Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China / 生物医学与环境科学（英文）

OBJECTIVE@#To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake, China.@*METHODS@#Ten smear samples were collected in March 2019. Metagenomic sequencing was performed to delineate bacterial and viral diversity. Taxonomic analysis was performed using the Kraken2 and Bracken methods. A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase (RdRp) region of picornavirus.@*RESULTS@#We identified 363 bacterial and 6 viral families. A significant difference in microbial and viral abundance was found between samples S01-S09 and S10. In S01-S09, members of Flavobacteriia and Gammaproteobacteria were the most prevalent, while in S10, the most prevalent bacteria class was Actinomycetia. Among S01-S09, members of Myoviridae and Herelleviridae were the most prevalent, while the dominant virus family of S10 was Picornaviridae. The full genome of the pigeon mesivirus-like virus (NC-BM-233) was recovered from S10 and contained an open reading frame of 8,124 nt. It showed the best hit to the pigeon mesivirus 2 polyprotein, with 84.10% amino acid identity. Phylogenetic analysis showed that RdRp clustered into Megrivirus B.@*CONCLUSION@#This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples, broadens our knowledge of viral and bacterial diversity, and is a way to discover potential pathogens in wild birds.

Erratic migration of Ascaridia hermaphrodita (Nematoda: Ascaridida) in a blue-fronted Amazon parrot (Amazona aestiva) from illegal wildlife trade: case report / [Migração errática de Ascaridia hermaphrodita (Nematoda: Ascaridida) em papagaio-verdadeiro (Amazona aestiva) oriundo do comércio ilegal: relato de caso]

Ascaridiasis by Ascaridia hermaphrodita is a common parasitic disease in blue-fronted Amazon parrots (Amazona aestiva) and the contamination occurs by ingestion of eggs. Illegal trade of wild birds can increase the frequency of visceral erratic migration by this parasite. Hence, this report describes the erratic migration of A. hermaphrodita and associated lesions in a blue-fronted Amazon parrot. This is a retrospective study, which originated from several apprehension of illegal birds in the state of Paraíba, Brazil. Necropsy revealed intense intestinal ascarid infestation. Hepatic lesions were also observed associated with the parasite migration. Stereoscopy allowed the identification of the morphology of the parasites. Summarizing, this condition in wild birds is not fully understood and may be associated with illegal trade.(AU)

Ascaridíase por Ascaridia hermaphrodita é uma doença parasitária comum em papagaios-verdadeiros. Sua contaminação ocorre pela ingestão de ovos. O tráfico de aves silvestres pode facilitar a migração errática visceral desse parasita. Este relato descreve a migração errática de A. hermaphrodita e lesões associadas em papagaio-verdadeiro. Trata-se de um relato retrospectivo, analisado a partir de uma série de apreensões de aves no estado da Paraíba, Brasil. A necropsia revelou intensa infestação ascarídea intestinal. Também foram observadas lesões hepáticas em uma ave, associadas à migração do parasita. A estereoscopia permitiu distinguir a morfologia dos parasitas. Resumidamente, essa condição em aves silvestres é pouco conhecida e pode ser considerada, inclusive, associada à comercialização ilegal.(AU)

Occurrence of Chlamydia spp. In wild birds in Thailand

Objective: To determine the occurrence of Chlamydia spp. in wild birds in Thailand. Methods: Cloacal and tracheal swabs of 313 wild birds from 11 orders, 27 families, and 51 species were tested to determine the occurrence of Chlamydia infection. The outer membrane protein A (ompA) gene was amplified from positive samples to construct a phylogenetic tree. Results: At the time of sample collection, none of the birds showed clinical signs of any disease. Of 313 wild birds, two Asian openbill stork (Anastomus oscitans) were positive for Chlamydia spp., representing 0.64% (2/313) and 4.9% (2/41) occurrence for birds overall and for the Asian openbill stork, respectively. Phylogram analysis based on deduced amino acid of the ompA gene showed that Chlamydia spp. in Asian openbill storks was closely related to that in wildfowl (Pica pica and Cygnus olor) from Poland in a different branch with a 95% bootstrap value and had a shorter evolutionary distance to Chlamydia abortus. Conclusions: Asymptomatic Asian openbill storks could be a potential source of Chlamydia infection in domestic animals, poultry, and humans who share their habitat.

The difference of detection rate of avian influenza virus in the wild bird surveillance using various methods

Korea is located within the East Asian-Australian flyway of wild migratory birds during the fall and winter seasons. Consequently, the likelihood of introduction of numerous subtypes and pathotypes of the Avian influenza (AI) virus to Korea has been thought to be very high. In the current study, we surveyed wild bird feces for the presence of AI virus that had been introduced to Korea between September 2017 and February 2018. To identify and characterize the AI virus, we employed commonly used methods, namely, virus isolation (VI) via egg inoculation, real-time reverse transcription-polymerase chain reaction (rRT-PCR), conventional RT-PCR (cRT-PCR) and a newly developed next generation sequencing (NGS) approach. In this study, 124 out of 11,145 fresh samples of wild migratory birds tested were rRT-PCR positive; only 52.0% of VI positive samples were determined as positive by rRT-PCR from fecal supernatant. Fifty AI virus specimens were isolated from fresh fecal samples and typed. The cRT-PCR subtyping results mostly coincided with the NGS results, although NGS detected the presence of 11 HA genes and four NA genes that were not detected by cRT-PCR. NGS analysis confirmed that 12% of the identified viruses were mixed-subtypes which were not detected by cRT-PCR. Prevention of the occurrence of AI virus requires a workflow for rapid and accurate virus detection and verification. However, conventional methods of detection have some limitations. Therefore, different methods should be combined for optimal surveillance, and further studies are needed in aspect of the introduction and application of new methods such as NGS.

Occurrence of Chlamydia spp. In wild birds in Thailand

Objective: To determine the occurrence of Chlamydia spp. in wild birds in Thailand. Methods: Cloacal and tracheal swabs of 313 wild birds from 11 orders, 27 families, and 51 species were tested to determine the occurrence of Chlamydia infection. The outer membrane protein A (ompA) gene was amplified from positive samples to construct a phylogenetic tree. Results: At the time of sample collection, none of the birds showed clinical signs of any disease. Of 313 wild birds, two Asian openbill stork (Anastomus oscitans) were positive for Chlamydia spp., representing 0.64% (2/313) and 4.9% (2/41) occurrence for birds overall and for the Asian openbill stork, respectively. Phylogram analysis based on deduced amino acid of the ompA gene showed that Chlamydia spp. in Asian openbill storks was closely related to that in wildfowl (Pica pica and Cygnus olor) from Poland in a different branch with a 95% bootstrap value and had a shorter evolutionary distance to Chlamydia abortus. Conclusions: Asymptomatic Asian openbill storks could be a potential source of Chlamydia infection in domestic animals, poultry, and humans who share their habitat.

Causes of bird losses recorded in a captive-bred wild bird flock between 2011 and 2015 / Perdas registradas em um plantel de aves silvestres criadas em cativeiro, entre 2011 e 2015

ABSTRACT: This study discusses the causes of bird deaths recorded in a small aviary dedicated to the breeding of a few exotic, wild bird species. Findings from 28 birds were examined over a period of five years. About 40% of the deaths occurred in the first two weeks after hatching in the two most numerous species in the flock and such losses were mainly a result of starvation caused by inadequate nutritional management. Additionally, 28% of the cases affected recently introduced birds. Despite frequent treatment with anthelmintics; a total of 21% of the deaths in the flock could be attributed to parasitic diseases, most of them in recently acquired birds. Only three of the deaths could be associated with advanced age, all of the further cases were also attributable to management fails. Our results indicated that propagation of these and other species requires an improvement of the management of the newly hatched and newcomer birds to considerably enhance the flock’s performance. Such information may be useful in conservation initiatives and may justify, at least in part, captivity of these animals.

RESUMO: Este estudo discute as causas de morte de aves registradas em um pequeno criadouro de umas poucas espécies de aves silvestres exóticas. As mortes de 28 aves foram examinadas em um período de cinco anos. Cerca de 40% dos casos ocorreram na primeira semana de vida de filhotes das duas espécies mais numerosas no plantel e essas perdas foram consequentes à desnutrição por falhas no manejo nutricional. Outros 28% de casos ocorreram em aves, recentemente introduzidas, ou em fase de adaptação, no criadouro. Ainda que as aves do plantel sejam frequentemente dosificadas com anti-helmínticos, 21% das mortes no plantel foram secundárias a doenças parasitárias; a maioria afetou aves recentemente adquiridas. Exceto por três mortes que foram associadas com desordens atribuídas à idade avançada, todas as demais foram associadas com inadequações no manejo das aves. Esses resultados sugerem que, em sistemas dessa natureza, as aves recém-nascidas e as recém-introduzidas são categorias críticas que demandam concentração de esforços para o atendimento sistemático de suas necessidades. Tais dados podem ser aplicáveis em iniciativas de conservação de outras espécies e podem justificar, ainda que parcialmente, a manutenção desses animais, em cativeiro.

Molecular characterization of highly pathogenic avian influenza H5N8 viruses isolated from Baikal teals found dead during a 2014 outbreak in Korea

Nineteen highly pathogenic avian influenza (HPAI) H5N8 viruses were isolated from wild birds in the Donglim reservoir in Gochang, Jeonbuk province, Korea, which was first reported to be an outbreak site on January 17, 2014. Most genes from the nineteen viruses shared high nucleotide sequence identities (i.e., 99.7% to 100%). Phylogenetic analysis showed that these viruses were reassortants of the HPAI H5 subtype and the H4N2 strain and that their hemagglutinin clade was 2.3.4.4, which originated from Eastern China. The hemagglutinin protein contained Q222 and G224 at the receptor-binding site. Although the neuraminidase protein contained I314V and the matrix 2 protein contained an S31N substitution, other mutations resulting in oseltamivir and amantadine resistance were not detected. No substitutions associated with increased virulence and enhanced transmission in mammals were detected in the polymerase basic protein 2 (627E and 701D). Non-structural-1 was 237 amino acids long and had an ESEV motif with additional RGNKMAD amino acids in the C terminal region. These viruses caused deaths in the Baikal teal, which was unusual, and outbreaks occurred at the same time in both poultry and wild birds. These data are helpful for epidemiological understanding of HPAI and the design of prevention strategies.

Surveillance of wild birds for avian influenza virus in Korea / 대한수의학회지

Avian influenza viruses (AIV) have been isolated from a wide range of domestic and wild birds. Wild birds, predominantly ducks, geese and gulls form the reservoir of AIV in nature. The viruses in wild bird populations are a potential source of widespread infections in poultry. Active surveillance for AIV infection provides information regarding AIV distribution, and global AIV surveillance can play a key role in the early recognition of highly pathogenic avian influenza (HPAI). Since 2003 in Korea, there have been four H5N1 HPAI outbreaks caused by clade 2.5, 2.2 and 2.3.2. Therefore, improvement of AIV surveillance strategy is required to detect HPAI viruses effectively. This article deals with the major events establishing the role of wild birds in the natural history of influenza in Korea. We highlighted the need for continuous surveillance in wild birds and characterization of these viruses to understand AIV epidemiology and host ecology in Korea.

Serosurveillance for Japanese encephalitis virus in wild birds captured in Korea

Climate change induced by recent global warming may have a significant impact on vector-borne and zoonotic diseases. For example, the distribution of Japanese encephalitis virus (JEV) has expanded into new regions. We surveyed the levels of hemagglutination-inhibition (HI) antibodies against JEV (Family Flaviviridae, genus Flavivirus) in wild birds captured in Korea. Blood samples were collected from 1,316 wild birds including the following migratory birds: Oceanodroma castro (n = 4), Anas formosa (n = 7), Anas penelope (n = 20), Fulica atra (n = 30), Anas acuta (n = 89), Anas crecca (n = 154), Anas platyrhynchos (n = 214), Aix galericulata (n = 310), and Anas poecilorhyncha (n = 488). All were captured in 16 locations in several Korea provinces between April 2007 and December 2009. Out of the 1,316 serum samples tested, 1,141 (86.7%) were positive for JEV. Wild birds captured in 2009 had a higher seroprevalence of ant-JEV antibodies than those captured in 2007. Wild birds with an HI antibody titer of 1 : 1,280 or higher accounted for 21.2% (280/1,316) of the animals tested. These findings indicated that wild birds from the region examined in our study have been exposed to JEV and may pose a high risk for introducing a new JEV genotype into Korea.