The nucleotide sequence and N-, C-terminal amino acid sequences of alpha,beta-subunit of glutaryl 7-ACA acylase C130 from Pseudomonas sp. 130 were determined. The alignment of the acylase C130 with the other acylases shows that it has high homology with the acylases from Pseudomonas sp. GK16 and C427, but low homology with the others. There is large difference in the N-terminal of alpha-subunit, while the N-terminal of beta-subunit has significant conservation.
Amino Acid Sequence ; Base Sequence ; DNA, Bacterial ; analysis ; Genes, Bacterial ; Molecular Sequence Data ; Penicillin Amidase ; genetics ; Pseudomonas ; enzymology ; genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo study the EV71 Chinese strain SHZH98 and analyze its genetic evolution using 3c gene as index.

METHODSThe 3C gene cDNA of EV71 Chinese strain SHZH98 was amplified by PCR, the PCR product was sequenced.

RESULTSThe EV71 Chinese mainland strain SHZH98 3C segment was 549 bps in length. Comparison of nucleotide sequences from other enteroviruses which have been published, revealed a higher homology to strain MS, 78.7% at nucleotide level and 93.45% at deduced amino acid level. The homology to strain BrCr was 76.7% at nucleotide level and 89.1% at deduced amino acid level. Taiwan strains POLY,NCKU,TW2086,TW2272 shared a lower homology with Chinese mainland strain SHZH98, 74.0%, 73.8%, 71.9%, 69.8% at nucleotide level and 90.7%, 90.2%, 84.2%, 82.5% at deduced amino acid level. The genetic progress analysis revealed that EV71 Chinese mainland strain SHZH98 3C segment shares more homology with European and American strains than Taiwan strains.

CONCLUSIONThe non-structural protein of EV71 Chinese strains may have different evolutionary process from Taiwan strains.

Amino Acid Sequence ; Base Sequence ; Enterovirus ; genetics ; isolation & purification ; Genes, Viral ; Humans ; Molecular Sequence Data ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo investigate the genetic characteristics of coxsackievirus A10(CV-A10) strains isolated from hand, foot and mouth disease (HFMD) cases in Ningxia province.

METHODSBased on the HFMD laboratory network surveillance system, 2 470 patients clinical specimens including 450 faeces and 2 020 throat swaps were collected from various regions people's hospital in Ningxia Hui Autonomous Region during January, 2013 to December, 2014. All specimens were isolated using rhabdomyosarcoma cells. VP1 regional gene of isolated strains was amplified by RT-PCR using degenerate primers and sequenced. Sequences were compared with the database of GenBank by the Blast algorithm to identify the enterovirus genotypes. All the CV-A10 strains were performed the homology and phylogenetic evolution analysis.

RESULTS450 specimens identified as non-EV-A71, non-CV-A16 enterovirus were collected and 36 CV-A10 strains were isolated, 6 strains were isolated in 2013 and 30 strains were isolated in 2014. The homology of nucleotides and amino acids among 36 CV-A10 strains were 90.6%-100.0% , and 90.2%-100.0%, respectively. Compared 36 strains with genotype A, B, C, D representative strains, it has the highest homology with the genotype C, the nucleotide and amino acids homogeneity were 90.2%-98.9% and 95.7%-99.7%. The phylogenetic tree showed 36 strains and genotype C representative strains located in the same evolutionary branch.

CONCLUSIONCV-A10 was one of the most common pathogen of HFMD in Ningxia Hui Autonomous Region. All CV-A10 strains belonged to genotype C and contained wide homology range.

China ; Enterovirus ; genetics ; Genotype ; Hand, Foot and Mouth Disease ; virology ; Humans ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo characterize HA1 gene of influenza B virus circulated in 1990 through 2000 in China.

METHODSViral RNA was extracted and transcribed into cDNA by reverse transcriptase and amplified by PCR. The product of PCR was purified and sequenced by ABI377. The sequence data were analyzed with epidemic records.

RESULTS1. Two major lineages of influenza B virus always circulated during the period of 1990-2000 in China; the Yamagata lineage was the main lineage, but in 1994 and 1997 the Victoria lineage was more active. 2. During 1992-2000 the Yamagata lineage evolved into two minor groups whose distance in HAI amino acid sequences was about 6%. 3. Large and non-reverse mutators led the development of influenza B epidemics in 1990-2000 in China. 4. Except for a few strains, there was little difference among the influenza B viruses of the same major lineages circulated in the same year in China.

CONCLUSIONSTwo major lineages of influenza B virus always circulated during the period from 1990-2000 in China,and the Yamagata lineage diverged into two minor groups in recent years. Exchanges of the lineages and the appearance of large non-reverse mutators possibly had important epidemic significance.

China ; epidemiology ; Genes, Viral ; genetics ; Influenza B virus ; classification ; genetics ; RNA, Viral ; genetics ; Sequence Analysis ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo identify a novel human leukocyte antigen (HLA) allele.

METHODSHLA typing was carried out with PCR-SSOP. Molecular cloning and DNA sequencing were used to identify the sequence of a potential novel allele and the difference between this new allele and other known alleles was analyzed.

RESULTSHLA genotyping of one sample gave different results. The sequencing results showed that the HLA B alleles of the proband were B*151101 and a novel allele. The nucleotide sequence of the novel allele was different from all other known B alleles. It had one nucleotide change from the closest matching allele B*460101 at nucleotide 527 (A to T) in exon 3, resulting in an amino acid change from E (GAG) to V (GTG) at codon 176.

CONCLUSIONA novel HLA B allele was identified and officially designated as HLA B*4609 by WHO Nomenclature Committee for Factors of the HLA System in November, 2006.

Alleles ; Amino Acid Substitution ; Base Sequence ; Cloning, Molecular ; HLA Antigens ; genetics ; immunology ; HLA-B Antigens ; genetics ; immunology ; Humans ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Sequence Homology, Nucleic Acid

Thirteen field isolates of infectious bronchitis virus (IBV) were isolated from broiler flocks in Thailand between January and June 2008. The 878-bp of the S1 gene covering a hypervariable region was amplified and sequenced. Phylogenetic analysis based on that region revealed that these viruses were separated into two groups (I and II). IBV isolates in group I were not related to other IBV strains published in the GenBank database. Group 1 nucleotide sequence identities were less than 85% and amino acid sequence identities less than 84% in common with IBVs published in the GenBank database. This group likely represents the strains indigenous to Thailand. The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). This finding indicated that the recent Thai IBVs evolved separately and at least two groups of viruses are circulating in Thailand.
Animals ; Chickens ; Coronavirus Infections/*veterinary/virology ; Infectious bronchitis virus/*genetics/*isolation & purification ; Molecular Sequence Data ; Phylogeny ; Poultry Diseases/*virology ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Thailand ; Viral Proteins/chemistry

OBJECTIVETo understand the molecular epidemiologic characteristics of hantavirus Shandong isolate JNL virus strain.

METHODSThe complete M and S gene of the JNL virus isolated from Shandong Province was amplified by RT- PCR, and the purified PCR product was cloned into T vector for sequencing.

RESULTSThe results revealed that the JNL M segment was 3615 bp in length, encoding 1135 amino acids, and the S segment was 1698 bp encoding 429 amino acids, JNL belongs to HTN virus. The comparison of homology with HTN and SEO types showed that the difference of M and S complete sequences between JNL and all other HTN virus strains reached 20.0%-20.6%, and 15.5%-16.0%, respectively. Phylogenetic tree also showed that the position of JNL is located at a different clade.

CONCLUSIONSHTN virus Shandong local isolate JNL strain is a new specific HTN subtype virus.

DNA, Viral ; analysis ; Hantaan virus ; classification ; genetics ; isolation & purification ; Hemorrhagic Fever with Renal Syndrome ; virology ; Humans ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo determine the distribution and sequence conservation of pagC gene in Salmonella paratyphi A isolates, and the immunogenicity and immunoprotection of its recombinant expression products (rPagC).

METHODSThe distribution of pagC gene in Salmonella paratyphi A isolates and its sequence conservation were examined by PCR and sequencing. A prokaryotic expression system of pagC gene was constructed and the expressed rPagC was extracted by Ni-NTA affinity chromatography. SDS-PAGE and Bio-Rad Gel Image Analyzer were applied to examine the expression and yield of rPagC. The antigenicity and immunoreactivity of rPagC were detected by immunodiffusion test, ELISA and Western Blot assay. The immunoprotective effect of rPagC against infection of Salmonella paratyphi A in mice was determined, while the agglutinative effect of sera from rPagC-immunized mice was measured by micro-Widal's test.

RESULTSAll the Salmonella paratyphi A isolates tested had the pagC gene, the similarity of nucleotide and amino acid sequences was 99.1 %-100 % and 98.4 %-100 %, respectively. The constructed prokaryotic expression system expressed rPagC with high efficiency. The rPagC immunized rabbit produced a high level antibody and it also combined with antiserum against whole cell of S. paratyphi A to generate a positive Western hybridization signal. ELISA results indicated that 97.1 % (66/68) paratyphoid patients infected with Salmonella paratyphi A were positive for rPagC antibody in their serum specimens. When mice were immunized with 100 μg or 200 μg rPagC, the immunoprotective rates were 73.3 % (11/15) or 86.7 % (13/15), respectively. The sera from rPagC-immunized mice offered 1:10-1:40 agglutination titers with the H antigens of Salmonella paratyphi A and Salmonella typhi.

CONCLUSIONPagC gene has an extensive distribution in Salmonella paratyphi A isolates. rPagC can be used as the candidate antigen in genetic engineering vaccine due to its fine immunogenicity and powerful immunoprotective effect.

Agglutination Tests ; Animals ; Antibodies, Bacterial ; blood ; Antigens, Bacterial ; genetics ; immunology ; Bacterial Proteins ; genetics ; immunology ; Bacterial Vaccines ; Membrane Proteins ; genetics ; immunology ; Mice ; Rabbits ; Recombinant Proteins ; genetics ; immunology ; Salmonella paratyphi A ; genetics ; immunology ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo study the gene characterization of enterovirus 71 (EV71) virus strains isolated from clinical specimens of children with hand-foot-and-mouth disease (HFMD) in Zhejiang province.

METHODSVirus were isolated from clinical samples including stool, throat swab and vesicle from patients with HFMD. The EV71 isolates were identified by microneutralization assay and reverse transcriptase PCR (RT-PCR) with specific primer pair for VP1 genes of EV71. Complete VP1 gene sequences (891 nucleotides) for recent 6 EV71 isolates were determined and compared with that of A, B, C genotype reference EV71 strains and 11 EV71 China isolates available from GeneBank by homogeneity and phylogenetic tree analyses.

RESULTS9 strains of EV were isolated from 14 clinical specimens. Data from microneutralization and RT-PCR results indicated that all the strains belong to EV71. The nucleotide and amino acid homogeneity of these 6 Zhejiang strains with the representative isolates of A and B genotypes were 82.9%-85.5% and 94.9%-98.0% respectively; with the representative isolates of C were 89.2%-94.1% and 97.0%-99.0% respectively. There were 91.0%-92.2%, 90.2%-90.3%, 89.2%-89.5%, 96.7%-96.9% nucleotide, homology with representative strains of C1, C2, C3,C4 subgenotypes of EV71. The nucleotide homogeneity of these 6 EV71 isolated strains with 9 previously isolated Chinese strains appeared to be 93.8%-97.1%. These 6 EV71 isolated strains were within genotype C subgenogroup C4 in the phylogenetic tree.

CONCLUSIONThe recently identified EV71 isolates in Zhejiang province belonged to subgenogroup C4.

Child ; China ; Enterovirus ; classification ; genetics ; isolation & purification ; Genes, Viral ; Genotype ; Hand, Foot and Mouth Disease ; virology ; Humans ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid

OBJECTIVETo determine the molecular characterization of full-length genome of Japanese encephalitis virus (JEV) genotype V.

METHODSThe full-length nucleotide sequences of JEV strains isolated from different locations and sources were used in sequence and phylogenetic analysis.

RESULTSThe full-length genome of genotypes V JEV, XZ0934, and Muar strain were composed of 10 983 and 10 988 nucleotides respectively and shared a lower level of identity with JEV genotypes I-IV, ranging from 78.4% (G I, KV1899) to 79.7% (G III, JaGAr01), for the nucleotide sequences, and from 90.0% (G I, KV1899) to 91.8% (G III, JaGAr01) for the amino acid sequences. The open reading frame (ORF) of JEV genotype V spanned nucleotides 96 to 10 397 and encoded 3 433 amino acids. Interestingly, a comparison with JEV genotype I-IV revealed that 3 nucleotides (encoded with a serine residue) were inserted in the NS4A gene of JEV genotype V, and the insertion of nucleotides was also found in downstream of the ORF stop codon in 3'-untranslated region. Moreover, numerous amino acid mutations were observed in 3 functional domains of the E gene of JEV genotype V.

CONCLUSIONThe molecular characterization of JEV genotype V is significantly different from that of the known genotypes I-IV. The mutations located in the coding region and the non-coding region may be molecular markers of JEV genotype V and warrant further studies to determine their effects on biology and immunogenicity of genotype V strains.

Amino Acid Sequence ; Animals ; Base Sequence ; Culex ; virology ; Encephalitis Virus, Japanese ; genetics ; Genome, Viral ; Genotype ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Tibet ; Young Adult