A spotted towhee, one of 11 species whose survival estimates seem to have rebounded after being affected by West Nile virus. Paul Higgins.

Since its introduction in 1999, West Nile virus has devastated native bird populations in North America. It spread across the continent in just five years, and it’s been linked to the deaths of millions of birds. But what’s happened since?

Researchers analyzing 16 years of data on a quarter-million birds reveal that far more species were hit than we thought; nearly half of the bird species they studied were negatively affected. And while half of those afflicted species managed to rebound within a year or two, the other half have yet to recover. The findings are published in Proceedings of the National Academy of Sciences this week.

Previous analyses uncovered negative effects of the virus in roughly one-fifth to one-third of the species examined. But these studies relied on bird count data that might have underestimated virus susceptibility. Recruitment and immigration, for example, could mask population declines.

Now, to fully document the demographic impacts of West Nile virus across North American populations, UCLA’s Ryan Harrigan and colleagues analyzed mark-recapture data on 49 bird species collected between 1992 and 2007 from over 500 bird-banding stations across the U.S. That method requires you to catch a bird, band it, and then see it or catch it again. By counting how many times you re-catch a bird over the course of migratory seasons, you can get a better estimate of the survival rate for the population or species, Harrigan explained to IFLScience.

They found significant declines in the survival rates of 23 of the 49 species investigated. That’s 47%. "Clearly we didn't see the whole picture," study coauthor Joseph LaManna from Washington University said in a statement. "Half the species we studied had significant die-offs."

Among those 23 negatively affected species, there was a clear divide: birds that were only impacted during the disease’s initial spread and those that still show no signs of recovery. Eleven species recovered to their pre-virus levels. These include the field sparrow, downy woodpecker, spotted towhee (pictured above), and red-eyed vireo (pictured above right). In fact, crows, jays, and other corvids – who were so strongly associated with the disease on its arrival – seem to be some of the most resilient ones.

For the remaining 12 species, average survival dropped and remained below pre-virus levels in subsequent years. Swainson’s thrush (pictured right), the purple finch and tufted titmouse may have suffered long-term population declines.

It’s still unclear why some species fare better than others. Phylogenetic analyses, however, did identify the groups that were disproportionally affected by West Nile virus – New World sparrows, finches, and vireos – which suggests an evolutionary dimension to disease risk.

Images in the text: Red-eyed Vireo (top) and Swainson's thrush. Both by Randy Korotev.