BackgroundOver the past 20 years, many marine seabird populations have been gradually declining and the factors driving this ongoing deterioration are not always well understood. Avipoxvirus infections have been found in a wide range of bird species worldwide, however, very little is known about the disease ecology of avian poxviruses in seabirds. Here we present two novel avipoxviruses from pacific shearwaters (Ardenna spp), one from a Flesh-footed Shearwater (A. carneipes) (SWPV-1) and the other from a Wedge-tailed Shearwater (A. pacificus) (SWPV-2).ResultsEpidermal pox lesions, liver, and blood samples were examined from A. carneipes and A. pacificus of breeding colonies in eastern Australia. After histopathological confirmation of the disease, PCR screening was conducted for avipoxvirus, circovirus, reticuloendotheliosis virus, and fungal agents. Two samples that were PCR positive for poxvirus were further assessed by next generation sequencing, which yielded complete Shearwaterpox virus (SWPV) genomes from A. pacificus and A. carneipes, both showing the highest degree of similarity with Canarypox virus (98% and 67%, respectively). The novel SWPV-1 complete genome from A. carneipes is missing 43 genes compared to CNPV and contains 4 predicted genes which are not found in any other poxvirus, whilst, SWPV-2 complete genome was deemed to be missing 18 genes compared to CNPV and a further 15 genes significantly fragmented as to probably cause them to be non-functional.ConclusionThese are the first avipoxvirus complete genome sequences that infect marine seabirds. In the comparison of SWPV-1 and −2 to existing avipoxvirus sequences, our results indicate that the SWPV complete genome from A. carneipes (SWPV-1) described here is not closely related to any other avipoxvirus genome isolated from avian or other natural host species, and that it likely should be considered a separate species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3680-z) contains supplementary material, which is available to authorized users.

ABSTRACT:We report the recent emergence of a novel beak and feather disease virus (BFDV) genotype in the last remaining wild population of the critically endangered Orange-bellied Parrot (Neophema chrysogaster). This virus poses a significant threat to the recovery of the species and potentially its survival in the wild. We used PCR to detect BFDV in the blood of three psittacine beak and feather disease (PBFD)-affected wild Orange-bellied Parrot fledglings captured as founders for an existing captive breeding recovery program. Complete BFDV genome sequence data from one of these birds demonstrating a 1,993-nucleotide-long read encompass the entire circular genome. Maximum-likelihood (ML) and neighbor-joining (NJ) phylogenetic analysis supported the solitary position of this viral isolate in a genetically isolated branch of BFDV. On Rep gene sequencing, a homologous genotype was present in a second wild orange-bellied parrot and the third bird was infected with a distantly related genotype. These viruses have newly appeared in a population that has been intensively monitored for BFDV for the last 13 yr. The detection of two distinct lineages of BFDV in the remnant wild population of Orange-bellied Parrots, consisting of fewer than 50 birds, suggests a role for other parrot species as a reservoir for infection by spillover into this critically endangered species. The potential for such a scenario to contribute to the extinction of a remnant wild animal population is supported by epidemiologic theory.

Phylogenetic analyses of the highly genetically diverse but antigenically conserved, single-stranded circular, DNA genome of the avian circovirus, beak and feather disease virus (BFDV) from cockatoo species throughout Australia demonstrated a high mutation rate for BFDV (orders of magnitude fall in the range of 10(-4) substitutions/site/year) along with strong support for recombination indicating active cross-species transmission in various subpopulations. Multiple variants of BFDV were demonstrated with at least 30 genotypic variants identified within nine individual birds, with one containing up to 7 variants. Single genetic variants were detected in feathers from 2 birds but splenic tissue provided further variants. The rich BFDV genetic diversity points to Australasia as the most likely geographical origin of this virus and supports flexible host switching. We propose this as evidence of Order-wide host generalism in the Psittaciformes characterised by high mutability that is buffered by frequent recombination and slow replication strategy.

Antibiotic-free broiler meat production is becoming increasingly popular worldwide due to consumer perception that it is superior to conventional broiler meat. Globally, broiler farming impacts the income generation of low-income households, helping to alleviate poverty and secure food in the countryside and in semi-municipal societies. For decades, antibiotics have been utilized in the poultry industry to prevent and treat diseases and promote growth. This practice contributes to the development of drug-resistant bacteria in livestock, including poultry, and humans through the food chain, posing a global public health threat. Additionally, consumer demand for antibiotic-free broiler meat is increasing. However, there are many challenges that need to be overcome by adopting suitable strategies to produce antibiotic-free broiler meat with regards to food safety and chicken welfare issues. Herein, we focus on the importance and current scenario of antibiotic use, prospects, and challenges in the production of sustainable antibiotic-free broiler meat, emphasizing broiler farming in the context of Bangladesh. Moreover, we also discuss the need for and challenges of antibiotic alternatives and provide a future outlook for antibiotic-free broiler meat production.

The assembly and regulation of viral capsid proteins into highly ordered macromolecular complexes is essential for viral replication. Here, we utilize crystal structures of the capsid protein from the smallest and simplest known viruses capable of autonomously replicating in animal cells, circoviruses, to establish structural and mechanistic insights into capsid morphogenesis and regulation. The beak and feather disease virus, like many circoviruses, encode only two genes: a capsid protein and a replication initiation protein. The capsid protein forms distinct macromolecular assemblies during replication and here we elucidate these structures at high resolution, showing that these complexes reverse the exposure of the N-terminal arginine rich domain responsible for DNA binding and nuclear localization. We show that assembly of these complexes is regulated by single-stranded DNA (ssDNA), and provide a structural basis of capsid assembly around single-stranded DNA, highlighting novel binding interfaces distinct from the highly positively charged N-terminal ARM domain.

Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of beak and feather disease virus (BFDV) infection in the orange-bellied parrot (Neophema chrysogaster). Detailed health monitoring and the small population size (<300 individuals) of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16) and Rep gene sequences (n = 35) revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved Rep gene and immunogenic capsid (Cap) gene with a high evolutionary rate (3.41×10−3 subs/site/year) approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another.

Since the characterization of psittacine beak and feather disease (PBFD) in 1984, a wide range of avian circoviruses have been discovered with varying pathogenic effects amongst a diverse range of avian hosts. Until recently these circovirus species were thought to be restricted to within avian Orders such as the Psittaciformes for beak and feather disease virus (BFDV) and Columbiformes for pigeon circovirus with little evidence of cross-family transmission or replication. We report evidence of a naturally occurring novel host switch event with self-limiting BFDV infection in a group of rainbow bee-eaters (Merops ornatus) a species of Coraciiformes unrelated to parrots and not previously known to be susceptible to any avian circovirus. The outbreak highlights important and unexpected aspects of disease emergence and host-switching pertinent to other situations when viruses might cross species boundaries as well as the potential of avian circoviruses to infect disparate host species.

The study was carried out to investigate the prevalence of Peste des petitis ruminants (PPR) in goats in Rajshahi District of Bangladesh, and its relation to age, sex, breeds and seasonal influence. In total, 627 goats were examined where 305 were males and 322 were females. The overall prevalence of PPR in goats was found to be 20.57% (n=129). From the various risk factors analysed, age categories of goats, sex, breed and seasonal influence were found to be significantly associated (p<0.01) with the prevalence of PPR. Findings suggested that the seasonal influence on outbreaks of this disease was significantly higher. The clinical prevalence of PPR was highest in the month of December (31.68%) and lowest in June (9.52%). The influence of sex on PPR outbreaks was found to be higher in male (28.52%) than female (13.04%) goats. As regards to age, PPR was significantly higher in young (31.06%) compared to sucklers (13.14%) and adult (10.15%). The susceptibility of Black Bengal goats to PPR was higher than other breeds. The results of this study showed that PPR is an important goat disease in the studied areas. Thus, an appropriate control strategy has to be designed and applied, which could involve prevention of contact with infected goats and vaccination against the PPR virus.