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PubMed1983

Monoclonal antibodies against five structural components of measles virus. I. Characterization of antigenic determinants on nine strains of measles virus.

Monoclonal antibodies against five structural proteins of measles virus were used to determine the degree of antigenic variation within these proteins amongst nine strains of measles virus (four fresh wild-type isolates, two vaccine and two laboratory strains, and a strain derived from a case of subacute sclerosing panencephalitis) giving lytic infections in cell culture. The major surface proteins showed limited variations in their epitopes between the nine strains. No variations in the fusion (F) protein and only three variations in the hemagglutinin (H) protein epitopes were detected by radioimmune precipitation assay and other serological tests using a panel of 11 monoclonal antibodies against each protein. These antibody panels consisted of at least nine and six different binding groups for the H and F proteins, respectively. The two innermost proteins, the nucleocapsid and polymerase proteins, also appeared to be antigenically stable as no variation was detected between strains using in each case a panel of six hybridomas. In sharp contrast, the epitopes on the matrix (M) protein of different strains showed extensive variation in their reactivity with the nine anti-M monoclonal antibodies. The possible use of M protein epitopic markers in classification of measles virus strains is discussed.

Antibodies, Monoclonal↗
PubMed2003

Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region.

The 65 human enterovirus serotypes are currently classified into five species: Poliovirus (3 serotypes), Human enterovirus A (HEV-A) (12 serotypes), HEV-B (37 serotypes), HEV-C (11 serotypes), and HEV-D (2 serotypes). Coxsackie A virus (CAV) serotypes 1, 11, 13, 15, 17, 18, 19, 20, 21, 22, and 24 constitute HEV-C. We have determined the complete genome sequences for the remaining nine HEV-C serotypes and compared them with the complete sequences of CAV21, CAV24, and the polioviruses. The viruses were most diverse in the capsid region (4 to 36% amino acid difference). A high degree of capsid sequence conservation (96% amino acid identity) suggests that CAV15 and CAV18 should be classified as strains of CAV11 and CAV13, respectively. In the 3CD region, CAV1, CAV19, and CAV22 differed from one another by only 1.2 to 1.4% and CAV11, CAV13, CAV17, CAV20, CAV21, CAV24, and the polioviruses differed from one another by only 1.2 to 3.6%. The two groups, however, differed from one another by 14.6 to 16.2%. The polioviruses as a group were monophyletic only in the capsid region. Only one group of serotypes (CAV1, CAV19, and CAV22) was consistently monophyletic in multiple genome regions. Incongruities among phylogenetic trees based on different genome regions strongly suggest that recombination has occurred between the polioviruses, CAV11, CAV13, CAV17, and CAV20. The close relationship among the polioviruses and CAV11, CAV13, CAV17, CAV20, CAV21, and CAV24 and the uniqueness of CAV1, CAV19, and CAV22 suggest that revisions should be made to the classification of these viruses.

Amino Acid Sequence↗
PubMed1993

Nucleotide sequence of the capsid protein cistrons from six potato virus Y (PVY) isolates infecting tobacco.

Complementary DNA libraries representing the capsid protein cistron of the potato virus Y (PVY) isolate 'Chilean', 'Hungarian', MsNr, NsNr, O, and 'Potato US' were synthesized and used as template for polymerase chain reaction (PCR) amplification. An AUG codon for initiating a discrete capsid protein (CP) open reading frame was embedded upstream of the first codon of the CP cistrons. PCR-amplified products of the expected size of 0.8 kilo bases were cloned into the transcription vector pBS(+). The fidelity of each PCR-amplified PVY CP cistron was tested by transcribing recombinant plasmids in vitro and translating the transcripts in two cell free translation systems. Translation analysis of in vitro transcribed PVY CP cistrons consistently yielded a polypeptide co-migrating with authentic CP that was immunoprecipitated by anti PVY 'Chilean' antibodies. The nucleotide sequence of each capsid protein gene was determined by dideoxy sequence analysis. Each capsid protein gene was determined to be 801 nucleotides in length, encoding a deduced protein of 267 amino acids with calculated M(r) ranging from 29,799 to 29,980. The nucleic acid sequence similarity between the six isolates ranged between 89 to 97% and the amino acid similarity between 91 to 99%. The high level of amino acid sequence similarity confirms the classification of these viruses as isolates of PVY.

Amino Acid Sequence↗
PubMed1996

The genomic structure of a new simian T-lymphotropic virus, STLV-PH969, differs from that of human T-lymphotropic virus types I and II.

A new simian T-lymphotropic virus, STLV-PH969, was recently isolated from a wild-born Hamadryas baboon. Previous analysis had revealed that it differs sufficiently from the other HTLV/STLVs to be considered a new type, provisionally designated primate T-lymphotropic virus-L. Here we analyse a 3850 bp cDNA fragment spanning the 3' part of the STLV-PH969 genome. The fragment encodes three major proteins: Env, Tax and Rex. Sequence comparison and phylogenetic analysis indicate that in general STLV-PH969 tends to be more closely related to HTLV-II than to HTLV-I, although separate gene regions might have evolved under different constraints. Detailed comparison of the Env, Tax and Rex proteins among the HTLV-I, -II and STLV-PH969 prototypes reveals that the amino acid sequence of each protein shows a preferential conservation of functionally important domains. RNA-PCR on cytoplasmic messengers demonstrated splicing between a splice donor site immediately downstream of the env start codon, and two splice acceptor sites identified in the pX region. The predominant spliced messenger encodes both Tax and Rex. The other messenger potentially encodes a new viral protein from the proximal part of the pX region that is similar in amino acid composition to p12I and p10xI of HTLV-I and HTLV-II respectively. This genomic organization of the proximal pX region of STLV-PH969 is different from that found in HTLV-I and HTLV-II. Therefore, the distinct classification of this virus can be justified, not only in terms of sequence divergence but also in terms of its different genomic structure.

Amino Acid Sequence↗
PubMed1992

Genomic organization and expression of simian foamy virus type 3 (SFV-3).

The complete nucleotide sequence of simian foamy virus type 3 (SFV-3) strain LK-3, isolated from an African green monkey, was determined. In addition to translation frames representing the gag, pol, and env genes, two open reading frames are located in the region between the env gene and the 3' long terminal repeat (LTR). Both SFV-3 and SFV-1 encode two open reading frames between env and the 3' LTR, whereas HFV encodes three open reading frames in this region. Northern blot analysis of cell cultures infected with SFV-3 revealed subgenomic RNAs for these open reading frames. The protease of SFV-3 is encoded by the pol gene in contrast to HFV which encodes the protease in the gag gene. Notably, the pol gene of SFV-3 in the +1 translational frame relative to the gag gene; this observation is in agreement with SFV-1, but differs for HFV and all other retrovirus genomes reported. Thus, gag-pol precursors of the SFVs appear to be expressed by a +1 frameshift. Nucleotide and deduced amino acid alignments of SFV-3, SFV-1, and HFV revealed an unexpected homology pattern; highest homologies are observed in the pol and env genes but low homologies are noted in the gag genes and the additional open reading frames. Analysis of phylogenetic trees confirms the classification of foamy viruses as a subfamily of retroviruses, distinct from the lentiviruses and oncoviruses.

Amino Acid Sequence↗
PubMed2004

[The spectrum of lymphoproliferations and malignant lymphoma after organ transplant].

Lymphoproliferative disease in patients with organ transplantation has increasingly been diagnosed in recent years. It is caused by immunosuppression after organ transplantion. A large percentage of these tumors is associated with Epstein-Barr virus infection. The classification differentiates between early lesions, polymorphic and monomorphic lymphoproliferations. Whereas the early lesions are often polyclonal, the remaining groups are mostly monoclonal. Polymorphic lymphoproliferative disease shows a wide spectrum of B-cell differentiation, whereas monomorphic proliferations resemble sproadic malignant lymphomas. The latter also show genetic abberations of the c-myc-, Ras-, p53- and Bcl6-genes. With reference to the germinal center reaction, posttransplant lymphoproliferations have to be assigned to the post-follicular activated B-cell type. While until 1991 only 2% of the cases of PTLD had an EBV-association, the EBV-associated PTLD have been frequently observed in recent times and presently constitute about 20% of the cases. EBV-negative PTLD constitute a negative prognostic factor. Posttransplant lymphomas might also represent a model for sporadic lymphoproliferative disease, that for example also occurs at elderly patients.

B-Lymphocytes↗
PubMed1991

Cloning of the maize rough dwarf virus genome: molecular confirmation of the plant-reovirus classification scheme and identification of two large nonoverlapping coding domains within a single genomic segment.

The segmented double-stranded RNA genome of maize rough dwarf virus, a plant-infecting reovirus of the genus Fijivirus, was cloned and partially characterized. Nucleotide sequence analysis of full-length cDNA clones corresponding to genomic segments S6, S7, and S8 revealed each segment to contain the conserved terminal oligonucleotide sequences (+) 5' AAGUUUUUU------UGUC 3' and adjacent, segment-specific, regions of inverted complementarity (inverted repeats), a structural motif previously reported for members of the genus Phytoreovirus. Genomic segment S6 was completely sequenced and found to consist of 2193 base pairs. Computer analysis indicated that the coding strand contained two large nonoverlapping open reading frames consisting of 363 and 310 codons and located in the 5'- and 3'-terminal domains, respectively. This was confirmed by cell-free translation studies with synthetic transcripts and denatured genomic RNA. However, only the product of the 5'-proximal open reading frame, a 40-kDa polypeptide, was efficiently expressed in vitro from the full-length S6 coding strand. This represents the first case in which a reovirus genomic segment was found to contain two large open reading frames in a nonoverlapping configuration, suggesting possible alternative strategies for regulation of gene expression by members of this genus. The combined results provide a molecular confirmation of the current classification scheme for plant-infecting reoviruses. Furthermore, the fact that the same terminal structural motif is conserved across genera provides additional evidence that these elements serve an important functional role during genome transcription or replication.

Amino Acid Sequence↗
PubMed1975

Comparative analyses of members of the Venezuelan equine encephalomyelitis virus complex.

Polyacrylamide gel electrophoretic examination of viruses selected from the Venezuelan equine encephalomyelitis (VEE) complex revealed distinct strain to strain differences in profiles of the two virion envelope proteins. The core protein was identical in all viruses tested. We detected five electrophoretic patterns into which the virus strains could be classified and these were designated alpha (alpha), beta (beta), gamma (gamma), delta (delta), and episolon (episolon). Isolates representing variant E of subtype I exhibited a profile characterized by only one apparent envelope band. The epizootic subtypes I-A, I-B, I-C and the sylvatic subtype II viruses contained at least two envelope proteins which differed in molecular weight according to virus strain but which were not necessarily specific for antigenic variety. These results generally, though not uniformly, support the serologic classification of the VEE virus complex and suggested that the usefulness of the classification scheme could be complemented by the inclusion of biochemical criteria.

Animals↗
PubMed2006

The phylogenetic analysis of hepatitis C virus isolates obtained from two Iranian carriers revealed evidence for a new subtype of HCV genotype 3.

Classification of hepatitis C virus is based on phylogenetic analysis of the strains reported world wide. Different strains are classified within 6 major genotypes and several minor groups (subtypes). In addition to epidemiologic value of determining genotype/subtype of this virus, the result may change the therapeutic strategy used for a patient. During a survey on hepatitis C in Iran, we found two cases assigned as 1b genotype by PCR-RFLP on 5' UTR, but three based on core region sequencing. Fragments from 5' UTR, Core and NS5b regions were PCR-amplified and sequenced followed by phylogenetic analysis. Although the 5' UTR of this new strain is very similar to genotypes 1 and 6, analysis of core region classifies it in a separate branch of genotype 3, close to subtypes h and k. Further analysis of NS5b region put this new strain in a separate branch near other subtypes of genotype 3 and 4. These data are suggestive of a new subtype within genotype 3.

5' Untranslated Regions↗
PubMed2005

Relationship of genotypes of hepatitis B virus to mutations, disease progression and response to antiviral therapy.

SUMMARY: Phylogenetic analysis has led to the classification of hepatitis B virus into eight genotypes, designated A to H. The genotypes have differences in biological properties and show heterogeneity in their global distribution. These attributes of the genotypes may account not only for differences in the prevalence of hepatitis B virus mutants in various geographic regions, but also be responsible for differences in the clinical outcome and response to antiviral treatment in different population groups.

Antiviral Agents↗
PubMedDate not supplied

Molecular epidemiology of vertical human immunodeficiency virus type 1 transmission in Greece: evidence of non-B subtypes.

OBJECTIVES: To investigate the subtype classification of the circulating virus strains among human immunodeficiency virus type 1 (HIV-1)-infected children in Greece. STUDY DESIGN/METHODS: Since the beginning of the acquired immunodeficiency syndrome (AIDS) epidemic in Greece in 1982, 23 children have been reported to be vertically infected with HIV-1. Blood samples were available for 19 of these children, and the C2-C4 env region was successfully amplified by nested polymerase chain reaction (PCR) for 16 subjects. HIV-1 subtype was established by the heteroduplex mobility assay (HMA) in 16 subjects and confirmed by DNA sequencing and phylogenetic analysis in 8 subjects. RESULTS: Most subjects (9; 56%) fell into subtype B. However, a substantial proportion (44%) were classified as subtypes A (3; 19%), C (1; 6%), D (1; 6%), and I (2; 12%). According to epidemiologic information, 5 of 7 children infected with non-B HIV-1 subtypes were born to Greek parents. CONCLUSION: These findings clearly suggest that non-B strains have been introduced into Greece, providing evidence that HIV epidemic in this country will probably change profile over time. In addition, subtype I was identified in 2 HIV-1-infected children, both of whom were born to Greek parents.

Adolescent↗
PubMed1994

Mapping the subgroup epitopes of rotavirus protein VP6.

VP6, the most abundant protein of rotaviruses, contains epitopes that allow the classification of these viruses into four subgroups (SG), depending on the presence or absence of two epitopes called I and II. The subgroup-specific epitopes are conformational and appear to be present on trimeric but not monomeric VP6. We have identified on VP6 some of the amino acids that determine the reactivity of the subgroup-specific mAbs 255/60 and 631/9. A single amino acid mutation at positions 172 (Met to Ala) or 305 (Asn to Ala) was sufficient to change the subgroup specificity of the human rotavirus Wa VP6 protein from SGII to SGI/II, since either of these mutations allowed the protein to be recognized by the SGI mAb 255/60, while retaining its capacity to interact with the SGII mAb 631/9. In the case of the SGII epitope, the mutation of two contiguous amino acids (Ala305 Asn306 to Asn305 Ala306) in the porcine rotavirus YM VP6 protein (SGI) enabled the protein to be efficiently recognized by the SGII mAb 631/9, while causing the YM VP6 protein to lose its capacity to interact with mAb 255/60. These results suggest that both subgroup Abs interact with an antigenic domain in VP6 that is composed of at least two regions of the protein that, although distant in the linear sequence, might be in close proximity in the structured VP6 trimer.

Amino Acid Sequence↗
PubMed1994

Biochemical and genomic characterization of muscovy duck parvovirus.

A duck parvovirus (DPV) isolated from muscovy ducks during the epizootic in France in 1989 was purified from inoculated allanto-amniotic fluids by CsCl density gradient centrifugation and characterized. Full and empty non-enveloped icosahedral viral particles were observed banding at densities of 1.39 to 1.42 and 1.38 respectively, with a diameter of 22 to 23 nm. Viral proteins were analyzed by SDS-PAGE and the estimated molecular weights of the 3 major proteins were 91, 78 and 58 kDa. The nucleic acid was shown to be a single-stranded DNA of about 5,300 bases with terminal palindromic hairpins. These results confirm the previous classification of the virus in the family Parvoviridae established by Jestin et al. [14] on morphological and serological bases. The DPV DNA was reannealed indicating that complementary DNA strands were encapsidated. A partial restriction endonuclease map was also established. This work constitutes the first biochemical and genomic description of a muscovy duck parvovirus.

Animals↗
PubMed2005

Conservation of the N-terminus of some phage tail proteins.

To study the interaction between lipopolysaccharide and protein, a comparative approach was employed using seven Salmonella enterica serovar Typhimurium typing phages as the protein model systems. This interaction has been studied in detail in the Salmonella enterica serovar Typhimurium phage P22 system and involves only the viral tailspike protein. Similarity between these phages and phage P22 was monitored in this Report by assaying restriction endonuclease digestions, capsid size, reactivity to the P22 tailspike protein monoclonal antibody, mAb92, which reacts with the N-terminus of the P22 tail protein and the ability to produce a PCR fragment using primers made to the ends of the P22 tailspike gene. The data indicate that tailspike similarity exists between most of these phages and a scheme reclassifying them is presented and that the N-terminus of the P22 tailspike protein may be a motif for many phage systems and may serve as a aid in the taxonomy of phages. The data suggest a classification scheme in which the N-terminus of some tailspike proteins (head-binding region in some tail proteins) may play a critical element role in the classification of Salmonella viruses.

Antibodies, Monoclonal↗
PubMed1998

Sequence comparison of the major capsid protein gene from 18 diverse iridoviruses.

Insect iridoviruses (IV) have been found on all continents of the world and in a broad range of insect hosts. The host range for a single strain can cross several insect orders. This along with a paucity of molecular information on all but a few members has led to confusion in the taxonomy and classification of these viruses and in the identification of potentially novel isolates. To address this problem consensus PCR primers were designed to amplify and sequence a 500 bp region of the major capsid protein (MCP) gene. PCR products were amplified from eighteen IVs belonging to the genus Iridovirus. No product was observed for the chloriridovirus IV3. Phylogenetic analysis of the partial MCP gene sequence showed that the iridovirus genus can be divided into three groups. These results support previous studies where a range of molecular techniques were used. Group I contained PjIV and IV31, group II contained IV6 (CIV), IV21, and IV28, and group III contained IV1 (TIV), IV2 (SIV), IV9 (WIV), IV10, IV16, (CzIV), IV18, IV22, IV23 (BbIV), IV24, IV29, IV30, AgIV and an undescribed weevil IV. There was no correlation of relatedness with host of isolation but there was some correlation with geographic region of isolation. Sequence analysis also raised issues concerning the purity of some virus stocks and supported the view that some isolates should be considered as variants of one virus species.

Base Sequence↗
PubMed2005

Isolation and characterization of a new Vesivirus from rabbits.

This report describes the isolation, cDNA cloning, complete genome nucleotide sequence, and partial characterization of a new cultivable calicivirus isolated from juvenile feeder European rabbits (Oryctolagus cuniculus) showing symptoms of diarrhea. Absence of neutralization by type-specific neutralizing antibodies for 40 caliciviruses and phylogenetic sequence comparisons of the open reading frame 1-encoded polyprotein with those of other caliciviruses demonstrate that this new calicivirus is a putative novel member of the Vesivirus genus which is closely related to the marine calicivirus subgroup. According to its putative classification, this new virus has been named rabbit vesivirus.

Animals↗
PubMed1998

[Importance of molecular biology in retrovirus and herpesvirus infections].

Molecular biology has long been used as a tool for basic research in virology. Its medical use is recent and has been supported both by numerous technical improvements and the discovery of new human viruses. This is illustrated by the emergence of human immunodeficiency virus (HIV)-1, HIV-2, human T-cell leukemia virus (HTLV)-I/II, and human herpesviruses (HHV) 6, 7 and 8. Polymerase chain reaction (PCR) gave a major boost to an extended use of molecular biology techniques. This resulted in a better knowledge of human viral infections as illustrated by studies on HIV and HHV-8. New viruses have been characterized. Molecular markers have permitted analysis of virus transmission cases, classification of genetic variants and detection of mixed infections. The quantitation of viral load has led to a better understanding of chronic infections and reactivations. As a tool for diagnosis, molecular biology is not yet considered as a universal alternative to classical procedures such as serology and antigen detection. However, major improvements in molecular biology techniques might question current diagnosis strategies in the very near future.

HIV↗
PubMed1999

V3 serotyping of HIV-1 infection: correlation with genotyping and limitations.

HIV-1 V3 serotyping is a classification of immunodeficiency viruses based on antibody binding to V3 peptides that allows obtaining information on circulating subtypes that could be important for population-based epidemiologic studies. Recently, several laboratories have developed V3 enzyme-immunoassays (EIAs) using V3 peptides of subtypes A to E. In the present study, the utility of including additional peptides of subtypes F to H to the EIA was evaluated on a panel of 203 well-characterized serum samples from patients with diverse geographic origins (22 countries) and known HIV-1 genotype (79 A, 61 B, 21 C, 7 D, 7 E, 21 F, 6 G, 1 H). The results indicate a high predictive value (ppv) for serotypes B (> or =0.86), D (1) and E (0.88), and confirm the difficulty of predicting genotype A or C based on serotype A or C. Results also indicate that inclusion of the F peptide in the V3 EIAs may be useful (ppv = 0.61), but introduction of peptides G and H failed to demonstrate significant sensitivity or specificity for these subtypes. Correlation between serotyping and amino-acid sequences of the V3 region from 103 samples allowed the identification of key amino-acids that appear essential for subtype-specific seroreactivity.

Amino Acid Sequence↗