Chikungunya virus ; genetics ; isolation & purification ; China ; Genome, Viral ; RNA, Viral ; genetics ; Sequence Analysis, RNA

Epstein-Barr virus(EBV) has been implicated in the pathogenesis of B-lymphoproliferative disorders, T-cell lymphomas and Hodgkin's disease. In this report, we performed an in situ hybridization study on EBV genome in 10 cases of nasal non-Hodgkin's lymphoma(NHL), 20 cases of Waldeyer's ring(WR) NHL, and 20 cases of nodal NHLs to document EBV association with lymphomas in Koreans. For immunophenotyping, monoclonal antibodies for CD 20, MB 2, CD 45Ro & CD 43 were used. For in situ hybridization study, EBV DNA probe for Bam HI 'V' fragment and EBV RNA probe for EBER and BHLF were used. Twenty two cases(44%) of malignant lymphomas were positive for EBV genome. Generally, T-cell lymphomas showed a higher positive rate(61%) than B-cell lymphomas(24%). Among T-cell lymphomas, nasal lymphomas showed a higher positive rate(80%) than WR(50%) or nodal lymphomas(50%). Of 22 EBV genome positive cases, 10 cases were positive for EBER, 10 cases for BHLF, and 2 cases for both EBER and BHLF. The histologic types by Working Formulation(WF) were not correlated with EBV genome positive rate, whereas lymphomas showing the histologic spectrum of polymorphic reticulosis(PR) showed a higher positive rate(65%) than lymphomas without PR-like features(40%). These results indicate that nasal T-cell lymphomas with the histologic spectrum of PR are strongly associated with EBV and that the anatomic site may be an important factor in this association.
DNA, Viral/analysis ; Genome, Viral ; Herpesvirus 4, Human/*genetics ; Human ; *In Situ Hybridization ; Lymphoma, Non-Hodgkin/*virology ; RNA, Viral/analysis

China ; DNA, Viral ; blood ; Hepacivirus ; classification ; Hepatitis C ; diagnosis ; etiology ; therapy ; Humans ; RNA, Viral ; analysis

OBJECTIVETo learn the prevalence of infection of human and animals severe fever with thrombocytopenia syndrome bunyavirus (SFTSV) in Yantai, Shandong province, and to analyze the pathogenic features of SFTSV as well as its relationship between human and animal hosts.

METHODSFrom April to November in 2011, 3 576 serum samples were collected from domesticated animals, including sheep, cattle, pigs, dogs, chickens, in Laizhou and Penglai areas where fever with thrombocytopenia syndrome frequently occurred among local residents. Total SFTSV antibodies and virus-specific nucleic acids of the serum were tested by ELISA and Real time RT-PCR, respectively. SFTSV infection on each animal was observed in different months. 2 590 human serum samples were also collected in Laizhou and Penglai areas, with IgG antibodies tested by ELISA. Virus was isolated with Vero cells from the serum which SFTSV viral nucleic acids were positive. S fragments were amplified by RT-PCR and sequenced, with homology analysis conducted on these sequences.

RESULTSThe overall positive rate of serum samples from animals on the total SFTSV antibodies was 40.24% (1 439/3 576) while the positive rate for specific nucleic acids was 4.56% (163/3 576). The positive rates for SFTSV antibodies were 62.78%, 52.97%, 45.56%, 28.73%, 1.45% and the positive rates for specific nucleic acids were 5.72%, 4.63%, 3.02%, 5.25% and 3.73%, in sheep, cattle, chickens, dogs, pigs, respectively. The antigens/antibodies for SFTSV in animals changed seasonally. The overall positive rate for SFTSV IgG antibody from 2 590 human samples was 5.41%. Thirteen virus strains were isolated from these serum samples (10 strains from human and 3 strains from animals). The nucleotide homology of 13S fragments' sequences ranged from 95.23% to 100.00% and the nucleotide homology with the isolates from other provinces were between 94.72% and 99.13%. The homology was considered to be high.

CONCLUSIONHigh prevalence of SFTSV infections occurred both in human and domestic animals in Yantai city. The nucleotide sequences of SFTSV were highly homologous among human and domestic animals. The findings suggested that domesticated animals might serve as SFTSV proliferation and the hosts for transmission thus should be attached great importance.

Animals ; Antibodies, Viral ; blood ; Bunyaviridae Infections ; epidemiology ; China ; epidemiology ; Humans ; Prevalence ; RNA, Viral ; blood ; Sequence Analysis, RNA

This paper proposed a new kind of visualized method of genome. Using cellular automation theory, the visual method transfers one-dimensional RNA sequence into two-demension visual image. Applying this method to SARS RNA sequence analysis, the characteristic of SARS-CoV differing from Non-SARS is discovered. This paper extracts characteristic genome fragment, visualize them, and study them with some pattern recognition method such as PCA and SVM. The result shows that the characteristic of SARS-CoV is classifiable. Some combined methods can use the characteristic more sufficient as an un-routine method.
Genome, Viral ; Image Processing, Computer-Assisted ; methods ; RNA, Viral ; genetics ; SARS Virus ; genetics ; Sequence Analysis, RNA ; methods

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 compare the molecular characteristics of 3 Crimean-Congo hemorrhagic fever viruses(CCHFV) isolated in Xinjiang province.

METHODSYL05035, YT05099 and LT05146 were isolated in 2005 from Hyalomma ticks and viral RNA was extracted from suckling mouse brains infected with these three strains respectively. The polymerase chain reaction(PCR) products of S segments from the 3 strains of CCHFV were directly sequenced.

RESULTSThe full-length'S RNA from the 3 strains of CCHFV all comprised 1673 nucleotides with ORF of them including 1449 nucleotides and encoding a protein which comprised 482 amino acids in a viral complementary sense. The sequences indicated that the three strains of CCHFV isolated from ticks in Xinjiang province were highly homologenic. Data from the phylogenetic analysis showed that the obtained sequences were identical. The homology between 3 strains of CCHFV was 99.5%. Their homologies compared with that of the other strains isolated from other region of Xinjiang were also high at nucleotide levels (92.7%-99.8%). The three strains which were clustered together with 7001 strain and 79121 strain (isolated from patient and rat in Xinjiang respectively) was only different by 2%-3%. The genetic difference from the prototype CCHFV Nigerian strain IBAR10200 was 13%. In comparison, the Nigerian CCHFV tick isolate was more divergent when compared with the reference China strains 66019 and with the three variants mentioned above.

CONCLUSIONThe CCHFV isolated from China comprised a group of genetically high conserved strains.

Animals ; Brain ; virology ; China ; Genes, Viral ; Hemorrhagic Fever Virus, Crimean-Congo ; genetics ; isolation & purification ; Mice ; RNA, Viral ; analysis

OBJECTIVETo investigate the viral contamination of invasive medical instruments in dentistry and to provide health administrative institutions with surveillance data.

METHODSSterilized samples were randomly collected from the department of dentistry to detect HBV-DNA, HCV-RNA, HIV-RNA and HBsAg.

RESULTSOf the invasive medical instruments that were sterilized with 2% glutaraldehyde, one of the samples was positive for HBV-DNA, and another sample was positive for HBsAg.

CONCLUSIONThough massive virus contamination of invasive medical instruments in dentistry has been reduced to a low level, the occurrence of contamination still remains.

DNA, Viral ; analysis ; Dental Instruments ; virology ; Equipment Contamination ; HIV ; isolation & purification ; Hepacivirus ; isolation & purification ; Hepatitis B Surface Antigens ; analysis ; Hepatitis B virus ; isolation & purification ; Humans ; RNA, Viral ; analysis

BACKGROUNDAs with many studies carried out in European countries, a quality assurance program has been established by the National Center for Clinical Laboratories in China (NCCL). The results showed that the external quality assessment significantly improves laboratory performance for quantitative evaluation of hepatitis C virus (HCV) RNA.

METHODSSerum panels were delivered twice annually to the clinical laboratories which performed HCV RNA detection in China. Each panel made up of 5 coded samples. All laboratories were requested to carry out the detection within the required time period and report on testing results which contained qualitative and/or quantitative test findings, reagents used and relevant information about apparatus. All the positive samples were calibrated against the first International Standard for HCV RNA in a collaborative study and the range of comparison target value (TG) designated as +/- 0.5 log.

RESULTSThe numbers of laboratories reporting on qualitative testing results for the first and second time external quality assessment were 168 and 167 in the year of 2003 and increased to 209 and 233 in 2007; the numbers of laboratories reporting on quantitative testing results were 134 and 147 in 2003 and rose to 340 and 339 in 2007. Deviation between the mean value for quantitative results at home in 2003 and the target value was above 0.5 log, which was comparatively high. By 2007, the target value was close to the national average except for the low concentrated specimens (10(3) IU/ml). The percentage of results within the range of GM +/- 0.5 log(10) varied from 8.2% to 93.5%. Some laboratories had some difficulties in the exact quantification of the lowest (3.00 log IU/ml) as well as of the highest viral levels (6.37 log IU/ml) values, very near to the limits of the dynamic range of the assays.

CONCLUSIONSThe comparison of these results with the previous study confirms that a regular participation in external quality assessment (EQA) assures the achievement of a high proficiency level in the diagnosis of HCV infection. During the 5-year external quality assessment, sensitivity and accuracy of detection in most of the clinical laboratories have been evidently improved and the quality of kits has also been substantially improved.

Hepacivirus ; genetics ; Humans ; Laboratories ; standards ; Polymerase Chain Reaction ; Quality Control ; RNA, Viral ; analysis ; Reagent Kits, Diagnostic

OBJECTIVEIn order to fully understand hepatitis c virus (HCV) genotype 3b, 1a, 2b and 6a infection in China, We built HCV 5'-noncoding region (5'-NCR) of different genotypes and subtypes.

METHODSThe classification HCV into variable genotypes (subtypes) was carried on by programs A, B and C A. Using a combination of three restriction endonuclease BHH' (BsrB I, Hae II, Hinf I) digestions at the same time. The distinct genotypes were classified into 5 groups: genotype 1 (1a, 1b), 6a, 2 (2a, 2b), genotype 3 (3a, 3b), genotype4 (4a). B. With regard to genotype 1, we could distinguish subtype 1a from 1b using BstU I digestion. C. Using restriction endonuclease Hae III, genotype 2a, 2b, 3b, 4a, 6a are differentiated respectively.

RESULTS(1) HCV genotype 1a, 1b, 2a, 2b, 3a, 3b, 4a, 6a are fully discriminated by comparison with the genotypes regular samples. (2) Of the 93 patients, HCV genotype distribution in China was 66.67% for 1b, 18.28% for 2a, 3.23% for 1b/2b, 3b, 2b respectively. 2.15% for 2a/2b, 1b/2a respectively. 1.08% for 1a.

CONCLUSIONThis research indicated that adoption of HCV 5'-NCR A B C restriction endonuclease digestions techniques, might be sensitive and efficient to detect HCV and discriminate HCV genotype (subtypes) 1a to 6a.

5' Untranslated Regions ; chemistry ; DNA Restriction Enzymes ; Genotype ; Hepacivirus ; classification ; genetics ; RNA, Viral ; analysis