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.
Animals ; Animals, Wild/genetics* ; Lakes ; Phylogeny ; Picornaviridae/genetics* ; Viruses/genetics* ; China ; Metagenomics ; Genome, Viral

Animals ; Animals, Wild ; microbiology ; Genes, rRNA ; RNA, Ribosomal, 16S ; genetics ; Rats ; Rickettsia ; classification ; genetics ; Rickettsia Infections ; microbiology ; veterinary

Maintaining genetic diversity is a major issue in conservation biology. In this study, we demonstrate the differences of genetic diversity levels between wild and captive individuals of Elliot's Pheasant Syrmaticus ellioti. Wild individuals showed a higher genetic diversity level than that of the captive individuals. Nucleotide diversity and haplotype diversity of wild individuals were 0.00628 and 0.993, while those of captive individuals were 0.00150 and 0.584 respectively. Only 3 haplotypes of mtDNA control region sequence were identified among 36 captive individuals, while 16 unique haplotypes were identified among the 17 wild individuals in this study. One captive haplotype was shared by a wild individual from Anhui Province. It is concluded that a low number of founders was the likely reason for the lower level genetic diversity of the captive group. Careful genetic management is suggested for captive populations, particularly of such an endangered species, to maintain genetic variability levels.
Animals ; Animals, Wild ; genetics ; Animals, Zoo ; genetics ; Base Sequence ; DNA, Mitochondrial ; genetics ; Galliformes ; genetics ; Genetic Variation ; genetics ; Haplotypes ; Molecular Sequence Data ; Polymorphism, Genetic ; genetics

Encephalomyocarditis virus (EMCV) is a natural epidemic zoonotic pathogen. However, no reports have been published regarding the isolation, identification and full-length genome of EMCV from a local aardvark population. In present study, an EMCV isolate HNXX13 was isolated from aardvarks named Huainan-pig in Henan Province. The systematic identification, full-length genome sequencing and molecular characteristic analysis of the isolate HNXX13 were conducted. The result showed that the isolate was spherical with a diameter of 24-30 nm, neither heat- nor acid-resistant, sensitive to trypsin, insensitive to chloroform, not protected by bivalent cationic, and the specific fluorescence was observed in the cytoplasm of BHK-21 cells infected with the isolate by using indirect fluorescence assay. The full-length genome of EMCV HNXX13 generated a 7 725bp sequence (GenBank: F771002), with 81.0%-99.9% nucleotide identity to reference strains from different animals, and 99.5% with a Chinese reference strain isolated earlier from a commercial pig herd. The phylogenetic tree based on the full-length genome and ORF sequences identified that all EMCV strains were divided into three groups G1, G2 and G3, and strain HNXX13 belonging to the G1 group with other Chinese reference strains. The result also identified that this EMCV infection could cause severe clinical signs in a local aardvark population, and enriches the molecular epidemiological data of EMCV in China. Regional differences exist in EMCV genome and transmission is limited within a certain area. However, the cross-infection and transmission of EMCV between aardvark and mice appears most likely. Mutations have occurred in some amino acids of EMCV strain HNXX13 during the transmission in local aardvark herd and these mutations might make the virus easier to infect the aardvark.
Animals ; Animals, Wild ; virology ; Cardiovirus Infections ; veterinary ; virology ; China ; Encephalomyocarditis virus ; classification ; genetics ; isolation & purification ; Genome, Viral ; Mice ; Molecular Sequence Data ; Phylogeny ; Xenarthra ; virology

Wild birds (mainly Anseriformes and Charadriiformes) are recognized as the natural reservoir of avian influenza viruses (AIVs). The long-term surveillance of AIVs in wild birds has been conducted in North America and Europe since 1970s. More and more surveillance data revealed that all the HA and NA subtypes of AIVs were identified in the wild ducks, shorebirds, and gulls, and the AIVs circulating in wild birds were implicated in the outbreaks of AIVs in poultry and humans. Therefore, the AIVs in wild birds pose huge threat to poultry industry and human health. To gain a better understanding of the ecology and epidemiology of AIVs in wild birds, we summarize the transmission of AIVs between wild birds, poultry, and humans, the main results of surveillance of AIVs in wild birds worldwide and methods for surveillance, and the types of samples and detection methods for AIVs in wild birds, which would be vital for the effective control of avian influenza and response to possible influenza pandemic.
Animals ; Animals, Wild ; virology ; Birds ; virology ; Humans ; Influenza A virus ; genetics ; isolation & purification ; physiology ; Influenza in Birds ; epidemiology ; transmission ; virology ; Influenza, Human ; epidemiology ; transmission ; virology ; Sentinel Surveillance ; veterinary

In order to examine the prevalence of Cryptosporidium infection in wild rodents and insectivores of South Korea and to assess their potential role as a source of human cryptosporidiosis, a total of 199 wild rodents and insectivore specimens were collected from 10 regions of South Korea and screened for Cryptosporidium infection over a period of 2 years (2012-2013). A nested-PCR amplification of Cryptosporidium oocyst wall protein (COWP) gene fragment revealed an overall prevalence of 34.2% (68/199). The sequence analysis of 18S rRNA gene locus of Cryptosporidium was performed from the fecal and cecum samples that tested positive by COWP amplification PCR. As a result, we identified 4 species/genotypes; chipmunk genotype I, cervine genotype I, C. muris, and a new genotype which is closely related to the bear genotype. The new genotype isolated from 12 Apodemus agrarius and 2 Apodemus chejuensis was not previously identified as known species or genotype, and therefore, it is supposed to be a novel genotype. In addition, the host spectrum of Cryptosporidium was extended to A. agrarius and Crosidura lasiura, which had not been reported before. In this study, we found that the Korean wild rodents and insectivores were infected with various Cryptosporidium spp. with large intra-genotypic variationa, indicating that they may function as potential reservoirs transmitting zoonotic Cryptosporidium to livestock and humans.
Animals ; Animals, Wild/*parasitology ; Cryptosporidiosis/*parasitology ; Cryptosporidium/classification/*genetics/*isolation & purification ; Feces/parasitology ; Genotype ; Insectivora/*parasitology ; Molecular Sequence Data ; Murinae ; Phylogeny ; Republic of Korea ; Rodent Diseases/*parasitology

The virus strains were isolated from the liver and spleen of the dead young ducks characterized with symptoms of hemorrhagic-necrotic hepatitis. These isolates could cause the death of muscovy duck-embryo and chick-embryo. 1-day-old birds infected with these isolates had the same character with clinically dead birds and the virus could be isolated from artificially infected birds. These isolates could proliferate in MDEF and result in CPE. The virus could proliferate in the cytoplasm in order of crystals and arranged in the latlic-like. The viron was shown spherical, icosahedron, cubic symmetry, no-envelope, with double-layered capsid, about 70 nm in diameter by electron microscopy. The genome segments of the virus were consisted of L1-3, M1-3 and S1-4, which were similar to that of avian reovirus (ARV). Compared to 68.2%, 69.3% - 70.1%, respectively. The system evolution analysis showed that S3 gene coding sigmaB protein was placed in different branch of MDRV and ARV, indicating that S3 gene of the virus was different from ARV and MDRV. The main clinical symptoms and lesions of ducklings caused by the virus were different from the diseases caused by MDRV and ARV. It was concluded that the virus was a Novel duck reovirus belonging to Orthoreovirus genus of the Reoviridae family.
Animals ; Animals, Wild ; virology ; Bird Diseases ; pathology ; virology ; Chick Embryo ; China ; Ducks ; Molecular Sequence Data ; Orthoreovirus, Avian ; classification ; genetics ; isolation & purification ; Phylogeny ; Reoviridae Infections ; pathology ; veterinary ; virology ; Viral Proteins ; genetics

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.
Animal Migration ; Animals ; Animals, Wild ; Bird Diseases/*epidemiology/virology ; Birds ; Encephalitis Virus, Japanese/genetics/*isolation & purification ; Encephalitis, Japanese/blood/epidemiology/*veterinary/virology ; Genotype ; Hemagglutination Inhibition Tests ; Population Surveillance ; Republic of Korea/epidemiology ; Seroepidemiologic Studies

With the development of biotechnology, forensic DNA identification technology in protection of wild animals has been used more and more widely. This review introduces the global status of wildlife crime and the relevant protection to wildlife, outlines the practical applications of forensic DNA identification technology with regard to species identification, determination of geographic origin, individual identification and paternity identification. It focus on the techniques commonly used in DNA typing and their merits and demerits, as well as the problems and prospects of forensic DNA technology for wildlife conservation.
Animals ; Animals, Wild/genetics* ; Commerce/legislation & jurisprudence* ; Conservation of Natural Resources ; Crime/legislation & jurisprudence* ; DNA/genetics* ; DNA Fingerprinting/methods* ; DNA, Mitochondrial/genetics* ; Forensic Genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/methods* ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; Species Specificity