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Objective:To conduct in-depth study of the distribution and diversity of viruses in poultry is of great importance in monitoring the emergence of interspecies transmission of novel viruses that may cause epidemics with public health significance. Poultry is an economically important source of meat, eggs and feathers which plays an important role as natural reservoirs of many pathogenic viruses. Compared with wild animals, poultry have more frequent interactions and therefore opportunities to transmit their viruses to human.Methods:To study the viromes of different types of poultry in Hainan, China, we used metagenomics for deep viral nucleic acid sequencing of the faecal samples collected from chickens, ducks and pigeons from a live poultry market in Haikou.Result:The poultry viromes were identified by sequence similarity comparisons of viral reads (BLASTxE score, <5) against viral reference database. A total of 15 309 viral reads were obtained, approximately 13 063, 1 370 and 876 viral reads were generated from the chicken, duck, pigeon faecal samples, respectively. The majority of the sequences were homologous to the animal virus of Adenoviridae, Herpeaviridae, Picobirnaviridae, Reoviridae, Retroviridae, Circoviridae, Paramyxoviridae, Astroviridae, Caliciviridae, Coronaviridae, Picornaviridae, and Orthomyxoviridae. The VP4 and VP7 segments of a pigeon rotavirus, similar to fox rotavirus in group A, were sequenced and phylogenetically analyzed. The near full genome of a pigeon circovirus was also analyzed.Conclusion:The major types of poultry in a Haikou harbor many different families of viruses in their feces which may have the potential for interspecies transmissions. Further studies should be conducted to identify the most prevalent and important viruses among a larger number of poultry in Haikou and other areas in Hainan.
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Objective:Torque teno virus(TTV), are reported in a wide range of mammals. In this study, we sequenced and analyzed the complete genome of a genetic variant of Rodent TTV, RoTTV3-HMU1 (Hainan Medical University). The virus was harbored by a Rattus norvegicus in the residential areas of Hainan Island, China.Methods:Torque Teno virus (TTV) was found widely distributed throughout the world infecting an extensively wide range of mammals .We extracted the viral DNA from a Rattus norvegicus liver which was caught from the residential areas of Hainan Island. Purifying the amplicons in the range of 250-500 bp. Then Five hundred nanograms DNA was subjected to high-throughput sequencing. The contigs were compared with the NCBI nucleiotide database, designed the primers to cover the genome by PCR amplification and amplicons of each PCR which have been cloned and sequenced. Finally the genome was annotated by using NCBI ORF finder and FGENESV0. Phylogenetic analysis was implemented by the neighbor-joining method in the MEGA6 software package.Results:We sequenced the complete genome of a genetic variant of Rodent TTV, RoTTV3- HMU1. The genomic sequence of RoTTV3-HMU1 has been deposited in GenBank under accession number MF688246.1. The complete genome of RoTTV3-HMU1 is 2 570 nucleotides (nt) in length with a G+C content of 46.93%. RoTTV3-HMU1 encoded 3 unidirectional overlapping open reading frames (ORF). Sequence analysis indicated that the genome of RoTTV3-HMU1 virus was most closely related to RN_2_15 (GenBank accession no. KM668486.1). Phylogenetic analysis based on both ORF1 and the total genome sequence placed RoTTV3-HMU1 in to the clad RoTTV3 of the RoTTV.Conclusions:Hainan Island faces mainland across the sea, however, the same genotype of RoTTV was identified in both Hainan Island and the other part of China. The detection of RoTTV3-HMU1 contributed to a better understanding about the origin and evolution of RoTTV.
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Objective:Microsporidia have been rapidly emerging as pathogens in both immunocompromised and immunocompetent humans. Enterocytozoon bieneusi (E. bieneusi) is the most common microsporidial species found in human. E. bieneusi has also been found in a wide range of animals and is considered to be a potentially important zoonotic pathogen. The epidemiological and genetic characterization of E. bieneusi among long-tailed macaques [Macaca fascicularis (M. fascicularis) is not fully understood. Here, we conducted the first molecular epidemiological investigation of E. bieneusi among M. fascicularis in Hainan Province, the southernmost part of China.Methods:A total of 193 fecal specimens of M. fascicularis were collected from a breeding base housing non-human primates for experimental use in Hainan Province, China. E. bieneusi was identified and genotyped by nested PCR analysis of the internal transcribed spacer (ITS) region of the rRNA gene. Phylogenetic analysis was performed by constructing a neighboring-joining tree of the ITS gene sequences using MEGA6.Results:A total of 59 (30.6%) of the M. fascicularis were PCR-positive for E. bieneusi. All 59 samples were sequenced successfully and 16 ITS genotypes were identified. These included nine known genotypes: Type IV (n=19), D (n=11), CM1 (n=8), PigEBITS7 (n=4), Pongo2 (n=4), Peru 8 (n=3), Peru11 (n=1), WL21 (n=1) and CM2 (n=1). Additionally, seven novel genotypes named as HNM-I to HNM-VII (one each) were identified. Importantly, genotypes D, Type IV, Peru8, PigEBITS7, and Peru11, which were the predominant (38/59, 64.4%) genotypes identified among M. fascicularis in this study, are also well-known human-pathogenic genotypes. All the genotypes of E. bieneusi identified in this study, including the seven novel ones, belonged to zoonotic group 1.Conclusions:This is the first report of the identification of E. bieneusi in M. fascicularis in Hainan Province, China. The findings of numerous known human-pathogenic types and seven novel genotypes (HNM-I to HNM-VII) of E. bieneusi all belong to zoonotic group 1 indicate the possibility of transmission of this important pathogenic parasite between M. fascicularis and humans.
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PURPOSE: Efficacy of the new rotavirus vaccines (Rotarix(R), RotaTeq(R)) recently developed can be affected by the rotavirus genotypes prevalent in communities. We performed this study to identify the recent distribution of rotavirus genotypes prevalent in Jeju. METHODS: Genotyping of human rotaviruses was performed using 81 samples collected from 154 inpatients and outpatients with rotavirus gastroenteritis at Cheju National University Hospital between July 2005 and June 2006. All six (1, 2, 3, 4, 8, 9) G serotypes were identified by amplification of segments of the gene for VP7 using the reverse transcription-polymerase reaction (RT- PCR). RESULTS: The results of RT-PCR for 81 samples were all positive. G typing of the VP7 protein showed that G1 was the most dominant circulating genotype (65.5%) followed by G2 (14.8%), G3 (13.6%), G8 (1.2%), G9 (1.2%), G4 (0%), and a combination of G1/G3 (3.7%). CONCLUSION: This distribution of rotavirus VP7 genotypes in Jeju is different from that in other domestic areas; the most dominant circulating genotype was G1.