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.

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.

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.

A multiplex PCR for detection of poxvirus and papillomavirus in cutaneous warts from live birds and museum skins

Viral cutaneous lesions are frequent in some bird populations, though we are generally ignorant of the causal agent. In some instances, they represent a threat to livestock and wildlife health. We present here a multiplex PCR which detects and distinguishes infection by two such agents, avipoxviruses and papillomaviruses, in avian hosts. We assayed biopsies and superficial skin swabs from field and preserved museum skin specimens. Ninety-three percent of samples from symptomatic specimens tested positive for the presence of avipox (n = 23) or papillomavirus (n = 5). Sixteen and five sequences, corresponding to the P4b and L1 genes, were obtained from avipox and papillomavirus, respectively. One museum specimen, of Fringilla coelebs (chaffinch), was apparently infected with both viruses. Although papillomavirus sequences proved identical to previously published sequences, four novel avipox sequences were generated and used to build a neighbor-joining phylogenetic tree. Our tree recovered a similar topology to that of several recent authors; however, we also propose here two new minor avipox clades (B1b and B3). This multiplex PCR technique shows improved sensitivity compared to other avipox and papillomavirus assays, is able to detect a wide range of avipox and papillomavirus types (it amplifies all three avian-derived papillomavirus genera described thus far and sequences from both major avipox clades), and was even able to detect ancient viral DNA contained in museum specimens of greater than 75 years antiquity for both viruses.

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.

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.