You will find appropriate guidance in order to prevent personnel and animal contamination from avian flu in the Live Animal Regulations. In particular, subsections 10.7.1 through to 10.7.4& (32nd ed.) cover hygiene measures including the cleaning and disinfection of air cargo compartments and animal holding areas.
Liaise with national health authorities
Airlines must approach their health authorities to obtain information on adequate disinfectant solutions or materials as there is no standard applicable to all diseases.
Once a potential list of disinfectants has been established, they must coordinate with their maintenance and engineering departments, who in turn should liaise with airframe manufacturers to establish which solution is most suitable to prevent aircraft corrosion and damage.
See the US CDC example of country-issued standard precautions in addition to instructions on health care environment respiratory and droplet prevention techniques.
On the basis of regular contact with authorities specialized in pandemics protection and prevention, such as the EU Dangerous Goods Consumer protection, IATA has developed these Avian Flu - Cargo guidelines for carriers (pdf)
On an international basis, animal diseases are usually dealt with via the World Animal Health organization (OIE) as well as the World Health Organization (WHO). You can subscribe to the OIE-Info Distribution List to receive information via e-mail on any animal disease outbreak.
In case of disease outbreaks, specimens are dispatched to health laboratories for identification purposes. For example in the EU, samples (virological and serological) are transported to the Community Reference Laboratory based in Weybridge (UK) from the countries affected. OIE reference laboratories and disease experts list.
Packaging
In order to ensure timely delivery in transportation by air, packaging should follow the requirements applying to infectious substances.