Magnetic hydrogel particles improve nanopore sequencing of SARS-CoV-2 and other respiratory viruses.

Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with Nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40 × improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher automation platform.

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

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.

Evaluation of corn fiber, cottonseed hulls, oat hulls and soybean hulls as roughage sources for ruminants.

An in situ trial (randomized complete block design) using cows, and a site and extent of digestion trial (Latin square design) using sheep were conducted to study the potential of corn fiber (CF), cottonseed hulls (CSH), oat hulls (OH) and soybean hulls (SH) as roughage sources for ruminants. Two feedlot trials with steers and one with lambs (completely randomized design with factorial arrangements of treatments) were conducted to study the potential of CF and SH as energy supplements relative to corn. In situ rate of ruminal dry matter (DM) disappearance (3 to 36 h) and extent of DM disappearance (36 h) indicated that CF and SH were more fermentable in the rumen compared with OH or CSH, with SH being the most fermentable. Total tract digestibilities of DM, organic matter (OM), neutral detergent fiber (NDF) and acid detergent fiber (ADF) were above 70% for sheep fed CF and SH diets, and were 50% or less for sheep fed OH and CSH diets. A ranking of by-products in terms of nutritive value followed the trend: CF greater than SH greater than OH greater than CSH. Lamb feedlot trial data showed that CF was of similar nutritive value to corn and of higher nutritive value than SH at the 50% level of supplementation. Corn-fed lambs responded better than CF- or SH-fed lambs at the 70% level of supplementation. Data from steer feedlot trials showed that CF was of similar quality to corn and of higher quality than SH. Dramatic differences exist in by-product feed utilization by ruminants. All by-products tested appeared to have some usefulness as dietary components.