Detection of norovirus, sapovirus, and human astrovirus in fecal specimens using a multiplex reverse transcription-PCR with fluorescent dye-labeled primers

An Inexpensive System for Rapid and Accurate On-site Detection of Garlic-Infected Viruses by Agarose Gel Electrophoresis Followed by Array Assay

Garlic can be infected by a variety of viruses, but mixed infections with leek yellow stripe virus, onion yellow dwarf virus, and allexiviruses are the most damaging, so an easy, inexpensive on-site method to simultaneously detect at least these three viruses with a certain degree of accuracy is needed to produce virus-free plants. The most common laboratory method for diagnosis is multiplex reverse transcription polymerase chain reaction (RT-PCR). However, allexiviruses are highly diverse even within the same species, making it difficult to design universal PCR primers for all garlic-growing regions in the world. To solve this problem, we developed an inexpensive on-site detection system for the three garlic viruses that uses a commercial mobile PCR device and a compact electrophoresis system with a blue light. In this system, virus-specific bands generated by electrophoresis can be identified by eye in real time because the PCR products are labeled with a fluorescent dye, FITC. Because the electrophoresis step might eventually be replaced with a lateral flow assay (LFA), we also demonstrated that a uniplex LFA can be used for virus detection; however, multiplexing and a significant cost reduction are needed before it can be used for on-site detection.

Application of the Peroxidase‒like Activity of Nanomaterials for the Detection of Pathogenic Bacteria and Viruses

Infectious diseases caused by pathogenic bacteria and viruses pose a significant threat to human life and well-being. The prompt identification of these pathogens, characterized by speed, accuracy, and efficiency, not only aids in the timely screening of infected individuals and the prevention of further transmission, but also facilitates the precise diagnosis and treatment of patients. Direct smear microscopy, microbial culture, nucleic acid-based polymerase chain reaction (PCR), and enzyme-linked immunosorbent assay (ELISA) based on microbial surface antigens or human serum antibodies, have made substantial contributions to the prevention and management of infectious diseases. Due to its shorter processing time, simple equipment requirements, and no need for professional and technical personnel, ELISA has inherent advantages over other methods for detecting pathogenic bacteria and viruses. Horseradish peroxidase mediated catalysis of substrate coloration is the key for the detection of target substances in ELISA. However, the variability, high cost, and environmental susceptibility of natural peroxidase greatly limit the application of ELISA in pathogen detection. Compared with natural enzymes, nanomaterials with enzyme-mimicking activity are inexpensive, highly environmentally stable, easy to store and mass producing, etc. Based on their peroxidase-like activities and unique physicochemical properties, nanomaterials can greatly improve the efficiency and ease of use of ELISA-like detection methods for pathogenic bacteria and viruses. This review introduces recent advances in the application of nanomaterials with peroxidase-like activity for the detection of pathogenic bacteria (both gram-negative bacteria and gram-positive bacteria) and viruses (both RNA viruses and DNA viruses). The emphasis is on the detection principle and the evaluation of effectiveness. The limitations and prospects for future translations are also discussed.

Noroviruses-The State of the Art, Nearly Fifty Years after Their Initial Discovery

Human noroviruses are recognised as the major global cause of viral gastroenteritis. Here, we provide an overview of notable advances in norovirus research and provide a short recap of the novel model systems to which much of the recent progress is owed. Significant advances include an updated classification system, the description of alternative virus-like protein morphologies and capsid dynamics, and the further elucidation of the functions and roles of various viral proteins. Important milestones include new insights into cell tropism, host and microbial attachment factors and receptors, interactions with the cellular translational apparatus, and viral egress from cells. Noroviruses have been detected in previously unrecognised hosts and detection itself is facilitated by improved analytical techniques. New potential transmission routes and/or viral reservoirs have been proposed. Recent in vivo and in vitro findings have added to the understanding of host immunity in response to norovirus infection, and vaccine development has progressed to preclinical and even clinical trial testing. Ongoing development of therapeutics includes promising direct-acting small molecules and host-factor drugs.

Astrovirus Diagnostics

Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.

Detection of gastroenteritis viruses among pediatric patients in Hiroshima Prefecture, Japan, between 2006 and 2013 using multiplex reverse transcription PCR-based assays involving fluorescent dye-labeled primers

Multiplex reverse transcription (RT)-polymerase chain reaction (PCR)-based assays involving fluorescent dye-labeled primers were modified to detect 10 types of gastroenteritis viruses by adding two further assays to a previously developed assay. Then, these assays were applied to clinical samples, which were collected between January 2006 and December 2013. All 10 types of viruses were effectively detected in the multiplex RT-PCR-based assays. In addition, various viral parameters, such as the detection rates and age distributions of each viral type, were examined. The frequency and types of mixed infections were also investigated. Among the 186 virus-positive samples, genogroup II noroviruses were found to be the most common type of virus (32.7%), followed by group A rotaviruses (10.6%) and parechoviruses (10.3%). Mixed infections were observed in 37 samples, and many of them were detected in patients who were less than 2 years old. These observations showed that the multiplex RT-PCR-based assays involving fluorescent dye-labeled primers were able to effectively detect the viruses circulating among pediatric acute gastroenteritis patients and contributed to the highly specific and sensitive diagnosis of gastroenteritis. J. Med. Virol. 89:791-800, 2017. © 2016 Wiley Periodicals, Inc.

Epidemiology of gastroenteritis viruses in Japan: Prevalence, seasonality, and outbreak

Acute gastroenteritis has been recognized as one of the most common diseases in humans and continues to be a major public health problem worldwide. Several groups of viruses have been reported as the causative agents of acute gastroenteritis, including rotavirus, norovirus, sapovirus, human astrovirus, adenovirus, and an increasing number of others which have been reported more recently. The epidemiology, prevalence, seasonality, and outbreaks of these viruses have been reviewed in a number of studies conducted in Japan over three decades. Rotavirus and norovirus were the two most common viruses detected almost equally in children under 5 years of age who were suffering from acute gastroenteritis. Like many other countries, the main rotavirus strains circulating in pediatric patients in Japan are G1P[8], G2P[4], G3P[8], and G9P[8]. Norovirus GII.4 was involved in most outbreaks in Japan and found to be associated with the emergence of new variants Sydney_2012. The classic human astrovirus, MLB, and VA clades astroviruses were also commonly found in pediatric patients with acute diarrhea. The sapovirus and adenovirus have been identified as the minor viral causative agents for acute gastroenteritis in Japan.

Comprehensive review of human sapoviruses

Sapoviruses cause acute gastroenteritis in humans and animals. They belong to the genus Sapovirus within the family Caliciviridae. They infect and cause disease in humans of all ages, in both sporadic cases and outbreaks. The clinical symptoms of sapovirus gastroenteritis are indistinguishable from those caused by noroviruses, so laboratory diagnosis is essential to identify the pathogen. Sapoviruses are highly diverse genetically and antigenically. Currently, reverse transcription-PCR (RT-PCR) assays are widely used for sapovirus detection from clinical specimens due to their high sensitivity and broad reactivity as well as the lack of sensitive assays for antigen detection or cell culture systems for the detection of infectious viruses. Sapoviruses were first discovered in 1976 by electron microscopy in diarrheic samples of humans. To date, sapoviruses have also been detected from several animals: pigs, mink, dogs, sea lions, and bats. In this review, we focus on genomic and antigenic features, molecular typing/classification, detection methods, and clinical and epidemiological profiles of human sapoviruses.

Molecular detection and genotyping of noroviruses

Noroviruses (NoVs) are a major cause of gastroenteritis worldwide in humans and animals and are known as very infectious viral agents. They are spread through feces and vomit via several transmission routes involving person-to-person contact, food, and water. Investigation of these transmission routes requires sensitive methods for detection of NoVs. As NoVs cannot be cultivated to date, detection of these viruses relies on the use of molecular methods such as (real-time) reverse transcriptase polymerase chain reaction (RT-PCR). Regardless of the matrix, detection of NoVs generally requires three subsequent steps: a virus extraction step, RNA purification, and molecular detection of the purified RNA, occasionally followed by molecular genotyping. The current review mainly focused on the molecular detection and genotyping of NoVs. The most conserved region in the genome of human infective NoVs is the ORF1/ORF2 junction and has been used as a preferred target region for molecular detection of NoVs by methods such as (real-time) RT-PCR, NASBA, and LAMP. In case of animal NoVs, broad range molecular assays have most frequently been applied for molecular detection. Regarding genotyping of NoVs, five regions situated in the polymerase and capsid genes have been used for conventional RT-PCR amplification and sequencing. As the expected levels of NoVs on food and in water are very low and inhibition of molecular methods can occur in these matrices, quality control including adequate positive and negative controls is an essential part of NoV detection. Although the development of molecular methods for NoV detection has certainly aided in the understanding of NoV transmission, it has also led to new problems such as the question whether low levels of human NoV detected on fresh produce and shellfish could pose a threat to public health.

Detection and forecasting of oyster norovirus outbreaks: recent advances and future perspectives

Norovirus is a highly infectious pathogen that is commonly found in oysters growing in fecally contaminated waters. Norovirus outbreaks can cause the closure of oyster harvesting waters and acute gastroenteritis in humans associated with consumption of contaminated raw oysters. Extensive efforts and progresses have been made in detection and forecasting of oyster norovirus outbreaks over the past decades. The main objective of this paper is to provide a literature review of methods and techniques for detecting and forecasting oyster norovirus outbreaks and thereby to identify the future directions for improving the detection and forecasting of norovirus outbreaks. It is found that (1) norovirus outbreaks display strong seasonality with the outbreak peak occurring commonly in December-March in the U.S. and April-May in the Europe; (2) norovirus outbreaks are affected by multiple environmental factors, including but not limited to precipitation, temperature, solar radiation, wind, and salinity; (3) various modeling approaches may be employed to forecast norovirus outbreaks, including Bayesian models, regression models, Artificial Neural Networks, and process-based models; and (4) diverse techniques are available for near real-time detection of norovirus outbreaks, including multiplex PCR, seminested PCR, real-time PCR, quantitative PCR, and satellite remote sensing. The findings are important to the management of oyster growing waters and to future investigations into norovirus outbreaks. It is recommended that a combined approach of sensor-assisted real time monitoring and modeling-based forecasting should be utilized for an efficient and effective detection and forecasting of norovirus outbreaks caused by consumption of contaminated oysters.