Hydrogel particles improve detection of SARS-CoV-2 RNA from multiple sample types

Abstract

Here we present a rapid and versatile method for capturing and concentrating SARS-CoV-2 from contrived transport medium and saliva samples using affinity-capture magnetic hydrogel particles. We demonstrate that the method concentrates virus from 1 mL samples prior to RNA extraction, substantially improving detection of virus using real-time RT-PCR across a range of viral titers (100–1,000,000 viral copies/mL) and enabling detection of virus using the 2019 nCoV CDC EUA Kit down to 100 viral copies/mL. This method is compatible with commercially available nucleic acid extraction kits (i.e., from Qiagen) and a simple heat and detergent method that extracts viral RNA directly off the particle, allowing a sample processing time of 10 min. We furthermore tested our method in transport medium diagnostic remnant samples that previously had been tested for SARS-CoV-2, showing that our method not only correctly identified all positive samples but also substantially improved detection of the virus in low viral load samples. The average improvement in cycle threshold value across all viral titers tested was 3.1. Finally, we illustrate that our method could potentially be used to enable pooled testing, as we observed considerable improvement in the detection of SARS-CoV-2 RNA from sample volumes of up to 10 mL.

An ultrafast SARS-CoV-2 virus enrichment and extraction method compatible with multiple modalities for RNA detection

“…Although RNA obtained via enriched rnaGEM extraction was readily detected with C t values of 20±2 units in all dilutions, the values of commercial extracts were ∼3 cycles lower. A similar phenomenon was observed by Barclay et al, who suspected viral saturation of the nanoparticles at very high titers; 22 virions were likely sterically prevented from binding with the particles and were lost in the discarded supernatant prior to extraction. Still, Barclay et al suggests that nanoparticle saturation does not affect the utility of enrichment-aided extractions since it does not prevent qualitative SARS-CoV-2 identification.…”

“…Still, Barclay et al suggests that nanoparticle saturation does not affect the utility of enrichment-aided extractions since it does not prevent qualitative SARS-CoV-2 identification. 22 We believe this to be especially true as it pertains to high titer samples such as the one in question, since regardless of extraction method, amplification occurred well below the cut-off cycle and SARS-CoV-2 was readily detected.…”

“… 8 As the pandemic continued, commercial nucleic acid preparation kits became supply-chain limited and existing laboratory infrastructure has been largely overwhelmed. 22 , 23 To enable the required expansion of testing capabilities, alternative analytical strategies must be implemented. One such strategy proposed by the United States Department of Human Health and Safety for surveillance in asymptomatic or low disease prevalence populations involves pooling samples from up to 20 individuals in a single test.…”

Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus

“…Briefly, 10 ml of raw sewage was concentrated using an automated affinity capture magnetic hydrogel particle (Ceres Nanosciences Inc., USA)-based concentration method using a KingFisher Flex liquid-handling robot platform (Thermo Fisher Scientific, USA) ( 13 ). The concentrated viral RNA was then extracted using the MagMAX Microbiome Ultra Nucleic Acid isolation kit (catalog no.…”

Hydrogels and Their Role in Biosensing Applications

“…[1] This need exemplifies the importance of fast, efficient, and reliable testing and demonstrates the value of biosensors and bioanalytical tests. [2,3] Even before the COVID-19 outbreak, however, biosensors and bioanalytical detection methods played a major role in the fields of clinical diagnostics, pointof-care testing, personalized medicine, and pharmaceutical research, with a key objective of understanding interaction processes at the molecular level. [4,5] In this area, highly sensitive detection platforms with excellent specificity are required for their ability to provide useful insights into individual's health.…”