Preserving Viral Genome Integrity: Best Practices for Scientists
Ensuring the integrity of viral genomes helps to maintain the safety and efficacy of virus-based biological systems
Virus-based biological systems are versatile tools for multiple biomedical and biotechnological applications, including delivering therapeutic genes to target cells and producing vaccines. Central to the functionality of these systems is the integrity of viral genomes.
Why does viral genome integrity matter?
The genetic material within viruses shapes their behavior and interaction with host cells. Ensuring the integrity of these genomes is pivotal to maintaining the stability and functionality of viruses, which ultimately safeguards the safety and efficacy of virus-based biological systems.
Consider a gene therapy vector. In this case, scientists engineer a virus to deliver a therapeutic gene into a patient’s cells to prevent or cure a genetic disease. If the viral genome within the vector undergoes unexpected changes, the delivered gene might not function as intended, leading to therapeutic failure. In a worst-case scenario, these alterations could even introduce health risks to the patient.
Viral genome integrity is also crucial in vaccine development. Some vaccines rely on weakened or inactivated viruses to stimulate an immune response without causing disease. If these viruses lose their genetic integrity, they might not trigger an immune response, resulting in a less potent—or ineffective—vaccine.
Genome integrity is equally critical in oncolytic virotherapy. This innovative cancer treatment employs modified viruses, known as oncolytic viruses, which are engineered to selectively target cancer cells and induce a robust anti-tumor immune response. Any unintended changes or mutations in the viral genome could compromise their specificity for cancer cells or their ability to stimulate the immune system effectively.
By preserving viral genomes, scientists can ensure that the systems they construct, manipulate, and employ remain reliable, predictable, and safe.
Navigating the pathways to integrity
Achieving viral genome integrity requires a multi-faceted approach. Here, we outline practices that scientists can implement to ensure the stability of viral genomes:
Precision sequencing techniques
Accurate sequencing serves as the foundation for understanding and preserving viral genomes.
While most genetic changes within a virus's genome might not affect the host cell, a select few might be important. Detecting and tracking these changes over time is essential. The insight granted by genome sequencing empowers scientists to monitor and respond to mutations, make informed decisions, anticipate potential issues, and develop strategies to preserve viral genetic integrity.
Two main methods are currently used for viral genome sequencing: polymerase chain reaction (PCR) and next-generation sequencing.
Harnessing bioinformatics
Bioinformatics tools are essential for analyzing vast amounts of sequencing data. These tools identify mutations, track their distribution, and predict potential outcomes. For example, tools like the Basic Local Alignment Search Tool (BLAST) and Multiple Alignment using Fast Fourier Transform (MAFFT) help researchers compare sequences and uncover variations in the genomes of viruses.
Genomics and bioinformatics also streamline the vector design process. By understanding the genetic factors influencing vector performance, scientists can choose which viral vector to use for a specific purpose. This enhances the efficiency of vector selection and optimization.
Meticulous laboratory practices
By practicing sterile techniques and careful handling, scientists increase the likelihood of preserving the genomes of their virus-based biological systems. Ensure that instruments like DNA sequencers, PCR machines, and centrifuges function accurately and consistently. Regular maintenance and calibration of equipment prevent errors in sequencing techniques and minimize the introduction of technical artifacts during experimental procedures.
Proper documentation practices are indispensable too, especially at early clinical development stages when critical production and analytical parameters may still be identified. In addition, protecting sample integrity by maintaining the cold chain is vital for transportation and storage of clinical samples that will be used for direct virological methods.
Reference strains as anchors
Reference strains typically have well-characterized genomes. Attempting to analyze a newly sequenced genome without a reference strain for comparison is like trying to identify a misspelled word in an unknown language. With a well-characterized reference strain to compare against, spotting any unusual mutations or discrepancies in the new sequence becomes much easier.
When discrepancies are detected, scientists can delve deeper to understand the implications and assess whether these mutations might affect the virus’s behavior, function, or treatment response.
Continuous surveillance
Continuous surveillance allows scientists to detect any mutations or genetic changes that may occur in the viruses. This ensures that the viruses within biological systems continue to function reliably and safely.
Surveillance also aids in the adaptation and optimization of virus-based biological systems. By monitoring genetic changes, scientists can potentially harness new viral variants with advantageous properties for their intended applications. For example, a slight mutation might enhance a virus’s ability to target specific cells for gene therapy.
By staying vigilant and proactive, scientists can adapt and optimize their biological systems while minimizing the risk of unexpected issues due to genetic changes in the viruses they employ.
Collaborative monitoring
Collaborative monitoring is not just about sharing data; it’s about creating a unified front to improve public health intelligence and generate evidence for decision-making. This collective effort enhances our ability to adapt, respond, and optimize virus-based products while mitigating the risks associated with viral genetic changes.
An illustrative example of effective collaborative viral genomic surveillance comes from an article published in July 2023. The authors established a SARS-CoV-2 variant surveillance model that focused on expanding next-generation genome sequencing capabilities at universities located in or near rural areas in Louisiana, Georgia, and Mississippi. The resulting genomic surveillance network has generated more than a thousand SARS-CoV-2 genomes. These include the first confirmed case of Omicron in northeast Louisiana, and the first and sixth confirmed cases of the emergent BA.2.75 and BQ.1.1 variants in Georgia.
This initiative underscores how collaborative monitoring directly contributes to the tailoring of vaccination strategies and treatment protocols in response to evolving viral dynamics.
Virus-based biological systems hold immense promise for advancements in medicine and biotechnology. Nevertheless, the success of these systems depends on the integrity of the viral genome. Scientists engaged in virus-based biological research bear the responsibility of preserving this integrity, and by employing the strategies outlined here, they can ensure that these systems remain reliable, secure, and efficient.
