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

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 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

Animals ; DNA, Fungal ; Phosphorylation ; RNA Polymerase II ; Sequence Homology, Nucleic Acid ; T-Box Domain Proteins ; genetics

OBJECTIVETo investigate a 272 base pair section of the 5'-non-coding region of genomic DNA from the peripheral blood monounuclear cells of healthy hepatitis virus C (HCV)-negative human subjects (not patients).

METHODSThis sequence section bears interest because (1) it harbors several potential methylation (Cp-rich) sites, and (2) it represents the largest part of its internal ribosomal entry site. A pre-PCR digestion protocol was established making consistent use of four restriction endonucleases selected for certain features: SmaI, XmaCI, MspI, and HpaII are inhibited if methylation(s) are present at certain cytosines within their cutting sequences.

RESULTSThe suspected HCV-specific sequence was found in the DNA of each subject tested. The pre-PCR digestion assay reveals individual differences in their pattern of methylation, which may be due to possible epigenetic phenomena.

CONCLUSIONSThe results provide formal proof that these HCV-specific sequences are contained in the genomic or extra chromosomal target DNA, and probably belong to a new class of endogenous sequences.

DNA Methylation ; Hepacivirus ; genetics ; Humans ; Restriction Mapping ; Sequence Homology, Nucleic Acid

Porcine sapoviruses (SaVs), which belong to the family Caliciviridae, have been considered potential zoonotic agents for human infection, and several cases have been reported in Asian countries. In this study, a total of 200 porcine fecal samples collected from Lulong county of China were tested. Among 200 samples, porcine sapoviruses were detected by RT-PCR in 17 samples (8.5%) showing their circulation in China. 14 out of 17 positive sapovirus strains were genetically related to the genogroup III (GIII) and were further divided into three different clusters or genotypes according to the phylogenetic analysis. In addition, the remaining three sapovirus strains belonged to GVII (one strain) and a potential novel genogroup (two strains) according to the phylogenetic analysis and the nucleotide identity and amino acid identity. These data suggested the genetic diversity of porcine sapoviruses in China.
Animals ; China ; Genetic Variation ; Genotype ; Phylogeny ; Sapovirus ; classification ; genetics ; Sequence Homology, Nucleic Acid ; Swine ; virology

OBJECTIVETo analyse the genetic relationship of local strains of dengue type 1 viruses isolated in different years and regions from Guangdong Province, and to explore the genetic links with strains of adjacent countries by comparing with the sequences of relevant strains in Genbank.

METHODSThe viral RNAs were extracted and used for one-step reverse transcriptase polymerase chain reaction (RT-PCR) to amplify the partial nucleotide fragments in E/NS1 gene junction which were then cloned into the plasmid pBluescript II SK for sequencing, the results were analysed by DNASTAR software.

RESULTSThe phylogenetic tree of the sequenced 14 strains of dengue type 1 viruses branches into two genotypic groups. The nucleotide sequences showed a maximal homologies of 99.2% with Indonesia strains, 100% with Philippines strains and 98.8% with Thailand strains.

CONCLUSIONSThe dengue type 1 viruses of Guangdong Province are closely related to the Philippines, Indonesia and Thailand strains, which may indicate the possibility of importation from those countries.

Base Sequence ; China ; Dengue Virus ; classification ; genetics ; isolation & purification ; Genes, Viral ; genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid

OBJECTIVEThis research focused on analyzing the differences of 5S rRNA gene spacer sequences on Swertia mussotii and its commonly used adulterants, including S. franchetiana, S. wolfangiana and S. chirayita.

METHODDNA was extracted from the collected Swertia samples. 5S rRNA intergenic spacers were amplified by PCR, sequenced and analyzed.

RESULT5S rRNA gene spacer sequences were different between S. mussotii and its other three adulterants. Sequence divergence among species ranged from 30.6% to 65.0%.

CONCLUSION5S rRNA spacers may be used as molecular authentication markers to differentiate S. mussotii and other commonly used Swertia adulterants. This result provides reliable and simple reference for the authentication of Swertia genus species.

Base Sequence ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 5S ; genetics ; Sequence Homology, Nucleic Acid ; Swertia ; classification ; genetics

OBJECTIVETo investigate the molecular genetic basis for a human leukocyte antigen (HLA) novel allele HLA-A*9206 in the Chinese population.

METHODSDNA was extracted from whole blood by PEL-FREEZ DNA extraction kit. The amplification of HLA-A exons 1-8 of the proband was preformed and the PCR products were sequenced using ABI sequencing kit. Both strands of exons 2, 3 and 4 of the amplified product were sequenced. The polymerase chain reaction-sequence specific primer (PCR-SSP) was performed to split the two alleles apart and confirm the mutations detected by sequencing.

RESULTSThe sequencing results showed that the HLA-A alleles of the proband were A*1101 and a novel allele. The sequence of the novel allele has been submitted to GenBank (EF062306). After Blast analysis, the novel allele shows one nucleotide different from the HLA-A*0206 in exon 3 at nucleotide position 530 (C to T). This results in an amino acid change from Ala to Val at codon 153.

CONCLUSIONThis allele is a novel allele and has been officially named A*9206 by the WHO Nomenclature Committee.

Alleles ; Asian Continental Ancestry Group ; Base Sequence ; HLA-A Antigens ; genetics ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid