cavallo

et al. 2023

Preprint

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“…This capability has been demonstrated with Nanotrap particles used in a coinfection scenario with HIV and Rift Valley fever virus in bovine serum (Shafagati et al, 2013 ). Since the COVID-19 pandemic, Nanotrap particles have been used to detect SARS-CoV-2 (Karthikeyan et al, 2021a , b ; Zhan et al, 2022 ; Ahmed et al, 2023 ) and other respiratory viruses (Shafagati et al, 2016 ; Anderson et al, 2021 ) in wastewater. For example, Anderson et al ( 2021 ) showed that Nanotrap particles can be used for the concentration and detection of SARS-CoV-2, influenza, and respiratory syncytial viruses in wastewater simultaneously.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Nanotrap® Microbiome A Particles, membrane filtration, and skim milk workflows for SARS-CoV-2 concentration in wastewater

et al. 2023

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IntroductionSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA monitoring in wastewater has become an important tool for Coronavirus Disease 2019 (COVID-19) surveillance. Grab (quantitative) and passive samples (qualitative) are two distinct wastewater sampling methods. Although many viral concentration methods such as the usage of membrane filtration and skim milk are reported, these methods generally require large volumes of wastewater, expensive lab equipment, and laborious processes.MethodsThe objectives of this study were to compare two workflows (Nanotrap® Microbiome A Particles coupled with MagMax kit and membrane filtration workflows coupled with RNeasy kit) for SARS-CoV-2 recovery in grab samples and two workflows (Nanotrap® Microbiome A Particles and skim milk workflows coupled with MagMax kit) for SARS-CoV-2 recovery in Moore swab samples. The Nanotrap particle workflow was initially evaluated with and without the addition of the enhancement reagent 1 (ER1) in 10 mL wastewater. RT-qPCR targeting the nucleocapsid protein was used for detecting SARS-CoV-2 RNA.ResultsAdding ER1 to wastewater prior to viral concentration significantly improved viral concentration results (P < 0.0001) in 10 mL grab and swab samples processed by automated or manual Nanotrap workflows. SARS-CoV-2 concentrations in 10 mL grab and Moore swab samples with ER1 processed by the automated workflow as a whole showed significantly higher (P < 0.001) results than 150 mL grab samples using the membrane filtration workflow and 250 mL swab samples using the skim milk workflow, respectively. Spiking known genome copies (GC) of inactivated SARS-CoV-2 into 10 mL wastewater indicated that the limit of detection of the automated Nanotrap workflow was ~11.5 GC/mL using the RT-qPCR and 115 GC/mL using the digital PCR methods.DiscussionThese results suggest that Nanotrap workflows could substitute the traditional membrane filtration and skim milk workflows for viral concentration without compromising the assay sensitivity. The manual workflow can be used in resource-limited areas, and the automated workflow is appropriate for large-scale COVID-19 wastewater-based surveillance.

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“…A48383) using the automated nucleic acid extractor KingFisher™ Apex Magnetic Particle Processor. The protocol was completed as described previously 7 . The RT‐PCR analyses were performed using the TaqPath COVID‐19 CE‐IVD RT‐PCR Kit (Life Technologies, Carlsbad, CA).…”

Section: Methodsmentioning

confidence: 99%

“…The disease transmission dynamics and the pandemic progression within many African countries, including Angola, are still not investigated in detail. Angola lacks a strong genomic surveillance network, despite the emergence of two variants of concern (VOCs) within the southern African region, 6,7 and outbreaks of reemerging infectious diseases 8–11 . This may hamper the timely detection and early warning of newly emerging VOCs, variants of interest (VOIs), and other outbreaks of infectious diseases of global importance.…”

Section: Introductionmentioning

confidence: 99%

“…As a result, crucial national sectors such as healthcare and disease surveillance networks become constrained. This lack of infrastructure is especially concerning during infectious disease outbreaks, where the robustness of the healthcare system and pathogen surveillance initiatives are heavily dependent on it to facilitate effective disease control and prevention 6–10 …”

Section: Introductionmentioning

confidence: 99%

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Insights into SARS‐CoV‐2 in Angola during the COVID‐19 peak: Molecular epidemiology and genome surveillance

Francisco,

van Wyk,

Moir

et al. 2023

Influenza Resp Viruses

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BackgroundIn Angola, COVID‐19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS‐CoV‐2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID‐19 pandemic in Angola.MethodsWe generated 1210 whole‐genome SARS‐CoV‐2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Virus movement events were inferred using ancestral state reconstruction.ResultsThe epidemic in Angola was marked by four distinct waves of infection, dominated by 12 virus lineages, including VOCs, VOIs, and the VUM C.16, which was unique to South‐Western Africa and circulated for an extended period within the region. Virus exchanges occurred between Angola and its neighboring countries, and strong links with Brazil and Portugal reflected the historical and cultural ties shared between these countries. The first case likely originated from southern Africa.ConclusionA lack of a robust genome surveillance network and strong dependence on out‐of‐country sequencing limit real‐time data generation to achieve timely disease outbreak responses, which remains of the utmost importance to mitigate future disease outbreaks in Angola.

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Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses

Cited by 3 publications

References 32 publications

Evaluation of Simple and Convenient Methods for SARS-CoV-2 Detection in Wastewater in high and Low Resource Settings

Evaluation of Simple and Convenient Methods for SARS-CoV-2 Detection in Wastewater in high and Low Resource Settings

Comparison of Nanotrap® Microbiome A Particles, membrane filtration, and skim milk workflows for SARS-CoV-2 concentration in wastewater

Insights into SARS‐CoV‐2 in Angola during the COVID‐19 peak: Molecular epidemiology and genome surveillance

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