A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron.

The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to understand transmission patterns and loads on healthcare resources. Next-generation sequencing (NGS) is the primary method for detecting and tracing new variants, but it is expensive, and it can take weeks before sequence data are available in public repositories. This article describes a customizable reverse transcription PCR (RT-PCR)-based genotyping approach which is significantly less expensive, accelerates reporting, and can be implemented in any lab that performs RT-PCR. Specific single-nucleotide polymorphisms (SNPs) and indels were identified which had high positive-percent agreement (PPA) and negative-percent agreement (NPA) compared to NGS for the major genotypes that circulated through September 11, 2021. Using a 48-marker panel, testing on 1,031 retrospective SARS-CoV-2 positive samples yielded a PPA and NPA ranging from 96.3 to 100% and 99.2 to 100%, respectively, for the top 10 most prevalent World Health Organization (WHO) lineages during that time. The effect of reducing the quantity of panel markers was explored, and a 16-marker panel was determined to be nearly as effective as the 48-marker panel at lineage assignment. Responding to the emergence of Omicron, a genotyping panel was developed which distinguishes Delta and Omicron using four highly specific SNPs. The results demonstrate the utility of the condensed panel to rapidly track the growing prevalence of Omicron across the US in December 2021 and January 2022.

Bioinspirational understanding of flexural performance in hedgehog spines.

In this research, the flexural performance of hedgehog spines is investigated in four ways. First, X-ray micro-computed tomography (µCT) is employed to analyze the complex internal architecture of hedgehog spines. µCT images reveal distinct structural morphology, characterized by longitudinal stringers and transverse central plates, which enhance flexural performance. Second, computer-aided design (CAD) is utilized to create and produce different three-dimensional (3D) computational models that gradually approach resemblance to hedgehog spines. Various levels of models are constructed by including and excluding key internal features of hedgehog spines, resulting in the formation of model levels from the simplest to the most realistic form. Third, finite element analysis (FEA) is exploited to simulate flexural behavior of hedgehog spines undergoing three-point bending. FEA results aim to identify and elucidate how internal structural features affect flexural stiffness and bending stress contours. Fourth, flexural analytical modeling is performed to calculate flexural shear flow and twist angle during transverse loading. The effects of the number of hedgehog outer cells, the spine wall thickness ratio and radius ratio are theoretically investigated to predict the shear stress and twist angle of the hedgehog spine structure. Results demonstrate that longitudinal stringers of the hedgehog spine significantly increase the overall flexural stiffness, while the transverse central plates provide support and rigidity to prevent spines from buckling and collapsing. Interestingly, the 3D model level that most realistically resembles the actual hedgehog spine is evidenced to have the highest specific bending stiffness, demonstrating nature's most efficient design. The findings of this study may be useful for developing hedgehog-inspired lightweight, high-stiffness, impact-tolerant structures. STATEMENT OF SIGNIFICANCE: This research has given much needed insight on the inner morphology of hedgehog spines and the structure-property relationship to the spine's flexural performance. X-ray µCT images reveal inner structural morphology, characterized by longitudinal stringers and transverse plates. Finite element analysis shows that longitudinal stringers significantly increase flexural stiffness, while the transverse plates provide support and rigidity to prevent buckling. The model that resembles the actual hedgehog spine is evidenced to have the highest specific bending stiffness, demonstrating nature's most efficient design. Analytical model studies influence on cell number, spine geometrical ratios, and further confirms nature's perfect design with lowest flexural shear flow and twist angle during transverse loading. This work paths future design for hedgehog-inspired lightweight, high-stiffness, impact-tolerant structures.

Static flexural properties of hedgehog spines conditioned in coupled temperature and relative humidity environments.

Hedgehogs are agile climbers, scaling trees and plants to heights exceeding 10m while foraging insects. Hedgehog spines (a.k.a. quills) provide fall protection by absorbing shock and could offer insights for the design of lightweight, material-efficient, impact-resistant structures. There has been some study of flexural properties of hedgehog spines, but an understanding of how this keratinous biological material is affected by various temperature and relative humidity treatments, or how spine color (multicolored vs. white) affects mechanics, is lacking. To bridge this gap in the literature, we use three-point bending to analyze the effect of temperature, humidity, spine color, and their interactions on flexural strength and modulus of hedgehog spines. We also compare specific strength and stiffness of hedgehog spines to conventional engineered materials. We find hedgehog spine flexural properties can be finely tuned by modifying environmental conditioning parameters. White spines tend to be stronger and stiffer than multicolored spines. Finally, for most temperature and humidity conditioning parameters, hedgehog spines are ounce for ounce stronger than 201 stainless steel rods of the same diameter but as pliable as styrene rods with a slightly larger diameter. This unique combination of strength and elasticity makes hedgehog spines exemplary shock absorbers, and a suitable reference model for biomimicry.

Dynamic impact testing of hedgehog spines using a dual-arm crash pendulum.

Hedgehog spines are a potential model for impact resistant structures and material. While previous studies have examined static mechanical properties of individual spines, actual collision tests on spines analogous to those observed in the wild have not previously been investigated. In this study, samples of roughly 130 keratin spines were mounted vertically in thin substrates to mimic the natural spine layout on hedgehogs. A weighted crash pendulum was employed to induce and measure the effects of repeated collisions against samples, with the aim to evaluate the influence of various parameters including humidity effect, impact energy, and substrate hardness. Results reveal that softer samples-due to humidity conditioning and/or substrate material used-exhibit greater durability over multiple impacts, while the more rigid samples exhibit greater energy absorption performance at the expense of durability. This trend is exaggerated during high-energy collisions. Comparison of the results to baseline tests with industry standard impact absorbing foam, wherein the spines exhibit similar energy absorption, verifies the dynamic impact absorption capabilities of hedgehog spines and their candidacy as a structural model for engineered impact technology.