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PubMed1990

The impact of oral examination on the Centers for Disease Control classification of subjects with human immunodeficiency virus infection.

Seventy patients infected with human immunodeficiency virus (HIV) have been included in this study to evaluate the impact of oral examination on the Centers for Disease Control (CDC), Atlanta, Ga, classification of HIV disease. Based on clinical data prior to oral examination, 22 patients were classified in the CDC group 2, 11 in CDC group 3, and 37 in CDC group 4. Twelve patients (55%) initially classified as CDC 2, and 4 patients (36%) initially classified as CDC 3 had to be reallocated to CDC group 4 due to the presence of oral candidiasis, hairy leukoplakia, or oral Kaposi's sarcoma. We conclude that oral examination has a large impact on the CDC classification of HIV-infected subjects. Since this classification system is used to select asymptomatic HIV-infected subjects (CDC groups 2 and 3) for clinical trials receiving antiretroviral therapy in early HIV disease, it is suggested that accurate oral examination is mandatory before inclusion of patients in such studies.

Adult↗
PubMed1996

A reevaluation of the higher taxonomy of viruses based on RNA polymerases.

In order to assess the validity of classifications of RNA viruses, published alignments and phylogenies of RNA-dependent RNA and DNA polymerase sequences were reevaluated by a Monte Carlo randomization procedure, bootstrap resampling, and phylogenetic signal analysis. Although clear relationships between some viral taxa were identified, overall the sequence similarities and phylogenetic signals were insufficient to support many of the proposed evolutionary groupings of RNA viruses. Likewise, no support for the common ancestry of RNA-dependent RNA polymerases and reverse transcriptases was found.

Animals↗
PubMed1996

Does the classification system fit disease progression in perinatal human immunodeficiency virus infection?

The objective was to test the applicability of the new classification for paediatric human immonodeficiency virus infection. The person-time of each state, transition probabilities and survival (+/- standard errors) at 5 years, and median sojourn-time were calculated on 39 perinatally infected children followed up from the first month of life for a median of 64.5 (1.2-120.1) months. The person-times of the N2, N3, B1, C1, and C2 states were low. The transition probabilities and sojourn-times were similar for A (48.1 +/- 10.8%; 63.5 months), B (50.5 +/- 15.5%; 44.9 months) and C (74.6 +/- 15.1%; 43.1 months) clinical categories, which differed (p < 0.025) from the N category (87.9 +/- 5.5%; 12.05 months). The survival probabilities after 5 years of entering the A, B and C categories were 84.8 +/- 10.7%, 60.5 +/- 19.8% and 14.8 +/- 13.5%, respectively (p < 0.001). Immunological category 3 had lower transition probabilities and longer sojourn-times (58.8 +/- 16.6%; 53.3 months) than categories 1 (71.3 +/- 8.1%; 33.2 months) and 2 (75.6 +/- 10.5%; 19.8 months) (p < 0.01). The transition probabilities to C3 for states N3, A3 or B3 were 52.5 +/- 13.5%. In conclusion, the classification fits the clinical history better than the immunological history.

Age Factors↗
PubMed2006

Geographical distribution of hantaviruses in Thailand and potential human health significance of Thailand virus.

Phylogenetic investigations, sequence comparisons, and antigenic cross-reactivity studies confirmed the classification of Thailand virus (THAIV) as a distinct hantavirus species. The examination of sera from 402 rodents trapped in 19 provinces of Thailand revealed that five greater bandicoot rats (Bandicota indica) and one lesser bandicoot rat (B. savilei) from four provinces were focus reduction neutralization test (FRNT) antibody-positive for THAIV. One of 260 patients from Surin province in Thailand (initially suspected of having contracted leptospirosis, but found to be negative) showed symptoms compatible with hemorrhagic fever with renal syndrome (HFRS). The serum of this patient showed high titers of hantavirus-reactive IgM and IgG. FRNT investigations confirmed virus-neutralizing antibodies against THAIV. These observations suggest that THAIV or THAI-like viruses occur throughout Indochina and may represent an additional causative agent of HFRS.

Animals↗
PubMed1992

Comparison of the amino acid sequences of nine different serotypes of hepatitis B surface antigen and genomic classification of the corresponding hepatitis B virus strains.

The surface (S) genes of 12 hepatitis B viruses (HBVs) encoding nine different serotypes of hepatitis B surface antigen (HBsAg) were amplified by the polymerase chain reaction and sequenced. These represented the eight strains of HBV, P1 to P8, defined at an international workshop on HBsAg subtypes in Paris in 1975, and the adrq- subtype. The S genes from additional HBV strains, one ayw4, one adw4 and one ayw1, of sub-Saharan African origin, were also sequenced. The relationship of these 12 new S gene sequences to those of the 20 published previously was investigated by constructing a phylogenetic tree, which confirmed a previous classification into four groups, designated A to D, based on 18 complete HBV genomes. When relating our sequenced S genes to these genomic groups, ayw1 of African origin and P6 (adw2) were both allocated to group A, the reference P1 (ayw1 of Vietnamese origin) was allocated to group B, P5 (ayr), P8 (adr) and adrq- were all related to group C, and P2 (ayw2) and P3 (ayw3) could both be allocated to group D. Interestingly, the S genes of w4 serotype viruses, i.e. P4 (ayw4) and P7 (adw4q-), differed by 4% or more from both previous groups and from each other, suggesting their classification into two new groups, for which the designations E and F are proposed. Genomes specifying ayw were also found in groups A and B; previously sequenced genomes specifying the ayw subtype have all been confined to group D. There were indications that the epitope for subdeterminants of w resided at amino acid positions 125 to 127. Thus, at positions 125 and 127, ayw1, ayw2 and adw2 had T and P residues, respectively, whereas M and T residues were at the corresponding positions of ayw3. Both ayw4 and adw4 had L at residue 127, and all strains expressing r, apart from P5, had an I instead of a T residue at position 126.

Amino Acid Sequence↗
PubMed2005

Classification of single-projection reconstructions for cryo-electron microscopy data of icosahedral viruses.

We present a novel strategy for classification of heterogeneous electron microscopy data of icosahedral virus particles. The effectiveness of the procedure, which is based on classification of single-projection reconstructions (SPRs), is first investigated using simulated data. Of several reconstruction approaches examined, best results were obtained with algebraic reconstruction techniques (ART) when providing prior information about the reconstruction in the form of a starting volume. The results presented indicate that SPR-classification is sufficiently sensitive to classify assemblies with differences of only a few percent of the total mass. The usefulness of this procedure is illustrated by application to a heterogeneous cryo-electron microscopy dataset of adenovirus mutant dl313, lacking minor coat protein IX. These data were successfully divided into two distinct classes, in agreement with gel analysis and immuno-electron microscopy results. The classes yielded a wildtype-like reconstruction and a reconstruction representing the polypeptide IX-deficient dl313 virion. As the largest difference between these volumes is found at the location previously assigned to the external portion of minor coat protein polypeptide IIIa, questions arise concerning the current adenovirus model.

Adenoviruses, Human↗
PubMed2002

Proposed criteria for classification of new genotypes of mumps virus.

The nucleotide sequences of a 300 bp segment carrying the small hydrophobic (SH) protein gene of a large number of virus strains, belonging to 10 different mumps virus genotypes denoted A-J, were compared. When virus strains belonging to the same genotype were compared intra-genotypically, a variation in the range 2-4% was recorded. The level of inter-genotypical variation was higher (8-18%). A consistent finding was the more pronounced variation found when the A genotype was compared to the B-J genotypes than when the B-J genotypes were compared among themselves. A similar relatively more pronounced genetic variation between the A and B-D genotypes has also been found previously with the hemagglutinin-neuraminidase and fusion protein genes. It is concluded that the establishment of a new genotype should be founded on a nucleotide variation of the SH gene of > or = 6% in relation to previously described genotypes.

Classification↗
PubMed1987

The capsid polypeptides of the 190S virus of Helminthosporium victoriae.

SDS-PAGE of the 190S virus of Helminthosporium victoriae, using a discontinuous buffer system, revealed two major capsid polypeptides of mol. wt. 88K and 83K (p88 and p83) and a minor polypeptide, p78. Peptide mapping by both limited proteolysis and selective chemical cleavage showed p83 and p78 to be closely related to p88. The origin of p83/p78 could not be explained by proteolysis of p88 during virus preparation and storage. In rabbit reticulocyte lysates, denatured dsRNA directed the synthesis of a single major translation product which was identical to capsid polypeptide p88 on the basis of coelectrophoresis, immunoprecipitation and peptide mapping. No translation products comparable in size to p83 or p78 were detected in vitro. These data indicated that the capsid of the 190S virus is encoded by a single gene and verified the classification of the virus as a member of the family Totiviridae. Radioiodination of intact virus under conditions considered optimum for surface-specific iodination showed p88 to be more readily available for labelling than p83 or p78. Furthermore, when Western blots of capsid polypeptides were reacted with an antiserum to glutaraldehyde-stabilized virus (190S-G), p88 was more reactive to 190S-G antibodies than was p83/p78. These results suggest p88 is external to p83/p78 in the capsid.

Capsid↗
PubMed1989

Bovine ephemeral fever.

Ephemeral fever remains a viral disease of considerable importance to many countries including Australia. The virus has been only partly characterised and still awaits final classification. Although BEF virus was first thought to contain 6 structural proteins there is increasing evidence to suggest that it contains the 5 proteins characteristic of the Rhabdoviridae. Although BEF is thought to be arthropod borne, the vector has yet to be identified but it is clear from the distribution of BEF that more than one vector is capable of transmitting the disease. Despite rigorous investigation of the clinical signs and the pathology of ephemeral fever, little progress has been made on the pathogenesis of the disease. This has been partly due to the difficulty of propagating BEF virus in vitro and the inability to define the site of replication. However, there is mounting evidence to suggest that BEF is immunopathologic in nature and that the clinical expression of the disease is influenced by the release of one or more mediators of inflammation. The disease is characterised by a number of haematological and biochemical changes and early and prolonged treatment with phenylbutazone is capable of reversing a number of these changes. The intravenous administration of calcium can now be considered a justifiable addition to the treatment regimen together with prolonged phenylbutazone therapy. The vaccines currently available are prepared from either live attenuated or killed virus and may be less than reliable. There appears to be a need for a reliable, inexpensive, cold-chain independent alternative vaccine.

Animals↗
PubMed1993

[Case reports of hemorrhagic diathesis in calves with bovine diarrhea virus infection].

Clinical and pathological findings in six veal calves suffering from haemorrhagic diathesis are reported. Further pathological and virological results were highly suggestive of mucosal disease (BVD). No virus isolation or classification was possible. The post mortem results indicated that the virus might have been cytopathogenic. The cases are discussed and compared with similar field and experimental publications dealing with thrombocytopenia in veal calves in the USA. These are the first reports of cases published in Germany.

Animals↗
PubMed2005

Molecular characterization of isolates of anagyris vein yellowing virus, plantago mottle virus and scrophularia mottle virus -- comparison of various approaches for tymovirus classification.

The complete nucleotide sequences were determined for the genomic RNAs of three tymoviruses, i.e. isolates of anagyris vein yellowing virus (AVYV), plantago mottle virus (PlMoV) and scrophularia mottle virus (SrMV) which are all serologically closely related to ononis yellow mosaic virus (ibid) and to Nemesia ring necrosis virus (NeRNV), a recently described recombinant virus which is widely spread in commercially grown ornamental plant species belonging to the Scrophulariaceae. Total nucleotide and coat protein amino acid sequence identities revealed similar groupings in the genus tymovirus as serological studies did. The latter, however, tended to suggest much closer relationships than the molecular data and may fail to recognise the distinctiveness of new tymovirus species. The usefulness of various species demarcation criteria for the classification of tymoviruses is discussed.

Genome, Viral↗
PubMed1996

[The characterization of influenza viruses by the immunoperoxidase method using monoclonal antibodies. Its setup and validation].

The immunoperoxidase method for the rapid classification of influenza viruses in type and subtype was applied and validated for the first time in Cuba. The method is based on a rapid culture in MDCK-L cells and on the use of monoclonal antibodies for the classification in type and subtype. A pool of antibodies against influenza A and another against influenza B and HA1-71 and HA2-76 monoclonal antibodies are used for the subtyping in H1 and H3. The validation was carried out by applying this method to 21 international reference strains and to 23 human influenza virus strains that were isolated and previously classified by hemagglutination inhibition. All the strains reacted to the monoclonal antibodies according to their hemagglutinin type and subtype. 6 reference strains and 9 isolations were characterized within the H1N1 subtype: 9 reference strains and 10 isolations in the H3N2 subtype; and 6 reference strains and 4 isolations in type B. There were neither unspecific nor crossed reactions among the controls established. There was 100% of sensitivity, specificity and coincidence. The technique used proved to be fast and convenient for the characterization in type and subtype of the isolated influenza virus strains. It may substitute the classic hemagglutination inhibition method when it is required the rapid characterization of outbreaks or epidemics of acute respiratory infections, which is very important due to the high morbidity they cause mainly in risk groups and to their economic repercussion.

Antibodies, Monoclonal↗
PubMed1994

Phylogenetic classification of human T cell leukaemia/lymphoma virus type I genotypes in five major molecular and geographical subtypes.

Proviral DNA was obtained from ex vivo peripheral blood mononuclear cells of 75 human T cell leukaemia/lymphoma virus type I (HTLV-I)-infected individuals who were either asymptomatic or had adult T cell leukaemia or tropical spastic paraparesis/HTLV-I-associated myelopathy. Amplified long terminal repeats (LTRs) were analysed for restriction fragment length polymorphisms (RFLPs). The results, together with previously published LTR data (a total of 180 specimens analysed), showed the presence of 12 different RFLP profiles with four major molecular subtypes. Furthermore, a fragment of 413 bp (nucleotides 22 to 434) of the U3/R region was sequenced for 12 new HTLV-I specimens originating from Central and West Africa (8 cases), Iran (1 case), Caribbean (2 cases) and Reunion Island (1 case). Phylogenetic analysis using three different techniques (maximum parsimony, neighbour-joining and UPGMA) comparing these 12 strains (including four new African HTLV-I variants) with the 30 published partial HTLV-I LTR sequences (nt 120 to 434) showed the existence of clusters of molecular variants in discrete geographical areas. The topology of the phylogenetic trees is thought to reflect HTLV-I evolution and the migrations of virally infected populations in the recent or distant past. Furthermore, there was a nearly perfect concordance between the clustering based on the LTR sequence homologies and the LTR RFLP subtypes suggesting that this rapid and simple technique is well suited to the investigation of HTLV-I molecular epidemiology. These results allow a new phylogenetic classification of HTLV-I genotypes into five major molecular subtypes: Cosmopolitan (C) subtype widespread all over the world, Japanese (J) subtype, West African (WA) subtype. Central African (CA) subtype and Melanesian (M) subtype.

Africa↗
PubMed1972

Inactivation of the hemagglutinins of type A influenza viruses by physical and chemical means: an aid to classification.

The effects of temperature and treatment with sodium dodecyl sulfate, Tween 20, dithiothreitol, trypsin, or guanidine on the hemagglutinating capacity of six strains of type A influenza virus (A(0)/PR8/34, A(1)/CAME/46, A(2)/J305/57, A(2)/Bethesda/63, A(2)/HK/Aichi/68, and A(2)/HK/80/68), one strain of swine virus (A/Swine/76/?), and one equine strain (A/Equi-2/63) were determined. The two Hong Kong strains could be readily distinguished from the earlier A(2) strains by the resistance of their hemagglutinins to trypsin treatment and their inability to recover hemagglutinating capacity after removal of dithiothreitol from treated virus preparations. In these respects, the equine strain most closely resembled the Hong Kong variants. The pattern of hemagglutination inactivation also set the swine, PR8, and CAME strains apart from each other as well as from the other five strains. The results suggest that separation of type A viruses into groups by the pattern of inactivation of their hemagglutinins may be a valuable adjunct to standard serology for a more definite classification of these viruses.

Animals↗
PubMed1986

env genes of avian retroviruses: nucleotide sequence and molecular recombinants define host range determinants.

The env gene of avian sarcoma and leukosis retroviruses is allelic in the virus population permitting the virus to use different host cell receptors. This polymorphism has allowed the classification of these viruses into different subgroups. In order to understand further the role of viral sequences involved in determining this host range phenomenon, we constructed molecular recombinants between subgroup A, B, and E viruses and showed that the host range determinant defining subgroup specificity was located within a 1.1-kb region of the genome that included most of the coding region for the env gene product gp85. We also determined the nucleotide sequence of the region of the env gene encoding gp85 for virus isolates representing subgroup A and B viruses. We compared the predicted amino acid sequences of gp85 to themselves and to the previously published sequences of subgroup B, C, and E env genes. Based on these comparisons, we draw the following conclusions: Within the gp85 coding domain, there are four variable regions (VR-1 to VR-4) ranging in size from 9 to 52 amino acids. The variable regions are located in the same relative positions for each of the env gene alleles compared. The variable regions range in homology from 42% (A compared to B) to 57% (C compared to E) in pairwise comparisons; the flanking conserved domains are on average 95% homologous. The sequences of three different subgroup B virus isolates are highly homologous in both the conserved and variable regions. Secondary structure predictions suggest that gp85 is composed mostly of beta sheet topology. Hydrophilic loops within the variable regions may define sites of receptor interaction and binding sites for subgroup specific neutralizing antibodies.

Alleles↗