The influence of food matrices on aptamer selection by SELEX (systematic evolution of ligands by exponential enrichment) targeting the norovirus P-Domain

Sample Processing and Concentration Methods for Viruses from Foods and the Environment Prior to Detection

Viruses are the leading cause of foodborne illness globally. Concentration of viruses from samples is important for detection because viral contamination of foods often occurs at low levels. In general, virus concentration methods can be classified as either nonspecific, exploiting the relatively homogeneous physicochemical properties of the virus to separate/concentrate it from the sample matrix, or specific, relying on recognition elements such as antibodies to specifically capture and separate viruses from foods. Numerous nonspecific and specific techniques for virus concentration have been reported, each with its own advantages and limitations. Factors to consider can include reagent and equipment costs, time-to-result, ease of use, and potential to eliminate matrix-associated inhibitors. The purpose of this review is to survey the different foodborne virus concentration techniques and their efficacy in various food and environmental matrices as well as discuss some emerging techniques for purification and concentration of viral pathogens from food samples.

Selection and application of highly specific Salmonella typhimurium aptamers against matrix interference

In practical applications, the structure and performance of aptamers can be influenced by the presence of sample matrices, which interferes with the specific binding between the aptamer and its target. In this work, to obtain aptamer chains resistant to matrix interference, four typical food matrices were introduced as negative selection targets and selection environments in the process of selecting aptamers for Salmonella typhimurium using the systematic evolution of ligands by exponential enrichment (SELEX) technology. As a result, some highly specific candidate aptamers for Salmonella typhimurium (BB-34, BB-37, ROU-8, ROU-9, ROU-14, ROU-24, DAN-3, NAI-12, and NAI-21) were successfully obtained. Based on the characterization results of secondary structure, affinity, and specificity of these candidate aptamers, ROU-24 selected in the pork matrix and BB-34 selected in the binding buffer were chosen to develop label-free fluorescence aptasensors for the sensitive and rapid detection of the Salmonella typhimurium and verify the performance against matrix interference. The ROU-24-based aptasensor demonstrated a larger linear range and better specificity compared to the BB-34-based aptasensor. Meanwhile, the recovery rate of the ROU-24-based aptasensor in real sample detection (ranging from 94.2% to 110.7%) was significantly higher than that of the BB-34-based aptasensor. These results illustrated that the negative selection of food matrices induced in SELEX could enhance specific binding between the aptamer and its target and the performance against matrix interference. Overall, the label-free fluorescence aptasensors were developed and successfully validated in different foodstuffs, demonstrating a theoretical and practical basis for the study of aptamers against matrix interference.

Establishment of fumonisin B1 detection method for catalytic fluorescence detection of aptamer-regulated carbon dots

Mycotoxin, common in agricultural products, is a small secondary metabolite with strong toxicity. Fumonisin B₁ (FB₁) is the most common and the most toxic. Establishing a rapid detection method is important for preventing and controlling FB₁ pollution. This study prepared carbon dots (CDs) from 2,2'-dithiosalicylic acid (DTSA). Tetramethylbenzidine (TMB) can be catalyzed to produce fluorescence by CDs, while FB₁ can adhere to the surface of CDs, decreasing fluorescence. Aptamer F10 of FB₁ combines with FB₁ attached to the surface of CDs to restore the catalytic ability of CDs and increase the fluorescence value. This method has good linearity in the FB₁ concentration range from 0 to 1.0 μg mL^-1. The standard curve was Y = -0.2512x + 661.4, R² = 0.9903, the limit of detection (LOD) was 17.67 ng mL^-1 and limit of quantitation (LOQ) was 53.55 ng mL^-1. The recovery of the corn sample was 89.83-98.62%, and the detection time was 30 min.

Microfluidic Paper-Based Analytical Devices for the Determination of Food Contaminants: Developments and Applications

Food safety is an issue that cannot be ignored at any time because of the great impact of food contaminants on people's daily life, social production, and the economy. Because of the extensive demand for high-quality food, it is necessary to develop rapid, reliable, and efficient devices for food contaminant detection. Microfluidic paper-based analytical devices (μPADs) have been applied in a variety of detection fields owing to the advantages of low-cost, ease of handling, and portability. This review systematically discusses the latest progress of μPADs, including the fundamentals of fabrication as well as applications in the detection of chemical and biological hazards in foods, hoping to provide suitable screening strategies for contaminants in foods and accelerating the technology transformation of μPADs from the lab into the field.

Viral outbreaks detection and surveillance using wastewater-based epidemiology, viral air sampling, and machine learning techniques: A comprehensive review and outlook

A viral outbreak is a global challenge that affects public health and safety. The coronavirus disease 2019 (COVID-19) has been spreading globally, affecting millions of people worldwide, and led to significant loss of lives and deterioration of the global economy. The current adverse effects caused by the COVID-19 pandemic demands finding new detection methods for future viral outbreaks. The environment's transmission pathways include and are not limited to air, surface water, and wastewater environments. The wastewater surveillance, known as wastewater-based epidemiology (WBE), can potentially monitor viral outbreaks and provide a complementary clinical testing method. Another investigated outbreak surveillance technique that has not been yet implemented in a sufficient number of studies is the surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in the air. Artificial intelligence (AI) and its related machine learning (ML) and deep learning (DL) technologies are currently emerging techniques for detecting viral outbreaks using global data. To date, there are no reports that illustrate the potential of using WBE with AI to detect viral outbreaks. This study investigates the transmission pathways of SARS-CoV-2 in the environment and provides current updates on the surveillance of viral outbreaks using WBE, viral air sampling, and AI. It also proposes a novel framework based on an ensemble of ML and DL algorithms to provide a beneficial supportive tool for decision-makers. The framework exploits available data from reliable sources to discover meaningful insights and knowledge that allows researchers and practitioners to build efficient methods and protocols that accurately monitor and detect viral outbreaks. The proposed framework could provide early detection of viruses, forecast risk maps and vulnerable areas, and estimate the number of infected citizens.

Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers

Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.

Potential applications of aptamers in veterinary science

Aptamers are small nucleic acids that fold in a three-dimensional conformation allowing them to bind specifically to a target. This target can be an organic molecule, free or carried in cells or tissues, or inorganic components, such as metal ions. Analogous to monoclonal antibodies, aptamers however have certain advantages over the latter: e.g., high specificity for their target, no to low immunogenicity and easy in vitro selection. Since their discovery more than 30 years ago, aptamers have led to various applications, although mainly restricted to basic research. This work reviews the applications of aptamers in veterinary science to date. First, we present aptamers, how they are selected and their properties, then we give examples of applications in food and environmental safety, as well as in diagnosis and medical treatment in the field of veterinary medicine. Because examples of applications in veterinary medicine are scarce, we explore the potential avenues for future applications based on discoveries made in human medicine. Aptamers may offer new possibilities for veterinarians to diagnose certain diseases—particularly infectious diseases—more rapidly or “at the patient’s bedside”. All the examples highlight the growing interest in aptamers and the premises of a potential market. Aptamers may benefit animals as well as their owners, breeders and even public health in a “One Health” approach.

Detection and disinfection of COVID-19 virus in wastewater

The coronavirus disease 2019, COVID-19, caused by the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, appears as a major pandemic having adverse impact on public health and economic activities. Since viral replication in human enterocytes results in its faecal shedding, wastewater surveillance is an ideal, non-invasive, cost-effective and an early warning epidemiological approach to detect the genetic material of SARS-CoV-2. Here, we review techniques for the detection of SARS-CoV-2 in municipal wastewater, and disinfectants used to control viral spread. For detection, concentration of ribonucleic acid involves ultrafiltration, ultracentrifugation and polyethylene glycol precipitation. Identification is done by reverse transcriptase amplification, nucleic acid sequence-based amplification, helicase dependent amplification, loop-mediated isothermal amplification, recombinase polymerase amplification, high throughput screening and biosensor assays. Disinfectants include ultraviolet radiations, ozone, chlorine dioxide, hypochlorites and hydrogen peroxide. Wastewater surveillance data indicates viral presence within longer detection window, and provides transmission dynamics earlier than classical methods. This is particularly relevant for pre-symptomatic and asymptomatic COVID-19 cases.

Selection of Specific DNA Aptamers for Hetero-Sandwich-Based Colorimetric Determination of Campylobacter jejuni in Food

Herein, a high-affinity single-stranded DNA aptamer (59 nt) against Campylobacter jejuni, defined as CJA1, was obtained using the whole-bacterium-based systemic evolution of ligands by exponential enrichment procedure. CJA1 was analyzed with a stable secondary structure and low dissociation constant (K_d) value of 1.37 ± 0.28 nM. The potential use of CJA1 was exemplified by the construction of a hetero-sandwich platform, in which C. jejuni was bound with a biotin-tagged CJA1 to perform a colorimetric reaction that is associated with visible color changes and detectable optical responses. Dependent upon this sensing platform, C. jejuni can be detected from 1.7 × 10¹ to 1.7 × 10⁶ colony-forming units (CFU)/mL. The limit of detection (LOD) is obtained as 10 CFU/mL in PBS. The specificity study showed that the sensing platform is easy to distinguish C. jejuni from other common pathogens. Moreover, the C. jejuni-contaminated milk samples can also be accurately probed (LOD = 13 CFU/mL) without sacrificing its assay abilities, indicating the promising prospect of CJA1 in the fields of biosensing and diagnostics.

A Survey of Analytical Techniques for Noroviruses

As the leading cause of acute gastroenteritis worldwide, human noroviruses (HuNoVs) have caused around 685 million cases of infection and nearly $60 billion in losses every year. Despite their highly contagious nature, an effective vaccine for HuNoVs has yet to become commercially available. Therefore, rapid detection and subtyping of noroviruses is crucial for preventing viral spread. Over the past half century, there has been monumental progress in the development of techniques for the detection and analysis of noroviruses. However, currently no rapid, portable assays are available to detect and subtype infectious HuNoVs. The purpose of this review is to survey and present different analytical techniques for the detection and characterization of noroviruses.

Aptamer-functionalized chitosan magnetic nanoparticles as a novel adsorbent for selective extraction of ochratoxin A

The preparation and application of aptamer-functionalized chitosan magnetic nanoparticles (Fe₃O₄@CTS@Apt nanoparticles) for selective extraction and determination ochratoxin A (OTA) were described in this study. Magnetic nanoparticle was synthesized by the coprecipitation method followed by coating with chitosan to improve its stability and biocompatibility. Further characterization was performed by scan electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), thermogravimetric analysis (TGA) and magnetic property measurement, and the results clearly indicated that the obtained magnetic chitosan nanoparticle was composed of magnetic core and chitosan coating layer. Aptamers specific to OTA were coupled onto the magnetic chitosan nanoparticles, and an extraction procedure was developed by optimization. When challenged with food samples fortified with OTA at 5 and 10 μg/kg, recoveries ranging from 91.3% to 99.1% with relative standard deviation (RSD) ≤ 4.2% were achieved by aptamer-functionalized magnetic extraction, which is very close to the results obtained by immunoaffinity chromatography extraction, indicating that this magnetic adsorbent could be hopefully used to achieve a fast and efficient extraction and detection of OTA in food samples.