Emergence of a novel avian pox disease in British tit species

Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity

Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.

Molecular and pathological screening of the current circulation of fowlpox and pigeon pox virus in backyard birds

Avian pox is a disease that has devastating impacts on both poultry and wild bird species. Avian pox is caused by various strains of avipoxviruses (APV). Nevertheless, the virus has been detected in pigeons and chickens that are raised in backyard areas, leading to substantial financial damage for small-scale producers. There is a lack of comprehensive information regarding the transmission of APV among birds in the backyards and residential areas. Hence, the present investigation closely monitored and observed APV in domesticated birds residing in backyard areas, with the aim of impeding the transmission of the virus to nearby poultry farms. In 2023, a total of fifty backyard flocks were surveyed for the presence of avian pox disease. Sixteen backyards (14 pigeons and 2 chickens) exhibited warty nodular lesions on their heads and nonfeathered body parts. APV was confirmed in nodular lesions by polymerase chain reaction (PCR) amplification and genetic sequencing. All samples from the lesions showed successful amplification of the p4b locus (core protein p4b). Four confirmed samples were tested for pathogenicity on the chicken embryo chorioallantoic membrane (CAM). Histopathological examination revealed ballooning degeneration and numerous intracytoplasmic inclusion bodies (Bollinger bodies) in the ectoderm of the infected CAM. Phylogenetic analysis revealed that the strains clustered into main clade A, with 11 in subclade A2 and 5 in subclade A1. Amino acid identity showed 100% similarity between the vaccine (fowlpox/VSVRI/Egypt) and some detected strains (PP537574 and PP537575). In addition, the PP537576.1 to PP537580.1 and PP537582.1 to PP537585.1 had 2-point mutations compared to the fowlpox/VSVRI/Egypt vaccine. The overall finding of low biosecurity levels in the investigated backyard birds emphasizes the significance of establishing sanitary measures and control vectors to reduce virus transmission routes and disease severity. In conclusion, it is necessary to emphasize the tracking of APV in backyard birds. Concurrently, we advised enhancing hygiene protocols, vector management, and subsequent vaccination to restrict the occurrence of APV outbreaks and prevent their transmission to neighboring poultry farms. Furthermore, it is crucial to incorporate molecular studies in order to enhance the vaccine seeds for disease management.

Emerging and Novel Viruses in Passerine Birds

There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.

Current situation and genomic characterization of fowlpox virus in lower Egypt during 2022

A total of 45 samples of vaccinated and non-vaccinated layer chickens were collected from farms in the Egyptian governorates of Sharqia, Ismailia, Menofia, Gharbia, Kafr El Sheikh, Qalyubia, and Dakahlia in the year 2022. They exhibited nodular lesions on their combs, mouth corners, and eyelids, suggesting they were infected with pox disease, which was associated with a 3 to 5% mortality rate. The samples were grown on the chorioallantoic-membrane of embryonated chicken eggs to ensure their viability. In both vaccinated and non-vaccinated farms, 35 of 45 virus isolates were confirmed positive via polymerase chain reaction (PCR) of fpv167 (P4b), based on the amplicon length of the fpv167 gene locus. The 6 strains from various Egyptian governorates were chosen for sequencing and genetic characterization. Phylogenetic investigation of the fpv167 (P4b) gene of sequenced strains clustered within sub clade A1 showed 100% correlation between FWPVD, TKPV13401 and fowlpox-AN2, fowlpox-AN3, and fowlpox-AN6, but only a 98.6% correlation between fowlpox-AN1, fowlpox-AN4, and fowlpox-AN5. Comparing the fowlpox-AN1, fowlpox-AN4, and fowlpox-AN5 strains with commercial vaccine strains (HP1-444-(FP9), vaccine-VSVRI), they had 98.6% identity, while other strains had 100% identity. The results of this study's mutation research showed that fowlpox-AN1, fowlpox-AN4, and fowlpox-AN5 had acquired novel mutations; fowlpox-AN1 had R201G and T204A; fowlpox-AN4 and fowlpox-AN5 had L141F and H157P. Further research is required to determine the effectiveness of the current vaccine in order to develop a new vaccine.

Transcriptomic responses of Galápagos finches to avian poxvirus infection

Emerging pathogens can have devastating effects on naïve hosts, but disease outcomes often vary among host species. Comparing the cellular response of different hosts to infection can provide insight into mechanisms of host defence. Here, we used RNA-seq to characterize the transcriptomic response of Darwin's finches to avian poxvirus, a disease of concern in the Galápagos Islands. We tested whether gene expression differs between infected and uninfected birds, and whether transcriptomic differences were related either to known antiviral mechanisms and/or the co-option of the host cellular environment by the virus. We compared two species, the medium ground finch (Geospiza fortis) and the vegetarian finch (Platyspiza crassirostris), to determine whether endemic Galápagos species differ in their response to pox. We found that medium ground finches had a strong transcriptomic response to infection, upregulating genes involved in the innate immune response including interferon production, inflammation, and other immune signalling pathways. In contrast, vegetarian finches had a more limited response, and some changes in this species were consistent with viral manipulation of the host's cellular function and metabolism. Many of the transcriptomic changes mirrored responses documented in model and in vitro studies of poxviruses. Our results thus indicate that many pathways of host defence against poxviruses are conserved among vertebrates and present even in hosts without a long evolutionary history with the virus. At the same time, the differences we observed between closely related species suggests that some endemic species of Galápagos finch could be more susceptible to avian pox than others.

Outbreaks of Avipoxvirus Clade E in Vaccinated Broiler Breeders with Exacerbated Beak Injuries and Sex Differences in Severity

Avipoxvirus affects chickens and wild birds, and it is characterized by lesions on the nonfeathered parts of the body (the cutaneous form), or necrotic lesions in the upper respiratory tract (the diphtheritic form). In poultry farming, avian pox is usually controlled by live attenuated vaccines. However, there have been many reports of outbreaks, even in flocks of vaccinated birds. In the present study, different outbreaks of the emerging clade E avipoxvirus were detected in commercial breeder flocks of chickens vaccinated against fowlpox virus in Southeast Brazil. Clinical manifestations of these outbreaks included a marked prevalence of moderate to severe progressive lesions in the beaks of affected birds, especially in roosters with increased mortality (up to 8.48%). Also, a reduced hatchability (up to 20.77% fewer hatching eggs) was observed in these flocks. Analysis of clinical samples through light and transmission electron microscopy revealed the presence of Bollinger bodies and poxvirus particles in epithelial cells and affecting chondrocytes. PCR, sequencing, and phylogenetic analysis of major core protein (P4b) and DNA polymerase (pol) genes identified this virus as clade E avipoxvirus. We also developed qPCR assays for open reading frames (ORFs) 49, 114, and 159 to detect and quantify this emergent virus. These results show the arrival and initial spread of this pathogen in the poultry industry, which was associated with harmful outbreaks and exacerbated clinical manifestations in vaccinated commercial breeder flocks. This study also highlights the relevance of permanent vigilance and the need to improve sanitary and vaccination programs.

Genomic associations with poxvirus across divergent island populations in Berthelot's pipit

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot's pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses indicates that pathogen-mediated selection may play a role in shaping genomic variation among relatively recently colonised island bird populations and highlights the utility of genotype-environment associations for identifying candidate genes potentially involved in host-pathogen interactions.

A Review on the Prevalence of Poxvirus Disease in Free-Living and Captive Wild Birds

Avian pox is a widespread infection in birds caused by genus Avipoxvirus pathogens. It is a noteworthy, potentially lethal disease to wild and domestic hosts. It can produce two different conditions: cutaneous pox, and diphtheritic pox. Here, we carry out an exhaustive review of all cases of avian pox reported from wild birds to analyze the effect and distribution in different avian species. Avian poxvirus strains have been detected in at least 374 wild bird species, a 60% increase on a 1999 review on avian pox hosts. We also analyze epizootic cases and if this disease contributes to wild bird population declines. We frequently observe very high prevalence in wild birds in remote island groups, e.g., Hawaii, Galapagos, etc., representing a major risk for the conservation of their unique endemic avifauna. However, the difference in prevalence between islands and continents is not significant given the few available studies. Morbidity and mortality can also be very high in captive birds, due to high population densities. However, despite the importance of the disease, the current detection rate of new Avipoxvirus strains suggests that diversity is incomplete for this group, and more research is needed to clarify its real extent, particularly in wild birds.

HEALTH SCREENING OF THE EUROPEAN ENDANGERED SPECIES PROGRAM CAPTIVE POPULATION OF THE PINK PIGEON (NESOENAS MAYERI)

The population of the Mauritian pink pigeon (Nesoenas mayeri) fell to fewer than 20 individuals in the 1970s. Following intensive conservation efforts, the free-living population is now estimated to be 470 individuals. However, because of the population bottleneck the species remains at risk of extinction because of genetic loss and inbreeding depression. A European captive population was established in 1977 and a European Endangered Species Program (EEP) was formalized in 1992. As birds in the EEP captive population possess unique alleles not observed in the surviving free-living birds, the EEP management plan recommends transferring EEP birds to Mauritius to improve genetic diversity. Health screening of the current EEP population to identify circulating pathogens was performed. Forty-two birds from three collections in the United Kingdom and one in Jersey were screened for a wide range of pathogens, present clinically or subclinically, including important viruses, bacteria, protozoa, and helminths. Eleven birds tested positive for at least one pathogen: Trichomonas spp. (5), Yersinia kristensenii (2), Yersinia aleksiciae (1), coccidial oocysts (3), and strongyle ova (3). None of the positive birds showed overt signs of clinical disease, although two birds with Trichomonas spp. had suboptimal body condition. Genotyping of one Trichomonas gallinae sample revealed a type-C strain (low pathogenicity). The results from this screening will contribute towards a disease risk assessment, to create a pre-export protocol for translocation of captive EEP birds to Mauritius.

WHOLE GENOME SEQUENCING OF AN AVIPOXVIRUS ASSOCIATED WITH INFECTIONS IN A GROUP OF AVIARY-HOUSED SNOW BUNTINGS (PLECTROPHENAX NIVALIS)

Avipoxvirus infections have been reported in both free-ranging and domestic birds worldwide. Fowlpox and canarypox viruses belong to the genus Avipoxvirus among the virus family Poxviridae. They cause cutaneous lesions with proliferative growths on the unfeathered parts of the skin and/or diphtheritic lesions generally associated with necrosis in the upper respiratory and digestive tracts. In this study, a poxvirus has been identified in wild-caught snow buntings (Plectrophenax nivalis) housed in an outdoor aviary in the region of Rimouski, Quebec. During the falls and winters of 2015 and 2016, eight snow buntings affected by this infection were examined. Macroscopic and microscopic lesions observed were characteristic of an avipoxvirus infection. Electron microscopy imaging of an ultrathin section of the histopathological lesions of two birds confirmed the presence of the poxvirus. Afterward, the presence of the poxvirus was confirmed in three birds by a specific polymerase chain reaction assay that amplified a segment of the gene encoding the fowlpox virus 4b core protein. A 576-nucleotide amplicon was obtained from one of them and sequenced. The analyses revealed a 99% homology to other previously described avipoxviruses. Using high-throughput sequencing, almost the entire viral genome of this avipoxvirus was revealed and found to possess a 359,853-nucleotide sequence in length. Bioinformatic analyses revealed that the virus was genetically related to canarypox virus. To our knowledge, this is the first confirmed case and full description of a poxviral infection in this species. This episode suggests a high susceptibility of this northern species of passerine to avipoxviruses circulating in southeastern Canada during the summer months. Even if the source of the viral infections remains undetermined, transmission by local biological vectors is suspected. Management of poxviral infections in snow buntings housed outdoors in southeastern Canada could rely on the control of biting insects.

The emergence of subclades A1 and A3 avipoxviruses in India

During the years 2010-2018, avipoxvirus (APV) outbreaks were observed in the domestic chickens and pigeons present in the eastern Indian state of Odisha. Based on typical pox lesions, followed by molecular techniques, the overall morbidity was found to be 18%-19.23% and 16.92%-23% in chickens and pigeons, respectively. The cutaneous forms of the disease were observed with varied rates of mortality, being 47.36%-52.77% in chickens and 39.13%-92% in pigeons. PCR amplification targeting the viral P4b core protein-coding gene and the DNA polymerase gene confirmed the presence of APV strains in 10 birds. Subsequent phylogenetic analysis of these two genes confirmed that the circulating strains were members of APV clade A. The subclade analysis revealed the introduction of A1 and A3 subclades in Indian chickens and pigeons, respectively. This study is the first molecular record of APVs circulating in eastern Indian birds (Odisha) and involves the first use of the polymerase gene to reveal the circulating clades of Indian APVs.

Insights into pathological and molecular characterization of avipoxviruses circulating in Egypt

1. Avipoxvirus (APV) infections are one of many threats inflicting economic losses within the poultry industry, particularly in tropical and subtropical countries. A proper and comprehensive study for APVs is needed to increase the knowledge concerning the diversity and evolution of the virus.2. For this purpose, 136 bird flocks of different species and breeding types were examined for APV infection between October 2016 and November 2017. One hundred and thirty samples had visible pocks on the chorioallantoic membrane (CAM) which were designated as fowl pox-like viruses via amplification of 578 bp from the P4b gene and 1800 bp from the fpv140 locus.4. A comprehensive phylogenetic analysis of fpv167 locus (P4b), fpv140 locus (fpv139 and fpv140) and fpv94 (DNA polymerase) revealed that all the analysed strains belong to fowl pox-like viruses (clade A; subclade A1 and A2). Based on the fpv140 locus full nucleotide sequence, three turkey originated strains were seen to be divergent from chicken originated sequences and branched into novel subclade A1.b.5. Trees comparison, within the term of speculation of virus-host specificity, clearly highlighted a high order specific subgrouping among subclades in the case of the fpv140 locus (including fpv139 and fpv140). Hence, the fowl poxvirus, turkey poxvirus and pigeon poxvirus strains clustered into distinct host-specific subclades A1a, A1.b and A2, respectively, which could not be seen in the FWPV-P4b and DNA polymerase phylogeny.

Avian Poxvirus Infection in Polish Great Tits (Parus Major)

Introduction

Avian poxvirus infections are widespread in the domestic poultry population but are also reported in wild birds. In poultry, these infections cause significant economic losses, while wild birds may be a reservoir for poxvirus which affects breeding poultry. However, wild birds may also exhibit characteristic anatomopathological changes. This study concerns the infection of wild-living great tits (Parus major) with the avian poxvirus in Poland.

Material and Methods

Samples of internal organs and skin collected from great tits were homogenised and total cellular DNA was isolated. In PCR, the primers complementary to gene encoding the core protein 4b of the HP44 strain of fowl poxvirus (FPV) were used.

Results

After electrophoresis in 2% agarose gel, the PCR product of 578 bp characteristic for FPV was obtained in DNA samples isolated from skin lesions and the heart. The analysis of the nucleotide sequence of the virus strain showed 99% similarity to many poxviruses previously isolated from great tits and other free birds at various sites in the world.

Conclusions

This paper is the first clinically documented evidence obtained in laboratory conditions of avian poxvirus cases in great tits in Poland.

Health hazards to wild birds and risk factors associated with anthropogenic food provisioning

Provision of supplementary food for wild birds at garden feeding stations is a common, large-scale and year-round practice in multiple countries including Great Britain (GB). While these additional dietary resources can benefit wildlife, there is a concomitant risk of disease transmission, particularly when birds repeatedly congregate in the same place at high densities and through interactions of species that would not normally associate in close proximity. Citizen science schemes recording garden birds are popular and can integrate disease surveillance with population monitoring, offering a unique opportunity to explore inter-relationships between supplementary feeding, disease epidemiology and population dynamics. Here, we present findings from a national surveillance programme in GB and note the dynamism of endemic and emerging diseases over a 25-year period, focusing on protozoal (finch trichomonosis), viral (Paridae pox) and bacterial (passerine salmonellosis) diseases with contrasting modes of transmission. We also examine the occurrence of mycotoxin contamination of food residues in bird feeders, which present both a direct and indirect (though immunosuppression) risk to wild bird health. Our results inform evidence-based mitigation strategies to minimize anthropogenically mediated health hazards, while maintaining the benefits of providing supplementary food for wild birds.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'.

Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing

Avian pox is an infectious disease caused by avipoxviruses (APV), resulting in cutaneous and/or tracheal lesions. Poxviruses share large genome sizes (from 130 to 360 kb), featuring repetitions, deletions or insertions as a result of a long-term recombination history. The increasing performances of next-generation sequencing (NGS) opened new opportunities for surveillance of poxviruses, based on timely and affordable workflows. We investigated the application of the 3^rd generation Oxford Nanopore Minion technology to achieve real-time whole-genome sequencing directly from lesions, without any enrichment or isolation step. Fowlpox lesions were sampled on hens, total DNA was extracted and processed for sequencing on a MinION, Oxford Nanopore. We readily generated whole APV genomes from cutaneous or tracheal lesions, without any isolation or PCR-based enrichment: Fowlpox virus reads loads ranged from 0.75% to 2.62% and reads up to 61 kbp were generated and readily assembled into 3 APV complete genomes. This long read size eases the assembly step and lowers the bioinformatics capacity requirements and processing time compared to huge sets of short reads. The complete genome analysis confirmed that these Fowlpox viruses cluster within clade A1 and host full length reticuloendotheliovirus (REV) inserts. The pathobiological relevance of REV insert, although a classical feature of fowlpoxviruses (FPVs), should be further investigated. Surveillance of emerging poxviruses could greatly benefit from real-time whole genome sequencing.

Outbreak of cutaneous form of avian poxvirus disease in previously pox-vaccinated commercial turkeys

ABSTRACT: This study describes an outbreak of avian poxvirus disease in previously pox-vaccinated turkeys in Brazil. The turkeys had suggestive gross lesions of cutaneous avian poxvirus in the skin of the head and cervical area without changes in the flock mortality rates. In the slaughterhouse, 30 carcasses were removed from the slaughter line to collect tissue from cutaneous lesions for histological analyses and characterization of the virus. The virus was identified by conventional polymerase chain reaction (PCR) and subsequent gene sequencing. Acanthosis, hyperkeratosis, and hydropic degeneration were seen on skin histopathology. Eosinophilic intracytoplasmic inclusion bodies (Bollinger) on keratinocytes were observed in 46.6% of the samples. Avian poxvirus DNA was detected on PCR in 83.3% of the total samples. PCR associated with histopathology had 93.3% of positivity for avian poxvirus. In the phylogenetic study, samples show 100% matching suggesting that the outbreak occurred by a single viral strain and was different from those strains affecting other wild birds such as canaries and sparrows. A single mutation (Adenine for Guanine) was detected in our study’s strain and in the strains of turkey, chickens, and vaccine strains published in GenBank. Also, when the sequence strain of the present study and sequences from GenBank of canarypox and sparrowpox strains were aligned, a Thymine was found replacing the Adenine or Guanine. The in ovo vaccination method as single-use in turkeys of this study apparently did not provide adequate protection against avianpox disease, but additional vaccination administered by wing-web when turkeys were 45-60 days old in the new flocks controlled the disease. In the subsequent year, new cases of this disease were not found. It was not possible to confirm the source of the virus strain, but infection with a field strain derived from chickens is one possibility, considering the poultry farm population in the area and biosecurity aspects. For wide characterization of avipoxvirus and differentiation among strains, the complete sequence of the viral genome is required.

Characterization of an Avipoxvirus From a Bald Eagle ( Haliaeetus leucocephalus ) Using Novel Consensus PCR Protocols for the rpo147 and DNA-Dependent DNA Polymerase Genes

A juvenile female bald eagle ( Haliaeetus leucocephalus ) was presented with emaciation and proliferative periocular lesions. The eagle did not respond to supportive therapy and was euthanatized. Histopathologic examination of the skin lesions revealed plaques of marked epidermal hyperplasia parakeratosis, marked acanthosis and spongiosis, and eosinophilic intracytoplasmic inclusion bodies. Novel polymerase chain reaction (PCR) assays were done to amplify and sequence DNA polymerase and rpo147 genes. The 4b gene was also analyzed by a previously developed assay. Bayesian and maximum likelihood phylogenetic analyses of the obtained sequences found it to be poxvirus of the genus Avipoxvirus and clustered with other raptor isolates. Better phylogenetic resolution was found in rpo147 rather than the commonly used DNA polymerase. The novel consensus rpo147 PCR assay will create more accurate phylogenic trees and allow better insight into poxvirus history.

Prevalence and Genetic Diversity of Avipoxvirus in House Sparrows in Spain

Avipoxvirus (APV) is a fairly common virus affecting birds that causes morbidity and mortality in wild and captive birds. We studied the prevalence of pox-like lesions and genetic diversity of APV in house sparrows (Passer domesticus) in natural, agricultural and urban areas in southern Spain in 2013 and 2014 and in central Spain for 8 months (2012-2013). Overall, 3.2% of 2,341 house sparrows visually examined in southern Spain had cutaneous lesions consistent with avian pox. A similar prevalence (3%) was found in 338 birds from central Spain. Prevalence was higher in hatch-year birds than in adults. We did not detect any clear spatial or temporal patterns of APV distribution. Molecular analyses of poxvirus-like lesions revealed that 63% of the samples were positive. Molecular and phylogenetic analyses of 29 DNA sequences from the fpv167 gene, detected two strains belonging to the canarypox clade (subclades B1 and B2) previously found in Spain. One of them appears predominant in Iberia and North Africa and shares 70% similarity to fowlpox and canarypox virus. This APV strain has been identified in a limited number of species in the Iberian Peninsula, Morocco and Hungary. The second one has a global distribution and has been found in numerous wild bird species around the world. To our knowledge, this represents the largest study of avian poxvirus disease in the broadly distributed house sparrow and strongly supports the findings that Avipox prevalence in this species in South and central Spain is moderate and the genetic diversity low.

AN EPIZOOTIC OF EMERGING NOVEL AVIAN POX IN CARRION CROWS (CORVUS CORONE) AND LARGE-BILLED CROWS (CORVUS MACRORHYNCHOS) IN JAPAN

In 2006-10, an epizootic of emerging avian pox occurred in Carrion Crows ( Corvus corone ) and Large-billed Crows ( Corvus macrorhynchos ), leading to mortality of juvenile crows in Hokkaido, the northernmost island of Japan. We diagnosed 27 crows with proliferative skin lesions (19 carcasses and eight biopsied cases [one in zoo captivity]) as avian pox clinically, histopathologically by detection of Avipoxvirus-specific 4b core protein (P4b) gene, and epidemiologically. The fatal cases demonstrated intensively severe infection and aggressive lesions with secondary bacterial infection. Since the first identification of avian pox in Sapporo, Japan, in 2006, the frequency of mortality events has increased, peaking in 2007-08. Mortalities have subsequently occurred in other areas, suggesting disease expansion. In Sapporo, prevalence of avian pox evaluated by field censuses during 2007-12 was 17.6% (6.6-27.2%), peaked during 2007-08 and 2008-09, and then decreased. All diseased crows were juveniles, except for one adult. The number of crows assembling in the winter roosts had been stable for >10 yr; however, it declined in 2007-08, decreased by about 50% in 2008-09, and recovered to the previous level in 2009-10, correlated with the avian pox outbreak. Thus, avian pox probably contributed to the unusual crow population decline. All P4b sequences detected in six specimens in Sapporo were identical and different from any previously reported sequences. The sequence detected in the zoo-kept crow was distinct from any reported clades, and interspecies transmission was suspected. This report demonstrates an emerging novel avian pox in the Japanese avifauna and in global populations of Carrion Crows and Large-billed Crows. Longitudinal monitoring is needed to evaluate its impact on the crow population.

Citizen Science and Wildlife Disease Surveillance

Achieving effective wildlife disease surveillance is challenging. The incorporation of citizen science (CS) in wildlife health surveillance can be beneficial, particularly where resources are limited and cost-effectiveness is paramount. Reports of wildlife morbidity and mortality from the public facilitate large-scale surveillance, both in time and space, which would otherwise be financially infeasible, and raise awareness of incidents occurring on privately owned land. CS wildlife disease surveillance schemes benefit scientists, the participating public and wildlife alike. CS has been employed for targeted, scanning and syndromic surveillance of wildlife disease. Whilst opportunistic surveillance is most common, systematic observations enable the standardisation of observer effort and, combined with wildlife population monitoring schemes, can allow evaluation of disease impacts at the population level. Near-universal access to digital media has revolutionised reporting modalities and facilitated rapid and economical means of sharing feedback with participants. Here we review CS schemes for wildlife disease surveillance and highlight their scope, benefits, logistical considerations, financial implications and potential limitations. The need to adopt a collaborative and multidisciplinary approach to wildlife health surveillance is increasingly recognised and the general public can make a significant contribution through CS.

Drowning is an apparent and unexpected recurrent cause of mass mortality of Common starlings (Sturnus vulgaris)

Drowning is infrequently reported as a cause of death of wild birds and such incidents typically involve individual, rather than multiple, birds. Over a 21-year period (1993 to 2013 inclusive), we investigated 12 incidents of mortality of multiple (2 - 80+) Common starlings (Sturnus vulgaris) in Great Britain that appeared to be due to drowning. More than ten birds were affected in ten of these reported incidents. These incidents always occurred during the spring and early summer months and usually involved juvenile birds. In all cases, circumstantial evidence and post-mortem examinations indicated drowning to be the most likely cause of death with no underlying disease found. A behavioural explanation seems likely, possibly related to the gregarious nature of this species combined with juvenile inexperience in identifying water hazards. A review of data from the ringed bird recovery scheme across Great Britain (1909-2013 inclusive) of both starlings and Common blackbirds (Turdus merula), also a common garden visitor, identified additional suspected drowning incidents, which were significantly more common in the former species, supporting a species predisposition to drowning. For each species there was a marked seasonal peak from April to August. Drowning should be included as a differential diagnosis when investigating incidents of multiple starling mortality, especially of juveniles.

Outbreaks of Pox Disease Due to Canarypox-Like and Fowlpox-Like Viruses in Large-Scale Houbara Bustard Captive-Breeding Programmes, in Morocco and the United Arab Emirates

Infectious diseases can be serious threats for the success of reinforcement programmes of endangered species. Houbara Bustard species (Chlamydotis undulata and Chlamydotis macqueenii), whose populations declined in the last decades, have been captive-bred for conservation purposes for more than 15 years in North Africa and the Middle East. Field observations show that pox disease, caused by avipoxviruses (APV), regularly emerges in conservation projects of Houbara Bustard, despite a very strict implementation of both vaccination and biosecurity. Data collected from captive flocks of Houbara Bustard in Morocco from 2006 through 2013 and in the United Arab Emirates from 2011 through 2013 were analysed, and molecular investigations were carried out to define the virus strains involved. Pox cases (n = 2311) were observed during more than half of the year (88% of the months in Morocco, 54% in the United Arab Emirates). Monthly morbidity rates showed strong variations across the time periods considered, species and study sites: Four outbreaks were described during the study period on both sites. Molecular typing revealed that infections were mostly due to canarypox-like viruses in Morocco while fowlpox-like viruses were predominant in the United Arab Emirates. This study highlights that APV remain a major threat to consider in bird conservation initiatives.

Chlamydiosis in British Garden Birds (2005-2011): retrospective diagnosis and Chlamydia psittaci genotype determination

The significance of chlamydiosis as a cause of mortality in wild passerines (Order Passeriformes), and the role of these birds as a potential source of zoonotic Chlamydia psittaci infection, is unknown. We reviewed wild bird mortality incidents (2005-2011). Where species composition or post-mortem findings were indicative of chlamydiosis, we examined archived tissues for C. psittaci infection using PCR and ArrayTube Microarray assays. Twenty-one of 40 birds tested positive: 8 dunnocks (Prunella modularis), 7 great tits (Parus major), 3 blue tits (Cyanistes caeruleus), 2 collared doves (Streptopelia decaocto, Order Columbiformes), and 1 robin (Erithacus rubecula). Chlamydia psittaci genotype A was identified in all positive passerines and in a further three dunnocks and three robins diagnosed with chlamydiosis from a previous study. Two collared doves had genotype E. Ten of the 21 C. psittaci-positive birds identified in the current study had histological lesions consistent with chlamydiosis and co-localizing Chlamydia spp. antigens on immunohistochemistry. Our results indicate that chlamydiosis may be a more common disease of British passerines than was previously recognized. Wild passerines may be a source of C. psittaci zoonotic infection, and people should be advised to take appropriate hygiene precautions when handling bird feeders or wild birds.

Diversity of avipoxviruses in captive-bred Houbara bustard

Implementation of conservation breeding programs is a key step to ensuring the sustainability of many endangered species. Infectious diseases can be serious threats for the success of such initiatives especially since knowledge on pathogens affecting those species is usually scarce. Houbara bustard species (Chlamydotis undulata and Chlamydotis macqueenii), whose populations have declined over the last decades, have been captive-bred for conservation purposes for more than 15 years. Avipoxviruses are of the highest concern for these species in captivity. Pox lesions were collected from breeding projects in North Africa, the Middle East and Central Asia for 6 years in order to study the diversity of avipoxviruses responsible for clinical infections in Houbara bustard. Molecular and phylogenetic analyses of 113 and 75 DNA sequences for P4b and fpv140 loci respectively, revealed an unexpected wide diversity of viruses affecting Houbara bustard even at a project scale: 17 genotypes equally distributed between fowlpox virus-like and canarypox virus-like have been identified in the present study. This suggests multiple and repeated introductions of virus and questions host specificity and control strategy of avipoxviruses. We also show that the observed high virus burden and co-evolution of diverse avipoxvirus strains at endemic levels may be responsible for the emergence of novel recombinant strains.

Polymerase chain reaction detection of avipox and avian papillomavirus in naturally infected wild birds: comparisons of blood, swab and tissue samples

Avian poxvirus (avipox) is widely reported from avian species, causing cutaneous or mucosal lesions. Mortality rates of up to 100% are recorded in some hosts. Three major avipox clades are recognized. Several diagnostic techniques have been reported, with molecular techniques used only recently. Avipox has been reported from 278 different avian species, but only 111 of these involved sequence and/or strain identification. Collecting samples from wild birds is challenging as only few wild bird individuals or species may be symptomatic. Also, sampling regimes are tightly regulated and the most efficient sampling method, whole bird collection, is ethically challenging. In this study, three alternative sampling techniques (blood, cutaneous swabs and tissue biopsies) from symptomatic wild birds were examined. Polymerase chain reaction was used to detect avipoxvirus and avian papillomavirus (which also induces cutaneous lesions in birds). Four out of 14 tissue samples were positive but all 29 blood samples and 22 swab samples were negative for papillomavirus. All 29 blood samples were negative but 6/22 swabs and 9/14 tissue samples were avipox-positive. The difference between the numbers of positives generated from tissue samples and from swabs was not significant. The difference in the avipox-positive specimens in paired swab (4/6) and tissue samples (6/6) was also not significant. These results therefore do not show the superiority of swab or tissue samples over each other. However, both swab (6/22) and tissue (8/9) samples yielded significantly more avipox-positive cases than blood samples, which are therefore not recommended for sampling these viruses.

Wildlife health investigations: needs, challenges and recommendations

In a fast changing world with growing concerns about biodiversity loss and an increasing number of animal and human diseases emerging from wildlife, the need for effective wildlife health investigations including both surveillance and research is now widely recognized. However, procedures applicable to and knowledge acquired from studies related to domestic animal and human health can be on partly extrapolated to wildlife. This article identifies requirements and challenges inherent in wildlife health investigations, reviews important definitions and novel health investigation methods, and proposes tools and strategies for effective wildlife health surveillance programs. Impediments to wildlife health investigations are largely related to zoological, behavioral and ecological characteristics of wildlife populations and to limited access to investigation materials. These concerns should not be viewed as insurmountable but it is imperative that they are considered in study design, data analysis and result interpretation. It is particularly crucial to remember that health surveillance does not begin in the laboratory but in the fields. In this context, participatory approaches and mutual respect are essential. Furthermore, interdisciplinarity and open minds are necessary because a wide range of tools and knowledge from different fields need to be integrated in wildlife health surveillance and research. The identification of factors contributing to disease emergence requires the comparison of health and ecological data over time and among geographical regions. Finally, there is a need for the development and validation of diagnostic tests for wildlife species and for data on free-ranging population densities. Training of health professionals in wildlife diseases should also be improved. Overall, the article particularly emphasizes five needs of wildlife health investigations: communication and collaboration; use of synergies and triangulation approaches; investments for the long term; systematic collection of metadata; and harmonization of definitions and methods.

Two different avipoxviruses associated with pox disease in Magellanic penguins (Spheniscus magellanicus) along the Brazilian coast

A novel avipoxvirus caused diphtheritic lesions in the oesophagus of five and in the bronchioli of four Magellanic penguins (Spheniscus magellanicus) and also cutaneous lesions in eight Magellanic penguins housed in outdoor enclosures in a Rehabilitation Centre at Florianópolis, Santa Catarina State, Brazil. At the same time, another avipoxvirus strain caused cutaneous lesions in three Magellanic penguins at a geographically distinct Rehabilitation Centre localized at Vila Velha, Espírito Santo State, Brazil. Diagnosis was based on clinical signs, histopathology and use of the polymerase chain reaction (PCR). Clinical signs in the penguins included cutaneous papules and nodules around eyelids and beaks, depression and restriction in weight gain. The most common gross lesions were severely congested and haemorrhagic lungs, splenomegaly and cardiomegaly. Histological examination revealed Bollinger inclusion bodies in cutaneous lesions, mild to severe bronchopneumonia, moderate periportal lymphocytic hepatitis, splenic lymphopenia and lymphocytolysis. Other frequent findings included necrotizing splenitis, enteritis, oesophagitis, dermatitis and airsacculitis. Cytoplasmic inclusion bodies were seen within oesophageal epithelial cells in five birds and in epithelial cells of the bronchioli in four penguins. DNA from all samples was amplified from skin tissue by PCR using P4b-targeting primers already described in the literature for avipoxvirus. The sequences showed two different virus strains belonging to the genus Avipoxvirus of the Chordopoxvirinae subfamily, one being divergent from the penguinpox and avipoxviruses already described in Magellanic penguins in Patagonia, but segregating within a clade of canarypox-like viruses implicated in diphtheritic and respiratory disease.

Is low pathogenic avian influenza virus virulent for wild waterbirds?

Although low pathogenic avian influenza virus (LPAIV) is traditionally considered to have adapted to its wild waterbird host to become avirulent, recent studies have suggested that LPAIV infection might after all have clinical effects. Therefore, I reviewed the literature on LPAIV infections in wild waterbirds. The virulence of LPAIV was assessed in 17 studies on experimental infections and nine studies on natural infections. Reported evidence for virulence were reductions in return rate, feeding rate, body weight, long-range movement and reproductive success, as well as pathological changes in infected organs. However, major caveats in studies of experimental infections were unnatural route of LPAIV inoculation, animal husbandry not simulating natural stressors and low sensitivity of clinical assessment. Major caveats in studies of natural infections were incomplete measurement of LPAIV infection burden, quasi-experimental design and potential misclassification of birds. After taking these caveats into account, the only remaining evidence for virulence was that presence and intensity of LPAIV infection were negatively correlated with body weight. Based on this correlation, together with the demonstrated LPAIV tropism for the intestinal tract, I hypothesize that LPAIV reduces digestive tract function, and suggest how future studies could be directed to test this hypothesis.

Worldwide phylogenetic relationship of avian poxviruses

Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

Epidemiology of the emergent disease Paridae pox in an intensively studied wild bird population

Paridae pox, a novel avipoxvirus infection, has recently been identified as an emerging infectious disease affecting wild tit species in Great Britain. The incursion of Paridae pox to a long-term study site where populations of wild tits have been monitored in detail for several decades provided a unique opportunity to obtain information on the local-scale epidemiological characteristics of this novel infection during a disease outbreak. Using captures of >8000 individual birds, we show that, within two years of initial emergence, Paridae pox had become established within the population of great tits (Parus major) reaching relatively high peak prevalence (10%), but was far less prevalent (<1%) in sympatric populations of several other closely related, abundant Paridae species. Nonlinear smoothing models revealed that the temporal pattern of prevalence among great tits was characterised by within-year fluctuations indicative of seasonal forcing of infection rates, which was likely driven by multiple environmental and demographic factors. There was individual heterogeneity in the course of infection and, although recovery was possible, diseased individuals were far less likely to be recaptured than healthy individuals, suggesting a survival cost of infection. This study demonstrates the value of long-term monitoring for obtaining key epidemiological data necessary to understand disease dynamics, spread and persistence in natural populations.

Individual and population-level impacts of an emerging poxvirus disease in a wild population of great tits

Emerging infectious diseases of wildlife can have severe effects on host populations and constitute a pressing problem for biodiversity conservation. Paridae pox is an unusually severe form of avipoxvirus infection that has recently been identified as an emerging infectious disease particularly affecting an abundant songbird, the great tit (Parus major), in Great Britain. In this study, we study the invasion and establishment of Paridae pox in a long-term monitored population of wild great tits to (i) quantify the impact of this novel pathogen on host fitness and (ii) determine the potential threat it poses to population persistence. We show that Paridae pox significantly reduces the reproductive output of great tits by reducing the ability of parents to fledge young successfully and rear those young to independence. Our results also suggested that pathogen transmission from diseased parents to their offspring was possible, and that disease entails severe mortality costs for affected chicks. Application of multistate mark-recapture modelling showed that Paridae pox causes significant reductions to host survival, with particularly large effects observed for juvenile survival. Using an age-structured population model, we demonstrate that Paridae pox has the potential to reduce population growth rate, primarily through negative impacts on host survival rates. However, at currently observed prevalence, significant disease-induced population decline seems unlikely, although pox prevalence may be underestimated if capture probability of diseased individuals is low. Despite this, because pox-affected model populations exhibited lower average growth rates, this emerging infectious disease has the potential to reduce the resilience of populations to other environmental factors that reduce population size.