Tracking viral evolution during a disease outbreak: the rapid and complete selective sweep of a circovirus in the endangered Echo parakeet

Beak and feather disease virus (BFDV) persists in tissues of asymptomatic wild Crimson Rosellas

Infectious diseases can drive populations and species to extinction. Beak and feather disease virus (BFDV) is a circovirus of global conservation concern that can infect all Psittaciformes and some other species. Yet some parrot species, such as Crimson rosellas (Platycercus elegans), can live successfully with high BFDV prevalence (>40%) with no clinical signs reported in infected individuals. We assessed BFDV load in 10-12 tissues per bird, from n = 66 P. elegans, to reveal tissue tropism and BFDV persistence in tissues. Here we show that in 94% of individuals, BFDV was detected in one or more tissues. While BFDV replicated to high levels in subadults, in adults (some confirmed seropositive) the virus persisted in various tissues at much lower levels. Our findings reveal that BFDV is much more common in wild P. elegans than previously thought and suggest that current screening practices (mostly on blood) may substantially underestimate BFDV infection estimates, with implications for biosecurity and conservation programs globally.

The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton & E. Newton, 1876)

We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.

Prevalence, genotypes, and infection risk factors of psittacine beak and feather disease virus and budgerigar fledgling disease virus in captive birds in Hong Kong

Psittacine beak and feather disease virus (PBFDV) and budgerigar fledgling disease virus (BFDV) are significant avian pathogens that threaten both captive and wild birds, particularly parrots, which are common hosts. This study involved sampling and testing of 516 captive birds from households, pet shops, and an animal clinic in Hong Kong for PBFDV and BFDV. The results showed that PBFDV and BFDV were present in 7.17% and 0.58% of the samples, respectively. These rates were lower than those reported in most parts of Asia. Notably, the infection rates of PBFDV in pet shops were significantly higher compared to other sources, while no BFDV-positive samples were found in pet shops. Most of the positive samples came from parrots, but PBFDV was also detected in two non-parrot species, including Swinhoe's white-eyes (Zosterops simplex), which had not been reported previously. The ability of PBFDV to infect both psittacine and passerine birds is concerning, especially in densely populated urban areas such as Hong Kong, where captive flocks come into close contact with wildlife. Phylogenetic analysis of the Cap and Rep genes of PBFDV revealed that the strains found in Hong Kong were closely related to those in Europe and other parts of Asia, including mainland China, Thailand, Taiwan, and Saudi Arabia. These findings indicate the presence of both viruses among captive birds in Hong Kong. We recommend implementing regular surveillance for both viruses and adopting measures to prevent contact between captive and wild birds, thereby reducing the transmission of introduced diseases to native species.

The phylogenetic and phylogeographic landscape of the beak and feather disease virus, 1996-2022

The beak and feather disease virus (BFDV), causative agent of Psittacine beak and feather disease (PBFD), is a highly fatal and widespread virus that infects both the wild and captive Psittaciformes around the world. The BFDV genome is a ssDNA of approximately 2 kb in size, making it among the smallest known pathogenic viruses. Though, the virus is placed in Circoviridae family of the Circovirus genus, there is no classification system on clade and sub-clade level according to the International Committee on Taxonomy of Viruses and the strains are grouped on the bases of geographic locations. Thus, we provide the latest and robust phylogenetic classification of BFDVs in this study based on full-length genomic sequences, grouping all the available 454 strains detected during 1996-2022 into two distinct clades, e.g., GI and GII. The GI clade is further divided into six sub-clades (GI a-f), while GII into two sub-clades (GII a and b). In addition, the phylogeographic network identified high variability among the BFDV strains, showing several branches, where all the branches are connected to four strains, e.g., BFDV-ZA-PGM-70A-2008-South_Africa (GenBank ID: HM748921.1), BFDV-ZA-PGM-81A-2008-South_Africa (GenBank ID: JX221009.1), BFDV14-2010-Thailand (GenBank ID: GU015021.1) and BFDV-isolate-9IT11-2014-Italy (GenBank ID: KF723390.1). Furthermore, we identified 27 recombination events in the rep (replication-associated protein) and cap (capsid protein) coding regions using the complete genomes of BFDVs. Similarly, the amino acids variability analysis indicated that both the rep and cap regions are highly variable with values exceeding the variability coefficient estimation limit of 1.00, speculating the possible amino acids drift with the emergence of new strains. The findings provided in this study may offer the latest phylogenetic, phylogeographic and evolutionary landscape of the BFDVs.

Molecular detection and analysis of beak and feather disease viruses in Iran

The beak and feather disease virus (BFDV) is one of the few pathogens capable of causing extinction of psittacines. To determine the prevalence and the nature of BFDV mutation, this study investigated the presence of the BFDV among 1,095 individual birds of the 17 psittacine species in Iran followed by analyzing the DNA sequences of seven replication-associated protein (rep) and 10 capsid (cap) genomes of the virus. The BFDV was found to be the foremost pathogen among more than 12 psittacine species, and phylogenetic analysis showed that the BFDV GenBank-published sequences from Poland, Saudi Arabia, South Africa, Taiwan, and Thailand were most similar to those of this study. Evolutionary analysis concluded that arginine, leucine, and glycine were the amino acids frequently involved in the least-conserved substitution patterns of BFDV, and conversely, methionine, glutamine, and tryptophan were the amino acids that exhibited ultra-high conservation through the substitution patterns. The high substitution rate of arginine to lysine and glycine to serine also made greater contribution to the BFDV gene mutation. The relative synonymous codon usage between two genes revealed that the cap genome encoded proteins frequently used fewer codons, while the rep genome encoded proteins used more codons only at moderate frequency, explaining the broader divergence of the cap compared to the rep sequence. The data analysis also introduced a new variant of BFDV that exists in the rep and cap sequences of budgerigars. While the existence of more new variants was suspected, more solid evidence is required to substantiate this suspicion.

Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland

Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.

Apparent Lack of Circovirus Transmission from Invasive Parakeets to Native Birds

The transmission of pathogens to native species has been highlighted as one of the most important impacts of biological invasions. In this study, we evaluated the presence of psittacine beak and feather disease virus (BFDV) and other circoviruses in native bird species cohabiting with invasive populations of wild rose-ringed (Psittacula krameri) and monk parakeets (Myiopsitta monachus) that were found positive for a particular BFDV genotype in Sevilla, southern Spain. None of the 290 individuals from the 18 native bird species captured showed typical signs of disease caused by BFDV. A sample of 79 individuals from 15 native species showed negative results for the presence of the BFDV genotype previously detected in the sympatric invasive parakeets, as well as any other of the circoviruses tested. Although preliminary, this study suggests a lack of circovirus transmission from invasive parakeets to native birds at the study site. Further research is needed to determine if this apparent absence in transmission depends on the BFDV genotype present in the parakeets, which requires additional screening in other invasive and native populations living in sympatry.

Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations

Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. F_ST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.

Analysis of the beak and feather disease viral genome indicates evidence of multiple introduction events into Saudi Arabia

Psittacine beak and feather disease (PBFD), caused by beak and feather disease virus (BFDV) is a highly contagious disease in wild and captive psittacine populations and has an almost global presence. However, the BFDV infection in Saudi Arabia remains largely unknown. In the present study, we report the full genome sequence of BFDV strains from Saudi Arabia and its genetic diversity. The complete genome sequences were analyzed for 14 BFDV-infected birds representing 6 psittacine species. The complete genome sequence of BFDV strains was compared with 201 previously reported sequences to evaluate their diversity and possible recombination events, if any. Our analysis revealed that newly sequenced BFDV genomes from Saudi Arabia belonged to six different strains. Phylogenetic analysis suggested that the isolated BFDV genomes were highly recombinant with a high degree of diversity. It is evident from the study that psittacine species in Saudi Arabia are at risk from the spread of BFDV. As per the CITES trade database, about 190,000 parrots have been imported to Saudi Arabia since 1975 over a thousand instances. Presumably, during any of these trade events or unregulated trade of birds has predisposed the introduction of BFDV to Saudi Arabia. Understanding the epidemiology of BFDV is necessitated to address the threat posed by the virus to the psittacine population of Saudi Arabia.

Structural Perspectives of Beak and Feather Disease Virus and Porcine Circovirus Proteins

Circoviruses represent a rapidly expanding group of viruses that infect both vertebrate and invertebrate hosts. Members are responsible for diseases of veterinary and economic importance, including postweaning multisystemic wasting syndrome in pigs, and beak and feather disease (BFD) in birds. These viruses are associated with lymphoid depletion and immunosuppressive conditions in infected animals leading to systemic illness. Circoviruses are small nonenveloped DNA viruses containing a single-stranded circular genome, encoding two major proteins: the capsid-associated protein (Cap), comprising the entirety of the viral capsid, and the replication-associated protein (Rep). Cap is the only protein component of the virion and plays crucial roles throughout the virus replication cycle, including viral attachment, cell entry, genome uncoating, and packaging of newly formed viral particles. Rep mediates recognition of replication origin motifs in the viral genome sequence and is responsible for endonuclease activity enabling nicking of the circular DNA and initiation of rolling-circle replication (RCR). Porcine circovirus 2 (PCV2) was the first circovirus capsid structure to be solved at atomic resolution using X-ray crystallography. The structure revealed an assembly comprising 60 monomeric subunits to form virus-like particles. Each Cap monomer harbors a canonical viral jelly roll domain composed of two, four-stranded antiparallel β-sheets. Crystal structures of two distinct macromolecular assemblies from BFD virus Cap were also resolved at high resolution. In these structures, the exposure of the N-terminal arginine-rich motif, responsible for DNA binding and nuclear localization is reversed. Additional structural investigations have also elucidated a PCV2 type-specific neutralizing epitope, and interaction between the PCV2 capsid and polymers such as heparin. In this review, we provide a snapshot of the structural and functional aspects of circovirus proteins.

Active responses to outbreaks of infectious wildlife diseases: objectives, strategies and constraints determine feasibility and success

Emerging wildlife diseases are taking a heavy toll on animal and plant species worldwide. Mitigation, particularly in the initial epidemic phase, is hindered by uncertainty about the epidemiology and management of emerging diseases, but also by vague or poorly defined objectives. Here, we use a quantitative analysis to assess how the decision context of mitigation objectives, available strategies and practical constraints influences the decision of whether and how to respond to epidemics in wildlife. To illustrate our approach, we parametrized the model for European fire salamanders affected by Batrachochytrium salamandrivorans, and explored different combinations of conservation, containment and budgetary objectives. We found that in approximately half of those scenarios, host removal strategies perform equal to or worse than no management at all during a local outbreak, particularly where removal cannot exclusively target infected individuals. Moreover, the window for intervention shrinks rapidly if an outbreak is detected late or if a response is delayed. Clearly defining the decision context is, therefore, vital to plan meaningful responses to novel outbreaks. Explicitly stating objectives, strategies and constraints, if possible before an outbreak occurs, avoids wasting precious resources and creating false expectations about what can and cannot be achieved during the epidemic phase.

Beak and feather disease virus (BFDV) prevalence, load and excretion in seven species of wild caught common Australian parrots

Pathogens pose a major risk to wild host populations, especially in the face of ongoing biodiversity declines. Beak and feather disease virus (BFDV) can affect most if not all members of one of the largest and most threatened bird orders world-wide, the Psittaciformes. Signs of disease can be severe and mortality rates high. Its broad host range makes it a risk to threatened species in particular, because infection can occur via spill-over from abundant hosts. Despite these risks, surveillance of BFDV in locally abundant wild host species has been lacking. We used qPCR and haemagglutination assays to investigate BFDV prevalence, load and shedding in seven abundant host species in the wild in south-east Australia: Crimson Rosellas (Platycercus elegans), Eastern Rosellas (Platycercus eximius), Galahs (Eolophus roseicapillus), Sulphur-crested Cockatoos (Cacatua galerita), Blue-winged Parrots (Neophema chrysostoma), Rainbow Lorikeets (Trichoglossus moluccanus) and Red-rumped Parrots (Psephotus haematonotus). We found BFDV infection in clinically normal birds in six of the seven species sampled. We focused our analysis on the four most commonly caught species, namely Crimson Rosellas (BFDV prevalence in blood samples: 41.8%), Sulphur-crested Cockatoos (20.0%), Blue-winged Parrots (11.8%) and Galahs (8.8%). Species, but not sex, was a significant predictor for BFDV prevalence and load. 56.1% of BFDV positive individuals were excreting BFDV antigen into their feathers, indicative of active viral replication with shedding. Being BFDV positive in blood samples predicted shedding in Crimson Rosellas. Our study confirms that BFDV is endemic in our study region, and can inform targeted disease management by providing comparative data on interspecies variation in virus prevalence, load and shedding.

High Prevalence of Novel Beak and Feather Disease Virus in Sympatric Invasive Parakeets Introduced to Spain From Asia and South America

The psittacine beak and feather disease (PBFD) is a globally widespread infectious bird disease that mainly affects species within the Order Psittaciformes (parrots and allies). The disease is caused by an avian circovirus (the beak and feather disease virus, BFDV), which is highly infectious and can lead to severe consequences in wild and captive populations during an outbreak. Both legal and illegal trading have spread the BFDV around the world, although little is known about its prevalence in invasive parrot populations. Here, we analyze the BFDV prevalence in sympatric invasive populations of rose-ringed (Psittacula krameri) and monk parakeets (Myiopsitta monachus) in Southern Spain. We PCR-screened 110 blood samples (55 individuals from each species) for BFDV and characterized the genotypes of five positives from each species. About 33% of rose-ringed parakeets and 37% of monk parakeets sampled were positive for BFDV, while neither species showed disease symptoms. The circovirus identified is a novel BFDV genotype common to both species, similar to the BFDV genotypes detected in several parrot species kept in captivity in Saudi Arabia, South Africa and China. Our data evidences the importance of an accurate evaluation of avian diseases in wild populations, since invasive parrots may be bringing BFDV without showing any visually detectable clinical sign. Further research on the BFDV prevalence and transmission (individual–individual, captive–wild and wild–captive) in different bird orders and countries is crucial to understand the dynamics of the viral infection and minimize its impact in captive and wild populations.

Seasonal fluctuation of beak and feather disease virus (BFDV) infection in wild Crimson Rosellas (Platycercus elegans)

Understanding patterns of pathogen emergence can help identify mechanisms involved in transmission dynamics. Beak and feather disease virus (BFDV) poses a major threat world-wide to wild and captive parrots. Yet data from wild birds on seasonal fluctuations in prevalence and infection intensity, and thereby the potential high-risk times for virus transmission, have been lacking. We screened wild Crimson Rosellas (Platycercus elegans) for BFDV in blood and cloacal swabs. Prevalence in blood samples and cloacal swabs, as well as viral load varied with Julian date and in blood, were highest after the breeding season. Breeding birds had lower viral load and lower BFDV prevalence in blood than non-breeding birds (10.1% prevalence in breeding vs. 43.2% in non-breeding birds). BFDV prevalence was much higher in younger (<3 years) than older (≥3 years) birds for both blood samples (42.9% vs. 4.5%) and cloacal swabs (56.4% vs. 12.3%). BFDV status in blood and cloacal samples was not correlated within individuals. We show that, at least in P. elegans, BFDV infection seems to occur year-round, with seasonal changes in prevalence and load found in our samples. Our analyses suggest that the seasonal changes were associated primarily with the breeding season. We also discuss age and sex as important predictors of BFDV infection.

Monitoring of free-ranging and captive Psittacula populations in Western Europe for avian bornaviruses, circoviruses and polyomaviruses

Avian pathogens such as bornaviruses, circoviruses and polyomaviruses are widely distributed in captive collections of psittacine birds worldwide and can cause fatal diseases. In contrast, only little is known about their presence in free-ranging psittacines and their impact on these populations. Rose-ringed parakeets (Psittacula krameri) and Alexandrine parakeets (Psittacula eupatria) are non-native to Europe, but have established stable populations in parts of Western Europe. From 2012-2017, we surveyed free-ranging populations in Germany and France as well as captive Psittacula individuals from Germany and Spain for avian bornavirus, circovirus and polyomavirus infections. Samples from two out of 469 tested free-ranging birds (0.4%; 95% confidence interval [CI-95]: 0.1-1.5%) were positive for beak and feather disease virus (BeFDV), whereas avian bornaviruses and polyomaviruses were not detected in the free-ranging populations. In contrast, avian bornaviruses and polyomaviruses, but not circoviruses were detected in captive populations. Parrot bornavirus 4 (PaBV-4) infection was detected by RT-PCR in four out of 210 captive parakeets (1.9%; CI-95: 0.7-4.8%) from four different holdings in Germany and Spain and confirmed by detection of bornavirus-reactive antibodies in two of these birds. Three out of 160 tested birds (1.9%; CI-95: 0.5-5.4%) possessed serum antibodies directed against budgerigar fledgling disease virus (BuFDV). PaBV-4 and BuFDV were also detected in several psittacines of a mixed holding in Germany, which had been in contact with free-ranging parakeets. Our results demonstrate that Psittacula parakeets are susceptible to common psittacine pathogens and their populations in Western Europe are exposed to these viruses. Nevertheless, the prevalence of avian bornaviruses, circoviruses and polyomaviruses in those populations is very low.RESEARCH HIGHLIGHTS Psittacula parakeets are susceptible to bornavirus, circovirus and polyomavirus infection.Introduced Psittacula populations in Europe have been exposed to these viruses.Nevertheless, they may be absent or present at only low levels in free-ranging Psittacula populations.Free-ranging populations in Europe pose a minor threat of transmitting these viruses to captive Psittaciformes.

HEALTH ASSESSMENT OF CAPTIVE PSITTACINE SPECIES IN PRERELEASE PROGRAMS AT COSTA RICAN RESCUE CENTERS

With stricter laws regulating the capture and possession of wild animals in Costa Rica, local wildlife-rescue centers have been overwhelmed by an influx of confiscated or relinquished illegal pets, specifically of psittacine species. As part of a nationwide health-assessment program targeting these centers, 122 birds representing five psittacine species ( Ara macao, Amazona autumnalis, Amazona auropalliata, Amazona farinosa, Aratinga finschi) and one hybrid macaw ( Ara macao × Ara ambiguus) were examined and tested between January 2011 and October 2012. Physical examination, hematology, and serum biochemical analyses were performed. Blood and feathers were tested for psittacine beak and feather disease virus (PBFDV) and avian polyomavirus (APV) via PCR. A DNA-based prevalence and sequence analysis characterized the strains of PBFDV and APV isolated. Physical abnormalities observed in 36% of the 122 birds examined were limited to thin body condition and poor feather quality. None of the feather abnormalities were characteristic of disease caused by either PBFDV or APV. Results of hematological and biochemical analyses were within normal limits except for five birds with leukocytosis and heterophilia, three birds with uric acid values above 16 mg/dl, and two additional birds with AST values above 400 IU/L. No hemoparasites were detected during blood smear examination. Overall prevalences of 9.8% (12/122) for PBFDV and 3.3% (4/122) for APV were documented, with only one bird testing positive for both PBFDV and APV. Birds from two of the eight centers were negative for both viruses. Findings from this study constitute the beginning of a standardized surveillance program for Costa Rican rescue centers, targeting the management of avian species enrolled in propagation and reintroduction programs and expanding of the spectrum of pathogen surveillance and husbandry recommendations in prerelease centers.

The first reptilian circovirus identified infects gut and liver tissues of black-headed pythons

Viral metagenomic analysis of the liver of a black headed python (Aspidites melanocephalus) euthanized for a proliferative spinal lesion of unknown etiology yielded the first characterized genome of a reptile-infecting circovirus (black-headed python circovirus or BhPyCV). BhPyCV-specific in situ hybridization (ISH) showed that viral nucleic acids were strongly expressed in the intestinal lining and mucosa and multifocally in the liver. To investigate the presence of this virus in other snakes and its possible pathogenicity, 17 snakes in the python family with spinal disease were screened with ISH yielding a second BhP positive in intestinal tissue, and a Boelen’s python (Morelia boeleni) positive in the liver. BhPyCV specific PCR was used to screen available frozen tissues from 13 of these pythons, four additional deceased pythons with and without spinal disease, and fecal samples from 37 live snakes of multiple species with unknown disease status. PCR detected multiple positive tissues in both of the ISH positive BhP and in the feces of another two live BhP and two live annulated tree boas (Corallus annulatus). Preliminary analysis indicates this circovirus can infect BhPs where it was found in 4/5 BhPs tested (2/2 with spinal disease, 2/3 live with unknown status), Boelen’s python (1/2 with spinal disease), and annulated tree boa (2/6 live with unknown status) but was not detected in other python species with the same spinal lesions. This circovirus’ causal or contributory role in spinal disease remains speculative and not well supported by these initial data.

Hygiene and biosecurity protocols reduce infection prevalence but do not improve fledging success in an endangered parrot

Emerging Infectious Diseases (EIDs) are recognised as global extinction drivers of threatened species. Unfortunately, biodiversity managers have few tested solutions to manage them when often the desperate need for solutions necessitates a response. Here we test in situ biosecurity protocols to assess the efficacy of managing Psittacine beak and feather disease (PBFD), one of the most common and emergent viral diseases in wild parrots (Psittaciformes) that is currently affecting numerous threatened species globally. In response to an outbreak of PBFD in Mauritius “echo” parakeets (Psittacula eques), managers implemented a set of biosecurity protocols to limit transmission and impact of Beak and feather disease virus (BFDV). Here we used a reciprocal design experiment on the wild population to test whether BFDV management reduced viral prevalence and viral load, and improved nestling body condition and fledge success. Whilst management reduced the probability of nestling infection by approximately 11% there was no observed impact on BFDV load and nestling body condition. In contrast to expectations there was lower fledge success in nests with added BFDV biosecurity (83% in untreated vs. 79% in treated nests). Our results clearly illustrate that management for wildlife conservation should be critically evaluated through targeted monitoring and experimental manipulation, and this evaluation should always focus on the fundamental objective of conservation.

Psittacid Adenovirus-2 infection in the critically endangered orange-bellied parrot (Neophema chrysogastor): A key threatening process or an example of a host-adapted virus?

Psittacid Adenovirus-2 (PsAdv-2) was identified in captive orange-bellied parrots (Neophema chrysogastor) during a multifactorial cluster of mortalities at the Adelaide Zoo, South Australia, and an outbreak of Pseudomonas aeruginosa septicaemia at the Tasmanian Department of Primary Industries, Parks, Water and Environment captive breeding facility, Taroona, Tasmania. This was the first time that an adenovirus had been identified in orange-bellied parrots and is the first report of PsAdv-2 in Australia. To investigate the status of PsAdv-2 in the captive population of orange-bellied parrots, 102 healthy birds from five breeding facilities were examined for the presence of PsAdv-2 DNA in droppings and/or cloacal swabs using a nested polymerase chain reaction assay. Additionally, eight birds released to the wild for the 2016 breeding season were similarly tested when they were recaptured prior to migration to be held in captivity for the winter. PsAdv-2 was identified in all breeding facilities as well as the birds recaptured from the wild. Prevalence of shedding ranged from 29.7 to 76.5%, demonstrating that PsAdv-2 is endemic in the captive population of orange-bellied parrots and that wild parrots may have been exposed to the virus. PsAdv-2 DNA was detected in both cloacal swabs and faeces of the orange-bellied parrots, but testing both samples from the same birds suggested that testing faeces would be more sensitive than cloacal swabs. PsAdv-2 was not found in other psittacine species housed in nearby aviaries at the Adelaide Zoo. The source of the infection in the orange-bellied parrots remains undetermined. In this study, PsAdv-2 prevalence of shedding was higher in adult birds as compared to birds less than one year old. Preliminary data also suggested a correlation between adenovirus shedding prevalence within the breeding collection and chick survival.

Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range

While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.

Trade and conservation implications of new beak and feather disease virus detection in native and introduced parrots

Psittacine beak and feather disease (PBFD), caused by Beak and feather disease virus (BFDV), has spread rapidly around the world, raising concerns for threatened species conservation and biosecurity associated with the global pet bird trade. The virus has been reported in several wild parrot populations, but data are lacking for many taxa and geographical areas with high parrot endemism. We aimed to advance understanding of BFDV distribution in many data-deficient areas and determine phylogenetic and biogeographic associations of the virus in 5 parrot species across Africa, the Indian Ocean islands, Asia, and Europe and focused specifically on the highly traded and invasive Psittacula krameri. Blood, feather, and tissue samples were screened for BFDV through standard polymerase chain reaction. Isolates obtained from positive individuals were then analyzed in a maximum likelihood phylogeny along with all other publically available global BFDV sequences. We detected BFDV in 8 countries where it was not known to occur previously, indicating the virus is more widely distributed than currently recognized. We documented for the first time the presence of BFDV in wild populations of P. krameri within its native range in Asia and Africa. We detected BFDV among introduced P. krameri in Mauritius and the Seychelles, raising concerns for island endemic species in the region. Phylogenetic relationships between viral sequences showed likely pathways of transmission between populations in southern Asia and western Africa. A high degree of phylogenetic relatedness between viral variants from geographically distant populations suggests recent introductions, likely driven by global trade. These findings highlight the need for effective regulation of international trade in live parrots, particularly in regions with high parrot endemism or vulnerable taxa where P. krameri could act as a reservoir host.

Host heterozygosity and genotype rarity affect viral dynamics in an avian subspecies complex

Genetic diversity at community, population and individual levels is thought to influence the spread of infectious disease. At the individual level, inbreeding and heterozygosity are associated with increased risk of infection and disease severity. Host genotype rarity may also reduce infection risk if pathogens are co-adapted to common or local hosts, but to date, no studies have investigated the relative importance of genotype rarity and heterozygosity for infection in a wild, sexually reproducing vertebrate. With beak and feather disease virus (BFDV) infection in a wild parrot (Platycercus elegans), we show that both heterozygosity and genotype rarity of individual hosts predicted infection, but in contrasting ways. Heterozygosity was negatively associated with probability of infection, but not with infection load. In contrast, increased host genotype rarity was associated with lower viral load in infected individuals, but did not predict infection probability. These effects were largely consistent across subspecies, but were not evident at the population level. Subspecies and age were also strongly associated with infection. Our study provides novel insights into infection dynamics by quantifying rarity and diversity simultaneously. We elucidate roles that host genetic diversity can play in infection dynamics, with implications for understanding population divergence, intraspecific diversity and conservation.

Beak and feather disease virus in wild and captive parrots: an analysis of geographic and taxonomic distribution and methodological trends

Psittacine beak and feather disease (PBFD) has emerged in recent years as a major threat to wild parrot populations and is an increasing concern to aviculturists and managers of captive populations. Pathological and serological tests for screening for the presence of beak and feather disease virus (BFDV) are a critical component of efforts to manage the disease and of epidemiological studies. Since the disease was first reported in the mid-1970s, screening for BFDV has been conducted in numerous wild and captive populations. However, at present, there is no current and readily accessible synthesis of screening efforts and their results. Here, we consolidate information collected from 83 PBFD- and BFDV-based publications on the primary screening methods being used and identify important knowledge gaps regarding potential global disease hotspots. We present trends in research intensity in this field and critically discuss advances in screening techniques and their applications to both aviculture and to the management of threatened wild populations. Finally, we provide an overview of estimates of BFDV prevalence in captive and wild flocks alongside a complete list of all psittacine species in which the virus has been confirmed. Our evaluation highlights the need for standardised diagnostic tests and more emphasis on studies of wild populations, particularly in view of the intrinsic connection between global trade in companion birds and the spread of novel BFDV strains into wild populations. Increased emphasis should be placed on the screening of captive and wild parrot populations within their countries of origin across the Americas, Africa and Asia.

Discovery and complete genome sequence of a novel circovirus-like virus in the endangered rowi kiwi, Apteryx rowi

Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp., derived from faecal matter of the rowi kiwi (A. rowi) showing signs of verminous dermatitis. The entire 2085 nt genome was cloned and sequenced and contains both capsid and replicase genes, as well as a conserved 9 nt motif. Phylogenetic analyses place it within Circoviridae, adjacent to other environmental CRESS-DNA viruses, and most closely related to badger circovirus-like virus (Meles meles circovirus-like virus). As the rowi is the most critically endangered kiwi, it is vital to understand the role of rowi kiwi circovirus-like virus as a possible pathogen and also any potential cross-species transmission.

Comparison of beak and feather disease virus prevalence and immunity-associated genetic diversity over time in an island population of red-crowned parakeets

Pathogen outbreaks in the wild can contribute to a population's extinction risk. Concern over the effects of pathogen outbreaks in wildlife is amplified in small, threatened populations, where degradation of genetic diversity may hinder natural selection for enhanced immunocompetence. Beak and feather disease virus (BFDV) was detected for the first time in an island population of red-crowned parakeets (Cyanoramphus novaezelandiae) in 2008 on Little Barrier Island (Hauturu-o-Toi) of New Zealand. By 2013, the prevalence of the viral infection had significantly decreased within the population. We tested whether the population of red-crowned parakeets showed a selective response to BFDV, using neutral microsatellite and two immunity-associated genetic markers, the major histocompatibility complex (MHC) and Toll-like receptors (TLRs). We found evidence for selection at viral-associated TLR3; however, the ability of TLR3 to elicit an immune response in the presence of BFDV warrants confirmation. Alternatively, because red-crowned parakeet populations are prone to fluctuations in size, the decrease in BFDV prevalence over time may be attributed to the Little Barrier Island population dropping below the density threshold for viral maintenance. Our results highlight that natural processes such as adaptation for enhanced immunocompetence and/or density fluctuations are efficient mechanisms for reducing pathogen prevalence in a threatened, isolated population.

Evidence of a deep viral host switch event with beak and feather disease virus infection in rainbow bee-eaters (Merops ornatus)

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.

Emerging infectious disease or evidence of endemicity? A multi-season study of beak and feather disease virus in wild red-crowned parakeets (Cyanoramphus novaezelandiae)

Beak and feather disease virus (BFDV) is a single-stranded DNA virus that is the etiological agent of beak and feather disease in both wild and captive parrots. Given that BFDV is globally recognized as a conservation threat for wild parrots, between 2011-2013, red-crowned parakeets (Cyanoramphus novaezelandiae, n = 229), which are endemic to New Zealand, were captured in mist nets on Tiritiri Matangi Island and Hauturu-o-Toi/Little Barrier Island (LBI), New Zealand, for disease surveillance. Blood and feathers from all birds were tested by PCR for BFDV, and full genomes were recovered and sequenced. A subset of blood samples (n = 96) were tested for antibodies to BFDV by the haemagglutination inhibition (HI) test. A further 238 feather samples were obtained from red-crowned parakeets from three sites in the Wellington region of the North Island, and these were screened for BFDV. The DNA-based prevalence of BFDV infection determined on Tiritiri Matangi Island was 1.09% (CI 95 %, 0.1-3.9%); on Hauturu-o-Toi/LBI, 4.4% (95% CI, 0.5%-15.1%); on Kapiti Island, 3.4% (CI 95%, 1.1-7.8%); at the ZEALANDIA-Karori sanctuary, 1.6% (95% CI, 0-8.4%); and on Matiu-Somes Island, 0% (CI 95%, 0-12.3%). Seroprevalence for BFDV, indicating prior or current exposure, in the Tiritiri Matangi Island population, it was 2% (CI 95%, 0-10.1%), and in the Hauturu-o-Toi/LBI population was 14% (CI 95%, 5.3-27.9%). BFDV-positive birds showed no signs of clinical disease, with the exception of an individual bird obtained opportunistically from Shakespear Regional Park during the study period, which had classical signs of feather loss. Phylogenetic analysis of the 11 full genome sequences recovered from BFDV-positive red-crowned parakeets revealed evidence of ongoing viral flow between red-crowned parakeets and eastern rosellas (Platycercus eximius) in the Hauraki Gulf/Auckland region, with separate but closely related strains from the Wellington region of the North Island. This is the first study to report HI results for a New Zealand endemic parrot species, and the first epidemiological analysis of serial cross-sectional surveys in a BFDV-infected population of red-crowned parakeets in New Zealand. We postulate that although BFDV remains a threat to small, isolated or naïve populations of parrots globally, the low viral prevalence in this and other studies suggests that native parakeets in New Zealand may act as dead-end or spillover hosts.

Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses

The capsid genes from 14 pigeon circovirus (PiCV) sequences, collected from Taiwan between 2009 and 2010, were sequenced and compared with 14 PiCV capsid gene sequences from GenBank. Based on pairwise comparison, PiCV strains from Taiwan shared 73.9-100% nucleotide identity and 72-100% amino acid identity with those of the 14 reported PiCV sequences. Phylogenetic analyses revealed that Taiwanese PiCV isolates can be grouped into two clades: clade 1 comprising isolates from Belgium, Australia, USA, Italy and China, and clade 2 showing close relation to isolates from Germany and France. Recurrent positive selection was detected in clade 1 PiCV lineages, which may contribute to the diversification of predominant PiCV sequences in Taiwan. Further observations suggest that synonymous codon usage variations between PiCV clade 1 and clade 2 may reflect the adaptive divergence on translation efficiency of capsid genes in infectious hosts. Variation in selective pressures acting on the evolutionary divergence and codon usage bias of both clades explains the regional coexistence of virus sequences congeners prevented from competitive exclusion within an island such as Taiwan. Our genotyping results also provide insight into the aetiological agents of PiCV outbreak in Taiwan and we present a comparative analysis of the central coding region of PiCV genome. From the sequence comparison results of 28 PiCVs which differs in regard to the geographical origin and columbid species, we identified conserved regions within the capsid gene that are likely to be suitable for primer selection and vaccine development.

Detailed monitoring of a small but recovering population reveals sublethal effects of disease and unexpected interactions with supplemental feeding

Infectious diseases are widely recognized to have substantial impact on wildlife populations. These impacts are sometimes exacerbated in small endangered populations, and therefore, the success of conservation reintroductions to aid the recovery of such species can be seriously threatened by outbreaks of infectious disease. Intensive management strategies associated with conservation reintroductions can further compound these negative effects in such populations.

Exploring the sublethal effects of disease outbreaks among natural populations is challenging and requires longitudinal, individual life‐history data on patterns of reproductive success and other indicators of individual fitness.

Long‐term monitoring data concerning detailed reproductive information of the reintroduced Mauritius parakeet (Psittacula echo) population collected before, during and after a disease outbreak was investigated.

Deleterious effects of an outbreak of beak and feather disease virus (BFDV) were revealed on hatch success, but these effects were remarkably short‐lived and disproportionately associated with breeding pairs which took supplemental food. Individual BFDV infection status was not predicted by any genetic, environmental or conservation management factors and was not associated with any of our measures of immune function, perhaps suggesting immunological impairment. Experimental immunostimulation using the PHA (phytohaemagglutinin assay) challenge technique did, however, provoke a significant cellular immune response.

We illustrate the resilience of this bottlenecked and once critically endangered, island‐endemic species to an epidemic outbreak of BFDV and highlight the value of systematic monitoring in revealing inconspicuous but nonetheless substantial ecological interactions. Our study demonstrates that the emergence of such an infectious disease in a population ordinarily associated with increased susceptibility does not necessarily lead to deleterious impacts on population growth and that negative effects on reproductive fitness can be short‐lived.

Prevalence of beak and feather disease virus in wild Platycercus elegans: comparison of three tissue types using a probe-based real-time qPCR test

The detection of avian viruses in wild populations has considerable conservation implications. For DNA-based studies, feathers may be a convenient sample type for virus screening and are, therefore, an increasingly common technique. This is despite recent concerns about DNA quality, ethics, and a paucity of data comparing the reliability and sensitivity of feather sampling to other common sample types such as blood. Alternatively, skeletal muscle tissue may offer a convenient sample to collect from dead birds, which may reveal viraemia. Here, we describe a probe-based quantitative real-time PCR for the relative quantification of beak and feather disease virus (BFDV), a pathogen of serious conservation concern for parrots globally. We used this method to test for BFDV in wild crimson rosellas (Platycercus elegans), and compared three different sample types. We detected BFDV in samples from 29 out of 84 individuals (34.5%). However, feather samples provided discordant results concerning virus presence when compared with muscle tissue and blood, and estimates of viral load varied somewhat between different sample types. This study provides evidence for widespread infection of BFDV in wild crimson rosellas, but highlights the importance of sample type when generating and interpreting qualitative and quantitative avian virus data.

Phylogenetic analysis of beak and feather disease virus across a host ring-species complex

Pathogens have been hypothesized to play a major role in host diversity and speciation. Susceptibility of hybrid hosts to pathogens is thought to be a common phenomenon that could promote host population divergence and subsequently speciation. However, few studies have tested for pathogen infection across animal hybrid zones while testing for codivergence of the pathogens in the hybridizing host complex. Over 8 y, we studied natural infection by a rapidly evolving single-strand DNA virus, beak and feather diseases virus (BFDV), which infects parrots, exploiting a host-ring species complex (Platycercus elegans) in Australia. We found that host subspecies and their hybrids varied strikingly in both BFDV prevalence and load: both hybrid and phenotypically intermediate subspecies had lower prevalence and load compared with parental subspecies, while controlling for host age, sex, longitude and latitude, as well as temporal effects. We sequenced viral isolates throughout the range, which revealed patterns of genomic variation analogous to Mayr's ring-species hypothesis, to our knowledge for the first time in any host-pathogen system. Viral phylogeny, geographic location, intraspecific host density, and parrot community diversity and composition did not explain the differences in BFDV prevalence or load between subpopulations. Overall, our analyses suggest that functional host responses to infection, or force of infection, differ between subspecies and hybrids. Our findings highlight the role of host hybridization and clines in altering host-pathogen interactions, dynamics that can have important implications for models of speciation with gene flow, and offer insights into how pathogens may adapt to diverging host populations.

Beak and feather disease viruses circulating in Cape parrots (Poicepahlus robustus) in South Africa

Captive and wild psittacines are vulnerable to the highly contagious psittacine beak and feather disease. The causative agent, beak and feather disease virus (BFDV), was recently detected in the largest remaining population of endangered Cape parrots (Poicepahlus robustus), which are endemic to South Africa. Full-length genomes were isolated and sequenced from 26 blood samples collected from wild and captive Cape parrots to determine possible origins of infection. All sequences had characteristic BFDV sequence motifs and were similar in length to those described in the literature. However, BFDV coat protein (CP) sequences from this study did not contain a previously identified bipartite nuclear localisation signal (NLS) within residues 39-56, which indicates that an alternate NLS is involved in shuttling the CP into the nucleus. Sequences from the wild population shared a high degree of similarity, irrespective of year or location, suggesting that the disease outbreak occurred close to the time when the samples were collected. Phylogenetic analysis of full-length genomes showed that the captive Cape parrot sequences cluster with those isolated from captive-bred budgerigars in KwaZulu-Natal Province, South Africa. Exposure to captive-bred Cape parrots from a breeding facility in KwaZulu-Natal is suggested as a possible source for the virus infection. Phylogenetic analysis of BFDV isolates from wild and captive Cape parrots indicated two separate infection events in different populations, which highlights the potential risk of introducing new strains of the virus into the wild population. The present study represents the first systematic investigation of BFDV virus diversity in the southern-most population of Cape parrots.

Beak and feather disease virus: correlation between viral load and clinical signs in wild Cape parrots (Poicepahlus robustus) in South Africa

Psittacine beak and feather disease (PBFD), the most prevalent viral disease affecting psittacines, is caused by beak and feather disease virus (BFDV). This study assessed viral load using qPCR in a wild Cape parrot population affected by PBFD and compared it to overall physical condition based on clinical signs attributable to PBFD. A significant inverse correlation between viral load and overall physical condition was found, which confirmed that clinical signs may confidently be used to diagnose the relative severity of BFDV infections in wild populations. This is the first assessment of BFDV viral load in a wild psittacine population.

Clinical beak and feather disease virus infection in wild juvenile eastern rosellas of New Zealand; biosecurity implications for wildlife care facilities

CASE HISTORY

Four juvenile eastern rosellas (Platycercus eximius) were admitted to two separate wildlife care facilities in the Auckland region by members of the public. They had missing or dystrophic wing and tail feathers that rendered them flightless, suggestive of beak and feather disease virus (BFDV) infection. Two were subject to euthanasia after failing to re-grow their feathers, with samples taken for histopathology and PCR analysis. Blood samples were obtained from the other two birds at the time of examination, however these individuals were lost to follow up.

PATHOLOGICAL AND MOLECULAR FINDINGS

Basophilic inclusion bodies were observed in histological sections of the feather bulb, typical of BFDV infection, from the two euthanised individuals. Blood from all four birds tested positive by PCR for BFDV, and analysis of the recovered full BFDV genomes identified them as belonging to the BFDV-A strain.

DIAGNOSIS

Beak and feather disease virus infection.

CLINICAL RELEVANCE

This report highlights the clinical impacts of BFDV in juvenile eastern rosellas that may result in their admission to wildlife care facilities, creating a biosecurity risk in institutions that may host other native parrots intended for release. The environmental stability of BFDV and resistance to disinfection requires strict quarantine procedures to prevent contamination and spread within a facility. It is recommended that high-risk species such as wild eastern rosella be excluded from facilities that may also house native parrots.

Phylogeny of beak and feather disease virus in cockatoos demonstrates host generalism and multiple-variant infections within Psittaciformes

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.

Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses

The emergence of human-transmissible H5N1 avian influenza viruses poses a major pandemic threat. H5N1 viruses are thought to be highly genetically diverse both among and within hosts, but the effects of this diversity on viral replication and transmission are poorly understood. Here we use deep sequencing to investigate the impact of within-host viral variation on adaptation and transmission of H5N1 viruses in ferrets. We show that although within-host genetic diversity in hemagglutinin (HA) increases during replication in inoculated ferrets, HA diversity is dramatically reduced upon respiratory droplet transmission, where infection is established by only 1–2 distinct HA segments from a diverse source virus population in transmitting animals. Moreover, minor HA variants present in as little as 5.9% of viruses within the source animal become dominant in ferrets infected via respiratory droplets. These findings demonstrate that selective pressures acting during influenza virus transmission among mammals impose a significant bottleneck.

Mutability dynamics of an emergent single stranded DNA virus in a naïve host

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.

Identification of hepatotropic viruses from plasma using deep sequencing: a next generation diagnostic tool

We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids.

Differential expression of two isolates of beak and feather disease virus capsid protein in Escherichia coli

Expression of recombinant beak and feather disease virus (BFDV) capsid-associated protein (Cap) has relied on inefficient techniques that typically produce low yields or use specialized expression systems, which greatly increase the cost and expertise required for mass production. An Escherichia coli system was used to express recombinant BFDV Cap derived from two isolates of BFDV, from a Long-billed Corella (Cacatua tenuirostris) and an Orange-bellied parrot (OBP; Neophema chrysogaster). Purification by affinity and size exclusion chromatography was optimized through an iterative process involving screening and modification of buffer constituents and pH. A buffer containing glycerol, β-mercaptoethanol, Triton X-100, and a high concentration of NaCl at pH 8 was used to increase solubility of the protein. The final concentration of the corella-isolated BFDV protein was fifteen- to twenty-fold greater than that produced in previous publications using E. coli expression systems. Immunoassays were used to confirm the specific antigenicity of recombinant Cap, verifying its validity for use in continued experimentation as a potential vaccine, a reagent in diagnostic assays, and as a concentrated sample for biological discoveries.