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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Endemic Poultry Viral Diseases Research » Research » Publications at this Location » Publication #414679
Research Project: Elucidation of Molecular Determinants of Avian Herpesviruses Virulence and Evolution to Inform the Development of Safe and Effective Vaccines

Location: Endemic Poultry Viral Diseases Research

Title: Non-targeted RNA sequencing: towards the development of universal clinical diagnosis methods for human and veterinary infectious diseases

Author
item AFONSO, CLAUDIO - Base2bio
item Spatz, Stephen

Submitted to: Veterinary Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2024
Publication Date: 5/26/2024
Citation: Afonso, C., Spatz, S.J. 2024. Non-targeted RNA sequencing: towards the development of universal clinical diagnosis methods for human and veterinary infectious diseases. Veterinary Sciences. https://doi.org/10.3390/vetsci11060239.
DOI: https://doi.org/10.3390/vetsci11060239

Interpretive Summary: Traditional methods for diagnosing infections often miss the culprit or take a long time. Metagenomics, a technique that analyzes all the genetic material in a sample, offers a more comprehensive and accurate way to identify the cause of an infection. This new approach would be a godsend for doctors, but it's still too complex and expensive for everyday use in clinics. We propose using a specific type of metagenomics, RNA sequencing, as a standard for diagnosing infections. This method has the potential to be accurate, fast, and adaptable for many situations. By agreeing on common practices for collecting samples, analyzing data, and interpreting results, clinical labs can implement this powerful tool for everyday use. This would involve groups working together to figure out the best way to do each step and develop new technologies to bring down costs and speed things up. In the future, artificial intelligence might even help analyze the results even faster. With some collaboration and innovation, this new diagnostic technique could revolutionize how we identify culprits of infectious diseases.

Technical Abstract: Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology’s operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the “core” of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through “implementation research” by a consortium of interested institutions working on common samples.