Virus detection methods for different kinds of food and water samples – The importance of molecular techniques

Hrdy, Jakub; Petra, Vasickova

doi:10.1016/j.foodcont.2021.108764

Cited by 13 publications

(11 citation statements)

References 371 publications

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“…In some cases, the resulting concentrate can be in liquid or solid form, depending on the concentration method used. Similarly, specific nucleic acid recovery methods may also apply to foodstuff and air samples due to the nature of the samples and include, but are not limited to, direct extraction and/or proteinase K treatment [ 101 ]. Nucleic acid recovery in foodstuff and air samples depends, in turn, on how the samples are collected and how viruses are separated from the matrix and concentrated prior to nucleic acid recovery.…”

Section: Considerations and Limitations Of Viral Metagenomics For Mic...mentioning

confidence: 99%

“…Nucleic acid recovery in foodstuff and air samples depends, in turn, on how the samples are collected and how viruses are separated from the matrix and concentrated prior to nucleic acid recovery. Virus separation methods include elution techniques such as washing the viral particles from the matrix using appropriate buffers [ 101 ]. Virus concentration methods include, but are not limited to, Polyethylenglycol (PEG) precipitation, evaporation, ultracentrifugation, ultrafiltration, and flocculation, and may apply to different samples types such as water, foodstuff, and air samples [ 101 ].…”

Section: Considerations and Limitations Of Viral Metagenomics For Mic...mentioning

confidence: 99%

“…Virus separation methods include elution techniques such as washing the viral particles from the matrix using appropriate buffers [ 101 ]. Virus concentration methods include, but are not limited to, Polyethylenglycol (PEG) precipitation, evaporation, ultracentrifugation, ultrafiltration, and flocculation, and may apply to different samples types such as water, foodstuff, and air samples [ 101 ].…”

Section: Considerations and Limitations Of Viral Metagenomics For Mic...mentioning

confidence: 99%

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Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach

Santiago-Rodríguez

Hollister

2023

Viruses

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The One Health framework recognizes that human, animal, and environmental health are linked and highly interdependent. Fecal contamination of water, soil, foodstuff, and air may impact many aspects of One Health, and culture, PCR-based, and sequencing methods are utilized in the detection of fecal contamination to determine source, load, and risk to inform targeted mitigation strategies. Viruses, particularly, have been considered as fecal contamination indicators given the narrow host range many exhibit and their association with other biological contaminants. Culture- and molecular-based methods are considered the gold-standards for virus detection and for determining specific sources of fecal contamination via viral indicators. However, viral metagenomics is also being considered as a tool for tracking sources of fecal contamination. In the present review, studies tracking potential sources of fecal contamination in freshwaters, marine waters, foodstuff, soil, and air using viral metagenomics are discussed to highlight the potential of viral metagenomics for optimizing fecal source tracking. Limitations of the use of viral metagenomics to track fecal contamination sources, including sample processing, nucleic acid recovery, sequencing depth, and bioinformatics are also discussed. Finally, the present review discusses the potential of viral metagenomics as part of the toolbox of methods in a One Health approach.

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Section: Considerations and Limitations Of Viral Metagenomics For Mic...mentioning

confidence: 99%

Section: Considerations and Limitations Of Viral Metagenomics For Mic...mentioning

confidence: 99%

Section: Considerations and Limitations Of Viral Metagenomics For Mic...mentioning

confidence: 99%

See 1 more Smart Citation

Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach

Santiago-Rodríguez

Hollister

2023

Viruses

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“…This approach introduces novel perspectives for monitoring environmental communities, including viral pathogens [20]. To apply a specific detection method for viral pathogens biomonitoring, the method must be appropriate, optimized against possible limitations, verified for its applicability, reproducibility, sensitivity, specificity and, if possible, cost-and time-effective [21].…”

Section: Enteric Viruses In Water and Their Impact On Public Healthmentioning

confidence: 99%

Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring

Mostafa‐Hedeab

Allayeh

Elhady

et al. 2022

IJERPH

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Enteric viruses (EVs) occurrence within aquatic environments varies and leads to significant risk on public health of humans, animals, and diversity of aquatic taxa. Early and efficacious recognition of cultivable and fastidious EVs in aquatic systems are important to ensure the sanitary level of aquatic water and implement required treatment strategies. Herein, we provided a comprehensive overview of the conventional and up-to-date eco-genomic tools for aquatic biomonitoring of EVs, aiming to develop better water pollution monitoring tools. In combination with bioinformatics techniques, genetic tools including cloning sequencing analysis, DNA microarray, next-generation sequencing (NGS), and metagenomic sequencing technologies are implemented to make informed decisions about the global burden of waterborne EVs-associated diseases. The data presented in this review are helpful to recommend that: (1) Each viral pollution detection method has its own merits and demerits; therefore, it would be advantageous for viral pollution evaluation to be integrated as a complementary platform. (2) The total viral genome pool extracted from aquatic environmental samples is a real reflection of pollution status of the aquatic eco-systems; therefore, it is recommended to conduct regular sampling through the year to establish an updated monitoring system for EVs, and quantify viral peak concentrations, viral typing, and genotyping. (3) Despite that conventional detection methods are cheaper, it is highly recommended to implement molecular-based technologies to complement aquatic ecosystems biomonitoring due to numerous advantages including high-throughput capability. (4) Continuous implementation of the eco-genetic detection tools for monitoring the EVs in aquatic ecosystems is recommended.

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“…Therefore, simple, fast, accurate, and specific diagnostic techniques are in great demand for the early diagnosis, prognosis and surveillance of diseases, by targeting particular biomarkers/target sites. There are some reliable techniques which exist for virus detection such as cell culture, hemagglutination inhibition test, immuno-complexation, etc [ 3 , 4 ]. Furthermore, with advancement in technology, a few other techniques, for instance, ELISA, RIA, serological and PCR methods, have also been employed for virus detection [ 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

et al. 2022

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Viral infections are becoming the foremost driver of morbidity, mortality and economic loss all around the world. Treatment for diseases associated to some deadly viruses are challenging tasks, due to lack of infrastructure, finance and availability of rapid, accurate and easy-to-use detection methods or devices. The emergence of biosensors has proven to be a success in the field of diagnosis to overcome the challenges associated with traditional methods. Furthermore, the incorporation of aptamers as bio-recognition elements in the design of biosensors has paved a way towards rapid, cost-effective, and specific detection devices which are insensitive to changes in the environment. In the last decade, aptamers have emerged to be suitable and efficient biorecognition elements for the detection of different kinds of analytes, such as metal ions, small and macro molecules, and even cells. The signal generation in the detection process depends on different parameters; one such parameter is whether the labelled molecule is incorporated or not for monitoring the sensing process. Based on the labelling, biosensors are classified as label or label-free; both have their significant advantages and disadvantages. Here, we have primarily reviewed the advantages for using aptamers in the transduction system of sensing devices. Furthermore, the labelled and label-free opto-electrochemical aptasensors for the detection of various kinds of viruses have been discussed. Moreover, numerous globally developed aptasensors for the sensing of different types of viruses have been illustrated and explained in tabulated form.

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Virus detection methods for different kinds of food and water samples – The importance of molecular techniques

Cited by 13 publications

References 371 publications

Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach

Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach

Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

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