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Infected birds shed the virus in fecal and oculo-nasal discharges. Even though recovered flocks shed less virus than clinically ill flocks, recovered flocks will intermittently shed and should be considered infected for life.
Waterfowl (wild and domesticated) are the primary natural reservoir of influenza viruses. Wild waterfowl usually do not show clinical signs, but they can excrete the virus for long periods of time. In addition, waterfowl can be infected with more than one type of influenza virus. Detection is further complicated by the fact that they often do not develop a detectable antibody response after exposure to the virus.

Influenza virus has been recovered from water and organic material from lakes and ponds utilized by infected ducks. Co-mingling of these birds with range-reared flocks is a factor in some outbreaks.

The avian influenza virus can remain viable for long periods of time at moderate temperatures, and can survive indefinitely in frozen material. As a result, the disease can be spread through improper disposal of infected carcasses, manure, or poultry by-products.

The disease also can be easily spread by people and equipment contaminated with avian influenza virus. Avian influenza viruses can be transmitted on contaminated shoes, clothing, crates, egg flats, egg cases, vehicles, and other equipment. Any object located on an infected poultry farm must be considered contaminated and should be completely cleaned and disinfected before it is moved from that premises. Clothing worn on an infected farm should be laundered.

Insects and rodents may mechanically carry the virus from infected to susceptible poultry.

Influenza virus has been isolated from turkey eggs suggesting vertical transmission, although typically the virus kills the embryo. There is little or no evidence of egg-borne infection of poults. However, eggshell surfaces can be contaminated with the influenza virus, and thus are a means of transmission.

Avian influenza viruses have frequently been isolated from clinically normal, imported exotic birds. These infected birds are a potential threat to cage birds, wild birds, and poultry.

Live-bird markets are a reservoir of infection. Such markets serve as a focal point for gathering and housing many species of bird. These facilities are rarely cleaned or disinfected.