My first thought as well. They say it happened very fast though and it was contained within a relatively small radius... 5000 birds. Eerie.
My first thought was botulism poisoning in a near by water supply. We had a case of this in NM a while back...killed many ducks (and other small animals).
Once infected they can spread it to other animals that they come in contact with.
HANTAVIRUS
Hantavirus pulmonary syndrome is a severe respiratory illness that can be deadly. It is caused by the Sin Nombre virus, one of a family of viruses that is found worldwide. It can be transmitted by infected rodents through urine, droppings, or saliva.
Humans can contract the disease when they breathe in aerosolized virus. HPS was first recognized in 1993 and has since been identified throughout the United States. Although rare, HPS is potentially deadly. Rodent control in and around the home remains the primary strategy for preventing hantavirus infection.
Hantavirus Activity in New Mexico
(updated 10/14/2010)
Map of Human Cases of Hantavirus Pulmonary Syndrome in New Mexico, 2010
■The first case of hantavirus pulmonary syndrome in New Mexico this year has been confirmed in a McKinley County woman (see press release of 05/06/2010).
■New Mexico had four cases of hantavirus pulmonary syndrome in 2009. None of these was fatal.
■In 2008, New Mexico had two cases of hantavirus pulmonary syndrome, both of which were fatal.
■There were three cases in 2007, one of which was fatal.
■New Mexico has reported a total of 83 hantavirus pulmonary syndrome cases with 33 deaths since 1975.
Hantavirus Health Data in New Mexico - Epidemiology & Response Division