Virus isolate G6 was obtained from Hibiscus rosa-sinensis showing yellow and leaf curl symptoms in Guangzhou, Guangdong Province. The complete nucleotide sequence of DNA-A was determined to be 2 737 nucleotides encoding six potential ORFs. Comparison showed that G6 DNA-A had more than 89% sequence identify with all isolates of Cotton leaf curl Multan virus (CLCuMV) and shared the highest sequence identify (96.1%) with CLCuMV isolate 62. G6 DNA-A had 87.1%-89.8% sequence identity with those of CLCuRV isolates, while less than 87% identities with other begomoviruses. Phylogenetic analysis of G6 DNA-A and selected begomoviruses showed that G6 was most closely related to CLCuMV isolates, and they clustered together as a separate branch. Satellite DNA molecule (G6 DNAbeta) was found to be associated with G6 using the primers beta01 and beta02. G6 DNAbeta contains 1346 nucleotides, with a potential functional ORF (C1) in complementary sense DNA. Pairwise comparison indicated that G6 DNAbeta had the highest sequence identities with CLCuMV DNAbeta (92.1%) and CLCuRV DNAbeta (88.7%), but less than 80% sequence identities with other reported satellite DNA molecules. Phylogenetic analysis indicated that G6 DNAbeta was most closely related to CLCuMV DNAbeta and the two DNAbetas clustered together as a separate branch, and formed the main branch with DNAbeta of CLCuRV and MYVV-Y47. It is concluded that G6 infecting Hibiscus rosa-sinensis is an isolate of CLCuMV.
Base Sequence ; DNA, Satellite ; chemistry ; DNA, Viral ; chemistry ; Geminiviridae ; classification ; genetics ; Gossypium ; virology ; Hibiscus ; virology ; Phylogeny

Human bocavirus, which was firstly discovered in 2005, is a new human parvovirus associated with lower respiratory tract infection in children. In this study, a human bocavirus, named WLL-1 isolate, was identified in Wenlin County, Zhejiang Province. The genome of bocavirus WLL-1 has been sequenced and analyzed. Phylogenetic analyses showed that WLL-1 shares 99% homology with other bocaviruses recently reported, but also has some special variations.
Bocavirus ; classification ; genetics ; isolation & purification ; China ; DNA, Viral ; chemistry ; genetics ; Genome, Viral ; Humans ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA

DNA, Viral ; chemistry ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Torque teno virus ; classification ; genetics

This study was done to determine the effect of fixation time and freeze-thaw (FT) cycles on the quantitation and positivity of viral DNA. There were significant decreases in the viral DNA copies in the specimens subjected to formalin fixation more than 24 hours. However, The viral DNAs of specimens with FT cycles were not remarkably decreased as compare with those of fresh samples. These results implicate that there may be need to fix the samples less than 24 hours. Also, results of retrospective studies performed on specimens subjected to long-term fixation may be compromised.
DNA, Viral/*analysis/*genetics ; Freezing ; Herpesviridae/chemistry/genetics ; Polymerase Chain Reaction/methods ; Time Factors ; Virology/*methods

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

OBJECTIVESTo establish a Chinese national standard for a nucleic acid test (NAT) for HBV DNA.

METHODSThe candidate sample of HBV DNA positive plasma was diluted with HBV-negative human plasma. The sample was lyophilised with a concentration of approximately 300,000 copies/ml. The measurement methods used included Roche Amplicor assay (version 2.0) and real-time PCR. The lyophilised preparation was calibrated by the international standard (NIBSC code: 97/746) from NIBSC.

RESULTSThe quantity of this lyophilised preparation was (1.29+/-0.24) x 10(5)IU/ml in comparison with the international standard for HBV DNA 97/746. The stability test indicated that the sample was stable at room temperature (20 to 25 degrees C) for 2 weeks and at 37 degrees C for at least 1 week. Long-term stability was observed at 2 to 8 degrees C for 6 months and at -20 degrees C for more than 2 years with no significant changes. The vial-to-vial imprecision rate was 3.53%.

CONCLUSIONBased on the results of this study, our lyophilized sample can be used as a standard in China for the nucleic acid test (NAT) for HBV DNA.

DNA, Viral ; blood ; Hepatitis B virus ; genetics ; Humans ; Nucleic Acid Amplification Techniques ; standards ; Plasma ; chemistry

Integrase plays a critical role in the recombination of viral DNA into the host genome. Therefore, over the past decade, it has been a hot target of drug design in the fight against type 1 human immunodeficiency virus (HIV-1). Bovine immunodeficiency virus (BIV) integrase has the same function as HIV-1 integrase. We have determined crystal structures of the BIV integrase catalytic core domain (CCD) in two different crystal forms at a resolution of 2.45 Å and 2.2 Å, respectively. In crystal form I, BIV integrase CCD forms a back-to-back dimer, in which the two active sites are on opposite sides. This has also been seen in many of the CCD structures of HIV-1 integrase that were determined previously. However, in crystal form II, BIV integrase CCD forms a novel face-to-face dimer in which the two active sites are close to each other. Strikingly, the distance separating the two active sites is approximately 20 Å, a distance that perfectly matches a 5-base pair interval. Based on these data, we propose a model for the interaction of integrase with its target DNA, which is also supported by many published biochemical data. Our results provide important clues for designing new inhibitors against HIV-1.
Animals ; Catalytic Domain ; genetics ; Cattle ; DNA ; genetics ; DNA, Viral ; HIV-1 ; genetics ; metabolism ; Humans ; Immunodeficiency Virus, Bovine ; enzymology ; genetics ; Integrases ; chemistry ; genetics ; metabolism

The full-length genomic sequence of foot-and-mouth disease virus (FMDV) Asia1/YNBS/58 strain was determined by RT-PCR and compared with other 17 reference strains. The results showed that the complete genome of Asia1/YNBS/58 was 8164nt long including a 1061-nt 5' untranslated region (UTR), a 6990-nt open reading frame (ORF), and a 113-nt 3'UTR. The homology analysis indicated that the UTR regions and non-structural proteins were more conserved than the structural proteins in FMDV. VP1 exhibited the lowest conservation and VP4 was exceptionally conserved. The VP1-, VP2-, and VP3-based phylogenetic trees were divided into distinct clusters according to different serotypes, while the other gene-based phylogenetic trees exhibited some degree of intercross among serotypes. This study is the first description of the full-length genomic sequence of FMDV Chinese serotype Asia1.
3' Untranslated Regions ; chemistry ; Capsid Proteins ; genetics ; Foot-and-Mouth Disease Virus ; genetics ; Genome, Viral ; Phylogeny ; Sequence Analysis, DNA

BACKGROUNDTo study the antigenic and genetic characteristics of influenza (H3N2) virus circulated in China in 2004.

METHODSSingle-way and cross-way hemagglutination inhibition (HI) tests were firstly used to determine the reactivity with the reference serum of virus isolates. Based on the serological results, virus isolates were selected according to the different time and location in China in 2004. The HA1 domain of HA gene of those virus isolates were then sequenced in order to analyze the gene characterization.

RESULTSSingle-way HI test results showed that 52.3% of isolates showed 4 folds or more HI titer difference compared to A/Fujian/411/2002 (H3N2) itself (international reference strain in 2004). Cross-way HI test results showed that the antigenic ratio was 4. The nucleic acid and amino acid sequence data of HA1 domain showed that the mutated virus appeared in early February of 2004, and became the dominant circulating strain gradually. There were four important mutant positions, they were 159 Y>F, 189 S>N, 145 K>N, 226 V>I, respectively. The results also indicated that the mutated viruses originated from southern China, then transmitted to northern China, according to the analysis of time and location distribution.

CONCLUSIONThe HA1 domain of HA gene of influenza virus (H3N2) isolated from 2004 in China showed mutation and antigenic drift, and the mutated viruses were becoming the dominant circulating strain in China, and showed amino acid sequence difference compared to A/Fujian/411/2002 (H3N2) A/Wellington/1/2004 (H3N2), the vaccine components pronounced by WHO for 2004-2005 northern hemisphere and 2005 southern hemisphere respectively, which suggested that further surveillance should be conducted to monitor the virus mutation in circulation.

Animals ; Antibodies, Viral ; blood ; Antigens, Viral ; immunology ; Cell Line ; China ; DNA, Complementary ; chemistry ; genetics ; Humans ; Influenza A Virus, H3N2 Subtype ; classification ; genetics ; immunology ; Phylogeny ; RNA, Viral ; genetics ; isolation & purification ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA

OBJECTIVEHuman Parvovirus B19 (HPV B19) is a small (23 nm), non-enveloped DNA virus found in 1974. It has been proved that HPV B19 is associated with a variety of childhood diseases, such as erythema infectious, transient aplastic crisis, aplastic anemia, idiopathic thrombocytopenic purpura and arthropathy, etc. There have been no any effective vaccines to prevent HPV B19 infection so far. The HPV B19 genome is composed of 5.6 kb single strand DNA. This genome encodes a nonstructural protein NS1, two structural proteins VP1 and VP2. Most neutralizing linear epitopes of HPV B19 cluster in the VP1 unique and VP1-VP2 junction regions. Only proteins encoded by genes of the VP1 unique and VP1-VP2 junction regions can stimulate bodies to produce protective antibodies. Aim of the present study was to get the VP1 unique region gene of HPV B19 and to analyze the genetic diversity so as to further study its function and application.

METHODSThe VP1 unique region gene of HPV B19 was amplified from the serum of a child with idiopathic thrombocytopenic purpura by PCR. The purified PCR product was cloned into pGEM-T easy vector and transfected into the host strain E. coli (DH5 alpha). Positive clones were chosen and then the target gene was sequenced.

RESULTSThe target gene sequence of HPV B19 VP1 unique region was amplified and cloned successfully. It had 705 nucleotides. Compared with the relevant sequences published in Genbank, the sequencing results were revealed with two nucleotides changes in the HPV B19 VP1 unique region, but their coding amino acid were not changed.

CONCLUSIONIt is suggested that genetic diversity exists in the VP1 unique region of HPV B19. Construction of the recombinant plasmid of HPV B19 VP1 unique region gene might benefit to further study.

Capsid Proteins ; genetics ; Child ; DNA, Viral ; chemistry ; genetics ; Genetic Variation ; Humans ; Mutation ; Parvovirus B19, Human ; genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA