TRENDS IN THE LABORATORY DIAGNOSIS OF VIRAL INFECTIONS.
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Classification↗
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Occurrence of different types of infectious hematopoietic necrosis virus in fish.
The virion protein patterns of 71 isolates of infectious hematopoietic necrosis virus (IHNV) from the Pacific Northwest were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of [35S]-methionine-labeled virus. This analysis led to the classification of these virus isolates into four or more types. Type 1 virus was characterized by a nucleocapsid protein with an approximate molecular weight of 40,500. Type 2 and type 3 viruses have nucleocapsid proteins with molecular weights of 42,800 and 43,250, respectively. Type 2 virus was responsible for the recent epizootics of IHNV among fish in the lower Columbia River. The California IHNV isolates were type 3 with the exception of some of those isolated from fish at the Coleman Hatchery on the Sacramento River. These Coleman Hatchery isolates belonged to a type 4 virus group characterized by a larger glycoprotein of approximately 70,000 molecular weight. All other viruses examined had glycoproteins of 67,000 molecular weight. The "type 5" virus isolates were grouped together because they were not sufficiently distinct to warrant classification into a separate type. These findings have been useful in determining that a particular virus type is characteristic for a geographic area and will infect many different salmonid species in that area and the same type isolated from parental fish is responsible for the subsequent outbreak of the diseases in progeny.
Animals↗
Genetic classification of "Sapporo-like viruses".
"Sapporo-like viruses" (SLVs) and "Norwalk-like viruses" (NLVs) are an important cause of acute gastroenteritis in humans. While NLVs have been genetically classified into three major genetic groups consisting of 17 genetic subgroups, a classification of SLVs into comparable genetic groups remains to be determined. In an attempt to classify both SLVs and NLVs uniformly, the sequences of 2 SLV strains newly detected from French infants were analysed together with the published sequences of 9 SLV and 19 NLV strains. Distance and phylogenetic analyses were conducted on the sequences of the capsid gene, RNA polymerase gene, 3' open reading frame (3'ORF), ORF overlapping the capsid gene, and 3' untranslated region (3'UTR). The histogram showing frequency distribution of pairwise distances and the topology of the phylogenetic tree demonstrated that SLVs and NLVs could be classified uniformly on the basis of the entire capsid sequences and that the 11 SLV strains could be genetically classified into 3 major genetic groups, genogroups I, II and III, comprised of 5 genetic subgroups. The differentiation of the 11 SLV strains into these genetic groups was also maintained in the 4 remaining genome regions, while the sequences at the junction between the RNA polymerase and capsid genes were shown to be genogroup-specific.
3' Untranslated Regions↗
High sequence conservation among cucumber mosaic virus isolates from lily.
For classification of Cucumber mosaic virus (CMV) isolates from ornamental crops of different geographical areas, these were characterized by comparing the nucleotide sequences of RNAs 4 and the encoded coat proteins. Within the ornamental-infecting CMV viruses both subgroups were represented. CMV isolates of Alstroemeria and crocus were classified as subgroup II isolates, whereas 8 other isolates, from lily, gladiolus, amaranthus, larkspur, and lisianthus, were identified as subgroup I members. In general, nucleotide sequence comparisons correlated well with geographic distribution, with one notable exception: the analyzed nucleotide sequences of 5 lily isolates showed remarkably high homology despite different origins.
Capsid↗
Viral heterogeneity of the hepatitis C virus.
This review summarises the classification of hepatitis C virus as a flavivirus, the identification and detection of HCV genotypes, and reviews the current information concerning the geographical and risk group associations of the common genotypes in Europe.
Genetic Heterogeneity↗
[Isolation of a virus from sheep and its classification as a new serotype of ovine adenoviruses].
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Adenoviridae↗
Differentiation of the four viruses of the sugarcane mosaic virus subgroup based on cytopathology.
A cytological comparison has been made of representative isolates of johnsongrass mosaic (JGMV), maize dwarf mosaic (MDMV), sorghum mosaic (SrMV) and sugarcane mosaic (SCMV) viruses. These four viruses now encompass the complex of virus strains which were formerly considered as strains of sugarcane mosaic and/or maize dwarf mosaic viruses. The structure of the cytoplasmic cylindrical inclusions induced by these viruses, together with other cytological alterations, allow the four viruses to be distinguished. Pinwheels, scrolls and laminated aggregates were produced only by SCMV whereas JGMV, MDMV, and SrMV produced only pinwheels and scrolls. SrMV produced amorphous cytoplasmic inclusions which are not produced by JGMV and MDMV. The latter two were rather similar in cytological effects except that the SCMV-JG (U.S.A.) isolate of MDMV produced aggregates of needle-like structures in the cytoplasm which were not found with JGMV and the other MDMV isolates. The specific cytological effects induced by these viruses thus corroborate the recent classification of these viruses based mainly on the properties of the coat-protein gene, the 3' noncoding nucleotide sequences, and host reactions.
Cytopathogenic Effect, Viral↗
Morphogenesis of a cytomegalovirus from an American bison affected with malignant catarrhal fever.
A herpesvirus isolated from several organs of an American bison affected with malignant catarrhal fever was cultured in bovine foetal spleen cells and studied by electron microscopy. The fine structural features of the mature virion and the mode of virus morphogenesis were found to be similar to herpesviruses classified in the subgroup cytomegalovirus. The capsids were granular, hexagonal in shape and contained pleomorphic cores in thin sections. Envelopment of the capsids occurred primarily by budding on cytoplasmic membranes which appeared to be formed as extended vesicles of the Golgi apparatus; budding on nuclear membranes was only rarely observed. Cytoplasmic inclusions consisting of granular threads and amorphous electron-dense material were found in association with virions during the late stages of infection. The formation of cytoplasmic inclusions, the morphogenesis and ultrastructure of the virus are all consistent with classification of this virus as a cytomegalovirus.
Animals↗
Transmission of B virus infection between monkeys especially in relation to breeding colonies.
Studies of B virus (Herpesvirus simiae) antibody in several species of macaque lead to the following generalizations. Newborn monkeys are not infected with B virus, even when born of seropositive mothers. Young monkeys remain uninfected until they become adults. The majority of adults develop B virus antibody unless their physical contact with seropositive adults is restricted. These observations are consistent with sexual transmission of B virus and classification of the disease in monkeys as venereal. However, infection at oral and dermal sites also occurs and may play a part in monkey-to-monkey transmission. Epizootics of B virus occurred during early attempts to start B virus-free breeding colonies. They appeared to originate from reactivated latent B virus in adult monkeys which had only low titres of antibody. The stress produced when groups of adult strangers were assembled to form breeding colonies was the most effective known inducer of latent B virus. Total exclusion of animals with any trace of antibody has enabled the establishment of new breeding colonies which are free from B virus.
Age Factors↗
Sequence characterization and expression of the matrix protein gene of human parainfluenza virus type 1.
The nucleotide sequence of the M gene of human parainfluenza virus type 1 (hPIV1) was determined from genomic RNA and cDNA copies of the entire gene. The M gene contained 1173 nucleotides. It had one large open reading frame capable of encoding a protein of 348 amino acids (M(r) = 38,404). The predicted amino acid sequence of the hPIV1 M protein is highly basic (+20 at neutral pH). A pGEM-1 expression vector containing the M gene was used for cell-free transcription and translation. The resultant protein was confirmed to be M by electrophoretic mobility and immunoprecipitation. Among other paramyxoviridae the hPIV1 M amino acid sequence was most closely related to the Sendai virus M sequence (87% identity). The pattern of M gene relatedness observed from the alignment of 16 paramyxoviridae M protein amino acid sequences was not predicted by the viruses' taxonomic classification.
Amino Acid Sequence↗
Interference with superinfection and with cell killing and determination of host range and growth kinetics mediated by feline leukemia virus surface glycoproteins.
The functions of the surface glycoproteins (SU) of feline leukemia viruses (FeLVs) are of interest since these proteins mediate virus infection and interference and are critical determinants of disease specificity. In this study, we examined the biochemical and genetic determinants of SU important to virus entry and cell killing. In particular, we developed and used vesicular stomatitis virus (VSV)/FeLV pseudotype virus interference assays to determine interference subgroupings and assess mechanisms of host cell restriction. We also assessed roles of SU in virus growth kinetics and in the inhibition of cell killing caused by superinfection with cytopathic virus. Subgroup classification by VSV/FeLV pseudotype assay was in agreement with that defined previously by focus interference assay and was found to be determined by changes near the N terminus of SU for FeLV subgroups A (FeLV-A) and C. Virus host range restriction was found to be mediated at the level of virus entry in most cases, although postentry events mediated restriction in the failure of a subgroup A-like, T-cell cytopathic and immunodeficiency-inducing clone (FeLV-FAIDS-EECC) to replicate in feline fibroblasts. FeLV-FAIDS-EECC-induced cell killing was also inhibited by prior infection with one of two FeLV-A isolates. This inhibition could be conveyed by as few as four amino acid changes near the N terminus of the FeLV-A SU and also appeared to be mediated at a postentry level. Lastly, the SU-coding sequence was also found to determine differences in growth kinetics of viruses within the same subgroup. These studies demonstrate that subtle alterations in the FeLV SU, particularly in the N-terminal region, impart multiple significant functional differences which distinguish virus variants.
Amino Acid Sequence↗
Selection of vaccine strains of foot and mouth disease virus for use in southern Africa.
In the countries of Southern Africa, types SAT 1, SAT 2 and SAT 3 (SAT: Southern African Territories) of foot and mouth disease (FMD) virus are the most widely represented, especially the SAT 2 virus. Since 1982, examinations have been conducted on 139 isolates of these virus types. Other viruses, types O and A, have been detected in the north of this area. The typing and sub-typing of viruses with the complement fixation (CF) test can be improved by using panels of monoclonal antibodies (MAbs), which provide an accurate antigenic profile of a new strain. A total of 33 SAT 2 strains have been investigated using MAbs, and the results enable the classification of viruses into groups presenting the same profile. The author presents comparisons of isolates and vaccine viruses using conventional methods of serotyping--CF and virus neutralisation (VN) tests--as well as profiling the isolates using MAbs. Both manners of analysis provide information on the relationships between the viruses. The CF and VN tests give details on how animals responded against a particular isolate and how this antibody response would recognise another isolate; from this, the serological relationships can be proposed with respect to how different isolates might induce a humoral immune response. With MAb profiling, details of antigenic relationships between the isolates are obtained, enabling the identification of individual epitopic variations. These analyses can provide the potential to place different isolates into 'antigenic' groups. When compared with vaccine viruses, one can attempt to identify the vaccine virus with the closest profile to the isolate group. Immunological analysis (e.g. using the CF tests employed in this paper) can provide further information on the relationship between a particular vaccine and an antigenic group identified by MAb profiling. Of course, this MAb profiling can provide essential information in a very short time, which is of particular benefit in an emergency situation. Confirmation of the conclusions from the profiling would then be forthcoming through the serological analyses. Such combined analyses offer a more extensive identification of antigenic and immunogenic relationships between FMD virus isolates, as well as between isolates and vaccine viruses.
Africa, Southern↗
Clear detection and typing of herpes simplex virus types 1 and 2 by an indirect ELISA assay: comparison with three different combined methods--capture ELISA, restriction enzymes, and polymerase chain reaction.
The severity and recurrences of Herpes Simplex Virus (HSV) infection depend on the type of the infectious agent (HSV-1 or HSV-2), which induces the necessity of a nonambiguous detecting typing. The commonly used capture ELISA technique has to be often supported by DNA analysis to confirm the detection and the typing of HSV viruses in exposed patients. In this report, we describe a rapid and cheap indirect ELISA method using anti-HSV monospecific polyclonal antibodies prepared in the laboratory. The typing of the studied samples was clear, did not need series of dilution, and allowed the immediate classification of viruses without further control examination. We tested 51 specimens, which were typed 25 HSV-1 and 26 HSV-2 strains. The comparison with capture ELISA, restriction enzyme and polymerase chain reaction analysis definitely allowed our method to be assessed as a useful tool for a routine diagnostic.
Antibodies, Viral↗
Gene sequence and mapping data from Marek's disease virus and herpesvirus of turkeys: implications for herpesvirus classification.
Purified DNAs from Marek's disease virus (MDV) and the herpesvirus of turkeys (HVT) were randomly sheared and cloned into the M13 bacteriophage. Two-hundred and ten MDV and 130 HVT clones were sequenced to give representative samples of the genome sequences. The predicted amino acid sequences from these gammaherpes-viruses were compared to known sequences from other herpesviruses using computer analysis. Thirty-five MDV and 24 HVT genes were identified by comparison with varicella-zoster virus (VZV), an alphaherpesvirus. However, only 14 MDV and seven HVT genes, giving generally lower homology scores, were found by comparison with Epstein-Barr virus (EBV), a gammaherpesvirus, indicating that MDV and HVT sequences bear greater similarity to VZV than to EBV sequences. A number of sequences were mapped by hybridizing labelled M13 clones to Southern blots of restriction fragments of MDV or HVT DNA. The results were consistent with the MDV and HVT genomes being collinear with VZV.
Amino Acid Sequence↗
Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type 1 by using restriction fragment length polymorphism analysis.
The simultaneous presence of multiple HIV-1 subtypes has become common in communities with the growth of the pandemic. As a consequence, the potentiality for an increased frequency of HIV-1 mixed infections caused by viruses of distinct subtypes could be expected. Thus, there is a need to estimate the prevalence and geographic distribution of infections caused by viruses of a singular subtype as well as coinfections caused by two or more HIV-1 strains of distinct subtypes. To address this need, we have developed a genetic method based on restriction fragment length polymorphism (RFLP) to screen for these two types of infections within infected populations. In this assay, restriction enzymes may be used to predict the phylogroup of HIV-1 infected samples. A 297 bp pol fragment spanning the entire viral protease gene and a 311 bp fragment of the p24 gag region are used for this analysis. The viral regions are amplified by nested PCR using DNA templates from uncultured peripheral blood mononuclear cells (PBMC) or virus culture. Classification of HIV-1 strains to well defined subtypes B, D, F, and A/C is done by sequential endonuclease restriction analysis of a PCR amplified-protease gene followed by analysis of the p24 gag region. The electrophoretic migration patterns visualized by ethidium bromide staining or by radiolabeled probes are then determined on a 10% polyacrylamide gel. In infections caused by viruses of a singular subtype, a single restriction pattern is detected, whereas in multiple infections caused by two or more viral strains of different subtypes, the combination of different digestion patterns are observed in infected individuals. Using this methodology we have screened for genetic variations in HIV-1 proviral DNA from thirty-three Brazilian samples. Our RFLP procedure classified thirty-two samples as single infections caused by viruses of subtypes B (31) and F (1), and one sample as dual infection caused by distinct viral strains. Subsequent sequence and phylogenetic analysis of the viral protease gene in lymphocytes of all these patients confirmed our RFLP findings in single infections, and demonstrated the existence of two distinct HIV-1 strains of subtypes F and D in a patient which lymphocytes showed the simultaneous presence of two different digestion patterns. As up to now, single infections caused by subtype D variants were not identified in Brazil, our data provide the first evidence of subtype D HIV-1 in this country. Because sequencing of HIV proviral DNA is not particularly practical for large-scale molecular epidemiological studies, the protease/gag-based RFLP screening method will be useful to predict the phylogroup of HIV-1, and to identify multiple infections caused by HIV-1 strains of distinct subtypes. We believe that this information is crucial for both evaluation of the HIV-1/AIDS pandemic and intervention strategies.
Adult↗
The relationship of the receptors of a new strain of virus to those of the mumps-NDV-influenza group.
The interrelationships of the cellular receptors and the hemagglutinin inhibitors of a new strain of virus (1233) to members of the mumps-Newcastle disease-influenza group have been investigated. It was found that strain. 1233 does not destroy the receptors or inhibitors of the other group, nor does the latter destroy 1233 receptors or inhibitor. The sole exception to this statement was a moderate destruction of 1233 inhibitor in egg white by Newcastle disease virus. The classification of strain 1233 was discussed in the light of this evidence, evidence which tends to place strain 1233 in a different category from that of any other strain of the MNI group.
Animals↗
A classification of the murine leukemia viruses. Neutralization of pseudotypes of Friend spleen focus-forming virus by type-specific murine antisera.
Coinfection of neonatal BALB/c mice with helper-dependent Friend spleen focus-forming virus (SFFV), as contained in the Friend virus (FV) complex, and antigenically distinct Moloney leukemia virus (MolLV) resulted in the recovery of a MolLV pseudotype of SFFV, abbreviated SFFV(MolLV). The antigenic alteration of SFFV was observed by following its neutralization kinetics in vitro by specific Friend or Moloney typing antiserum. Effective pseudotype production was accomplished only when N-tropic LLV-F (the natural helper virus in the FV complex) was inhibited in B-type mice coinfected with an NB-tropic MolLV or other murine leukemia virus (MuLV) preparation. SFFV pseudotypes could not be prepared by using murine viruses other than leukemia viruses. SFFV prepared after two serial passages in the presence of MolLV was effectively neutralized by Moloney antiserum, but not by Friend typing antiserum; therefore, the envelope of the pseudotype virus, SFFV(MolLV), is homogeneous. Pseudotype virus was antigenically stable in the absence of continued mixed infection of BALB/c mice with SFFV(MolLV) and MolLV. However, SFFV(MolLV) was easily converted back to the LLV-F type after only one passage in BALB/c mice coinfected with NB-tropic LLV-F. The antigenic interconversion between LLV-F and MolLV types demonstrated that SFFV is defective with respect to the expression of neutralizable envelope antigens. Analysis of the neutralizable envelope antigens of nine SFFV(MuLV) pseudotypes by a panel of seven typing antisera made possible a "type-specific" SFFV(MuLV) envelope classification. Two major categories have been identified which correspond to the Gross (G) and Friend-Moloney-Rauscher (FMR) subgroups. Further, the FMR subgroup was divided into four types on the basis of distinct neutralization patterns. These results indicated that the specificity observed by cytotoxic G vs. FMR antisera is different from that observed by neutralization kinetics. We therefore suggest that the specific antigens revealed by virus neutralization tests be referred to as type specific.
Animals↗
NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.
MOTIVATION: Oncoviruses, pathogens known to cause or increase the risk of cancer, include both common viruses such as human papillomaviruses and rarer pathogens such as human T-lymphotropic viruses. Computational methods for detecting viral DNA from data acquired by modern DNA sequencing technologies have enabled studies of the association between oncoviruses and cancers. Those studies are rendered particularly challenging when multiple species of oncovirus are present in a tumor sample. In such scenarios, merely detecting the presence of a sequencing read of viral origin is insufficiently informative-instead, a more precise characterization of the viral content in the sample is required. RESULTS: We address this need with NextVir, to our knowledge the first multi-class viral classification framework that adapts genomic foundation models to detecting and classifying sequencing reads of oncoviral origin. Specifically, NextVir explores several foundation models-DNABERT-S, Nucelotide Transformer, and HyenaDNA-and efficiently fine-tunes them to enable accurate identification of the sequencing reads' origin. The results demonstrate superior performance of the proposed framework over existing deep learning methods and suggest downstream potential for foundational models in genomics.
Humans↗