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Emerging infectious diseases (EIDs) are key contributors to the current global biodiversity crisis. Psittaciformes (parrots) are one of the most vulnerable avian taxa and psittacine beak and feather disease (PBFD) is the most common viral disease in wild parrots. PBFD is caused by the beak and feather disease virus (BFDV), which belongs to the Circoviridae family and comprises a circular, single-stranded DNA genome. BFDV is considered to have spread rapidly across the world and, in 2005, an outbreak of PBFD was documented in the recovering population of the Mauritius parakeet (Alexandrinus eques). The Mauritius parakeet was once the world's rarest parrot and has been successfully recovered through 30 years of intensive conservation management. Molecular surveillance for the prevalence of BFDV was carried out across a 24-year sample archive spanning the period from 1993 to 2017, and DNA sequencing of positive individuals provided an opportunity to assess patterns of phylogenetic and haplotype diversity. Phylogenetic analyses show variation in the extent of viral diversification within the replicase protein (Rep). Timeseries of BFDV prevalence and number of haplotypes reveal that two subsequent waves of infection occurred in 2010/2011 and 2013/2014 following the initial outbreak in 2005. Continued disease surveillance to determine the frequency and intensity of subsequent waves of infection may benefit future translocation/reintroduction planning. The continued growth of the Mauritius parakeet population despite the presence of BFDV bodes well for its long-term persistence. [ABSTRACT FROM AUTHOR]