The University of Florida Emerging Pathogens Institute’s annual Research Day took place on Feb. 10 and featured 200 attendees for the poster session and 6,000 poster hits. One hundred and thirty people tuned in for the keynote talks given by Grant Stentiford, of the Centre for Environment, Fisheries, and Aquaculture Science, and Marco Salemi, a UF professor of pathology in the College of Medicine.
The keynotes spanned research investigating the phylogenomics of COVID-19 and emerging zoonoses to pathogens affecting aquaculture. They spotlighted the diverse array of research subjects encompassed within the lens of emerging pathogens. Stentiford presented emerging trends on risks in aquaculture that centered on four themes: food from water, healthy seafood, environment and people, and ecosystem change. Salemi presented on recent work applying phylogenomic tools to understand the spread and composition of genetic viral variants in COVID samples obtained from across Florida.
The One Health need in Aquaculture
Stentiford investigates marine diseases, aquatic pathology, aquatic invertebrates—such as wild and farmed mollusks—and has led development of the One Health Aquaculture movement. He pointed out that basic research describing new wild pathogens has critical connections to aquaculture.
“Knowledge of these pathogens in wild systems lead you to be able to describe more accurately the ones that emerge in aquaculture,” Stentiford said.
For example, he described a new type of Microsporidia in 2007 that infected wild edible crabs, Enterospora canceri. This discovery then helped to untangle the complex taxonomy of a novel parasite in target shrimp in Thailand, Enterocytozoon hepatopenaei. Now known as EHP, it is an important emergent disease in common white shrimp in Asia, where it is causing production issues and is linked to a pathogen that causes illness in immunosuppressed people.
Stentiford said his field is evolving from identifying and describing individual pathogens to placing them in context within a greater pathobiome in both plant and animal diseases. This involves looking at how pathogens interact within the symbiome and pathobiome to cause disease outcomes. From this holistic view, the field may begin to identify which pathogens are associated with pathobiomes and particular diseases, even if they are not solely causative.
“A lot more of what we will be doing in the next number of years will be profiling those sorts of consortia that live in these situations,” Stentiford said. “We will be moving from an approach where we are simply describing diseases and what happened to actually cataloging conditions conducive to health.”
This has implications for the future of aquaculture, he said. Currently about 50% of global consumption of fish is grown in fresh, ocean, or brackish waters. This so-called “blue food” is expected to increase to by 2050 when 70% of all seafood and fish will come from aquaculture sources. This expansion poses challenges to help aquaculture grow sustainably
“Aquaculture has a lot to offer, with the potential for very efficient production compared to other food sources, but if you follow the mainstream media and the literature on this, you’ll see that sustainability is not a given,” Stentiford said. “Unless we design sustainability into the systems we are looking to grow our food in.”
For example, aquaculture has been stymied by farmed fish escapes into wild habitats, mangrove destruction, overuse of therapeutics and even bonded labor. Stentiford said: “We need to face up to these issues and help nations to build sustainable aquaculture frameworks.”
Applying a One Health lens to aquaculture will positively affect human health, gender equity, organismal health, and environmental health, he said.
“It’s very difficult to do all this at once, it may take several years or decades to build into a sector,” he said. “But by focusing initially on prioritizing human and animal health aspects of the One Health approach, we get to the heart of current production inefficiencies and ensure we make a product that is safe to consume.”
Challenges on this path include identifying and controlling pathogens and hazards that cause these inefficiencies. Stentiford discussed examples such as toxic chemicals that harm the fish or environment, natural environmental pathogens that end up in the farmed fish, and human pathogens and substances that then get into farmed organisms—such as norovirus or antibiotics. He suggests that researchers must increasingly take an “all hazards” approach, rather than focus only on single hazards.
Another challenge centers on assessing risks more proactively, before disease or hazards harm animals or slow their growth through multifactorial causes and paths. Solutions to address this challenge should be centered upon promoting health, and not only upon mitigating disease, Stentiford said.
“It’s too late to tell farmers after the event, ‘this is what happened in this pond,’ because they have already experienced the losses and the outbreak, and the inefficiencies are already built into their system,” he said. “We need to start looking at what are the conditions in that pond in the preceding weeks and days before the outbreak occurs and, where possible, intervene to avert outbreaks.”
This will necessitate moving researcher’s focus form understanding the emergent phase to what he calls the pre-emergent phase. “High animal health and food safety is at the heart of aquaculture sustainability,” Stentiford said. “If we can’t create healthy animals and eat them, it’s not seafood.”
Phylogenomics and COVID-19 in Florida
Since the pandemic began, UF pathology professor Marco Salemi has been deeply involved in university research to genetically sequence COVID-19 samples obtained from Floridians infected with SARS-CoV-2. Salemi is based in the UF Department of Pathology, Experimental Pathology Division and is an EPI faculty member.
Using phylogenetic approaches, his research group—The Florida Coronavirus Genomic epidemiology Network (CGNet)—has tracked SARS-CoV-2 viral variants in Florida and emerging coronavirus zoonoses in the Caribbean. They also collaborated with UF research professor John Lednicky, and his team in the College of Public Health and Health Professions and the EPI, to retroactively uncover the first known genetic evidence of SARS-CoV-2 in Florida, found in a swab of a door handle on a public building.
In October 2020, Salemi and his team were awarded $250,000 from the UF Office of Research and the UF Clinical and Translational Science Institute to consolidate samples stored at separate institutions around Florida and which were known to be positive for coronavirus. His team sequenced these to gather information about the viral variants circulating in Alachua County and the state.
The team began receiving 400-800 samples per week from Alachua County, the Florida Department of Health, the University of Central Florida, the University of Miami, Bay Care hospitals in Ft Myers and Tampa, and Haiti (GHESKIO). They tested these for RNA and complementary DNA and analyzed full genomes to see which lineages were in Florida, if new variations were emerging, and tracked the viral spread in dissemination in populations of interest—such as the vaccinated/unvaccinated, students, the elderly, and farmworkers.
“We compare all of our sequences with those already found in GISAID, which is a huge database developed at the beginning of the coronavirus epidemic,” Salemi said.
Over the past 18 months, he and his team have encountered challenges and successes in developing the workflow and the bioinformatic analysis with this project.
“It’s a powerful pipeline. From the moment we get the samples to the moment we get the full report, it takes about three to five days,” Salemi said. “We can monitor the epidemic in nearly real time.”
The work provides insights to figure out how many lineages are circulating, the proportion of different lineages, and risk factors for different demographic populations.
One of the challenges is that there are millions of viral strains, and the genetic sequences are far from being uniform, he said. Another challenge is that the millions of data points from 15,000 samples are “all the result of convenience sampling.”
Despite this, his team has found that waves of infection in Florida follow national trends documented by the Coronavirus Resource Center maintained by Johns Hopkins University. Major spikes in infection rates tend to coincide with the emergence and spread of new viral variants of concern, such as delta and omicron.
Early in the pandemic, it was unclear if vaccinated people could still contract COVID, Salemi said.
“But we documented breakthrough cases, the first we found was in February 2021,” he recalled. “We considered these statistical oddities and not particularly worrisome.”
But then came delta. And within one month, his team found 100 breakthrough cases, almost all of which were delta. “The good news was that only 80% of these cases were mild, and 20% had no symptoms,” Salemi said. “This showed robust protection against severe illness and death in the vaccinated.”
They found that breakthrough infections were equally likely to occur at any time after vaccination. The CGNeT team also produced among the earliest evidence of breakthrough infections allowing vaccinated people to pass the virus to other vaccinated people. They confirmed the person-to-person transmission using contact tracing and evolutionary analysis of viral genomes (phylogenomics).
His team measured viral load in breakthrough cases and found that no matter the elapsed time from vaccination, 60% of their samples contained high viral loads above the threshold for transmission while 40% contained low viral loads insufficient for transmission.
“This basically means the vaccine, while doing a great job at preventing severe disease, did not do a good job of producing sterilizing immunity,” he said. “There is a great potential for ongoing transmission from vaccinated individuals.”
Future work needs to focus on developing ways to determine how transmissible or pathogenic a new viral variant may be when it emerges, he said.
The same pattern continued with omicron and may continue with other future viral variants too. “It is unlikely that the Omicron variant is the last variant we will see,” Salemi said.
“There may be weeks or months between detection of a new variant of concern and announcing it. Meanwhile it’s spreading and infecting people,” Salemi said. “We are currently using artificial intelligence to analyze data from the spike proteins in GSAID to learn how to detect if a new sequence is a variant of concern prior to a new wave of epidemic emerging.”
Missed our event? Watch the recorded keynote talks!
By; DeLene Beeland