[Characterization of capsid protein VP3-VP1 genes of hepatitis A virus prevalent strains circulated in China].
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To analyse the genetic characteristics of the capsid protein VP3-VP1 region of hepatitis A virus strains circulated in China.The nucleotide sequences of VP3-VP1-2A region of 42 HAV IgM positive serum samples were sequenced and analysed for nucleotide and amino acid identities and genetic characteristics of the VP3-VP1 region.The nucleotide and amino acid identities in the VP1-2A junction region among the 42 strains were 89.1% - 100% and 97.3% - 100%; while in the complete VP3-VP1 region, the identities were 87.6%-100% and 98.8%-100%. Strains with identical nucleotide sequences in the VP1-2A junction region had 98.4%-100% nucleotide identity in the complete VP3-VP1 region and 0-2 amino acid differences in this region. There were no amino acid changes at neutralizing antigenetic sites of VP3-VP1 region within the 42 HAV strains.All the 42 HAV strains belonged to genotype I, with 40 strains clustering to sub-genotype IA and 2 to sub-genotype IB. Different HAV strains analysed in this paper differed in the nucleotide sequences of the VP3-VP1 region, but the amino acid sequences were highly conserved with no changes at neutralizing antigenetic sites. Both the nucleotide and amino acid sequences of the strains with the same VP1-2A junction region were identical or closely related when compared in the complete VP3-VP1 region.Cite
The CD54 gene was amplified by RT-PCR from cells of milk of chinese cow mastis and cloned into pMD18-T for sequencing.The ORF of CD54 gene was 1608bp,encoding 535 amino acids.The initiative 28 amino acids consist of signal peptide.482～504 aa were transmembrane region,and 505～535 amino acids were inside region in deduced amino acid sequence.There are 13 N-glycosylation sites and one Ig-like domain.Compared with bovine CD54 gene reported in GenBank,there were 6 site-variations in the nucleotide sequence,which result in the changes of 4 amino acids,but without the difference in numbers and sites for N-glycosylation.Compared with CD54 genes of other different species,the nucleotide sequence of CD54 gene shares closer relationship with CD54 genes of sus scrofa,but displays some differences with homo sapiens,mus musculus,rattus norvegicus CD54 gene sequence.
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Homo sapiens
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Comparison of the amino acid sequence of the African swine fever virus attachment protein p12 from different field virus isolates, deduced from the nucleotide sequence of the gene, revealed a high degree of conservation. No mutations were found after adaptation to Vero cells, and a polypeptide with similar characteristics was present in an IBRS2-adapted virus. The sequence of the 5' flanking region was conserved among the isolates, whereas sequences downstream of the gene were highly variable in length and contained direct repeats in tandem that may account for the deletions found in different isolates. Protein p12 was synthesized in swine macrophages infected with all of the viruses tested.
Vero cell
Sequence (biology)
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To analyse the genetic characteristics of the capsid protein VP3-VP1 region of hepatitis A virus strains circulated in China.The nucleotide sequences of VP3-VP1-2A region of 42 HAV IgM positive serum samples were sequenced and analysed for nucleotide and amino acid identities and genetic characteristics of the VP3-VP1 region.The nucleotide and amino acid identities in the VP1-2A junction region among the 42 strains were 89.1% - 100% and 97.3% - 100%; while in the complete VP3-VP1 region, the identities were 87.6%-100% and 98.8%-100%. Strains with identical nucleotide sequences in the VP1-2A junction region had 98.4%-100% nucleotide identity in the complete VP3-VP1 region and 0-2 amino acid differences in this region. There were no amino acid changes at neutralizing antigenetic sites of VP3-VP1 region within the 42 HAV strains.All the 42 HAV strains belonged to genotype I, with 40 strains clustering to sub-genotype IA and 2 to sub-genotype IB. Different HAV strains analysed in this paper differed in the nucleotide sequences of the VP3-VP1 region, but the amino acid sequences were highly conserved with no changes at neutralizing antigenetic sites. Both the nucleotide and amino acid sequences of the strains with the same VP1-2A junction region were identical or closely related when compared in the complete VP3-VP1 region.
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The E2 strain of coxsackie B4 virus (CB4), which is of human origin, can induce a diabetes-like syndrome in mice. The cDNA of the genome of the E2 strain was cloned and sequenced. The E2 viral genome was found to comprise 7,396 bases, which appear to encode a polyprotein of 2,183 amino acids with an overall similarity of 94.91% to nondiabetogenic CB4 prototype JBV strain. The E2 genome is organized like other enteroviruses. It has a 5' noncoding region of 744 nucleotides, a single long open translational reading frame starting at nucleotide 745 and extending to nucleotide 7293, a 3' noncoding region of 100 nucleotides, and a poly (A) tract. Genomic sequence comparison of the E2 and JBV strains showed 1,369 nucleotide substitutions in the genome of the E2 strain, most of which are single and silent. There were 111 resultant amino acid changes arising from some of these substitutions, including 82 amino acid changes in the noncapsid proteins, and 29 amino acid changes in the capsid proteins VP1, VP2, VP3, and VP4, which showed 11, 13, 4, and 1 substitution(s), respectively. Noncapsid protein P2-C showed eight amino acid substitutions. On the basis of the sequence comparison of E2 and JBV strains of CB4, we suggest that some of the amino acid changes in the capsid and noncapsid proteins of the E2 strain may be involved in the determination of its diabetogenicity.
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Carnation mottle virus(CarMV) is one of the important viruses infecting Carnation.In this study,three genes of p7,p9 and CP of CarMV were isolated from twelve different cultivars of Carnation by RT-PCR and their sequences of nucleotides and amino acids were analyzed.The results showed that the p7,p9 and CP genes had higher stability by sequence alignment.The identities of the nucleotide and the amino acid sequence of p7 gene were 98.10% and 97.81 % respectively.There were evident variations at the 11th and 14th of amino acid position of p7 gene.While the identities of the nucleotide and amino acid sequence of p9 gene were 98.80% and 99.13% respectively.There was clear variations at the 4th amino acid position of p9 gene.However,the identities of the nucleotide and amino acid sequence of CP gene were 97.58% and 98.43% respectively.There was correlative between the 164th and 331th amino acid.Those variations of positions of CP were dispersive.The results also showed that the mutations of p7 and p9 were main located at N-terminal parts which exposed to interact with host.Those variations of positions of CarMV might relate to vial variation and interaction between the virus and host.
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Objective To provide a theoretical foundation for studying the aetiologic mutational loci of MSX1 and the etiology of the non-syndromic cleft lip and/or palate by analyzing the cDNA sequence and amino acid sequence of human MSX1 gene.Methods The full gene sequence and amino acid sequence of human MSX1 gene were obtained from NCBI,and analyzed comprehensively using software DNAMAN and GENtle,respectively.Results The full length of the human MSX1 gene was 1 944 bp.The translated region comprised 894 bp which was on the loci 247-1140,and the protein sequence included 298 amino acids.Hydrophobic amino acids were located in the N polar region,far distance of C terminal,and 14 regions in the middle of the full sequence.Hydrophilic amino acids were in 10 regions in the middle of protein sequence.The homology between human and gorilla was 100%,and the maximum of gene similarity with other species was 90%(canis).At the same time,452 bp were stable among MSX1 gene sequences in 8 species(account for 50.56%),and the numbers of similar base pairs were 91(10.18%).However,MSX1 gene in 8 species had no complete identical amino acid sequences,and only 11 nucleotides were basically identical(account for 3.74%).Conclusion Amino acid or protein sequences of MSX1 gene in 8 species have great difference and a batch of mutational loci.It is significant to reconsider and reassure the relationship between the mutation of MSX1 and non-syndromic cleft lip and/or palate.
Homology
Sequence (biology)
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Strain (injury)
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The amino terminus of VP2', the major capsid protein of the parvovirus H-1, was identified and mapped to the H-1 genome. The protein initiates at the start codon at nucleotide 2797 and is translated uninterrupted to the stop codon at nucleotide 4582. The primary sequence predicts a protein of 593 amino acids (65,500 daltons) with an amino acid composition which very closely matches the experimentally determined composition of the pure protein. The data suggest that the VP2' mRNA has a 5' leader sequence of ca. 650 bases and that protein translation initiates downstream from the sole splice junction.
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Protein sequencing
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A new isolate of hepatitis A virus (HAV), CY-145, was isolated from stool specimens obtained from cynomologus macaques naturally infected with this agent. Sequence analysis of the capsid region of the genome indicated that this virus differed from other sequenced HAV strains by about 20% at the nucleotide level and 7% at the amino acid level. Two amino acid residues (residues 70 of VP3 and 102 of VP1), previously identified as constituting an immunodominant site and conserved in all sequenced HAVs, were changed in the CY-145 virus. Sequence analysis of a second cynomolgus HAV isolate (CY-55), which came from a different geographical location, showed the same amino acid replacement at these two sites. In addition both isolates had an amino acid substitution at the VP3-VP1 cleavage site. These data suggest that the cynomolgus HAV differs genetically and antigenically from all other sequenced HAVs.
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