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.

Spatio-temporal dynamics and aetiology of proliferative leg skin lesions in wild British finches.

Proliferative leg skin lesions have been described in wild finches in Europe although there have been no large-scale studies of their aetiology or epizootiology to date. Firstly, disease surveillance, utilising public reporting of observations of live wild finches was conducted in Great Britain (GB) and showed proliferative leg skin lesions in chaffinches (Fringilla coelebs) to be widespread. Seasonal variation was observed, with a peak during the winter months. Secondly, pathological investigations were performed on a sample of 39 chaffinches, four bullfinches (Pyrrhula pyrrhula), one greenfinch (Chloris chloris) and one goldfinch (Carduelis carduelis) with proliferative leg skin lesions and detected Cnemidocoptes sp. mites in 91% (41/45) of affected finches and from all species examined. Fringilla coelebs papillomavirus (FcPV1) PCR was positive in 74% (23/31) of birds tested: a 394 base pair sequence was derived from 20 of these birds, from all examined species, with 100% identity to reference genomes. Both mites and FcPV1 DNA were detected in 71% (20/28) of birds tested for both pathogens. Histopathological examination of lesions did not discriminate the relative importance of mite or FcPV1 infection as their cause. Development of techniques to localise FcPV1 within lesions is required to elucidate the pathological significance of FcPV1 DNA detection.

Molecular identification of papillomavirus in ducks.

Papillomaviruses infect many vertebrates, including birds. Persistent infections by some strains can cause malignant proliferation of cells (i.e. cancer), though more typically infections cause benign tumours, or may be completely subclinical. Sometimes extensive, persistent tumours are recorded-notably in chaffinches and humans. In 2016, a novel papillomavirus genotype was characterized from a duck faecal microbiome, in Bhopal, India; the sixth papillomavirus genotype from birds. Prompted by this finding, we screened 160 cloacal swabs and 968 faecal samples collected from 299 ducks sampled at Ottenby Bird Observatory, Sweden in 2015, using a newly designed real-time PCR. Twenty one samples (1.9%) from six individuals (2%) were positive. Eighteen sequences were identical to the published genotype, duck papillomavirus 1. One additional novel genotype was recovered from three samples. Both genotypes were recovered from a wild strain domestic mallard that was infected for more than 60 days with each genotype. All positive individuals were adult (P = 0.004). Significantly more positive samples were detected from swabs than faecal samples (P < 0.0001). Sample type data suggests transmission may be via direct contact, and only infrequently, via the oral-faecal route. Infection in only adult birds supports the hypothesis that this virus is sexually transmitted, though more work is required to verify this.

Natural history of avian papillomaviruses.

Papillomaviruses (Family: Papillomaviridae) are small non-enveloped viruses that cause skin and mucosa infections in diverse vertebrates. The vast majority have been detected in mammals. However, the number of papillomaviruses described in birds is growing, especially because of metagenomic studies. Seven complete genomes and one partial sequence have been described, corresponding to five papillomavirus genera. These have been detected from various sample types, including skin, internal epithelium, and faecal material, from seven highly diverse wild and captive avian species. This review summarizes the molecular epidemiology of avian papillomaviruses, their genomic organization, evolutionary history and diagnostic techniques used for detection. The most commonly detected avian papillomavirus lesions are cauliflower-shaped papillomas, or warts, found on the tarsus and digits of common chaffinch (Fringilla coelebs) and occasionally brambling (Fringilla montifringilla). Similar warty growths have been detected in African grey parrot (Psittacus erithacus) and northern fulmar (Fulmarus glacialis), on the head and the foot, respectively. Papillomavirus has also been detected in avian tissue with no apparent lesions, similar to findings in humans and other mammals. Papillomavirus involvement was initially suspected to cause other types of lesions, such as internal papillomatosis of parrots (IPP) and proliferative pododermatitis in waterfowl. However, determined efforts failed to demonstrate papillomavirus presence. We briefly describe avian papillomavirus genomic organization and viral gene diversity. Furthermore, we performed a detailed analysis of avian papillomavirus non-coding regions and a preliminary computational analysis of their E9 proteins.

A Century of Shope Papillomavirus in Museum Rabbit Specimens.

Sylvilagus floridanus Papillomavirus (SfPV) causes growth of large horn-like tumors on rabbits. SfPV was described in cottontail rabbits (probably Sylvilagus floridanus) from Kansas and Iowa by Richard Shope in 1933, and detected in S. audubonii in 2011. It is known almost exclusively from the US Midwest. We explored the University of Kansas Natural History Museum for historical museum specimens infected with SfPV, using molecular techniques, to assess if additional wild species host SfPV, and whether SfPV occurs throughout the host range, or just in the Midwest. Secondary aims were to detect distinct strains, and evidence for strain spatio-temporal specificity. We found 20 of 1395 rabbits in the KU collection SfPV symptomatic. Three of 17 lagomorph species (S. nuttallii, and the two known hosts) were symptomatic, while Brachylagus, Lepus and eight additional Sylvilagus species were not. 13 symptomatic individuals were positive by molecular testing, including the first S. nuttallii detection. Prevalence of symptomatic individuals was significantly higher in Sylvilagus (1.8%) than Lepus. Half of these specimens came from Kansas, though new molecular detections were obtained from Jalisco-Mexico's first-and Nebraska, Nevada, New Mexico, and Texas, USA. We document the oldest lab-confirmed case (Kansas, 1915), pre-dating Shope's first case. SfPV amplification was possible from 63.2% of symptomatic museum specimens. Using multiple methodologies, rolling circle amplification and, multiple isothermal displacement amplification in addition to PCR, greatly improved detection rates. Short sequences were obtained from six individuals for two genes. L1 gene sequences were identical to all previously detected sequences; E7 gene sequences, were more variable, yielding five distinct SfPV1 strains that differing by less than 2% from strains circulating in the Midwest and Mexico, between 1915 and 2005. Our results do not clarify whether strains are host species specific, though they are consistent with SfPV specificity to genus Sylvilagus.

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.

Avian Influenza infections in nonmigrant land birds in Andean Peru.

As part of ongoing surveillance for avian influenza viruses (AIV) in Peruvian birds, in June 2008, we sampled 600 land birds of 177 species, using real-time reverse-transcription PCR. We addressed the assumption that AIV prevalence is low or nil among land birds, a hypodiesis that was not supported by the results-rather, we found AIV infections at relatively high prevalences in birds of the orders Apodiformes (hummingbirds) and Passeriformes (songbirds). Surveillance programs for monitoring spread and identification of AIV should thus not focus solely on water birds.

Continent-wide association of H5N1 outbreaks in wild and domestic birds in Europe.

The highly pathogenic avian influenza strain H5N1 was first detected in Europe in 2005, and has since been documented continent-wide in wild birds and poultry. However, the relative roles of each host group in transmission remain contentious. Using recently developed tools for analysis of ecological niches and geographic distributions of species, we compared ecological niche requirements for H5N1 between paired host groups (poultry versus wild birds, Anseriformes versus Falconiformes, swans versus non-swan Anseriformes). If environmental signals of different host groups are significantly different, the groups are likely to be involved in distinct transmission cycles. In contrast, models for which similarity cannot be rejected imply no unique ecological niches and no potential linkage of transmission cycles. In 24 similarity tests, we found significant similarity (13/24) or no significant differences (9/24). Although 2 of the 24 analyses showed significant differences, neither was unequivocal, so we conclude an overall signal of niche similarity among groups. We thus could not document distinct ecological niches for H5N1 occurrences in different host groups and conclude that the transmission cycles are broadly interwoven.

Ecological niche modeling of Francisella tularensis subspecies and clades in the United States.

Two subspecies of Francisella tularensis are recognized: F. tularensis subsp. tularensis (type A) and F. tularensis subsp. holartica (type B). Type A has been subdivided further into A1a, A1b, and A2, which differ geographically and clinically. The aim of this work was to determine whether or not differences among subspecies and clades translate into distinct ecological niches. We used 223 isolates from humans and wildlife representing all six genotypes (type A, B, A1, A2, A1a, or A1b). Ecological-niche models were built independently for each genotype, using the genetic algorithm for rule-set prediction. The resulting models were compared using a non-parametric multivariate analysis-of-variance method. A1 and A2 are ecologically distinct, supporting the previously observed geographic division, whereas ecological niches for types A and B overlapped notably but A1a and A1b displayed no appreciable differences in their ecological niches.

Ecology and geography of avian influenza (HPAI H5N1) transmission in the Middle East and northeastern Africa.

BACKGROUND: The emerging highly pathogenic avian influenza strain H5N1 ("HPAI-H5N1") has spread broadly in the past decade, and is now the focus of considerable concern. We tested the hypothesis that spatial distributions of HPAI-H5N1 cases are related consistently and predictably to coarse-scale environmental features in the Middle East and northeastern Africa.We used ecological niche models to relate virus occurrences to 8 km resolution digital data layers summarizing parameters of monthly surface reflectance and landform. Predictive challenges included a variety of spatial stratification schemes in which models were challenged to predict case distributions in broadly unsampled areas. RESULTS: In almost all tests, HPAI-H5N1 cases were indeed occurring under predictable sets of environmental conditions, generally predicted absent from areas with low NDVI values and minimal seasonal variation, and present in areas with a broad range of and appreciable seasonal variation in NDVI values. Although we documented significant predictive ability of our models, even between our study region and West Africa, case occurrences in the Arabian Peninsula appear to follow a distinct environmental regime. CONCLUSION: Overall, we documented a variable environmental "fingerprint" for areas suitable for HPAI-H5N1 transmission.

Easy visualization of the protist Oxyrrhis marina grazing on a live fluorescently labelled heterotrophic nanoflagellate.

Planktonic heterotrophic flagellates are ubiquitous eukaryotic microorganisms that play a crucial role in carbon and nutrient fluxes through pelagic food webs. Here we illustrate for the first time a grazing model of planktonic dinoflagellate, Oxyrrhis marina, on the heterotrophic nanoflagellate Goniomonas amphinema, using the DNA-binding fluorescent dye Hoechst 33342. A solution of 1 microg/mL of the fluorochrome allowed viability of the prey for at least 48 hours, provided low fluorescence quenching, and labelled the flagellate without masking the cytoplasm. After 2 hours of contact between the fluorescent prey and the predator, O. marina population had preyed on live G. amphinema at an ingestion rate of 2.2 prey Oxyrrhis (-1) h(-1). Results show that this model is a time-effective and inexpensive approach for the direct observation of heterotrophic flagellate grazing. The fact that prey remain alive while predation occurs, as well as the low rate of quenching, could be of help in studying the fate of real-time trophic interactions between protists in microbial webs.

Predictable ecology and geography of avian influenza (H5N1) transmission in Nigeria and West Africa.

The emerging virus strain termed highly pathogenic H5N1 avian influenza (HP-H5N1) has spread widely in the past decade and is now the focus of considerable concern in several sectors. We tested the hypothesis that spatial distributions of veterinary and human HP-H5N1 cases are related to coarse-scale environmental features in West Africa. We used ecological niche models to associate Nigerian HP-H5N1 occurrences with 1 km resolution digital data layers summarizing parameters of surface reflectance and landform. Predictive challenges included anticipating the spatial distribution of (i) random subsamples and (ii) spatially and temporally stratified subsamples of Nigerian occurrence data, and (iii) more limited occurrence data from across West Africa. In almost all tests, we found that HP-H5N1 cases were occurring under predictable environmental conditions, suggesting that elements of the transmission cycle have some form of ecological determination, here measured as differences in land-surface reflectance and plant phenology through the year. Considerable additional work is needed to establish how these differences affect HP-H5N1 transmission.