West Nile Virus may be a more dire problem for a far wider range of bird species than experts have previously thought, according to a new study conducted by a collaboration of research organizations including the Point Reyes Station-based Institute for Bird Populations. And some are being hit harder than others—though for reasons that remain unclear.

“What is clear is that West Nile has had a much greater effect on land birds than we thought,” said Dave DeSante, the institute’s founder and a longtime West Marin resident. 

Since the virus arrived in North America in 1999, studies have estimated that between one-fifth and one-third of all bird species have been negatively affected. But that tally may be closer to half, according to Mr. DeSante, whose team of researchers from the institute and several universities found that 23 out of 49 species they sampled—which encompassed tens of thousands of birds per species—were stricken with the virus.

Among affected species, survival rates for many—such as wrentit, Swainson’s thrush, purple finch and tufted titmouse—declined long after the virus’s introduction and have never recovered. That finding, Mr. DeSante said, was unexpected.

“We don’t have any idea why that’s happening,” Mr. DeSante said. “That’s the next step to try and find out.”

Mr. DeSante said most studies focusing on survival rates have relied on rough population field counts, mostly performed by bird enthusiasts. While eyeball-counts showed shrinking survival rates for many species, they gave an incomplete picture.

“It wasn’t clear whether these birds were declining due to a declining birth rate or an increasing death rate,” said Mr. DeSante, who has led West Marin counting groups. “But it seems now that the problem has more to do with death rates.”

Since 1992, his institute has spearheaded a more standardized method for tallying bird populations through the Monitoring Avian Productivity and Survivorship Program, or MAPS. Utilizing professional biologists and trained volunteers, MAPS involves netting and tagging individual birds at around 500 catch stations across the continent each year. From this effort, Mr. DeSante and his team developed a formula to calculate the probability of adult birds surviving year-to-year and pinpoint where and when these birds traveled.

Working with the University of California at Los Angeles, researchers extracted D.N.A. from the tail feathers of birds captured between 1999 and 2007 and analyzed the virus’s potential effects and the timing, locations and intensity of its arrival. They discovered that survival rates for some affected species recovered, while others continued to decline.

“You can’t see that [trend] unless you look at this data according to the year of the West Nile Virus’s arrival,” Mr. DeSante said. That finding, Mr. DeSante added, could help researchers unravel the mystery of why and how some species develop immunity and others do not.

Bird populations are plummeting because of other stresses, too, such as climate change and land development. “We’re trying to learn…what we have to do to turn the declines around,” Mr. DeSante said. “West Nile Virus is just another complicating factor that makes it more difficult.”