Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene.

Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima's D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.

Complete Genomic Characterization of Three Tick-Borne Encephalitis Viruses Detected Along the China-North Korea Border, 2011.

Tick-borne encephalitis virus (TBEV) causes neurological infections with serious sequelae in Europe and Northeast Asia. In China, the major epidemic areas are along the borders with Russia and North Korea. Although several TBEV isolates have been reported, the biological characteristics of the Chinese strains, especially those along the China-North Korea border, are unclear. In this study, we detected seven TBEV fragment sequences in 602 adult Dermacentor silvarum collected in the Changbai Mountain area of Jilin Province on the China-North Korea border and characterized the genome of three TBEV strains (JLCB11-08, JLCB11-35, and JLCB11-40). These three TBEV strains belong to the TBEV-Far Eastern (TBEV-FE) genotype and clustered most closely with the Svetlogorie and Kavalerovo strains from Russia. In addition, the TBEV strains from Northeast China clustered geographically within the TBEV-FE subtype branch. These findings will facilitate further research on the distinct genetic groupings of TBEV strains in China.

Identification and characterization of a novel rodent bocavirus from different rodent species in China.

Members in the genus Bocaparvovirus are closely related to human health and have a wide host range. The diverse hosts raise the possibility of crossing species barrier, which is a feature of emerging viruses. Among the mammalian hosts, rodents are generally acknowledged to be important reservoirs of emerging viruses. Here, rodent samples collected from six provinces and autonomous regions of China (Liaoning, Inner Mongolia, Tibet, Xinjiang, Guangxi and Yunnan) were used to investigate the prevalence and distribution of bocaparvoviruses. By using next-generation sequencing first, a partial non-structural protein 1 (NS1) gene belonging to a possible novel bocaparvovirus was discovered. Following this, PCR-based screening of NS1 gene was conducted in 485 rodent samples, with 106 positive results found in seven rodent species (Rattus norvegicus, Mus musculus, Apodemus agrarius, Cricetulus barabensis, Rattus flavipectus, Rattus rattus and Rhombomys opimus). Finally, six nearly full-length genomes and three complete CDS were obtained and the newly identified bocaparvovirus was tentatively named rodent bocavirus (RoBoV). RoBoV has three ORFs: NS1, NP1, and VP, which are characteristics of bocaparvoviruses. Phylogenetic analyses revealed that porcine bocavirus isolate PBoV-KU14, a member of Ungulate bocaparvovirus 4, was the most related virus to RoBoV, with 92.1-92.9% amino acid identities in NS1 protein. Alignments of RoBoV-related sequences showed RoBoV isolates could be classified into two clades, demonstrating an inter-host genetic diversity. The results indicate a potential interspecies transmission of RoBoV between rodents and swine and expand our knowledge on bocaparvoviruses in rodent populations.

First Molecular Detection of Rickettsia felis-Like Organism in Eulaelaps stabularis from the Changbai Mountain Area of China.

In 557 mites collected from rodents in the Changbai Mountain Area, 3 pools of Eulaelaps stabularis from Apodemus peninsulae and Apodemus agrarius showed a positive result by PCR amplifications of both the citrate synthase encoding gene (gltA) and outer membrane protein B encoding gene (ompB) of Rickettsia spp. Sequence analysis indicated that both gltA and ompB shared the high similarity (99%) to Rickettsia felis . The data presented in this paper extend the knowledge on the geographic distribution and host information of R. felis -like organism in China.

Complete Genome Sequence of a Novel Mutation of Seoul Virus Isolated from Suncus murinus in the Fujian Province of China.

Suncus murinus has been identified as the host for Seoul virus (SEOV). Here, we report the complete genome sequence of SEOV strain Fj372/2013, which was isolated from the lung tissue of Suncus murinus in the Fujian Province of China. A mutation A38C was observed in an open reading fragment of the middle segment.

[The analysis of hantavirus S gene in Apodemus agrarius in Changbai area].

To gain more insights into epidemiologic characteristics and genotype of hantavirus in Apodemus agrarius in Changbai Area. Complete hantavirus S segment sequences were amplified by RT-PCR and sequenced. The phylogenetic trees were constructed for analysis of genetic characters of hantavirus. A total of 58 Apodemus agrarius were trapped in the epidemic areas, and complete hantavirus S segment sequences were obtained from 4 lung samples of these rodents (6. 90%0). Phylogenetic analysis of the four S segment sequences indicated that all viruses isolated from Apodemu sagrarius were closely related to genotype 6 of Hantaan virus (95. 8%-96. 3%, nucleotide identity; 98. 6%-99. 5%, amino acid identity), all of them had a specific S387 different from other genotypes of Hantaan virus.

Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain SH04, Isolated from Chrysomya megacephala Collected from Pudong International Airport in China.

Wohlfahrtiimonas chitiniclastica bacilli that live in the larvae of a parasitic fly were recently isolated and are speculated to be the cause of fulminant sepsis. Here we report and analyze the complete genome sequence of Wohlfahrtiimonas chitiniclastica strain SH04. No complete genome sequence of a Wohlfahrtiimonas chitiniclastica isolate has been documented previously.

Complete genome sequence of an amur virus isolated from Apodemus peninsulae in Northeastern China.

Amur virus was recently identified as the causative agent of hemorrhagic fever with renal syndrome. Here we report the complete genome sequence of an Amur virus isolated from Apodemus peninsulae in Northeastern China. The sequence information provided here is critical for the molecular epidemiology and evolution of Amur virus in China.

Complete genome sequence of Seoul virus isolated from Rattus norvegicus in the Democratic People's Republic of Korea.

Seoul virus (SEOV) is responsible for 25% of cases of hemorrhagic fever with renal syndrome in Asia. Here we report the complete genome of strain DPRK08. The sequence information provided here is useful for understanding the molecular character of SEOV in the Democratic People's Republic of Korea (DPRK) and the circulation of SEOV in East Asia.

Real-time PCR for detecting circulating dengue virus in the Guangdong Province of China in 2006.

Dengue virus (DENV) causes a wide range of diseases in humans, from the acute febrile illness dengue fever (DF) to life-threatening dengue haemorrhagic fever/dengue shock syndrome. We developed four real-time quantitative PCR assays for each serotype of DENV based on computational analysis. These assays had high sensitivity and specificity without cross-reactivity for the four serotypes. To evaluate the performance of these assays in detecting and typing the virus in clinical samples, we analysed 64 serum samples from Guangdong during 2006. The results showed that 71 % of those samples were positive by the DEN-1 assay. The DENV assay results, in agreement with the serological tests and sequencing analysis, showed that the pathogen resulting in the DF explosion in Guangdong in 2006 belonged to DEN-1. Compared to the serological assays, the real-time PCR assays that we developed were much more sensitive in the 1-3 days after onset of the symptoms.

[Isolation and characterization of bacteriophages of Enterobacter sakazakii].

OBJECTIVE: To isolate bacteriophage of Enterobacter sakazaki from sewage using reference and isolated strains as indicators, and to observe the biological characteristics of the bacteriophage. METHODS: Bacteriophages were isolated from sewage with double layer agar. Specificity and host ranges of the bacteriophages were determined by reference bacterium from same genus and family. Phage particles were observed by electron microscope and its molecular character was analyzed by Random amplified polymorphic DNA. RESULTS: Five bacteriophages of E. sakazakii were isolated from sewage and showed relatively narrow host ranges, only E. sakazakii could be lysised. The phage SK2 isolated from ATCC 51329 could form plaques on 24 of all 27 E. sakazakii strains (89%). All five phage particles had the hexagonal heads and tails after observing with negatively stained method by electron microscope. Random amplified polymorphic DNA analysis showed the polymorphism of the five phages. CONCLUSION: E. sakazakii phages isolated from sewage were only sensitive to E. sakazakii, and had potential usage in typing, preventing, treating E. sakazakii and entironment protection.

[Generation of human recombinant antibody Fab fragment and its IgG to adeno-associated virus type II from phage display library].

BACKGROUND: To acquire the recombinant human monoclonal antibodies and IgG to adeno-associated virus type 2 (AAVs-2). METHODS: Construct and pan human Fab antibody library to AAVs-2 was established from normal volunteer donors by using phage display technology and secreted expression in E.Coli system. The positive Fab clones were selected and characterized through ELISA and immunofluorescent assay, and then the heavy and light chain were sequenced. The gene of light chain and heavy chain Fd fragment of recombinant mAb were inserted into baculovirus expression vector pAC-L-Fc and construct expression vectors of intact IgG, then transfected insert sf-9 cell secreted expression in Baculovirus/Insert system. Immunoprecipitation test was used to detect its recognizing region. RESULTS: One clone named AAVs-31 showed positive responses in ELISA and IFA, the Fab was composed of gamma chain and kappa chain IgG was positive in ELISA and IFA. The IgG failed to detect nonassembled or denatured capsid proteins, but recognized the AAVs-2 stock from immunoprecipitation test. CONCLUSION: The authors isolated a clone of Fab and IgG to adeno-associated virus type 2 by phage display technology, they perhaps recognize an epitope which is formed during capsid assembly.