Cross-species transmission of poultry pathogens in backyard farms: ducks as carriers of chicken viruses.

Pauly, Maude; Snoeck, Chantal J; Phoutana, Vannaphone; Keosengthong, Amphone; Sausy, Aurélie; Khenkha, Latdavone; Nouanthong, Phonethipsavanh; Samountry, Bounthome; Jutavijittum, Prapan; Vilivong, Keooudomphone; Hübschen, Judith M; Black, Antony P; Pommasichan, Sisavath; Muller, Claude P

In backyard farms of Lao People's Democratic Republic, mixed-species rearing of poultry is a breeding-ground for cross-species transmission. Here, the epidemiology of viruses circulating among backyard poultry in Vientiane Province was assessed to guide future control strategies. Oral/tracheal and cloacal swabs, collected from 605 poultry (308 ducks, 297 chickens) between 2011 and 2015, were screened by PCR for Newcastle disease virus (NDV), Coronavirus (CoV) and Chicken Anemia Virus (CAV). Chicken sera were screened for anti-NDV antibodies by ELISA. Statistical and phylogenetic analyses revealed transmission patterns and relationships. Closely related strains co-circulated in chickens and ducks. While CoV RNA was detected in oral/tracheal swabs of 9.3% of the chickens and 2.4% of the ducks, rates were higher in fecal swabs of both species (27.3% and 48.2%). RNA of Infectious bronchitis virus (IBV) and duck CoV was found in fecal swabs of chickens (19.7% and 7.1%) and of ducks (4.1% and 44.1%). Moreover, DNA of the generally chicken-specific CAV was detected in oral/tracheal swabs of chickens (18.1%) and sporadically of ducks (2.4%). Despite serological evidence of NDV circulation or vaccination (86.9%), NDV RNA was not detected. We found a high prevalence and indication for cross-species transmission of different CoV strains in backyard poultry. Interestingly, ducks served as biological or at least mechanical carrier of viral strains closely related not only to IBV, but also to CAV. Animal containment and poultry species separation could be first steps to avoid cross-species transmission and emergence of novel strains with broad host range and enhanced pathogenicity.