Psomagen was delighted to speak with one of our long-time customers last week! Dr. Arvind Varsani is an associate professor at Arizona State University, where he studies evolutionary virology. Much of his research focuses on plant and animal viruses, and how the interactions between species are changing the viral landscape.
His research is primarily academic, which presents unique challenges. “Most of the viruses we study are not yet known,” Dr. Varsani says. “So with that, there is a problem when it comes to identifying them. The best thing we can do is use sequencing platforms that do not require a prior knowledge of the sequences of these viruses.”
Identifying novel viruses and conducting genome sequencing make it possible for researchers to come up with mitigation strategies for viral infection and spread. As Dr. Varsani explained, “In animals the immune system has an adaptive arm to it. Plants do not have an adaptive immune system. Plants produce short interfering RNA as one mechanism to defend themselves against pathogens. You can also go into breeding programs where you breed for resistance to those pathogens [as a mitigation strategy].”
Take a look at the article below for insights from his research projects, his thoughts on ecosystem management, and ways in which scientific research is evolving.
Addressing Viral Disease in Plants
In 2010, Dr. Varsani and a team of researchers published research on a geminivirus responsible for the global spread of tomato yellow leaf curl virus (TYLCV). Geminiviridae cause damage to plant leaves, stunted growth, and a decrease in fruit production. Geminiviruses are transmitted by insects like aphids, leafhoppers, and treehoppers; TYLCV is transmitted by whiteflies.
An estimated 50% of emerging plant diseases are caused by viruses. In many cases, disease research in plants is a race against the clock. “Crop systems are monoculture in many instances.” Dr. Varsani says, “So if you have a pathogen that does come in, it hits hard and then moves across the crop very quickly.”
In virology, research often begins after a disease state is first observed. “There’s no way of determining [if a virus will be harmful],” Dr. Varsani elaborates. The only way that can be determined is once you start seeing an infection and a disease state…and then from there you work backwards to try to figure it out.”
This Geminiviridae research project, published in PLOS Pathogens, investigated past TYLCV movements throughout the world. By using recombination analysis and whole genome sequencing on TYLCV sequences, they were able to confirm that the virus first arose in the Middle East between 70 and 90 years ago. Global spread of the virus did not begin until the 1980s.
Although the most genetic diversity of TYLCV is found in the Middle East, this research suggests that those variants are not spreading globally. Instead, this project identified the Mediterranean basin as the most likely jumping-off point for global spread of TYLCV.
With a better understanding of a virus, researchers can then develop mitigation strategies. “A lot of my work is very academic,” Dr. Varsani explains, “but then other people tend to pick up our academic findings and use those in their applied settings.”
An abridged list of the plant species impacted by viruses and other microbes studied by Dr. Varsani and his team in the last several years.
For example, another geminiviridae study by Dr. Varsani and researchers from Iran and New Zealand used metagenomic sequencing to sequence the genomes of beet curly top Iran virus, turnip curly top viruses, oat dwarf virus, and wheat dwarf virus. These viruses are spread by leafhopper insects feeding on beet, parsley, pumpkin, and turnip plants.
Results identified viral and prokaryotic diseases being transmitted in Iran, and also identified oat dwarf virus in Iran for the first time. These viral genomes were then deposited in GenBank to allow for further research. Some insecticides with limited effectiveness have been identified, as have planting techniques designed to discourage the spread of disease-carrying insects.
Cross-Species Transmission in Animals
Dr. Varsani’s ecological focus has led him to conduct viral research on animals all over the world. His published studies have included animals native to Antarctica, North America, Ethiopia, and the Iberian Peninsula. In particular, his research with big cats has focused on diseases transmitted via interactions between wild and domesticated animals.
In the North American bobcat and African lion, Dr. Varsani’s research has identified novel smacoviruses. Smacoviruses have been previously identified in mammals, birds, and some insects. However, this is the first report of smacoviruses present in large feline predators.
An abridged list of the animal species and groups impacted by viruses and other microbes studied by Dr. Varsani and his team in the last several years.
Further research is necessary to determine how these viruses are related to other felid diseases and how they are transmitted. This will help researchers better understand the virus’s capacity to hop between species. “Cats are cats — at the end of the day they’re felines, so viruses that are similar in infecting cats will find their way into the wild animals and vice versa,” says Dr. Varsani.
Feline foamy virus (FFV) is a textbook example of this interaction. It is found frequently in domesticated cats, but can be transmitted to large cats. In a 2020 study, pumas in urban sites had an FFV prevalence of 77%, compared to 48% in puma samples from rural areas. This shows the capacity of viruses for cross-species transmission, particularly when previously segregated populations are brought together.
This cross-species interaction is an important focus for ecologists, as human development continues to encroach on animals’ natural habitats. “To be honest, there’s nothing that surprises me when you destroy nature’s systems and create an imbalance,” Dr. Varsani explains. “As soon as you create an imbalance in any type of ecosystem, there is going to be a consequence. In these kinds of systems it’s not surprising that you find viruses in wild animals that are also in domesticated animals.”
Virology & Environmental Changes
The effects of human expansion and climate change are still developing; however, virologists are already noticing changes in the systems at play. “From a pathogen perspective, you’ve got an expanded host range, you’ve got an expanded range for insects like mosquitoes to occupy new areas where they never were, to now eat from animals in those areas that are now going to get infected.”
These developments impact “not necessarily doing research, but certainly addressing research questions in those areas,” Dr. Varsani explained. “What are the impacts of elevated CO2 on pathogens — how do they behave, do they change their behavior? How do the hosts respond to those pathogens? In most cases, hosts and a variety of viruses have co-evolved with each other. So creating an imbalance in the environment has some effect on those dynamics.”
One example of this imbalance comes from the expansion of agriculture into natural areas. Crop species are more often analyzed for the presence of viruses and other microbes than uncultivated crops. This is a major gap in our understanding of plant virus spread; it also limits our ability to predict the consequences of agricultural expansion into certain areas.
In 2020, Dr. Varsani and a team of researchers conducted a two-year survey of agricultural and adjacent uncultivated plants in South Africa and France. Using geometagenomic approaches, this project identified 94 novel viral species. Most were from uncultivated plants.
As the world adapts to feed its growing population, converting natural areas to managed farmland will create interactions between native plants and non-native crops. This opens the door to previously undocumented outbreaks.
So what can research do to manage these changes? Dr. Varsani believes it begins with “actually managing our ecosystems. Our society is currently very individualistic, and not a society focused on the common good…. I think we need to start thinking more about not just this generation, not the next generation, but 200, 500, or 1,000 years beyond ourselves.”
Dr. Varsani’s current research is widespread, looking at seals and penguins in the Antarctic, as well as bobcats, mountain lions, and caracals in the United States and Africa. Over his career, he’s seen major improvements and advancements in sequencing technologies. “There’s a lot more we can do very rapidly…. Without that, I don’t think we would be able to do quite a lot. [Technologies] keep changing, getting cheaper and better, so I think overall we will see huge changes as a result of that.”
Looking for more insights from Psomagen customers? Take a look at how Dr. Taras Oleksyk’s “genome desert” research changed the genomics landscape in Puerto Rico.