Objective: To study the molecular epidemiological characteristics and genotypes of hantavirus carried by rodents in Shenzhen. Methods: Rodents were captured, and their lung samples were collected and grinded for RNA extraction. The hantavirus positive samples were classified by real-time fluorescence PCR. Rat lung nucleic acid samples were selected to amplify the nucleotide sequences of partial M fragments (G2 segment) and S fragments by reverse transcription-nested polymerase chain reaction (RT-nested PCR). The PCR products were then sequenced and homology and phylogenetic tree analyses were conducted. Results: A total of 200 rodents were captured, including 189 Rattus norvegicus, 9 Rattus flavipectus and 2 Mus musculus. The positive rate of hantavirus was 21.0% (42/200), all of the isolates were seoul virus (SEOV) strains. The positive rate of hantavirus in Bao'an district was highest (45.7%), and the difference in detection rate among districts were significant (χ²=25.60,P<0.05). A total of 25 G2 segment sequences and S fragment sequences of SEOV were obtained by virus gene sequencing, and their nucleotide homology was 95.3%-100.0% and 97.6%-100.0%, respectively. Compared with other reference sequences of S2 subtype, the nucleotide homology between the sample sequence and the reference sequence from Guangzhou was high. Analysis on nucleotide homology and phylogenetic tree showed that hantavirus carried by the rodents captured in Shenzhen belonged to SEOV S2 subtype. Analysis on amino acid variation sites revealed that there was a variation in the nucleocapsid protein encoded by S gene from Alanine to Threonine at the 973 position of BA-111. Conclusion: Hantavirus carried by rodents in Shenzhen belongs to S2 subtype of Seoul virus, which have little variation compared with the hantavirus strains obtained in other years in Shenzhen and surrounding provinces.
Mice ; Rats ; Animals ; Orthohantavirus/genetics* ; Rodentia ; Phylogeny ; Hantavirus Infections/veterinary* ; Communicable Diseases ; Nucleotides ; Real-Time Polymerase Chain Reaction

Most attempts at rational development of new analgesics have failed, in part because chronic pain involves multiple processes that remain poorly understood. To improve translational success, one strategy is to select novel targets for which there is proof of clinical relevance, either genetically through heritable traits, or pharmacologically. Such an approach by definition yields targets with high clinical validity. The biology of these targets can be elucidated in animal models before returning to the patients with a refined therapeutic. For optimal treatment, having biomarkers of drug action available is also a plus. Here we describe a case study in rational drug design: the use of controlled inhibition of peripheral tetrahydrobiopterin (BH4) synthesis to reduce abnormal chronic pain states without altering nociceptive-protective pain. Initially identified in a population of patients with low back pain, the association between BH4 production and chronic pain has been confirmed in more than 12 independent cohorts, through a common haplotype (present in 25% of Caucasians) of the rate-limiting enzyme for BH4 synthesis, GTP cyclohydrolase 1 (GCH1). Genetic tools in mice have demonstrated that both injured sensory neurons and activated macrophages engage increased BH4 synthesis to cause chronic pain. GCH1 is an obligate enzyme for de novo BH4 production. Therefore, inhibiting GCH1 activity eliminates all BH4 production, affecting the synthesis of multiple neurotransmitters and signaling molecules and interfering with physiological function. In contrast, targeting the last enzyme of the BH4 synthesis pathway, sepiapterin reductase (SPR), allows reduction of pathological BH4 production without completely blocking physiological BH4 synthesis. Systemic SPR inhibition in mice has not revealed any safety concerns to date, and available genetic and pharmacologic data suggest similar responses in humans. Finally, because it is present in vivo only when SPR is inhibited, sepiapterin serves as a reliable biomarker of target engagement, allowing potential quantification of drug efficacy. The emerging development of therapeutics that target BH4 synthesis to treat chronic pain illustrates the power of combining human and mouse genetics: human genetic studies for clinical selection of relevant targets, coupled with causality studies in mice, allowing the rational engineering of new analgesics.
Analgesics ; therapeutic use ; Animals ; Biopterin ; analogs & derivatives ; metabolism ; Chronic Pain ; drug therapy ; genetics ; Disease Models, Animal ; Drug Discovery ; GTP Cyclohydrolase ; genetics ; metabolism ; Humans ; Rodentia ; Signal Transduction ; drug effects ; genetics

To provide accurate information on geographic distribution of crude drug Sailonggu in the plateau, we identified zokor species (Eospalax spp.) in Qinghai-Tibet Plateau using molecular methods. Based on the mitochondrial cytochrome B (cytb) gene sequences, we then extracted haplotypes from these sequences and reconstructed phylogenetic trees for the haplotypes using both maximum likelihood (ML) and Bayesian inference (BI) methods. Based on the trees, the species of each sample were determined. Five hundred and three samples from 35 populations were sequenced and their whole cytb sequences (1140 bp) were obtained. From these sequences 150 haplotypes were detected, in which, 126 were Eospalax baileyi, 20 were E. cansus, and 4 were E. smithi of the 35 populations, 28 were E. baileyi type, 5 were E. cansus type, and the remaining 2 were mixed of E. baileyi + E. cansus (DT2) and E. baileyi + E. smithi (ZN3). The results showed that, the regions around the Qinghai lake and near the upper stream of Yellow River started at Guide could be viewed as the producing area of authentic Sailonggu, and also, the cytb gene is a powerful molecular marker to determine the species of zokors as well as for the authentication of geographic distribution of Sailonggu.
Animals ; Bone and Bones ; metabolism ; Haplotypes ; Medicine, Tibetan Traditional ; Phylogeny ; Rodentia ; classification ; genetics

OBJECTIVE: To investigate the infection in spotted fever group Rickettsiae (SFGR) in wild rodents from Heilongjiang, China. METHODS: Polymerase chain reaction (PCR) was used to detect the OmpA gene of SFGR in rodents collected in Heilongjiang. The PCR products amplified from rodent specimens were sequenced and compared with the corresponding part of the sequences deposited in the GenBank. Phylogenetic trees were constructed with Mega 5.0 software. RESULTS: A total of 514 rodents were collected from Heilongjiang during 2009-2011 and 11 species were included. The infection rate of SFGR in the rodents was 9.3% (95% CI: 7.1%-12.2%). Statistical analysis showed a significant difference in different areas of Heilongjiang (P=0.023). The highest prevalence was observed in Mudanjing area (12.42%). There were significant differences in different species of rodents (P=0.002). The infection rate of SFGR determined in Clethrionomys rufocanus was the highest (22.1%). Sequence analysis revealed SFGR belonged to R.heilongjiangensis and a new unknown rickettsia genotype. CONCLUSION R.heilongjiangensis has been presented in rodents in Heilongjiang, and a new SFGR genotype different from other rickettsiae genotypes may exist in this area.
Animals ; China ; DNA, Bacterial ; genetics ; isolation & purification ; Forests ; Phylogeny ; Polymerase Chain Reaction ; Rats ; Rickettsia ; classification ; genetics ; isolation & purification ; Rickettsia Infections ; microbiology ; veterinary ; Rodentia ; microbiology ; Sequence Analysis

Animals ; Borrelia burgdorferi ; genetics ; China ; DNA, Bacterial ; genetics ; isolation & purification ; Rodentia ; microbiology ; Sequence Analysis, DNA

OBJECTIVETo analyze the genetic evolution and bacterial type changes of Yersinia enterocolitica in the Ningxia area between year 1984 and 2011.

METHODSA total of 296 strains of Yersinia enterocolitica was collected from diarrhea patients, pig, rodents, sheep and dogs between year 1984 and 2011. The serotype, biotype, ail, ystA, ystB, yadA, virF and other toxic genes were detected. The PFGE subtypes of serotype O:3 and O:9 strains and the cluster features were analyzed.

RESULTSOut of 296 Yersinia enterocolitica strains, pig was the main host, accounting for 65.20% (193/296), followed by rodents, accounting for 32.43% (96/296). Serotype and biotype had their own respective dominant types in different periods. During 1984 and 1985, 2 strains of serotype O:3 and 3 strains of serotype O:9 were isolated, all belonged to biotype 3. Because of lack of strains, there were no obvious dominant types found. Between 1997 and 1999, 177 strains of serotype O:9 Yersinia enterocolitica were isolated as the dominant strain; and there were 178 strains of biotype 2 Yersinia enterocolitica were found. During 2007 and 2011, 54 strains of serotype O:3 Yersinia enterocolitica were isolated as dominant strain; followed by 26 strains of serotype O:5. There were separately 44 and 59 strains of biotype 1A and biotype 3. The PCR test divided the 248 strains into 4 types, including pathogenic strains as type I (ail(+), ystA(+), ystB(-), yadA(+), virF(+)). The PFGE divided the serotype O:3 into 12 types, in which K6GN11C30021 and K6GN11C30012 were the dominant types, accounting for 63.64% (42/66). The serotype O:9 were divided into 14 types, in which K6GN11C90010, K6GN11C90008, K6GN11C30018 and K6GN11C90003 were the dominant types, accounting for 89.01% (162/182).

CONCLUSIONThe different serotypes of isolated strains in Ningxia district showed different dominant bacteria in different periods; while the biotypes also changed with serotypes. The Yersinia enterocolitica isolated from different years showed great variation.

Animals ; DNA, Bacterial ; genetics ; Dogs ; Electrophoresis, Gel, Pulsed-Field ; Genes, Bacterial ; Genetic Variation ; Humans ; Rodentia ; Sheep ; Swine ; Yersinia Infections ; microbiology ; Yersinia enterocolitica ; classification ; genetics ; isolation & purification

In order to analyze the molecular epidemiology of Hantavirus (HV) in Zhejiang Province, the complete M and S genome sequences of 12 HV strains from different hosts and locations in Zhejiang Province of China during the period of 1981-2007 were analyzed on genetic evolution by DNAstar and MEGA 4.0 software in this research. Phylogenetic analyses revealed that HTN and SEO strains were co-circulating in Zhejiang Province, and the difference in sequence similarity and the phylogeny was closely related to the isolated regions, but had no distinct relationship with the isolate year and the host, indicating a relationship between epidemiology of HFRS and the distribution region, especially in HTNV. The isolates in the same region could be assigned in same or near phylogenetic clade sharing high sequence similarity. Interestingly, the Gou3 strain and ZJ5 strain isolated from Jiande region in Zhejiang Province formed a distinct phylogenetic lineage in SEOV clade, and different from the other SEOV variants outside China. We believed that the special SEOV variants were distributed in Jiande region.
Animals ; China ; Disease Reservoirs ; virology ; Evolution, Molecular ; Hantavirus ; classification ; genetics ; isolation & purification ; Hantavirus Infections ; virology ; Humans ; Molecular Sequence Data ; Phylogeny ; Rodentia ; virology ; Viral Proteins ; genetics

Prion proteins (PrPs) are infectious pathogens that cause a group of invariably fatal, neurodegenerative diseases, including Creutzfeldt-Jakob disease, by means of an entirely novel mechanism. They are produced by various species, including reptile, rodent, ruminant and mammals, during normal metabolic processes, but they can be slowly changed into pathogenic isoforms upon contact with other infectious PrP isoforms. This transmission can occur across species barriers. In the present study, phylogram for each PrP sequence was generated by PAUP* 4.0 program using Neighbor-Joining method with 1,000 times bootstrapping process for the phylogenetic analysis. The molecular dynamics (MD) simulations were performed by the SANDER module in the AMBER 7 package using Amber 99 force field. All the simulation process was conducted in the IBM p690 Supercomputing System in Korea Institute of Science and Technology Information. To reduce the calculation time, we used the Generalized Born (GB) model. We compared the sequences and structural characteristics of normal and pathogenic (E200K) human PrPs with those of other reptile, rodent, ruminant and mammalian PrPs. Phylogenetic analysis revealed that, although the turtle PrP sequence is the most distinct of the PrPs analyzed, it nonetheless retains five conserved secondary structural elements that are similar to those found in the mammalian PrPs, suggesting that these elements have important functions in vivo. The RMS deviation between the normal and E200K human PrPs was larger than that between the normal human and bovine PrPs, and all of the beta-sheet structures in human E200K PrP were very stable during MD simulations.
Animals ; Cattle ; *Computational Biology ; Humans ; Phylogeny ; Prions/*chemistry/classification/*genetics/isolation & purification ; Reptiles/metabolism ; Rodentia/metabolism ; Ruminants/metabolism ; Sequence Analysis, Protein ; Species Specificity

BACKGROUNDChina is the most severe endemic area of hemorrhagic fever with renal syndrome (HFRS) in the world with 30,000-50,000 cases reported annually, which accounts for more than 90% of total number of cases worldwide. The incidence rate of the syndrome in Shandong Province is one of the highest in China, which has ever reached 50 per 100,000 persons per year. However, the molecular characteristics of hantaviruses (HV) epidemic in Shandong Province remain unclear. Therefore it is useful to clarify nucleotide sequence and phylogenetic characteristics of HV isolated in Shandong Province in order to provide better advices to control and prevent HFRS.

METHODSRNAs were extracted from sera of clinically diagnosed patients and positive rodent lungs that were detected by indirect immunofluorescent assay (IFA). Partial M segments of HV were amplified from the RNAs with reverse transcription nested polymerase chain reactions (nested PCR) using hantavirus genotype specific primers. The nested PCR products were sequenced and compared with those from previously epidemic isolates in Shandong and with other representative HV sequences from GenBank. Phylogenetic tree analyses were performed based on the sequences of the M genes.

RESULTSThirty-four HV isolates in Shandong showed 67.1%-100% nucleotide identities. The nucleotide homologies among 6 Hantaan viruses (HTNV) isolates in Shandong were 78.1%-98.7%, while the homologies among 28 Seoul virus (SEOV) isolates in Shandong were 93.7%-100%. There were at least 3 subtypes HTNV (H2, H5, H9) and 2 subtypes SEOV (S2, S3) in Shandong Province.

CONCLUSIONSIn Shandong Province, the homologies of HTNV were lower and there were no predominant subtypes, while the homologies of SEOV were higher and S3 was the predominant subtype. The homologies of SEOV from rodents were higher than those from patients. The distribution of subtypes in Shandong was similar to that of the adjoining provinces. Phylogenetic analyses of the sequences showed geographic clustering of HV in Shandong.

Animals ; Antigens, Viral ; analysis ; Base Sequence ; Genetic Variation ; Hantavirus ; classification ; genetics ; Humans ; Lung ; virology ; Phylogeny ; RNA, Viral ; analysis ; Rodentia ; virology

OBJECTIVETo investigate the prevalence of Anaplasma phagocytophilum in rodents from forest areas in northeastern China.

METHODSPCR amplification, followed by sequence analysis was carried out. The sequences of 16S rRNA and gltA gene fragment amplified from rodent specimens were compared with corresponding part of the sequences deposited in GenBank.

RESULTSA total number of 276 rodents were tested, including 102 in Jilin province, 61 in Helongjiang province and 113 in Inner Mongolia autonomous region. The positive rates were 8.82%, 1.64% and 0.00%, respectively. The infection rate in rodents infected by ticks was 11.30 times higher than that in rodents without ticks (P = 0.002). The S. A. phagocytophilum 16S rRNA sequences from rodents in Jilin and Heilongjiang were identical and differed in 3-5 bases compared with the corresponding parts of A. phagocytophilum from America, Sweden and Japan. Compared with the sequences registered in GenBank, the nucleotide sequence of gltA varied from 87%-97% and its deduced amino acid sequence changed from 84%-99%.

CONCLUSIONA. phagocytophilum infection was presented in rodents from Jilin and Heilongjiang province.

Amino Acid Sequence ; Anaplasma phagocytophilum ; genetics ; isolation & purification ; Animals ; Bacterial Proteins ; analysis ; Base Sequence ; China ; Ehrlichiosis ; veterinary ; RNA, Ribosomal, 16S ; analysis ; Rodentia ; microbiology ; Ticks ; Trees