Real-time molecular methods to detect infectious viruses

Wastewater-Based Epidemiology as an Early Warning System for the Spreading of SARS-CoV-2 and Its Mutations in the Population

New methodologies based on the principle of "sewage epidemiology" have been successfully applied before in the detection of illegal drugs. The study describes the idea of early detection of a virus, e.g., SARS-CoV-2, in wastewater in order to focus on the area of virus occurrence and supplement the results obtained from clinical examination. By monitoring temporal variation in viral loads in wastewater in combination with other analysis, a virus outbreak can be detected and its spread can be suppressed early. The use of biosensors for virus detection also seems to be an interesting application. Biosensors are highly sensitive, selective, and portable and offer a way for fast analysis. This manuscript provides an overview of the current situation in the area of wastewater analysis, including genetic sequencing regarding viral detection and the technological solution of an early warning system for wastewater monitoring based on biosensors.

A Simple low-cost device enables four epi-illumination techniques on standard light microscopes

Back-scattering darkfield (BSDF), epi-fluorescence (EF), interference reflection contrast (IRC), and darkfield surface reflection (DFSR) are advanced but expensive light microscopy techniques with limited availability. Here we show a simple optical design that combines these four techniques in a simple low-cost miniature epi-illuminator, which inserts into the differential interference-contrast (DIC) slider bay of a commercial microscope, without further additions required. We demonstrate with this device: 1) BSDF-based detection of Malarial parasites inside unstained human erythrocytes; 2) EF imaging with and without dichroic components, including detection of DAPI-stained Leishmania parasite without using excitation or emission filters; 3) RIC of black lipid membranes and other thin films, and 4) DFSR of patterned opaque and transparent surfaces. We believe that our design can expand the functionality of commercial bright field microscopes, provide easy field detection of parasites and be of interest to many users of light microscopy.

Occurrence of human enteric viruses at freshwater beaches during swimming season and its link to water inflow

Human enteric viruses are significant etiological agents for many recreational waterborne illnesses. The occurrence and density of human enteric viruses such as human adenovirus (HAdV), human enterovirus (HEnV), and human norovirus genogroups I/II (HNoV GI/GII) were investigated using quantitative real-time PCR (qPCR) at freshwater beaches along with monitoring fecal indicators and environmental parameters. During the 2009 swimming season, water samples were collected from three inland freshwater beaches in Ohio, USA. Of the total samples, 40% (26/65) and 17% (11/65) were positive for HAdV and HEnV respectively, but HNoV GI/GII were not detected. There was no significant association among the detected human enteric viruses (HAdV and HEnV) and fecal bacteria indicators (Escherichia coli and Bacteroides) by Spearman correlation and principal component analyses. Logistic regression analysis also revealed that the odds of finding HAdV or HEnV was not influenced by levels of fecal bacteria indicators. However, there was a 14-fold increase in the odds of HEnV detection for each 1-log increase in daily water inflow (m(3)/s) into freshwater beach reservoirs (adjusted odds ratio=14.2; 95% confidence interval=1.19-171). In summary, the viral occurrence at the freshwater beaches was not readily explained by the levels of fecal bacteria indicators, but appeared to be more related to water reservoir inflows. These results suggest that hydrological data must be considered in future epidemiology efforts aimed at characterizing beach water safety.

Intrinsically conducting polymer nanowires for biosensing

The fabrication of conductive polymer nanowires and their sensing of nucleic acids, proteins and pathogens is reviewed in this feature article.

PCR em tempo real para detecção do vírus da doença de Aujeszky

O objetivo deste trabalho foi desenvolver uma PCR em tempo real (qPCR) para o diagnóstico rápido e sensível da doença de Aujeszky. Os iniciadores amplificaram um fragmento de 123 pares de base do gene codificante da glicoproteína D. A qPCR foi testada em 25 amostras de cérebro de suíno positivas e 85 amostras negativas para DA no isolamento viral e na soroneutralização. A sensibilidade analítica foi calculada com acréscimo de um isolado brasileiro do SuHV-1 titulado em amostras de cérebro de suíno negativas na soroneutralização e na PCR. A técnica apresentou sensibilidade analítica de 10-0,5 TCID50/50µL. A qPCR foi capaz de distinguir reações inespecíficas devido a dímero de oligonucleotídeos iniciadores ou amplificações, além do alvo designado (evitando, assim, os falso-positivos), e de obter resultados rápidos.

Analytical methods for the detection of viruses in food by example of CCL-3 bioagents

This critical review presents challenges and strategies in the detection of viral contaminants in food products. Adenovirus, caliciviruses, enteroviruses, and hepatitis A are emerging contaminant viruses. These viruses contaminate a variety of food products, including fruits, vegetables, shellfish, and ready-to-eat processed foods. The diversity of targets and sample matrices presents unique challenges to virus monitoring that have been addressed by a wide array of processing and detection methods. This review covers sample acquisition and handling, virus recovery/concentration, and the determination of targets using molecular biology and mass-spectrometric approaches. The concentration methods discussed include precipitation, antibody-based concentration, and filtration; the detection methods discussed include microscopy, polymerase chain reaction, nucleic acid sequence-based amplification, and mass spectrometry.

Multiplex detection and SNP genotyping in a single fluorescence channel

Probe-based PCR is widely used for SNP (single nucleotide polymorphism) genotyping and pathogen nucleic acid detection due to its simplicity, sensitivity and cost-effectiveness. However, the multiplex capability of hydrolysis probe-based PCR is normally limited to one target (pathogen or allele) per fluorescence channel. Current fluorescence PCR machines typically have 4–6 channels. We present a strategy permitting the multiplex detection of multiple targets in a single detection channel. The technique is named Multiplex Probe Amplification (MPA). Polymorphisms of the CYP2C9 gene (cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2C9*2) and human papillomavirus sequences HPV16, 18, 31, 52 and 59 were chosen as model targets for testing MPA. The allele status of the CYP2C9*2 determined by MPA was entirely concordant with the reference TaqMan® SNP Genotyping Assays. The four HPV strain sequences could be independently detected in a single fluorescence detection channel. The results validate the multiplex capacity, the simplicity and accuracy of MPA for SNP genotyping and multiplex detection using different probes labeled with the same fluorophore. The technique offers a new way to multiplex in a single detection channel of a closed-tube PCR.

Simultaneous detection of infectious human echoviruses and adenoviruses by an in situ nuclease-resistant molecular beacon-based assay

A multiplex methodology using two nuclease-resistant molecular beacons that target specific genomic regions of adenovirus 2 and echovirus 17 during simultaneous infection in A549 cells is presented. Using fluorescence microscopy, visualization of enteroviral and adenoviral replication was possible within 3 h postinfection.

PCR Multiplex para detecção dos principais herpesvírus neurológicos de ruminantes

Desenvolveu-se uma PCR multiplex (mPCR) para diagnóstico diferencial de encefalite bovina causada por herpesvírus suíno 1 (SuHV-1), herpesvírus bovino 1 (BoHV-1), herpesvírus bovino 5 (BoHV-5) e herpesvírus ovino 2 (OvHV-2). Os iniciadores foram projetados após alinhamento de sequências disponíveis no banco de genomas (GenBank) e a reação foi padronizada levando-se em consideração a concentração dos reagentes e os tipos diferentes de DNA polimerase. Após determinação da especificidade e sensibilidade, 65 amostras de encéfalo de bovinos com síndrome neurológica foram submetidas à análise. A sensibilidade analítica para detecção de BoHV-1, BoHV-5 e SuHV-1 foi, respectivamente, 10(1,2) TCID50/50µL, 10(1,0) TCID50/50µL, 10(1,3) TCID50/50µL na reação multiplex. Das 65 amostras analisadas, 10 foram positivas para BoHV-5, uma para BoHV-1 e cinco para OvHV-2. A mPCR descrita neste trabalho mostrou-se uma técnica útil para o diagnóstico diferencial de enfermidades relacionadas ao sistema nervoso central de bovinos.

Detection of murine norovirus-1 by using TAT peptide-delivered molecular beacons

A TAT peptide-delivered molecular beacon was developed and utilized to enumerate murine norovirus 1, a human norovirus (NoV) surrogate, in RAW 264.7 cells. This allowed the detection of a single infective virus within 6 h, a 12-fold improvement in time required for viral detection and quantification compared to that required by the conventional plaque assay.

Label-free chemiresistive immunosensors for viruses

We report development, characterization, and testing of chemiresistive immunosensors based on single polypyrrole (Ppy) nanowire for highly sensitive, specific, label free, and direct detection of viruses. Bacteriophages T7 and MS2 were used as safe models for viruses for demonstration. Ppy nanowires were electrochemically polymerized into alumina template, and single nanowire based devices were assembled on a pair of gold electrodes by ac dielectrophoretic alignment and anchored using maskless electrodeposition. Anti-T7 or anti-MS2 antibodies were immobilized on single Ppy nanowire using EDC-NHS chemistry to fabricate nanobiosensor for the detection of corresponding bacteriophage. The biosensors showed excellent sensitivity with a lower detection limit of 10(-3) plaque forming unit (PFU) in 10 mM phosphate buffer, wide dynamic range and excellent selectivity. The immunosensors were successfully applied for the detection of phages in spiked untreated urban runoff water samples. The results show the potential of these sensors in health care, environmental monitoring, food safety and homeland security for sensitive, specific, rapid, and affordable detection of bioagents/pathogens.