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.This study was funded by the Spanish Ministry of Science and Innovation (Project CGL2010-15734/BOS), the Spanish Ministry of Economy and Competitiveness (Project CGL2013-41642-P/BOS) and the Innovation and Development Agency of Andalusia (Spain) (P11-RNM-7038). Grants were awarded to JMP (Juan de la Cierva- JCI-2012-11868) and MAJM (FPIBES-2011-047609), Spanish Ministry of Economy and Competitiveness; RAJW (CEI-PICATA2012), CEI Campus of International Excellence; MM (FPU12/0568), Spanish Ministry of Education, Culture and Sports. RAJW was supported by the Craaford Foundation (grant 20160971) during the writing of this publication. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Diversity and host specificity of symbionts in neotropical birds

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Ciencias Biológicas, Departamento de Zoología y Antropología Física, leída el 15-07-2016¿Por qué hay tanta variación en la especificidad? La mayoría de los simbiontes (parásitos, mutualistas, comensales) son especialistas, i.e. han especializado su estilo de vida en una especie hospedadora, mientras otros son muy generalistas interactuando con muchas especies hospedadoras. En la presente tesis, queremos identificar determinantes históricos y ecológicos de la especificidad de parásitos sanguíneos y virus en aves Neotropicales. Los trópicos proveen un escenario ideal para explorar las relaciones entre especificidad y la diversidad de hospedadores, ya que lo último podría gobernar la evolución de la especificidad a través de los efectos de dilución e amplificación. A escala ecosistémica la especificidad también está determinada por la historia coevolutiva de hospedadores y simbiontes, ya que la coespeciación mantiene la especialización, y los cambios de hospedadores promueven la evolución de simbiontes generalistas. Estudiaremos el efecto de estos procesos históricos en la evolución de la especificidad de parásitos sanguíneos, Avipoxvirus y CRESS (circular rep-encoding single stranded) DNA virus. A escala interespecífica nos enfocaremos en los colibríes, cuyos parámetros sanguíneos ofrecen un nicho único para los parásitos sanguíneos. El concepto de la especialización ecológica es equivalente a la especialización en el nicho ecológico para las especies en general, y es importante para entender la arquitectura de las redes hospedador-parasito y cómo ocurre la diversificación. Como hemos trabajado en áreas neotropicales poco exploradas, una gran parte de la tesis esta también dedicada al biodescubrimiento, lo cual está presentado por la caracterización de nuevas especies de parásitos sanguíneos, cepas de Avipoxvirus, y genomas de CRESS DNA virus. En general, los análisis de la especificidad de los simbiontes aportarán al descubrimiento de nuevas especies e interacciones simbióticas, dando una oportunidad excelente para mejorar nuestro conocimiento sobre la evolución de relaciones hospedadoras-parásitos en ambientes megadiversos...Why is there such variation in host specificity? Most symbionts (parasites, mutualists, commensals) are specialist, i.e. they have specialized their lifestyle in one single host species, while others are generalist interacting with many host species. In this thesis, we aim to identify historical and ecological determinants of host specificity in avian blood parasites and viruses in Neotropical birds. The tropics provide an ideal scenario to explore the relationship between host specificity and host diversity, as the latter could govern the evolution of host specificity through dilution and amplification effects. At the ecosystem scale host range is also determined by the coevolutionary history of hosts and symbionts, where strict cospeciation maintains specialization, and host-switching promotes the evolution of generalist symbionts. We will study the influence of these historical processes on the evolution of host specificity of avian blood parasites, avipoxviruses and CRESS (circular rep-encoding single stranded) DNA viruses. At the interspecific scale we will focus on hummingbirds, whose particular blood features offer a unique niche for blood parasites. The concept of ecological specialization of symbionts is equivalent to niche specialization of free living species, and is crucial to understand the architecture of host parasite networks and how species diversification takes place. Since we worked in underexplored tropical areas, the thesis is also focused towards biodiscovery, which is presented by the characterization of new blood parasite species, Avipoxvirus strains and CRESS DNA viruses. Taken together, this comprehensive analysis of symbiont host specificity will contribute to the discovery of new species and symbiotic lifestyles, giving an excellent opportunity to improve our understanding on the evolution of host-symbiont interactions in megadiverse environments...Depto. de Biodiversidad, Ecología y EvoluciónFac. de Ciencias BiológicasTRUEunpu

Identification of two novel CRESS DNA viruses associated with an Avipoxvirus lesion of a blue-and-gray Tanager (Thraupis episcopus)

The discovery of circular rep-encoding single stranded (CRESS) DNA viruses has increased spectacularly over the past decade. They represent the smallest animal viruses known worldwide infecting a wide variety of invertebrates and vertebrates in different natural and human-made environments. The extremely low similarity of nucleotide and protein sequences among different CRESS DNA genomes has challenged their classification. Moreover, the existence of capsid proteins (Cp) remains difficult to demonstrate which is crucial to understand the structural properties of these viruses. Here we describe two unclassified CRESS DNA viruses isolated from a cutaneous lesion, caused by a strain of Avipoxvirus, from a blue-and-gray tanager (Thraupis episcopus) in Southern Ecuador. Both viruses present replication-associated proteins (Rep) and one to two open reading frames (ORF), one of which represents a putative Cp. The two new Rep are long proteins characterized by the existence of the several highly conserved amino acid residues characteristic of rolling circle replication. Within the putative Cp we detected intrinsically disordered regions (IDR), potential protein and DNA binding regions, and nuclear localization signals (NLS), providing further evidence of presumed Cp. Despite being found on the same host lesion, both viruses show low similarity between each other (< 60%) and other known CRESS DNA viruses. Furthermore, we analyze the evolutionary relationships within the CRESS DNA diversity. Additional sampling is needed to explore the possible pathogenic effects, prevalence and diversity (both phylogenetical and structural) of these viruses in wild bird populations

The biological background of a recurrently emerging infectious disease: prevalence, diversity and host specificity of Avipoxvirus in wild Neotropical birds

Understanding which factors promote disease emergence and transmission remains a major challenge of epidemiology. A problem with research on emerging diseases is that we seldom know to what extent pathogens circulate in natural popula-tions before emergence is already occurring. Moreover, it is critical to determine which pathogen characteristics are key to predict their emergence and invasion potential. We examined the prevalence, host specificity and evolutionary relationships of Avipoxvirus causing skin lesions in birds in two megadiverse and unexplored geographical regions of South America: an elevational gradient in the south Ecuadorian Andes, and a lowland Amazon rainforest in French Guiana. Next, we analyzed the host specificity and distribution of the worldwide Avipoxvirus diversity in order to understand their invasion potential. In French Guiana Avipoxvirus prevalence was 0% (n 889, 94 bird species). In Ecuador, prevalence was 0.3% (n 941, 132 bird species), with cases spanning the range of elevations between 1500 and 2500 m. ese were caused by two newly described strains, one of which belonged to an American clade of Avipoxvirus shared by different bird families, and another one closely related to a strain recovered from a different family of birds in Madeira. An analysis of the host specificity and geographic distribution of all Avipoxvirus strains known worldwide finds that these viruses are usually host generalists (particularly those in the fowlpox clade), and that many closely related strains are found on multiple continents. Our study at the community level suggests that distantly related Avipoxvirus strains circulate at very low prevalence in continental tropical South America. Avipoxvirus assemblages are composed of generalist strains with different ancestry and widespread distribution, a combination of characteristics which may make these typically scarce viruses perfect candidates to emerge under favorable ecological conditions

Genomic characterization of the first oral avian papillomavirus in a colony of breeding canaries (Serinus canaria)

Papillomaviruses are non-enveloped, DNA viruses that infect skin and mucosa of a wide variety of vertebrates, causing neoplasias or simply persisting asymptomatically. Avian papillomaviruses, with six fully sequenced genomes, are the second most studied group after mammalian papillomaviruses. In this study, we describe the first oral avian papillomavirus, detected in the tongue of a dead Yorkshire canary (Serinus canaria) and in oral swabs of the same bird and other two live canaries from an aviary in Madrid, Spain. Its genome is 8,071 bp and presents the canonical papillomavirus architecture with six early (E6, E7, E1, E9, E2, E4) and two late open reading frames (L1 and L2) and a long control region between L1 and E6. This new avian papillomavirus L1 gene shares a 64% pairwise identity with FcPV1 L1, so it has been classified as a new species (ScPV1) within the Ethapapillomavirus genus. Although the canary died after showing breathing problems, there is no evidence that the papillomavirus caused those symptoms so it could be part of the oral microbiota of the birds. Hence, future investigations are needed to evaluate the clinical relevance of the virus

Haemoproteus erythrogravidus n. sp. (Haemosporida, Haemoproteidae): Description and molecular characterization of a widespread blood parasite of birds in South America

The great diversity of birds and ecosystems in the Andean mountains has been understudied in terms of their parasite species. We describe a new Haemoproteus parasite, H. (Parahaemoproteus) erythrogravidus infecting Zonotrichia capensis (Rufous-Collared Sparrow) in South America. The description of this blood parasite species is supported by morphological and molecular data based on a fragment of cytochrome b gene (cyt b) and complete mitochondrial genome sequences. The new species is closely related to H. (Parahaemoproteus) coatneyi, and it can be readily distinguished from the latter parasite due to morphology of its blood stages, particularly 1) the formation of a marked protrusion on envelope of infected erythrocytes by the majority of developing gametocytes, a feature which is unique for this Haemoproteus species and 2) the extremely attenuated width of the growing dumbbell-shaped macro- and microgametocytes.Additionally, Haemoproteus erythrogravidus is shown to be a monophyletic taxon that diverges from Haemoproteus coatneyi atthe molecular level. We provide the complete mitochondrial DNA genome for both H. coatneyi and H. erythrogravidus. Molecular and morphological evidences indicate that H. erythrogravidus is present in Ecuador and Colombia, and genetic lineages with 100% of identity for the cyt b gene were reported in Chile, Perú, and Venezuela. Our study also indicates that H. erythrogravidus and H. coatneyi are sympatric sister taxa sharing Z. capensis as a host species across its distribution, which could be the result of sympatric speciation or complex biogeographic processes. Further studies on the distribution and evolutionary history of Z. capensis and its parasites H. erythrogravidus and H. coatneyi insight for our better understanding of the factors and dynamics driving parasite speciation

Comparative metagenomics of Palearctic and Neotropical avian cloacal viromes reveal geographic bias in virus discovery

Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing important diseases, and wild birds are threatened by viral spillovers associated with human activities. However, our knowledge of the avian virome may be biased towards poultry and highly pathogenic diseases. We describe and compare the fecal virome of two passerine-dominated bird assemblages sampled in a remote Neotropical rainforest in French Guiana (Nouragues Natural Reserve) and a Mediterranean forest in central Spain (La Herrería). We used metagenomic data to quantify the degree of functional and genetic novelty of viruses recovered by examining if the similarity of the contigs we obtained to reference sequences differed between both locations. In general, contigs from Nouragues were significantly less similar to viruses in databases than contigs from La Herrería using Blastn but not for Blastx, suggesting that pristine regions harbor a yet unknown viral diversity with genetically more singular viruses than more studied areas. Additionally, we describe putative novel viruses of the families Picornaviridae, Reoviridae and Hepeviridae. These results highlight the importance of wild animals and remote regions as sources of novel viruses that substantially broaden the current knowledge of the global diversity of viruses

Summary of total pox-like lesions, type of samples and molecular analysis of APV strains.

<p>Summary of total pox-like lesions, type of samples and molecular analysis of APV strains.</p