Non-targeted microbial sequencing of backyard chickens in Tanzania

The overall objective of the collaborative project between Sokoine University of Agriculture in Morogoro, Tanzania and the USDA-ARS Southeast Poultry Research Laboratory (SEPRL) in Athens, USA, was to identify and molecularly characterize Newcastle disease virus variants (NDVs) that may be circulating in backyard free-range chickens that are presented for sale at live bird markets (LBMs) in the cities of Dar es Salaam, Morogoro, Tanga, Arusha, Iringa and Mbeya. The chickens are transported from small-scale rural farms to the open-air LBMs (re-stocking is on average twice a week), where they are kept throughout in wired cages, with number of birds per trader ranging from 50-300 birds. The project approach is collection of a cloacal and an oropharyngeal swab from each bird using standard procedures, which are then shipped to SEPRL for non-targeted random next-generation sequencing (NGS) and data processing.