Confirming Virus Detection in Frozen Berries Using Genome Sequencing

Greg Howard
3rd May, 2024

Confirming Virus Detection in Frozen Berries Using Genome Sequencing

Image Source: Natural Science News, 2024

Key Findings

  • FDA study improves virus detection in frozen berries using genome sequencing
  • New method can confirm low-level viral contamination, aiding food safety
  • Technique outperforms standard tests, potentially preventing outbreaks
In recent years, the safety of our food supply has become a critical concern, particularly with the increasing number of foodborne illnesses linked to fruits and vegetables. Among these, frozen berries have been frequently implicated in outbreaks caused by enteric viruses, such as the hepatitis A virus (HAV) and human norovirus (HuNoV), which can lead to serious health issues even at low exposure levels. Detecting these viruses is challenging due to their low infectious doses and the complexity of food matrices. A breakthrough study by the U.S. Food and Drug Administration[1] has made significant strides in addressing this challenge. Researchers have innovated a method that combines whole-genome sequencing (WGS) with non-targeted pre-amplification techniques to confirm the presence of enteric viruses in contaminated frozen berries. This study's findings could revolutionize how we identify and confirm viral pathogens in our food, potentially preventing future outbreaks. Whole-genome sequencing is a method that determines the complete DNA sequence of an organism's genome at a single time. It offers a comprehensive view of the genetic information, which is invaluable for identifying and understanding pathogens. However, when it comes to foodborne viruses, their low numbers in food samples can make detection difficult. To overcome this, researchers used two pre-amplification methods, SPIA and SISPA, which amplify viral genetic material to levels detectable by WGS. The study's approach was tested on frozen raspberries, strawberries, and blackberries, known for their association with viral outbreaks. The results were promising; WGS could detect and confirm the presence of HuNoV and HAV in samples with very low genomic copy numbers. Impressively, it even identified viruses in samples that previously tested negative by the commonly used RT-qPCR method, a technique that quantifies the amount of viral RNA in a sample. However, the study also found that some RT-qPCR-positive samples could not be confirmed by WGS, and in samples with very high Ct values—indicating a low amount of viral genetic material—only a few viral reads were obtained. This highlights the need for further optimization of WGS techniques for routine application in food safety testing. The findings of this study are particularly significant when considering earlier research. For instance, studies have shown that fresh produce like lettuce harbors a diverse community of viruses[2], and frozen berries have been identified as a cause of foodborne disease outbreaks[3]. The review of berry-associated viral outbreaks emphasized the need for improved detection and processing methods to reduce contamination[4]. The current study builds upon these previous insights by providing a method that not only detects but also confirms the presence of foodborne viruses, which is crucial for outbreak investigations. It highlights the potential of WGS as a confirmatory method, which could complement existing RT-qPCR techniques. The ability to confirm viral contamination at such low levels is a significant step forward in food safety. The research underscores the importance of preventing viral contamination right from the farm to the consumer's fork, as emphasized by the identification of human and animal viruses in field lettuce samples[2]. It also aligns with the need for improved processing practices to reduce viral loads in berries[4], as current industrial practices have shown limited efficacy. In conclusion, the study by the U.S. Food and Drug Administration has demonstrated the potential of WGS combined with pre-amplification methods as a powerful tool for confirming low-level viral contamination in foods, particularly berries. While further optimization is needed for routine use, this method represents a significant advancement in our ability to ensure the safety of the food supply. It is a promising development in the ongoing effort to protect public health from foodborne illnesses.



Main Study

1) Whole-Genome Sequencing-Based Confirmatory Methods on RT-qPCR Results for the Detection of Foodborne Viruses in Frozen Berries

Published 30th April, 2024

Related Studies

2) Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses.

3) Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR.

4) Outbreaks, occurrence, and control of norovirus and hepatitis a virus contamination in berries: A review.

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