What Can We Learn From Animal and Plant Viruses?

The earthquake hit Christchurch, New Zealand around lunchtime. Although not as powerful as the one six months before, it caused more destruction, killing 185 people. The University of Canterbury, where I was working at the time, fortunately experienced no staff or student injuries and only minor damage to buildings. My lab had to close for four months and it was a critical time for our research. Fortunately, a collaborator, John Thomas, offered my research team and I an alternative for a month. Relocating our team and setting up a temporary lab in Brisbane, Australia was challenging, but many companies were extremely supportive, providing equipment and even lending us products. For example, Integrated DNA Technologies (IDT) quickly deployed a host of primers critical for completing our project on time — sending one set to my Christchurch home, duplicates to Brisbane, and a third set was waiting for me at the airport: all at no extra cost. This and other examples showed what a community could achieve together in the face of hardship, not unlike the more recent, global unison against the COVID-19 pandemic.

Then, as now, we achieved great work together as a global scientific community. Vendors also contributed, for instance, by improving access to various primer sets for sequencing the SARS-CoV-2 genome (important for detecting, tracking, and studying genetic mutations and understanding the evolution of the virus and its notable variants). The pandemic has pushed the world to achieve unprecedented success in rapidly developing and deploying a whole new modality of vaccines, revealing at the same time our common vulnerabilities and global interdependencies. Whether it is an earthquake in New Zealand or a disease outbreak in China, we now better understand how highly connected our apparently disparate ecosystems are across the globe. This connection is recapitulated in the ecosystems that my collaborators and I study through investigating the diversity, demographics and evolutionary dynamics of viral communities in various ecosystems.

More specifically, my team and I use a combination of traditional virology, microscopy (including transmission electron microscopy), and molecular and cellular biology techniques, in conjunction with next generation sequencing (NGS) techniques, synthetic biology, and bioinformatics to characterize viruses and understand their dynamics. We seek to understand the evolution and geographic spread of viruses by studying a wide range of viruses in their natural habitat. Many of these viruses are not pathogenic to humans, and can even be beneficial. Indeed, the vast majority of viruses that exist do not cause human disease and, as such, tend to be overlooked by researchers. However, these plant and other viruses can still tell us a lot about how viruses develop in general, as well as inform studies of viruses that are harmful to humans. The impact of humans on virus ecology can also be revealed, for example, when plants harbouring viruses are moved from one region to another, introducing new viruses into new geographic locations, which in turn, subsequently influences the evolution of the viruses through natural selection. Such anthropogenic behaviors also extend to the movement of animals, which can similarly be infected by viruses. Some of these viruses can then jump species into humans to cause zoonotic disease.

In fact, COVID-19 serves as a recent example of a disease that has zoonotic origins. It is caused by the SAR-CoV-2 virus, which is believed to have jumped species from bats to humans. Viruses that are pathogenic to humans constitute only a tiny fraction of all the viruses that exist today. Investigating viral dynamics gives us a much bigger picture of viral evolution, behavior, transmission among hosts, and geographic spread. All of these important elements can be used to better understand viruses, including those that are pathogenic to humans, as well as to other animals and plants. During the pandemic, my team and I have applied high-throughput NGS methods to sequence viral genomes from wastewater to investigate the community spread of the SARS-CoV-2 virus and the diversity of circulating variants. Wastewater-based epidemiology (WBE) provides viral surveillance at the community level and, through genetic correlation and the analysis of single nucleotide variants (SNVs), can give us a comprehensive snapshot of the SARS-CoV-2 genetic population structure and provide early warning of outbreaks.

One NGS panel designed to sequence SARS-Cov-2 is IDT’s SARS-CoV-2 SNAP research panel, which has been adopted by Psomagen, a genetic sequencing services company that I have been a long-time user of, and which is now part of IDT’s Align Preferred Sequencing Provider Program. IDT partners with some of the most comprehensive genomic sequencing service entities in the world, who are aligned in their commitment to collaboration and the resolve to break down research barriers. Collaboration between vendors like IDT and Psomagen is critical, not only to support researchers like myself in coping with disasters like the earthquake in Christchurch, but also in combating global threats such as the pandemic. If the pandemic has taught us anything, it is that we are all connected in complex and sometimes subtle ways. As such, it is vital that we learn to work together as a whole, not only on apparently diverse research projects that come together to give us a more complete understanding of our shared ecosystem — from humans to viruses and beyond — but also to facilitate innovation in how we interrogate these biological systems and ultimately manage them as responsible caretakers of our planet.