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The proteolytic cleavage of potyvirus coat N-terminal region is discussed with relation to host recovery and aphid transmission. The relationship of this coat protein region and the HC, may affect the host range and should be considered in this virus group classification.
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The concept of pathotype in Marek's disease (MD) probably dates from the recognition of a more virulent form of the disease in the late 1950s (Benton & Cover, 1957). Distinctions between MD virus strains were further expanded with the description of the vv pathotype in the early 1980s and of the vv+ pathotype in the 1990s. Pathotype designations reflect important biological properties that correlate with the break-through of vaccinal immunity in the field. However, pathotyping methods applied by various laboratories have not been uniform, preventing critical comparison of results. Better uniformity of pathotyping procedures is desirable.The Avian Disease and Oncology Laboratory (ADOL) method is based on induction of lymphoproliferative lesions in vaccinated chickens. This method has been used to pathotype more than 45 isolates and is the basis for the current pathotype classification of MD virus strains. Its limitations include requirements for a specific type of chickens (15x7 ab+), large numbers of animals, and a statistical method to compare lesion responses to those of JM/102W and Md5 control strains. Because of these limitations, it has not been and is not likely to be used in other laboratories. Comparability in pathotyping can be improved by the comparison of field isolates with standard prototype strains such as JM/102W, Md5 and 648A (American Type Culture Collection) or their equivalents. Data may be generated by different in vivo procedures that measure tumour induction, neurological disease (both neoplastic and non-neoplastic lesions), or solely non-neoplastic criteria (such as lymphoid organ weights or virus replication). Methods based on neoplastic criteria, especially when generated in MD-immunized chickens, will probably correlate most closely with that of the ADOL method and be most relevant to evolution of MD virus in the field. Based on data from several trials, a modification of the ADOL method that utilizes fewer chickens and can be conducted with commercial specific pathogen free strains is proposed. The modified method is based on "best fit" comparisons with prototype strains, and is expected to provide results generally comparable with the original method. A variety of other alternative criteria (see earlier) are also evaluated both for primary pathotyping and as adjuncts to other pathotyping methods. Advantages and disadvantages of alternative methods are presented.
Because immunologic classification of human immunodeficiency virus type 1 (HIV) might be more relevant than genotypic classification for designing polyvalent vaccines, studies were undertaken to determine whether immunologically defined groups of HIV ("immunotypes") could be identified. For these experiments, the V3 region of the 120-kDa envelope glycoprotein (gp120) was chosen for study. Although antibodies (Abs) to V3 may not play a major protective role in preventing HIV infection, identification of a limited number of immunologically defined structures in this extremely variable region would set a precedent supporting the hypothesis that, despite its diversity, the HIV family, like the V3 region, might be divisible into immunotypes. Consequently, the immunochemical reactivities of 1,176 combinations of human anti-V3 monoclonal Abs (MAbs) and V3 peptides, derived from viruses of several clades, were studied. Extensive cross-clade reactivity was observed. The patterns of reactivities of 21 MAbs with 50 peptides from clades A through H were then analyzed by a multivariate statistical technique. To test the validity of the mathematical approach, a cluster analysis of the 21 MAbs was performed. Five groups were identified, and these MAb clusters corresponded to classifications of these same MAbs based on the epitopes which they recognize. The concordance between the MAb clusters identified by mathematical analysis and by their specificities supports the validity of the mathematical approach. Therefore, the same mathematical technique was used to identify clusters within the 50 peptides. Seven groups of peptides, each containing peptides from more than one clade, were defined. Inspection of the amino acid sequences of the peptides in each of the mathematically defined peptide clusters revealed unique "signature sequences" that suggest structural motifs characteristic of each V3-based immunotype. The results suggest that cluster analysis of immunologic data can define immunotypes of HIV. These immunotypes are distinct from genotypic classifications. The methods described pave the way for identification of immunotypes defined by immunochemical and neutralization data generated with anti-HIV Env MAbs and intact, viable HIV virions.
An attempt was made to classify herpes simplex virus type 1 (HSV-1) isolates into subtypes on the basis of the combination of the gain or loss of specific cleavage sites of HSV-1 genomes with each of three restriction endonucleases (Bam HI, Kpn I, and Sal I). According to the criteria we used for the determination of HSV-1 subtypes, 93 strains of HSV-1 that were isolated in three areas of Japan (Sapporo, Tottori, and Kagawa) were tentatively classified into eight subtypes: subtypes A-H. The bulk of the strains (84 of 93) fell into three subtypes: A, C, and H. There were highly significant differences (P less than .01) in the proportion of subtypes A and H that were isolated in Sapporo as compared with those isolated in Tottori and in Kagawa, which are geographically far from Sapporo. No significant differences, however, were found in subtypes isolated in Tottori as compared with those isolated in Kagawa, which are geographically close to each other. These data suggest that there might be a correlation between the genome structure of HSV-1 and the areas of their isolation in Japan.
Hantaviruses (genus Hantavirus, family Bunyaviridae) represent a prime example of emerging viruses. Since isolation of the prototype Hantaan virus in the late 70s more than 20 new species have been described and the number is increasing fast thus demanding for a more refined classification. Taking into account that hantaviruses are difficult to isolate in cell culture, one should not be surprised that most of the "newcomers" were first described as distinct hantavirus genotypes. Moreover, the only "solid" characteristics of many hantavirus species still exist in the form of nucleotide sequences of their genome. The relatively short history of hantavirology can thus be taken to illustrate how genetics can contribute to (and even, perhaps, dominate) discovery, characterization and classification of viruses. In this review the following aspects of hantavirus genetics are discussed: (i) genome structure; (ii) genetic diversity and evolution; and (iii) use of genetic criteria in current taxonomy of hantaviruses. In addition, several examples of classification of hantavirus species (New York virus, Saaremaa virus and Hokkaido virus) are given, and future prospects are analyzed.
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Viruses evolve gradually through replication. Therefore, isolates of a virus species can have different genome sequences, albeit slightly, if isolates are epidemiologically unrelated. The difference in virus genome involves difference in virus functions and clinical manifestations of virus infection. Molecular epidemiology of virus infection is a relatively new field directed at infection in humans but not other animals. Analyses are based on genomic differences between virus strains with advances in methodology related to DNA analyses, progress is being made. Classification of virus strains, tracing of transmission of a strain, analyses of outbreaks (including nosocomial infection), and analyses of pathogenesis of virus infection in humans (a natural host) are given attention in molecular epidemiological studies. Human parvovirus B19 is a common human pathogen associated with a wide variety of diseases, including erythema infectiosum, aplastic crisis, hydrops fetalis, and arthritis. B19 is not propagatable in conventional cell lines, hence, molecular cloning of B19 DNA directly from clinical materials has to be done. Events concerning B19 infection were analyzed based on the concept of molecular epidemiology and studies proved to be productive to better understand the pathogenesis of B19 infection.
Viruses occupy a unique position in biology. Although they possess some of the properties of living systems such as having a genome, they are actually nonliving infectious entities and should not be considered microorganisms. A clear distinction should be drawn between the terms virus, virion, and virus species. Species is the most fundamental taxonomic category used in all biological classification. In 1991, the International Committee on Taxonomy of Viruses (ICTV) decided that the category of virus species should be used in virus classification together with the categories of genus and family. More than 50 ICTV study groups were given the task of demarcating the 1,550 viral species that were recognized in the 7th ICTV report, which was published in 2000. We briefly describe the changes in virus classification that were introduced in that report. We also discuss recent proposals to introduce a nonlatinized binomial nomenclature for virus species.
The main contributions of the author and collaborators about sialidase (EC 3.2.1.18) of influenza virus types A and B and O-acetylesterase (EC 3.1.1.53) of type C are summarized. After a short introduction on the topic, the negative results obtained by the author on inhibitors are commented. Then, the peculiarities of the three procedures assayed, based on the NADH determination as a measurement for the sialidase activity, are discussed. The spectrofluorimetric measurement of NADH concentration is a more sensitive and convenient procedure than that by spectrophotometry, although it is less sensitive than that based on bioluminiscence. Sialidase activity is generally higher in influenza virus type A than in type B; however, some differences have been found between the three sub-types A analysed. Furthermore, thermal stability and stability against changes in the pH values are higher for influenza virus from ducks, followed by those from humans and, finally, by those from pigs. O-acetylesterase of influenza virus type C shows a broad specificity; it acts on O-acetyl-containing compounds which may not be sialic acids. It seems that this enzyme might contribute to facilitate the action of sialidase of influenza virus types A and B. The peculiarities of influenza virus type C suggest to include this type as a new genus in the future classification of viruses.
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Hepatitis C virus (HCV) sequences from throughout the world have been grouped into six clades, based on recently proposed criteria. Here, the partial sequences and clade assignment are reported for three HCV isolates from chronic hepatitis C patients from Somalia, for whom conventional assays failed to identify the genotype. Phylogenetic analysis of the sequences of the core, envelope 1 and part of the non- structural 5b regions suggests that all three isolates belong to a distinct HCV genetic group, tentatively classified as subtype 3h. This novel HCV subtype shows the highest sequence similarity with HCV isolates from Indonesia. Despite the fact that these patients were infected with HCV clade 3, none of them responded to standard interferon treatment.
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Our discovery that the major coat protein of bacteriophage PRD1 resembles that of human adenovirus raised the unexpected possibility that viruses infecting bacteria could be related by evolution to those infecting animal hosts. We first review the development of this idea. We then describe how we have used structure-based modeling to show that several other viruses with no detectable sequence similarity are likely to have coats constructed from similar proteins-the "double-barrel trimer." There is evidence that the group includes a diversity of viruses infecting very different hosts in all three domains of life: Eukarya; Bacteria; and Archaea that diverged billions of years ago. The current classification of viruses obscures such similarities. We propose that the occurrence of a double-barrel trimer coat protein in an icosahedral dsDNA virus with large facets, irrespective of its host, is a very strong indicator of its membership in a lineage of viruses with a common ancestor.
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OBJECTIVE: To review 10 years' experience in a tertiary care paediatric hospital of erythema multiforme (EM), Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). In addition, to apply a recently described classification system for EM, SJS and TEN in children. DESIGN: Retrospective study of all children with a discharge diagnosis of EM, SJS or TEN over a 10-year period. SETTING: A university tertiary care paediatric hospital. PATIENTS: Sixty-one paediatric patients with a discharge diagnosis of EM, SJS or TEN. MAIN OUTCOME MEASURES: Epidemiology, laboratory features, causative factors, treatment methods, complications and mortality of EM, SJS and TEN in this group of patients. Comparison of correlation with aetiology of old and new classification systems in a paediatric population. RESULTS: Mucous membrane involvement was documented in 61% of patients. Ocular involvement was seen in 39%. Complications occurred in 21% cases, all of whom had SJS or TEN. Only one patient died as a result of their skin condition. Corticosteroids were used in 18% of cases; 95% of whom had a discharge diagnosis of SJS or TEN. The drugs most commonly identified as aetiological agents were sulphonamides and penicillins (26% each). The most frequently implicated infectious agent was herpes simplex virus (19.7%). Classification of study cases according to Bastuji-Garin et al. indicates a strong trend toward bullous EM cases being attributable to infection and SJS/TEN cases to drugs. There was no such clear trend with respect to aetiology when diagnosis was done without the classification system. CONCLUSION: EM, SJS and TEN rarely cause mortality but significant morbidity is seen. Infectious agents, particularly herpes simplex virus, and drugs, especially the sulphonamides and penicillins, are the most common aetiological agents. The classification system proposed by Bastuji-Garin et al. correlates better with aetiology than the practice that preceded it.
Virus genomics provides novel approaches for virus identification and classification. Based on the comparative analyses of sequenced lepidopteran-specific baculovirus genomes, degenerate oligonucleotides were developed that allow the specific amplification of several regions of the genome using polymerase chain reaction (PCR) followed by DNA sequencing. The DNA sequences within the coding regions of three highly conserved genes, namely polyhedrin/granulin (polh/gran), late expression factor 8 (lef-8), and late expression factor 9 (lef-9), were targeted for amplification. The oligonucleotides were tested on viral DNAs isolated from historical field samples, and amplification products were generated from 12 isolated nucleopolyhedrovirus (NPV) and 8 granulovirus (GV) DNAs. The PCR products were cloned or directly sequenced, and phylogenetic trees were inferred from individual and combined data sets of these three genes and compared to a phylogeny, which includes 22 baculoviruses using a combined data set of 30 core genes. This method allows a fast and reliable detection and identification of lepidopteran-specific NPVs and GVs. Furthermore, a strong correlation of the base composition of these three genome areas with that of the complete virus genome was observed and used to predict the base composition of uncharacterized baculovirus genomes. These analyses suggested that GVs have a significantly higher AT content than NPVs.