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PubMed1976

Equine infectious anemia virus: evidence favoring classification as a retravirus.

Equine infectious anemia virus (EIAV) has a density of 1.154 g/cm3 in sucrose a high-molecular-weight RNA similar in size to Rauscher murine leukemia virus, and an internal virion reverse transcriptase that utilizes the synthetic RNA template poly(rA) but not the synthetic DNA template poly(dA), both with (dT)12 as primer. Although capable of utilizing manganese at low concentrations (approximately 0.1 mM), EIAV reverse transcriptase showed highest activity in the presence of 9 mM magnesium. The major protein of EIAV has a slightly lower molecular weight than the comparable protein of type C viruses and co-electrophoresed with 125I-labeled p25 of Mason-Pfizer monkey virus. A reference horse serum with antibodies to the major EIAV protein reacted only with EIAV and not with other type C or non-type C retraviruses. Reciprocally, a broadly reactive serum to type C virus p30s and specific sera to a variety of non-type C retraviruses did not react with EIAV. We recommend the inclusion of EIAV in the family Retraviridae.

Antigens, Viral↗
PubMed1975

Antigenic characterization of the inclusion body hepatitis virus.

Proof that inclusion body hepatitis of chickens (IBHC) is caused by a virus (IBHV) was established in 1973. Characterization of IBHV has been conducted by employing the standard criteria for virus classification. The results have indicated that IBHV is a member of the avian adenovirus group. However, no antigenic relationship was found between IBHV and two other avian adenovirus isolates (CELO and Indiana C) as observed by hemagglutination (HA) and virus-serum neutralization tests. Another adenovirus isolate was found to be serologically different from IBHV (Tipton strain) but it incited typical IBHC in susceptible chicks. A novel antigen, detectable by the agar gel immunodiffusion test, was demonstrated in livers from chicks infected experimentally with IBHV. This antigen was able to give a specific precipitin reaction with serums from chickens previously exposed to IBHV. Repeated embryo passage of IBHV lowered its pathogenicity for susceptible chickens. Protection of chickens against IBHV challenge was obtained by vaccination with high embryo passage IBHV (Tipton strain). It was also found that subcutaneous administration of the vaccine virus induced a better immune response than the eye-drop route as observed by the virus-serum neutralization index obtained.

Adenoviridae↗
PubMed1989

[Probe seeks gene: nucleic acid hybridization as a current contribution to virologic diagnosis].

Molecular nucleic acid hybridization is based on the ability of single-stranded DNA/RNA to form hybrids with complementary labeled nucleic acids. This review shortly describes the components of this technique and presents the most important hybridization methods (spot-, Southern blot-, in situ-hybridization). The (potential) applications of nucleic acid hybridization as a diagnostic tool are discussed (e.g., for viruses which grow insufficiently or not at all in cell culture; virus latency; viruses with labile or antigenically variable envelope proteins, resp.; for virus classification) and yet existing limitations are indicated. An impetus for this technique in means of diagnostic application is expected to result from the Polymerase Chain Reaction (PCR) in the next future.

Animals↗
PubMed2001

The core region of the coat protein gene is highly useful for establishing the provisional identification and classification of begomoviruses.

Polymerase chain reaction (PCR) was applied to detect and establish provisional identity of begomoviruses through amplification of a approximately 575 bp fragment of the begomoviral coat protein gene (CP), referred to as the 'core' region of the CP gene (core CP). The core CP fragment contains conserved and unique regions, and was hypothesized to constitute a sequence useful for begomovirus classification. Virus relationships were predicted by distance and parsimony analyses using the A component (bipartite viruses) or full genome (monopartite viruses), CP gene, core CP, or the 200 5'-nucleotides (nt) of the CP. Reconstructed trees and sequence divergence estimates yielded very similar conclusions for all sequence sets, while the CP 5'-200 nt was the best strain discriminator. Alignment of the core CP region for 52 field isolates with reference begomovirus sequences permitted provisional virus identification based on tree position and extent of sequence divergence. Geographic origin of field isolates was predictable based on phylogenetic separation of field isolates examined here. A 'closest match' or genus-level identification could be obtained for previously undescribed begomoviruses using the BLAST program to search a reference core CP database located at our website and/or in GenBank. Here, we describe an informative molecular marker that permits provisional begomovirus identification and classification using a begomoviral sequence that is smaller than the presently accepted, but less accessible CP sequence.

Capsid↗
PubMed1986

Evidence that the amino acid composition of the particle proteins of plant viruses is characteristic of the virus group. II. Discriminant analysis according to structural biological and classification properties of plant viruses.

The amino acid composition (AAC) of the coat proteins (CPs) of 126 plant viruses or strains were analyzed by stepwise discriminant analysis. The criteria chosen for discrimination were: the structure of virus particles (3 clusters); the mode of of transmission of the viruses (6 clusters); and the grouping of viruses according to the classification of the International Committee on Taxonomy of Viruses (23 groups). Statistically significant correlations were obtained with different groups of discriminant amino acids. The results confirm that the AAC of the CPs contains all the information needed for a quantitative classification of plant viruses. These results and possible explanations of these clustering patterns are discussed.

Amino Acids↗
PubMed2007

Comparing sequences without using alignments: application to HIV/SIV subtyping.

BACKGROUND: In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment. RESULTS: In this paper, HIV (Human Immunodeficiency Virus) and SIV (Simian Immunodeficiency Virus) sequence data are used to evaluate this method. The program produces tree topologies that are identical to those obtained by a combination of standard methods detailed in the HIV Sequence Compendium. Manual alignment editing is not necessary at any stage. Furthermore, only one user-specified parameter is needed for constructing trees. CONCLUSION: The extensive tests on HIV/SIV subtyping showed that the virus classifications produced by our method are in good agreement with our best taxonomic knowledge, even in non-coding LTR (Long Terminal Repeat) regions that are not tractable by regular alignment methods due to frequent duplications/insertions/deletions. Our method, however, is not limited to the HIV/SIV subtyping. It provides an alternative tree construction without a time-consuming aligning procedure.

Animals↗
PubMed1984

Different recombinant murine leukemia viruses use different cell surface receptors.

Retroviruses can be grouped by viral interference measurements into classes which use common cell surface receptors. We previously tested a large number of isolates of mink cell focus-inducing (MCF) murine leukemia viruses (MuLVs), and reported that all of them share a distinct receptor on NIH/3T3 cells (A. Rein, Virology 120, 251, 1982). We now extend this generalization to several additional recombinant isolates, including two (SL3-2 and GPA-V2) which would not be considered MCFs on the basis of host-range data. We note the superiority of interference tests, based on positive, unambiguous data, over host-range tests for virus classification. We also show that in contrast to the MCFs, which are all derived from ecotropic MuLVs, a recombinant derived from wild mouse amphotropic MuLV (S. Rasheed et al., Int. J. Cancer 29, 345, 1982) uses a unique receptor on NIH/3T3 cells. This suggests that (a) mouse cells contain more than one type of endogenous env sequence; and (b) there is some specificity in the generation of recombinants, since ecotropic MuLVs appear to give rise only to MCFs, while amphotropic MuLV has generated a distinct type of recombinant. It also represents a second case (in addition to the MCFs) in which an env gene recombinant is more pathogenic than its exogenous parent. We also show that xenotropic MuLV does not interfere with MCFs in NZB mouse cells; thus, despite the close homology between MCF and xenotropic env sequences, the gp70 of xenotropic MuLV appears to have no detectable affinity for the MCF receptor.

Animals↗
PubMed2001

Molecular characterization of Menangle virus, a novel paramyxovirus which infects pigs, fruit bats, and humans.

Menangle virus (MenV), isolated in August 1997 following an outbreak of reproductive disease in a piggery in New South Wales, is the second previously unclassified member of the family Paramyxoviridae to be identified in Australia since 1994. Similar to Hendra virus (HeV), MenV appears to be a virus of fruit bats (flying foxes) in the genus Pteropus. No serological cross-reactivity was detected between MenV and other known paramyxoviruses and to facilitate virus classification a cDNA subtraction method was used to obtain viral-specific cDNA from MenV-infected cells. Cloning and sequencing of the products enabled the entire sequences of the NP, P/V, M, F, and HN genes to be determined. Comparison of the nucleotide and deduced amino acid sequences for each gene with members of the family Paramyxoviridae, determination of the P gene mRNA editing strategy, and phylogenetic analyses confirmed that MenV is a new member of the genus Rubulavirus. However the deduced protein sequence of MenV HN exhibited only limited sequence homology when compared with attachment proteins of other paramyxoviruses. Key differences within the amino acid residues considered important determinants of neuraminidase activity suggest MenV HN is unlikely to possess the same degree of neuraminidase activity characteristic of other rubulavirus and respirovirus HN proteins.

Amino Acid Sequence↗
PubMed2005

The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture.

Comparisons of bacteriophage PRD1 and adenovirus protein structures and virion architectures have been instrumental in unraveling an evolutionary relationship and have led to a proposal of a phylogeny-based virus classification. The structure of the PRD1 spike protein P5 provides further insight into the evolution of viral proteins. The crystallized P5 fragment comprises two structural domains: a globular knob and a fibrous shaft. The head folds into a ten-stranded jelly roll beta barrel, which is structurally related to the tumor necrosis factor (TNF) and the PRD1 coat protein domains. The shaft domain is a structural counterpart to the adenovirus spike shaft. The structural relationships between PRD1, TNF, and adenovirus proteins suggest that the vertex proteins may have originated from an ancestral TNF-like jelly roll coat protein via a combination of gene duplication and deletion.

Adenoviruses, Human↗
PubMed2005

Yersiniophage phiR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine.

Bacteriophage piR1-37 was isolated based on its ability to infect strain YeO3-R1, a virulence-plasmid-cured O antigen-negative derivative of Yersinia enterocolitica serotype O : 3. In this study, the phage receptor was found to be a structure in the outer core hexasaccharide of Y. enterocolitica O : 3 LPS. The phage receptor was present in the outer core of strains of many other Y. enterocolitica serotypes, but also in some Yersinia intermedia strains. Surprisingly, the receptor structure resided in the O antigen of Yersinia pseudotuberculosis O : 9. Electron microscopy demonstrated that phiR1-37 particles have an icosahedral head of 88 nm, a short neck of 10 nm, a long contractile tail of 236 nm, and tail fibres of at least 86 nm. This implies that the phage belongs to the order Caudovirales and the family Myoviridae in the ICTV (International Committee for Taxonomy of Viruses) classification. phiR1-37 was found to have a lytic life cycle, with eclipse and latent periods of 40 and 50 min, respectively, and a burst size of approximately 80 p.f.u. per infected cell. Restriction digestions and PFGE showed that the phiR1-37 genome was dsDNA and approximately 270 kb in size. Enzymically hydrolysed DNA was subjected to HPLC-MS/MS analysis, which demonstrated that the phiR1-37 genome is composed of DNA in which thymidine (T) is >99 % replaced by deoxyuridine (dU). The only organisms known to have similar DNA are the Bacillus subtilis-specific bacteriophages PBS1 and PBS2. N-terminal amino acid sequences of four major structural proteins did not show any similarity to (viral) protein sequences in databases, indicating that close relatives of phiR1-37 have not yet been characterized. Genes for two of the structural proteins, p24 and p46, were identified from the partially sequenced phiR1-37 genome.

DNA, Bacterial↗
PubMed1969

Studies on the nucleocapsid structure of a group A arbovirus.

When Sindbis virus (273S) was treated with sodium desoxycholate, a nonhemagglutinating 136S particle was liberated from the virion, representing the viral nucleocapsid (core). Electron microscopically it appeared as a spherical particle 35 nm in diameter, showing ringlike morphological units 12 to 14 nm in diameter on its surface. When the one- and two-sided images of core particles were correlated, their structure could be demonstrated to have the T = 3 arrangement of 32 hexamer-pentamer morphological units within a symmetrical surface lattice. The core contained a further spherical structure (12 to 16 nm in diameter) which was designated as the central core component. Two proteins were found associated with the core, a third viral protein belonged to the hemagglutinating surface structures. The significance of these findings for virus classification is discussed.

Arboviruses↗
PubMedDate not supplied

Usefulness of Lens culinaris agglutinin A-reactive fraction of alpha-fetoprotein (AFP-L3) as a marker of distant metastasis from hepatocellular carcinoma.

The objective of this study was to clarify the relationship between the serum level of the Lens culinaris agglutinin A-reactive fraction of alpha-fetoprotein (AFP-L3) and the clinical features including sex, age, Child's classification, virus markers, tumour size, tumour stage, distant metastasis, histopathologic findings, portal thrombus and outcome of hepatocellular carcinoma (HCC). We measured the AFP-L3 levels in 170 HCC cases at the time of diagnosis using lectin-affinity electrophoresis followed by antibody-affinity blotting. The patients were divided into two groups, those who were AFP-L3 positive (n=56; AFP-L3 >/=15% relative to the total alpha-fetoprotein (AFP) concentration) and those who were AFP-L3 negative (n=114; AFP-L3 <15%). Then we examined the association between the serum AFP-L3 level and the clinical features of HCC. No significant differences were found in age, sex, and virus markers between the AFP-L3-positive and -negative groups. However, patients in the positive group had worse liver function and larger tumours compared to the negative group. They also had more advanced cancer with poor tumour histology compared to the negative group. Distant metastasis was diagnosed significantly more often in the positive group than that in the negative group. There was no significant correlation between the AFP-L3 level and portal thrombus. Although the follow-up period was brief the prognosis for the positive group clearly was poor. These results suggest that AFP-L3 is a useful indicator of distant metastasis and a poor prognosis for HCC.

Adult↗
PubMed1971

A new influenza A virus infection in turkeys. VII. Comparative immunology.

Four influenza A strains isolated from turkeys in Ontario as well as strain Chicken/Scotland/59 were found to immunize turkeys against the lethal disease caused by virus Turkey/Ontario 7732/66 (V7732). These viruses form the avian influenza A serotype 5 (AA5). Immunoprotection against V7732 was not obtained with influenza viruses of other serotypes. Immunoprotective relationships among AA5 viruses were not always demonstrable in hemagglutination-inhibition (HI) and serum-neutralization (SN) tests, especially with turkey and mammalian antisera; better correlation between immunoprotection and these in vitro tests was seen with chicken antisera. The implications of these findings relative to virus classification, serodiagnosis and vaccination are discussed.

Animals↗
PubMed2002

Molecular evolution of hepatitis A virus: a new classification based on the complete VP1 protein.

Hepatitis A virus (HAV) is a positive-stranded RNA virus in the genus Hepatovirus in the family Picornaviridae So far, analysis of the genetic variability of HAV has been based on two discrete regions, the VP1/2A junction and the VP1 N terminus. In this report, we determined the nucleotide and deduced amino acid sequences of the complete VP1 gene of 81 strains from France, Kosovo, Mexico, Argentina, Chile, and Uruguay and compared them with the sequences of seven strains of HAV isolated elsewhere. Overall strain variation in the complete VP1 gene was found to be as high as 23.7% at the nucleotide level and 10.5% at the amino acid level. Different phylogenetic methods revealed that HAV sequences form five distinct and well-supported genetic lineages. Within these lineages, HAV sequences clustered by geographical origin only for European strains. The analysis of the complete VP1 gene allowed insight into the mode of evolution of HAV and revealed the emergence of a novel variant with a 15-amino-acid deletion located on the VP1 region where neutralization escape mutations were found. This could be the first antigenic variant of HAV so far identified.

Amino Acid Sequence↗
PubMed2026

FALCON2: compression-based metagenomic classification of ancient viruses.

MOTIVATION: Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100&#x2009;bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples. RESULTS: We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC&#x2009;=&#x2009;0.625), Kraken2 (AUPRC&#x2009;=&#x2009;0.184), and CLARK-S (AUPRC&#x2009;=&#x2009;0.013) on pooled micro-averaged metrics. FALCON2's advantage is most pronounced on ultra-short reads (20-40&#x2009;bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4-8 GB RAM for typical analyses. AVAILABILITY AND IMPLEMENTATION: FALCON2 is freely available at https://github.com/cobilab/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https://doi.org/10.5281/zenodo.17291214.

Metagenomics↗