Viral metagenomics in Brazilian Pekin ducks identifies two gyrovirus, including a new species, and the potentially pathogenic duck circovirus.

Viral metagenomics coupled to high-throughput sequencing has provided a powerful tool for large-scale detection of known and unknown viruses associated to distinct hosts and environments. Using this approach, known and novel viruses have been characterized from sylvatic and commercial avian hosts, increasing our understanding of the viral diversity in these species. In the present work we applied an exploratory viral metagenomics on organs (spleen, liver and bursa of Fabricious) of Pekin ducks from Southern Brazil. The virome contained sequences related to a known duck pathogen (duck circovirus) and a number of other circular ssDNA viruses. Additionally, we detected avian gyrovirus 9 (to date detected only in human feces) and one new avian gyrovirus species, to which is proposed the name avian gyrovirus 13 (GyV13). This study is expected to contribute to the knowledge of the viral diversity in Pekin ducks.

Phylogenetic characterization of a reassortant H5N2 influenza A virus from a resident Mexican duck (Anas diazi).

Congregation of different migratory and resident bird species on aquatic ecosystems during winter migration increases contact rates and enhances influenza A virus (IAV) transmission. However, scarce research has been focused on the resident bird's contribution to the viral ecology at a local scale. The Mexican duck (Anas diazi) is an endemic endangered anatid from Mexico. This resident species shares aquatic habitats with migratory birds in the wetlands of Central Mexico. Therefore, here we describe the phylogenetic analysis of an IAV (A/Mexican duck/EstadodeMexico; Lerma/UIFMVZ377/2016(H5N2)) isolated in this species, during spatiotemporal concurrence with migratory anatids in the winter season. All eight gene sequences were obtained by nextgeneration sequencing. Maximum Likelihood trees were constructed using MEGA-X, with General Time Reversible + Invariant (GTR+I), Subtree Pruning and Regrafting (SPR) heuristic method, and 1000 bootstrap replicates. Similarities with six different IAV subtypes were observed through a BLAST search: H6N5, H7N7, H5N2, H4N6, H9N2, and H11N9, detected in wild ducks during 2015 in the Pacific, Central and Mississippi flyways stop sites across the United States of America and Canada. The molecular identification of this reassortant H5N2 IAV highlights the importance of resident species as a reservoir host and its potential participation in the maintenance and transmission of IAV in wetlands surrounded by rural areas.

Loss of Fitness of Mexican H7N3 Highly Pathogenic Avian Influenza Virus in Mallards after Circulating in Chickens.

Outbreaks of highly pathogenic avian influenza (HPAI) virus subtype H7N3 have been occurring in commercial chickens in Mexico since its first introduction in 2012. In order to determine changes in virus pathogenicity and adaptation in avian species, three H7N3 HPAI viruses from 2012, 2015, and 2016 were evaluated in chickens and mallards. All three viruses caused high mortality in chickens when given at medium to high doses and replicated similarly. No mortality or clinical signs and similar infectivity were observed in mallards inoculated with the 2012 and 2016 viruses. However, the 2012 H7N3 HPAI virus replicated well in mallards and transmitted to contacts, whereas the 2016 virus replicated poorly and did not transmit to contacts, which indicates that the 2016 virus is less adapted to mallards. In vitro, the 2016 virus grew slower and to lower titers than did the 2012 virus in duck fibroblast cells. Full-genome sequencing showed 115 amino acid differences between the 2012 and the 2016 viruses, with some of these changes previously associated with changes in replication in avian species, including hemagglutinin (HA) A125T, nucleoprotein (NP) M105V, and NP S377N. In conclusion, as the Mexican H7N3 HPAI virus has passaged through large populations of chickens in a span of several years and has retained its high pathogenicity for chickens, it has decreased in fitness in mallards, which could limit the potential spread of this HPAI virus by waterfowl.IMPORTANCE Not much is known about changes in host adaptation of avian influenza (AI) viruses in birds after long-term circulation in chickens or other terrestrial poultry. Although the origin of AI viruses affecting poultry is wild aquatic birds, the role of these birds in further dispersal of poultry-adapted AI viruses is not clear. Previously, we showed that HPAI viruses isolated early from poultry outbreaks could still infect and transmit well in mallards. In this study, we demonstrate that the Mexican H7N3 HPAI virus after four years of circulation in chickens replicates poorly and does not transmit in mallards but remains highly pathogenic in chickens. This information on changes in host adaptation is important for understanding the epidemiology of AI viruses and the role that wild waterfowl may play in disseminating viruses adapted to terrestrial poultry.

Phylogenetic and pathotypic characterization of a Newcastle disease virus strain isolated from ducks and pigeons in Hubei, China

Newcastle disease is a highly contagious disease responsible for major outbreaks and considerable economic losses in the poultry industry in China. There is still little information available regarding gene characterization of the NDV, especially in ducks and pigeons. Therefore, the aim of this study was to investigate NDV isolated from ducks and pigeons in Hubei, China. In this study, three NDVs from ducks and pigeons were isolated between 2013 and 2015.The fusion protein (F) gene of the NDV isolates was sequenced and phylogenetically analyzed. The clinical signs and gross histopathological lesions were examined. Phylogenetic analysis of these strains indicated that all the sequences are classified as genotype II. The isolates shared a 112 G-R-Q-G-R-L 117motif at the F protein cleavage site, indicating that these three isolates strains are lentogenic. Necropsy and histopathology showed the typical pathological changes. It was concluded that commercial ducks and pigeons in Hubei province carry lentogenic NDV strains with regular genetic divergence, indicating that these species may act as the main reservoirs of NDV in poultry. Therefore, strategies and surveillance should be undertaken to reduce the risk of ND outbreaks.(AU)

Phylogenetic and pathotypic characterization of a Newcastle disease virus strain isolated from ducks and pigeons in Hubei, China

Newcastle disease is a highly contagious disease responsible for major outbreaks and considerable economic losses in the poultry industry in China. There is still little information available regarding gene characterization of the NDV, especially in ducks and pigeons. Therefore, the aim of this study was to investigate NDV isolated from ducks and pigeons in Hubei, China. In this study, three NDVs from ducks and pigeons were isolated between 2013 and 2015.The fusion protein (F) gene of the NDV isolates was sequenced and phylogenetically analyzed. The clinical signs and gross histopathological lesions were examined. Phylogenetic analysis of these strains indicated that all the sequences are classified as genotype II. The isolates shared a 112 G-R-Q-G-R-L 117motif at the F protein cleavage site, indicating that these three isolates strains are lentogenic. Necropsy and histopathology showed the typical pathological changes. It was concluded that commercial ducks and pigeons in Hubei province carry lentogenic NDV strains with regular genetic divergence, indicating that these species may act as the main reservoirs of NDV in poultry. Therefore, strategies and surveillance should be undertaken to reduce the risk of ND outbreaks.

Principais doenças em Anseriformes / Major diseases in Anseriforme

Anseriforme é uma ordem composta por inúmeras espécies de aves aquáticas. No Brasil as principais espécies criadas são patos e gansos em sua maioria criadas em sistemas de subsistência, poucos são os criatórios industriais. Mesmo com a produção informal o comércio de aves vivas, ovos e carne é pratica comum em todo território nacional, mas não se tem conhecimento da prevalência de enfermidades em aves aquáticas, podendo trazer risco a saúde pública. Anseriformes podem apresentar tanto doença clínica quanto inaparente, de etiologia viral, bacteriana, parasitária e micótica. Estudos sobre quadro clínico, aspectos epidemiológicos, achados anatomopatológicos são necessários para criar métodos diagnósticos eficazes para identificar aves doentes. Doenças virais são as mais relatadas e de maior impacto econômico em criações dessa ordem de aves, mais as enfermidades bacterianas, assim como micóticas e parasitárias também podem ocorrer. Por esse motivo, esse estudo tem como objetivo revisar as principais enfermidades presentes em aves aquáticas.

Anseriforme is an order composed of numerous species of waterfowl. In Brazil the mainspecies created are ducks and geese, mostly in sustenance systems, there are few industrial farms.Even with informal production trade in live poultry, eggs and meat is common practice throughoutthe country, but it isn’t aware of the prevalence of disease in waterfowl, may pose a risk to publichealth. Anseriformes can present both clinical disease and unapparent, viral diseases, bacterial,parasitic and fungal. Studies on clinical, epidemiological, pathological findings are needed to createeffective methods diagnostics to identify sick birds. Viral diseases are the most reported and greatereconomic impact in that order poultry farms, most bacterial diseases, as well as fungal and parasiticmay also occur. Therefore, this study aims to review the main diseases present in waterfowl.

Principais doenças em Anseriformes / Major diseases in Anseriforme

Anseriforme é uma ordem composta por inúmeras espécies de aves aquáticas. No Brasil as principais espécies criadas são patos e gansos em sua maioria criadas em sistemas de subsistência, poucos são os criatórios industriais. Mesmo com a produção informal o comércio de aves vivas, ovos e carne é pratica comum em todo território nacional, mas não se tem conhecimento da prevalência de enfermidades em aves aquáticas, podendo trazer risco a saúde pública. Anseriformes podem apresentar tanto doença clínica quanto inaparente, de etiologia viral, bacteriana, parasitária e micótica. Estudos sobre quadro clínico, aspectos epidemiológicos, achados anatomopatológicos são necessários para criar métodos diagnósticos eficazes para identificar aves doentes. Doenças virais são as mais relatadas e de maior impacto econômico em criações dessa ordem de aves, mais as enfermidades bacterianas, assim como micóticas e parasitárias também podem ocorrer. Por esse motivo, esse estudo tem como objetivo revisar as principais enfermidades presentes em aves aquáticas.(AU)

Anseriforme is an order composed of numerous species of waterfowl. In Brazil the mainspecies created are ducks and geese, mostly in sustenance systems, there are few industrial farms.Even with informal production trade in live poultry, eggs and meat is common practice throughoutthe country, but it isnt aware of the prevalence of disease in waterfowl, may pose a risk to publichealth. Anseriformes can present both clinical disease and unapparent, viral diseases, bacterial,parasitic and fungal. Studies on clinical, epidemiological, pathological findings are needed to createeffective methods diagnostics to identify sick birds. Viral diseases are the most reported and greatereconomic impact in that order poultry farms, most bacterial diseases, as well as fungal and parasiticmay also occur. Therefore, this study aims to review the main diseases present in waterfowl.(AU)

Pesquisa de enterobactérias em patos domésticos (Cairina moschata) de propriedades localizadas em quatro municípios do Ceará, Brasil / Survey of Enterobacteriaceae in domestic ducks (Cairina moschata) from properties located in four cities of the state of Ceará, Brazil

O objetivo deste trabalho foi isolar e identificar as enterobactérias presentes em patos domésticos (Cairina moschata) de propriedades localizadas em quatro municípios no estado do Ceará. Para isso, 47 esfregaços cloacais foram realizados, e 65 amostras de fezes de patos criados em propriedades localizadas nos municípios de Fortaleza, Boa Água, Eusébio e Cascavel foram coletadas. As amostras foram submetidas ao processamento microbiológico. No pré-enriquecimento, todas as amostras de fezes e dos esfregaços cloacais coletados foram alocadas em água peptonada tamponada 0,1%. Para o enriquecimento seletivo, alíquotas da água peptonada com as amostras foram transferidas para tubos contendo Rappaport-Vassilliadis e Selenito-Cistina. Placas de Verde-Brilhante e MacConkey foram semeadas com o conteúdo dos tubos do enriquecimento. Colônias suspeitas escolhidas com base em características morfológicas foram semeadas em provas bioquímicas (TSI: Tríplice Açúcar Ferro; LIA: Ágar Lisina Ferro; e SIM: Sulfeto, Indol, Motilidade). As bactérias foram identificadas com base nas características bioquímicas. Foi detectado, a partir do exame microbiológico, que as enterobactérias mais prevalentes isoladas das amostras de esfregaços cloacais e de fezes foram Citrobactersp., Proteus sp. e Enterobacter sp. Em menor frequência ocorreram Klebsiella sp., Hafnia sp., Escherichia coli, Shigella sp., Edwardsiella sp., Providencia sp. e Serratia sp. De acordo com a metodologia utilizada, concluiu-se que a microbiota intestinal dos patos avaliados não apresentava Salmonella sp., gênero bacteriano comumente associado a esta espécie de ave; entretanto, observou-se que a fauna microbiana era constituída pelas principais enterobactérias comuns a outras espécies de aves, sendo algumas potencialmente patogênicas aos animais e aos seres humanos.(AU)

This study aimed to isolate and identify members of the Enterobacteriaceae that were present in domestic ducks (Cairina moschata) from properties located in four cities in the State of Ceará, Brazil. Therefore, 65 stool samples and 47 cloacal swabs were collected from farms located in the following cities: Fortaleza, Boa Água, Eusébio and Cascavel. The samples were submitted to bacteriological processing. In pre-enrichment, all of the stool and swab samples were cultured in buffered peptone water 0.1%. For selective enrichment, aliquots from the tubes of the prior step after incubation were transferred to tubes containing Rappaport-Vassiliadis and Selenite Cystine broths. Plates with MacConkey and Brilliant Green agars were streaked with the content from the enrichment tubes after incubation. Colonies were chosen based on their morphological characteristics for the biochemical tests (TSI: Triple-Sugar-Iron; LIA: Lysine-Iron-Agar; and SIM: Sulfide-indole-motility). The bacteria were identified based on their biochemical characteristics. The mostly isolated bacteria were Citrobacter sp., Proteus sp., and Enterobacter sp. In a lower frequency, isolated enterobacteria were Klebsiella sp., Hafnia sp., Escherichia coli, Edwardsiella sp., Providencia sp. and Serratia sp. With the methodology applied, no Salmonella was isolated from the evaluated ducks, which is a genus commonly associated with this avian species; however the microbiota were composed by the main enterobacteria that are common to other species of birds, some of which are potentially pathogenic both to animals and humans.(AU)

Pesquisa de enterobactérias em patos domésticos (Cairina moschata) de propriedades localizadas em quatro municípios do Ceará, Brasil / Survey of Enterobacteriaceae in domestic ducks (Cairina moschata) from properties located in four cities of the state of Ceará, Brazil

O objetivo deste trabalho foi isolar e identificar as enterobactérias presentes em patos domésticos (Cairina moschata) de propriedades localizadas em quatro municípios no estado do Ceará. Para isso, 47 esfregaços cloacais foram realizados, e 65 amostras de fezes de patos criados em propriedades localizadas nos municípios de Fortaleza, Boa Água, Eusébio e Cascavel foram coletadas. As amostras foram submetidas ao processamento microbiológico. No pré-enriquecimento, todas as amostras de fezes e dos esfregaços cloacais coletados foram alocadas em água peptonada tamponada 0,1%. Para o enriquecimento seletivo, alíquotas da água peptonada com as amostras foram transferidas para tubos contendo Rappaport-Vassilliadis e Selenito-Cistina. Placas de Verde-Brilhante e MacConkey foram semeadas com o conteúdo dos tubos do enriquecimento. Colônias suspeitas escolhidas com base em características morfológicas foram semeadas em provas bioquímicas (TSI: Tríplice Açúcar Ferro; LIA: Ágar Lisina Ferro; e SIM: Sulfeto, Indol, Motilidade). As bactérias foram identificadas com base nas características bioquímicas. Foi detectado, a partir do exame microbiológico, que as enterobactérias mais prevalentes isoladas das amostras de esfregaços cloacais e de fezes foram Citrobactersp., Proteus sp. e Enterobacter sp. Em menor frequência ocorreram Klebsiella sp., Hafnia sp., Escherichia coli, Shigella sp., Edwardsiella sp., Providencia sp. e Serratia sp. De acordo com a metodologia utilizada, concluiu-se que a microbiota intestinal dos patos avaliados não apresentava Salmonella sp., gênero bacteriano comumente associado a esta espécie de ave; entretanto, observou-se que a fauna microbiana era constituída pelas principais enterobactérias comuns a outras espécies de aves, sendo algumas potencialmente patogênicas aos animais e aos seres humanos.(AU)

This study aimed to isolate and identify members of the Enterobacteriaceae that were present in domestic ducks (Cairina moschata) from properties located in four cities in the State of Ceará, Brazil. Therefore, 65 stool samples and 47 cloacal swabs were collected from farms located in the following cities: Fortaleza, Boa Água, Eusébio and Cascavel. The samples were submitted to bacteriological processing. In pre-enrichment, all of the stool and swab samples were cultured in buffered peptone water 0.1%. For selective enrichment, aliquots from the tubes of the prior step after incubation were transferred to tubes containing Rappaport-Vassiliadis and Selenite Cystine broths. Plates with MacConkey and Brilliant Green agars were streaked with the content from the enrichment tubes after incubation. Colonies were chosen based on their morphological characteristics for the biochemical tests (TSI: Triple-Sugar-Iron; LIA: Lysine-Iron-Agar; and SIM: Sulfide-indole-motility). The bacteria were identified based on their biochemical characteristics. The mostly isolated bacteria were Citrobacter sp., Proteus sp., and Enterobacter sp. In a lower frequency, isolated enterobacteria were Klebsiella sp., Hafnia sp., Escherichia coli, Edwardsiella sp., Providencia sp. and Serratia sp. With the methodology applied, no Salmonella was isolated from the evaluated ducks, which is a genus commonly associated with this avian species; however the microbiota were composed by the main enterobacteria that are common to other species of birds, some of which are potentially pathogenic both to animals and humans.(AU)

Avian influenza survey in migrating waterfowl in Sonora, Mexico.

A two-year survey was carried out on the occurrence of avian influenza in migrating birds in two estuaries of the Mexican state of Sonora, which is located within the Pacific flyway. Cloacal and oropharyngeal swabs were collected from 1262 birds, including 20 aquatic bird species from the Moroncarit and Tobari estuaries in Sonora, Mexico. Samples were tested for type A influenza (M), H5 Eurasian and North American subtypes (H5EA and H5NA respectively) and the H7 North American subtype (H7NA). Gene detection was determined by one-step real-time reverse transcription polymerase chain reaction (RRT-PCR). The results revealed that neither the highly pathogenic avian influenza virus H5 of Eurasian lineage nor H7NA were detected. The overall prevalence of avian influenza type A (M-positive) in the sampled birds was 3.6% with the vast majority in dabbling ducks (Anas species). Samples from two birds, one from a Redhead (Aythya americana) and another from a Northern Shoveler (Anas clypeata), were positive for the low-pathogenic H5 avian influenza virus of North American lineage. These findings represented documented evidence of the occurrence of avian influenza in wintering birds in the Mexican wetlands. This type of study contributes to the understanding of how viruses spread to new regions of North America and highlights the importance of surveillance for the early detection and control of potentially pathogenic strains, which could affect animal and human health.

Avian influenza in wild birds, central coast of Peru.

To determine genotypes of avian influenza virus circulating among wild birds in South America, we collected and tested environmental fecal samples from birds along the coast of Peru, June 2006-December 2007. The 9 isolates recovered represented 4 low-pathogenicity avian influenza strains: subtypes H3N8, H4N5, H10N9, and H13N2.

Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae

The nucleotide sequences of eight open reading frames (ORFs) located at the 5' end of the unique long region of the duck enteritis virus (DEV) Clone-03 strain were determined. The genes identified were designated UL1, UL2, UL3, UL4, UL5, UL6 and UL7 homologues of the herpes simplex virus 1 (HSV-1). The DEV UL3.5 located between UL3 and UL4 had no homologue in the HSV-1. The arrangement and transcription orientation of the eight genes were collinear with their homologues in the HSV-1. Phylogenetic trees were constructed based on the alignments of the deduced amino acids of eight proteins with their homologues in 12 alpha-herpesviruses. In the UL1, UL3, UL3.5, UL5 and UL7 proteins trees, the branches were more closely related to the genus Mardivirus. However, the UL2, UL4, and UL6 proteins phylogenetic trees indicated a large distance from Mardivirus, indicating that the DEV evolved differently from other viruses in the subfamily Alphaherpesvirinae and formed a single branch within this subfamily.

Pathogenicity and transmission studies of H5N2 parrot avian influenza virus of Mexican lineage in different poultry species.

In 2004, a low pathogenic H5N2 influenza virus (A/parrot/CA/6032/04) was identified in a psittacine bird for the first time in the United States. Sequence and phylogenetic analysis of the hemagglutinin gene grouped the parrot isolate under the Mexican lineage H5N2 viruses (subgroup B) with highest similarity to recent chicken-origin isolates from Guatemala. Antigenic analysis further confirmed the close relatedness of the parrot isolate to Mexican lineage viruses, the highest cross-reactivity being demonstrated to Guatemala isolates. In vivo studies of the parrot isolate in chickens, ducks and turkeys showed that the virus, though did not cause any clinical signs, could replicate to high titers in these birds and efficiently transmit to contact control cage mates. The possibility that the parrot harboring the virus was introduced into the United States as a result of illegal trade across the border provides additional concern for the movement of foreign animal diseases from neighboring countries. Considering the potential threat of the virus to domestic poultry, efforts should be continued to prevent the entry and spread of influenza viruses by imposing effective surveillance and monitoring measures.

An avian influenza virus from waterfowl in South America contains genes from North American avian and equine lineages.

Apart from an outbreak in commercial poultry in Chile in 2002, there have been few reports of avian influenza in South America. However, surveillance in free-flying birds has been limited. An avian influenza virus was isolated from a Cinnamon Teal (Anas cyanoptera) in Bolivia in 2001 from samples collected for an avian influenza virus and avian paramyxovirus surveillance study. This isolate was determined to be an H7N3 virus by gene sequencing. Analysis of all eight genes revealed that five genes were most closely related to the H7N3 in Chile in 2002. Two genes were most closely related to North American wild aquatic bird virus lineages and one gene was most closely related to an equine influenza virus from South America.