West Nile virus (WNV), a mosquito-borne pathogen that can kill both people and birds, is still causing havoc in North America, wiping out millions of birds every year across the continent, according to a new study. The research raises concerns about the long-term impacts of the disease, particularly on threatened and endangered species.

“It is really a fantastic but sobering study,” says Peter Marra, an ornithologist at the Smithsonian Institution's National Zoological Park in Washington, D.C., who was not involved in the work. “When combined with other threats, such as land use, climate change, cats, and buildings, it’s no wonder we’re seeing such strong declines in so many bird species across the United States.”

West Nile arrived in North America 16 years ago. Though it can infect and kill people, birds are the virus’s primary host. But North American avian species had never contracted WNV, and the novel pathogen spread across the continent in just 5 years, leaving millions of birds, from jays to sparrows to finches, dead in its wake. Previous studies indicated that a variety of factors, such as climate and habitat, affected how various bird species responded to the virus. For instance, researchers had shown that birds in urban environments seemed more likely to contract the ailment, although scientists do not yet know why.

To better understand such factors and to show the full impact of WNV, a team of scientists analyzed 16 years of data collected from 1992 to 2007 at more than 500 stations across the United States where birds are regularly trapped and banded. After 1999, these Monitoring Avian Productivity and Survivorship (MAPS) stations also began checking birds for WNV, and so had records of when the disease first appeared at each station and in each species, and whether the virus persisted. Using this information, the scientists were able to determine whether and to what extent the virus first affected various avian populations, and whether the birds’ numbers have recovered or are still declining. (The scientists weren’t able to include MAPS data after 2007 because these have not yet been processed by station volunteers and personnel. Nevertheless, the researchers are confident the trends they discovered have not changed.) Altogether, they looked at data on a quarter-million birds from 49 species in 14 avian families, focusing on adults so as to more accurately determine the number of survivors.

Twenty-three of the 49 species—or 47%—were negatively affected by WNV, the researchers report online today in the Proceedings of the National Academy of Sciences. They also uncovered several striking patterns in the disease’s impact. Some species initially suffered huge declines. Red-eyed vireo (Vireo olivaceus) populations, for instance, dropped about 29% when they first encountered the disease. Before WNV arrived, red-eyed vireos, a species that’s widely distributed across the continent, had an estimated population of 130 million birds. Ultimately, nearly 37 million of these vireos likely died from the virus, the scientists say. But this species’ populations only endured massive die-offs the first year WNV hit them. Their numbers subsequently recovered—which is the pattern that disease ecologists expect to see.

“It’s like after a flu outbreak,” says Ryan Harrigan, an infectious disease biologist at the University of California, Los Angeles, and one of the authors of the study. “Everyone builds up immunity, and the impact tends to wane.” Eleven of the 23 affected species in the study experienced this type of recovery.

But the other 12 species were not so lucky. Their populations are still declining from the disease. “Seeing the disease’s persistence was a shock,” Harrigan says. “We don’t know why these species are unable to recover. It’s alarming.” For example, populations of warbling vireos (Vireo gilvus) dropped only 8.7% when they contracted WNV. But instead of recovering, this species’ populations have continued to drop every year by roughly the same percentage, a trend the scientists expect is continuing. “It’s not that it was just an 8.7% decline one year; it’s an 8.7% decline on that smaller population the next year, and the year after that, so the effect is compounded,” Harrigan says.

He and his colleagues estimate that WNV has killed more than 15 million of these vireos, nearly one-third of their original population of 49 million. The Swaainson’s thrush (Catharus ustulatus), purple finch (Carpodacus purpureus), tufted titmouse (Baeolophus bicolor), and wrentit (Chamaea fasciata) were similarly affected.

To try to understand why some species are better than others at overcoming the disease, the researchers compared the birds’ habitats, looking to see whether those in more urban landscapes had larger declines as previous studies suggested. Here, too, results were mixed. The adult populations of 10 species, including the spotted towhee (Pipilo maculatus) and song sparrow (Melospiza melodia), were doing fine in these habitats, perhaps because they have more food resources thanks to human-provided bird feeders. But 11 other species in these same urban areas lost—and likely continue to lose—significant numbers of their adults.

The scientists also constructed a family tree of all the study species in order to see whether closely related birds responded similarly to the virus. Again, the pattern was mixed. New world sparrows and their close relatives, and vireos generally died off only the first year after contracting the virus, whereas finches typically experienced persistent declines. The scientists say they don’t yet know why some species are better than others at overcoming the disease.

“Is it because of differences in their immune systems or their habitats or the amount of their exposure to [WNV]?” Harrigan asks. He and his colleagues are now looking more closely at the regions they’ve identified as those where certain avian species are still dying from the disease to see whether they can spot the reason.

Other scientists expect that the study will lead to similar investigations. “As with all good studies, this one generates many new questions,” says Staffan Bensch, an animal ecologist at Lund University in Sweden, who wonders whether the virus has benefitted some songbird species by killing off their avian predators, jays and crows.

Another mystery: WNV did not affect at least three species, the black-capped chickadee (Parus atricapillus), American robin (Turdus migratorius), and house wren (Troglodytes aedon). “Those species went straight through without any problem,” Harrigan says. “How does a species have no effect from this disease?”

Answering these questions will require more long-term data of the type collected at the MAPS stations, the scientists say. “This won’t be the last time we see a disease like this,” Harrigan warns. And although the study didn’t focus on endangered species, all the scientists worry that the virus may be causing them further harm. “What’s the effect on birds with smaller populations and ranges?” he says. Like so many things about WNV, the scientists don’t yet know. They only know that the disease and its effects on North American birds—and people—are here to stay. Understanding more about how the virus affects birds and helping them overcome it will, thus, benefit humans, too, the scientists say.