Cotton leafroll dwarf virus (CLRDV) was officially detected in 2017 in Alabama, but new research finds that that virus has been lurking in the Cotton Belt since as early as 2006.

CLRDV has been detected in almost all states of the Cotton Belt, including Texas, Georgia, Mississippi, the Carolinas and Tennessee. While the virus hasn’t led to widespread damage in the Cotton Belt, localized economic damage has occurred. One study estimated yield reduction of 560 kg/ha over 25 percent of Alabama’s 2018 cotton acreage and a statewide farmgate income loss of $19 million as reported by Alabama A&M and Auburn Universities Extension offices. In South America’s commercial cotton industry, up to 80 percent yield loss has been observed due to CLRDV.

When Alejandro Olmedo-Velarde, assistant professor in plant pathology, entomology, and microbiology at Iowa State University, first began working with cotton and CLRDV something didn’t quite add up, he said. Instead of seeing severe outbreaks everywhere, the virus was present in fields with mild or hard-to-detect symptoms. A pathogen may cause major problems in one region or be relatively mild in another, especially if it has been present in that region for a long time, Olmedo-Velarde explained, and crops and pathogens can slowly adapt to each other, with local varieties developing some level of tolerance to the virus even without intentionally breeding for it.

“At the time, most reports suggested CLRDV was a newly introduced virus from South America or elsewhere. But when we looked closely at the genetic sequence of U.S. virus samples and compared them with those from South America, the data didn’t clearly support a recent introduction. The U.S. strains looked distinct,” he said. “That combination – mild or inconsistent symptoms in U.S. fields and genetic evidence that didn’t match the ‘recent introduction’ story – motivated us to dig deeper and ask a simple but important question: Has this virus actually been here longer than we think?”

To answer this question, Olmedo-Velarde and a team of researchers began data mining, a technique that involves reanalyzing publicly available datasets to answer research questions. Over the past 15 to 20 years, thousands of plant samples have been genetically sequenced and uploaded into public databases that scientists around the world can access, Olmedo-Velarde explained. Through searching a database called Serratus, which scans RNA sequencing data and identifies viral signatures, and using a tool called BLAST, which helped to find matches of CLRDV in older plant samples, the team made their discovery.

“Using these approaches, we found strong genetic evidence of CLRDV in cotton samples from Mississippi in 2006, Louisiana in 2015, and California in 2018. In each case, we were able to recover partial to nearly complete virus genomes that closely matched modern U.S. isolates,” Olmedo-Velarde said. “That told us it wasn’t contamination or a random fragment – the virus was genuinely present in those plants years before its official report in 2017.”

There are a few likely reasons why the virus went undetected for so long, Olmedo-Velarde said. One reason is that plants infected with CLRDV don’t consistently show obvious damage, making it difficult to know a new pathogen is present. Additionally, the symptoms of CLRDV overlap with other issues like nutrient stress, drought, and other known diseases, making it unlikely for growers to seek alternative explanations.

“There’s also an interesting possibility involving a condition called bronze wilt, which was reported in parts of the South in the 1990s and 2000s. Bronze wilt has an unclear cause, but some of its symptoms overlap with those associated with CLRDV,” he added. “It’s possible that some cases we thought were something else may actually have involved the virus. That’s still a hypothesis and would require further study to confirm.”

Olmedo-Velarde said future research steps include studying aphid pressure, which is strongly influenced by weather patterns.

“(The) next step is not just documenting presence, but refining risk prediction. We want to better integrate virus monitoring with aphid surveillance and weather data so growers can anticipate higher-risk seasons rather than react after symptoms appear,” he said. “We also need continued evaluation of cotton varieties under different environmental conditions to understand which ones perform better when virus pressure is high.”

Other research includes long-term regional monitoring to determine if the virus is stabilizing in production systems or if new genetic variants emerge over time and developing improved diagnostic tools.

Overall, the takeaway for farmers is that CLRDV is not a brand-new threat, which suggests U.S. cotton varieties may already have tolerance and knowing the true timeline of the pathogen helps to better understand risk, leading to research and progress on long-term management and monitoring.

“(It) reminds us that not every emerging disease is actually ‘new.’ Sometimes we only recognize a problem once it reaches a tipping point, maybe due to weather patterns, aphid pressure, changes in varieties or other stress factors,” Olmedo-Velarde said. “Understanding the history helps us avoid reacting purely out of alarm and instead respond with data-driven strategies.”