Identification and classification of human cytomegalovirus capsids in textured electron micrographs using deformed template matching

BACKGROUND

Characterization of the structural morphology of virus particles in electron micrographs is a complex task, but desirable in connection with investigation of the maturation process and detection of changes in viral particle morphology in response to the effect of a mutation or antiviral drugs being applied. Therefore, we have here developed a procedure for describing and classifying virus particle forms in electron micrographs, based on determination of the invariant characteristics of the projection of a given virus structure. The template for the virus particle is created on the basis of information obtained from a small training set of electron micrographs and is then employed to classify and quantify similar structures of interest in an unlimited number of electron micrographs by a process of correlation.

RESULTS

Practical application of the method is demonstrated by the ability to locate three diverse classes of virus particles in transmission electron micrographs of fibroblasts infected with human cytomegalovirus. These results show that fast screening of the total number of viral structures at different stages of maturation in a large set of electron micrographs, a task that is otherwise both time-consuming and tedious for the expert, can be accomplished rapidly and reliably with our automated procedure. Using linear deformation analysis, this novel algorithm described here can handle capsid variations such as ellipticity and furthermore allows evaluation of properties such as the size and orientation of a virus particle.

CONCLUSION

Our methodological procedure represents a promising objective tool for comparative studies of the intracellular assembly processes of virus particles using electron microscopy in combination with our digitized image analysis tool. An automated method for sorting and classifying virus particles at different stages of maturation will enable us to quantify virus production in all stages of the virus maturation process, not only count the number of infectious particles released from un infected cell.

Transduction characteristics of adeno-associated virus vectors expressing cap serotypes 7, 8, 9, and Rh10 in the mouse brain

Recombinant adeno-associated viral (AAV) vectors can transduce cells of the CNS, resulting in long-term expression. AAV vector transduction varies depending on the serotype used and the region of the brain injected. AAV serotypes 7, 8, 9, and Rh10 have recently become available, but the transduction capabilities of these serotypes within the CNS have not been determined. We show that AAV 7, 8, 9, and Rh10 vectors expressing cDNA for a lysosomal enzyme transduce neurons, but not astrocytes or oligodendrocytes, in the cortex, striatum, hippocampus, and thalamus. Although all of the vectors contained the same genome, there were markedly different transduction patterns that could be due only to the differences in capsid proteins. The AAV 9 vector was found to undergo vector genome transport to distal neuronal cell bodies via known axonal pathways. This facilitated the distribution of enzyme, resulting in correction of lysosomal storage lesions in regions of a diseased brain that would not be corrected if the genome were not transported.

Epidemic spread of recombinant noroviruses with four capsid types in Hungary

BACKGROUND

Noroviruses are common pathogens in gastro-enteritis outbreaks in humans worldwide. Noroviruses are genetically diverse group of viruses with multiple genogroups (GG) and genotypes. More recently, naturally occurring recombinant noroviruses were described. These viruses had a distinct polymerase gene sequence (designated GGIIb/Hilversum) and were disseminated through waterborne and food-borne transmission in Europe.

OBJECTIVES

Our aim was to characterize these emerging recombinant noroviruses causing outbreaks of gastro-enteritis in Hungary.

STUDY DESIGN

From January 2001 to May 2004, samples containing "GGIIb/Hilversum polymerase" (GGIIb-pol) were selected for analysis of the viral capsid region (ORF2) by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing.

RESULTS

Thirty-four (14.4%) of 236 confirmed norovirus outbreaks were caused by the variant lineage with the GGIIb-pol. Four different recombinants were detected with capsids of Hu/NLV/GGII/Mexico/1989 (n=9, 43%), Hu/NLV/GGII/Snow Mountain/1976 (n=6, 28%), Hu/NLV/GGII/Hawaii/1971 (n=4, 19%) and Hu/NLV/GGII/Lordsdale/1993 (n=1, 5%).

CONCLUSIONS

In Hungary, emerging recombinant noroviruses became the second most common norovirus variants-next to GGII-4/Lordsdale virus-causing epidemics of gastroenteritis in the last 4 years.

A refined circular template matching method for classification of human cytomegalovirus capsids in TEM images

An automatic image analysis method for describing, segmenting, and classifying human cytomegalovirus capsids in transmission electron micrograph (TEM) images of host cell nuclei has been developed. Three stages of the capsid assembly process in the host cell nucleus have been investigated. Each class is described by a radial density profile, which is the average grey-level at each radial distance from the center. A template, constructed from the profile, is used to find possible capsid locations by correlation based matching. The matching results are further refined by size and distortion analysis of each possible capsid, resulting in a final segmentation and classification.

Shrimp Taura syndrome virus: genomic characterization and similarity with members of the genus Cricket paralysis-like viruses

The single-stranded genomic RNA of Taura syndrome virus (TSV) is 10205 nucleotides in length, excluding the 3' poly(A) tail, and contains two large open reading frames (ORFs) that are separated by an intergenic region of 207 nucleotides. The ORFs are flanked by a 377 nucleotide 5' untranslated region (UTR) and a 226 nucleotide 3' UTR followed by a poly(A) tail. The predicted amino acid sequence of ORF1 revealed sequence motifs characteristic of a helicase, a protease and an RNA-dependent RNA polymerase, similar to the non-structural proteins of several plant and animal RNA viruses. In addition, a short amino acid sequence located in the N-terminal region of ORF1 presented a significant similarity with a baculovirus IAP repeat (BIR) domain of inhibitor of apoptosis proteins from double-stranded DNA viruses and from animals. The presence of this BIR-like sequence is the first reported in a single-stranded RNA virus, but its function is unknown. The N-terminal amino acid sequence of three TSV capsid proteins (55, 40 and 24 kDa) were mapped in ORF2, which is not in the same reading frame as ORF1 and possesses an AUG codon upstream of the structural genes. However, the intergenic region shows nucleotide sequence similarity with those of the genus Cricket paralysis-like viruses, suggesting a similar non-AUG-mediated translation mechanism. The structure of the TSV genome [5' UTR-non-structural proteins-intergenic UTR-structural proteins-3' UTR-poly(A) tail] is similar to those of small insect-infecting RNA viruses, which were recently regrouped into a new virus genus, Cricket paralysis-like viruses.

Molecular phylogeny and proposed classification of the simian picornaviruses

The simian picornaviruses were isolated from various primate tissues during the development of general tissue culture methods in the 1950s to 1970s or from specimens derived from primates used in biomedical research. Twenty simian picornavirus serotypes are recognized, and all are presently classified within the Enterovirus genus. To determine the phylogenetic relationships among all of the simian picornaviruses and to evaluate their classification, we have determined complete VP1 sequences for 19 of the 20 serotypes. Phylogenetic analysis showed that A13, SV19, SV26, SV35, SV43, and SV46 are members of human enterovirus species A, a group that contains enterovirus 71 and 11 of the coxsackie A viruses. SA5 is a member of human enterovirus species B, which contains the echoviruses, coxsackie B viruses, coxsackievirus A9, and enterovirus 69. SV6, N125, and N203 are related to one another and, more distantly, to species A human enteroviruses, but could not be definitely assigned to a species. SV4 and SV28 are closely related to one another and to A-2 plaque virus, but distinct from other enteroviruses, suggesting that these simian viruses are members of a new enterovirus species. SV2, SV16, SV18, SV42, SV44, SV45, and SV49 are related to one another but distinct from viruses in all other picornavirus genera, suggesting that they may comprise a previously unknown genus in Picornaviridae. Several simian virus VP1 sequences (N125 and N203; SV4 and SV28; SV19, SV26, and SV35; SV18 and SV44; SV16, SV42, and SV45) are greater than 75% identical to one another (and/or greater than 85% amino acid identity), suggesting that the true number of distinct serotypes among the viruses surveyed is less than 20.

Foot-and-mouth disease type O viruses exhibit genetically and geographically distinct evolutionary lineages (topotypes)

Serotype O is the most prevalent of the seven serotypes of foot-and-mouth disease (FMD) virus and occurs in many parts of the world. The UPGMA method was used to construct a phylogenetic tree based on nucleotide sequences at the 3' end of the VP1 gene from 105 FMD type O viruses obtained from samples submitted to the OIE/FAO World Reference Laboratory for FMD. This analysis identified eight major genotypes when a value of 15% nucleotide difference was used as a cut-off. The validity of these groupings was tested on the complete VP1 gene sequences of 23 of these viruses by bootstrap resampling and construction of a neighbour-joining tree. These eight genetic lineages fell within geographical boundaries and we have used the term topotype to describe them. Using a large sequence database, the distribution of viruses belonging to each of the eight topotypes has been determined. These phylogenetically based epidemiological studies have also been used to identify viruses that have transgressed their normal ecological niches. Despite the high rate of mutation during replication of the FMD virus genome, the topotypes appear to represent evolutionary cul-de-sacs.

Primary structure and phylogenetic analysis of the coat protein of a Toyama isolate of tobacco necrosis virus

The amino acid sequence of the coat protein (CP) of a tobacco necrosis virus (TNV) strain, Toyama isolate, was determined by a combination of peptide and cDNA sequencing. The deduced sequence of 276 residues was compared with CPs of other TNV isolates and other plant virus isolates of Tombusviridae. It showed the highest similarity to the TNV Nebraska isolate with 92% identity and moderate similarity to the TNV strain A with 51% identity, confirming the previous serological analysis. It also showed overall similarity with CPs of mostly genera Necrovirus and Sobemovirus, and partial similarity with CPs of genera Tombusvirus and Carmovirus. Among 13 CPs that showed overall similarity, there were 10 completely conserved residues. These included three residues that participate in Ca2+ ligation at the interfaces of virion subunits in TNV crystal structure, suggesting that similar metal binding occur in the viruses of genera Necrovirus and Sobemovirus.

Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated 'subtype I', reveals a unique complex A/G/H/K/? mosaic pattern

Human immunodeficiency virus type 1 (HIV-1) has been classified into three main groups and 11 distinct subtypes. Moreover, several circulating recombinant forms (CRFs) of HIV-1 have been recently documented to have spread widely causing extensive HIV-1 epidemics. A subtype, initially designated I (CRF04_cpx), was documented in Cyprus and Greece and was found to comprise regions of sequence derived from subtypes A and G as well as regions of unclassified sequence. Re-analysis of the three full-length CRF04_cpx sequences that were available revealed a mosaic genomic organization of unique complexity comprising regions of sequence from at least five distinct subtypes, A, G, H, K and unclassified regions. These strains account for approximately 2% of the total HIV-1-infected population in Greece, thus providing evidence of the great capability of HIV-1 to recombine and produce highly divergent strains which can be spread successfully through different infection routes.

[Inter-species transmission of the influenza virus]

Influenza is an infection of human beings and several animal species. It is caused by influenza viruses which belong to the Orthomyxoviridae family. Type A influenza viruses are the most important as they cause severe epidemics and are responsible of important pathological troubles. Type A influenza viruses are classified in different sub-types depending of the nature of their surface glycoproteins: haemagglutinin (H) and neuraminidase (N). The nature of the genome and the mode of replication of influenza viruses account for the high variability of these two proteins which are responsible for the immunity to the virus. The continuous appearance of point mutations in the gene coding for the H protein, leads to the progressive emergence of new viral strains. This event which is called antigenic drift makes it necessary to annually assess the composition of the human flue vaccine. Genetic reassortment is another mechanism of antigenic variation. When the gene coding for the H protein, or when both genes coding for H and N proteins are involved in genetic reassortment, a new viral sub-type occurs which replace the precedent. This event, which is termed antigenic shift, occurs occasionally every 10 to 30 years, and it is responsible of the great human pandemics. The role of the animals and particularly the importance of pigs and poultry in the emergence of these new viruses is discussed.

Multiple alignment and sorting of peptides derived from phage-displayed random peptide libraries with polyclonal sera allows discrimination of relevant phagotopes

Biopanning of phage-displayed random peptide libraries is a powerful technique for identifying peptides that mimic epitopes (mimotopes) for monoclonal antibodies (mAbs). However, peptides derived using polyclonal antisera may represent epitopes for a diverse range of antibodies. Hence following screening of phage libraries with polyclonal antisera, including autoimmune disease sera, a procedure is required to distinguish relevant from irrelevant phagotopes. We therefore applied the multiple sequence alignment algorithm PILEUP together with a matrix for scoring amino acid substitutions based on physicochemical properties to generate guide trees depicting relatedness of selected peptides. A random heptapeptide library was biopanned nine times using no selecting antibodies, immunoglobulin G (IgG) from sera of subjects with autoimmune diseases (primary biliary cirrhosis (PBC) and type 1 diabetes) and three murine ascites fluids that contained mAbs to overlapping epitope(s) on the Ross River Virus envelope protein 2. Peptides randomly sampled from the library were distributed throughout the guide tree of the total set of peptides whilst many of the peptides derived in the absence of selecting antibody aligned to a single cluster. Moreover peptides selected by different sources of IgG aligned to separate clusters, each with a different amino acid motif. These alignments were validated by testing all of the 53 phagotopes derived using IgG from PBC sera for reactivity by capture ELISA with antibodies affinity purified on the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2), the major autoantigen in PBC: only those phagotopes that aligned to PBC-associated clusters were reactive. Hence the multiple sequence alignment procedure discriminates relevant from irrelevant phagotopes and thus a major difficulty with biopanning phage-displayed random peptide libraries with polyclonal antibodies is surmounted.

Characterization of the coat protein gene of mite-transmitted blackcurrant reversion associated nepovirus

The nucleotide sequence of the 3' terminal 3105 nucleotides (nt) of RNA2 of blackcurrant reversion associated virus (BRAV), the first mite-transmitted member of the nepovirus group, has been determined. The sequence contains an open reading frame of 1744 nt in the virus-sense strand, a 3' untranslated region of 1360 nt and a 3' poly(A) tail. Analysis of the amino-terminal residues of purified coat protein (CP) suggests that the CP gene is located between nts 1361 and 2959 (from the 3' terminus) in the RNA2, and that Asp/Ser is the proteolytic cleavage site of CP in the RNA2 encoded polyprotein. The predicted translation product from the CP gene is a polypeptide of 533 amino acids with a calculated Mr of 57 561. The amino acid sequence of BRAV CP showed highest similarity to blueberry leaf mottle virus (BLMV), and tomato ringspot virus (ToRSV), two members of the proposed sub-group three of nepoviruses possessing large RNA2 components. Nucleic and amino acid sequence comparisons between BRAV CP and the CPs of other nepoviruses indicate that specific conserved nepovirus CP domains occur in the BRAV CP thus confirming that BRAV is a member of the subgroup three of nepoviruses. reserved.

Distribution of VP7 serotypes and VP4 genotypes among rotavirus strains recovered from Italian children with diarrhea

108 rotavirus strains obtained from children with diarrhea hospitalized in Palermo, Italy, in the years 1990-1994, were examined by seminested PCR to study the relative frequency and distribution of the four most common alleles of the gene 4. Such strains were selected from 344 human rotavirus strains recovered in palermo during those years after characterization by electropherotyping, subgrouping and G serotyping. One hundred and seven of the 108 strains could be classified into P types, the P[8], G1 (38.3%) and the P[8], G4 (52.3%) types being predominant. The unique strain whose P genotype could not be identified showed an unusual combination of long migration electrophoretic pattern and subgroup I specificity.

Chicken rotavirus Ch-1 shows a second type of avian VP6 gene

VP6 protein from chicken rotavirus Ch-1 showed more than 13% amino acid differences in comparison with pigeon and turkey VP6 sequences. This difference is greater than that observed between subgroup I and II mammalian rotavirus VP6 sequences. Phylogenetic tree analysis demonstrated that RV Ch-1 VP6 is not a link between avian and mammalian VP6 sequences. RV Ch-1 showed variant aa in 17 positions which were otherwise absolutely conserved in mammalian and avian group A RVs. The 17 replacements were scattered through the entire VP6 sequence except the C-terminal part implicated in the assembly of subviral particles. In RV Ch-1 the proline residue 309, reported to be critical for the trimerization of VP6, was replaced by leucine, but VP6 trimers were still observed. The sequence and hydrophilicity analysis of avian RV VP6 do not explain the anomalous electrophoretic migration behavior of avian VP6 proteins.

Sequence analysis of the gene encoding the capsid protein of the Snow Mountain human calicivirus

Snow Mountain virus (SMV) is the reference strain for serotype 3 as determined by immune electron microscopy of the human caliciviruses that are associated with epidemic gastroenteritis. In order to establish the genetic relationship of its capsid protein with those from other human caliciviriuses, the sequence of the open reading frame 2 (ORF2) encoding the SMV capsid protein was determined. The SMV ORF2 sequence was 1626 nucleotides in length and the deduced protein of 542 amino acids had a calculated molecular weight of 59.2 kD. The SMV capsid sequence showed approximately 48 and 77% amino acid sequence identity with the capsid proteins of the Norwalk (serotype 1) and Hawaii (serotype 2) human calicivirus reference strains, respectively, a finding consistent with its serotypic distinctiveness. Furthermore, the predicted amino acid sequence of the SMV capsid was found to share highest sequence identity (98%) with the Melksham human calicivirus in database searches.

Sequences of the three coat protein genes of a Malaysian isolate of rice tungro spherical virus reveal a close relationship to the Philippine isolate

Coat protein genes CP1, CP2 and CP3 of an isolate (MaP1) of rice tungro spherical virus (RTSV) from Malaysia were isolated, cloned and sequenced. Comparative analysis indicated that MaP1 isolate is closely related to the Philippine isolate.

Bovine rotavirus strain 678 possesses VP4 of serotype P7[5] specificity

Bovine rotavirus strain 678 is the first G8 strain of bovine origin but the literature is confusing as to its P type. In this study, two-way cross neutralization between 678 and 0510, a prototype G6P7[5] virus, was shown by plaque-reduction neutralization assays, establishing the P type of 678 as being P7[5]. The P7[5] specificity of 678 VP4 was reinforced by the finding that the VP8* portion of 678 VP4 had the highest amino acid identity with those of P7[5] bovine rotaviruses. Apparent contradiction with previous serological studies relates to intricacy of antigenicity and immunogenicity of UK VP4 in reassortants.

Bovine rotavirus 993/83 shows a third subtype of avian VP7 protein

VP7 genes of rotavirus (RV) 993/83 isolated from a German calf with diarrhea and of RV PO-13 isolated from a Japanese pigeon were sequenced. Alignment of the deduced VP7 amino acid sequence showed 98.8% sequence identity, while only 70% and 84% identity was seen with VP7 from chicken RV Ch-2 and turkey RV Ty-1, respectively. Over the antigenic regions A, B, and C mammalian RV 993/83 showed more aa identity with mammalian G3 RVs than with chicken RV Ch-2, which could explain the strong one-way cross-neutralization observed between RV 993/83 and G3 RVs. Despite marked VP7 sequence diversity avian RVs could not be differentiated into distinct G types.

Variability and phylogeny of the L1 capsid protein gene of human papillomavirus type 5: contribution of clusters of nonsynonymous mutations and of a 30-nucleotide duplication

We analyzed the variability and established the phylogeny of the L1 capsid protein gene of 33 isolates of human papillomavirus type 5 (HPV5) obtained from epidermodysplasia verruciformis patients from different continents. By comparing the sequences of a 419-bp fragment with those published for two Japanese isolates, we found 12.9% variable nucleotide positions, defining 25 variants with mutation rates ranging from 0.2 to 8.8%. Such a high intratypic diversity is unusual among HPVs. Nine of the 139 encoded amino acids were variable and 12 protein variants were identified. Fifteen of the 16 substitutions observed were clustered in two short regions. A 9-amino-acid insert, already reported for the Japanese HPV5b isolate, was found within one of the regions in five isolates. Our data support that the insert arose from the duplication of a 30-nucleotide sequence. Phylogenetic trees distributed the DNA variants into three subtypes (a to c) with a divergence higher than 4.5% and allowed the recognition of European and African lineages. By contrast with the trees based on the HPV5 E6 gene, HPV5a DNA variants and the HPV5b variants lacking the insert constituted a single group in the L1 amino acid tree, probably reflecting different levels of structural constraints for the HPV5 L1 and E6 proteins. In that respect, the short variable L1 sequences should represent less constrained regions.

Comparison of polymerase chain reaction and monoclonal antibodies for G-typing of group A bovine rotavirus directly from fecal material

A reverse transcriptase and polymerase chain reaction (RT-PCR)-based assay for G-typing of bovine rotaviruses (BRV) was compared with a monoclonal antibody-based immunoassay (MAbs-ELISA) in the characterization of BRV field strains obtained from calves in different regions of Quebec between 1992 and 1994. The strains were analysed for two G types (G6 and G10) which are the most predominate BRV field strains. Fecal samples positive for BRV by polyacrylamide gel electrophoresis (n = 74) were typed by both methods revealing 77% correlation. RT-PCR detected 10 more G6 and 2 more G10 serotypes than MAbs-ELISA. Nine of the 12 discrepant samples could be cultivated and were confirmed as G6 (8) or G10 (1) by both methods. RT-PCR was able to efficiently detect artificial mixes of G6 and G10 and detected two mixed field infections. Four additional infections considered as mixed by MAbs-ELISA and as only G6 by RT-PCR were possibly MAbs-ELISA cross-reactions. RT-PCR provided a very sensitive method for typing BRV field isolates.

The major echovirus group is genetically coherent and related to coxsackie B viruses

In order to determine the overall molecular heterogeneity of echoviruses (EVs) we performed a genetic analysis of the prototype strains. Nucleotide and derived amino acid sequences from different genomic regions (5'UTR, capsid protein-coding and 3D polymerase genes) were used for molecular comparisons. On the basis of a comparison of partial amino acid sequences from the capsid protein VP2, all the sequenced EVs excluding EV22 and EV23 form a single cluster which is genetically homogeneous. All previously sequenced coxsackie B viruses (CBVs) and coxsackievirus A9 also belong to this same genetic cluster. Similar results were obtained when the 5'UTR or 3D polymerase gene sequences were used in comparisons. When amino acid sequences of the major capsid proteins of EV1 and EV16 were compared to those of previously sequenced enteroviruses, the length of the loops connecting the beta-sheets appeared to be relatively constant in the EV/CBV cluster. It can be concluded that EVs and CBVs have diverged relatively late in evolution.

Classification of rotavirus VP4 and VP7 serotypes

Rotaviruses, members of the Reoviridae family, are major etiologic agents of acute nonbacterial gastroenteritis of the young in a wide variety of mammalian and avian species, including humans. The need for effective immunoprophylaxis against rotaviral gastroenteritis has stimulated interest in the biochemical, molecular, genetic, and clinical aspects of these agents with the aim of developing safe and effective vaccines. Because neutralizing antibodies appear to play an important role in protection against many viral diseases, rotavirus antigens that induce neutralizing antibodies have played a central role in research and development of a rotavirus vaccine. The VP7 glycoprotein and VP4 spike protein that constitute the outer capsid of a complete rotavirus particle have been shown to be independent neutralization antigens. Since type specificity of the outer capsid proteins of a rotavirus appears to play an important role in protection against disease in experimental animal models, continued efforts have been made for classification and typing of neutralization specificities on the VP7 or VP4 capsid protein. Based on a criterion of > 20-fold differences between the homologous and heterologous reciprocal neutralizing antibody titers, fourteen VP7 (G) serotypes have been established. Studies are underway to characterize and classify the VP4 (P) serotypes among the strains that exhibit the fourteen different G serotypes. Attempts to classify the VP4 serotypes based on the same criterion (i.e., > 20-fold antibody differences) that is applied to classification of VP7 serotypes are in progress. This standard of > 20-fold antibody differences can be applied with hyperimmune serum raised to a reassortant possessing the VP4 encoding gene (and an unrelated VP7 encoding gene). Genotypes can provide leads towards classification but the serotype of a strain should be based on neutralization.

VP4 and VP7 typing using monoclonal antibodies

Both rotavirus outer capsid proteins, VP4 and VP7, elicit neutralizing antibodies. Neutralizing mouse monoclonal antibodies (N-MAbs) to VP7 are easily derived and have been used widely and successfully to serotype both stool-derived and culture-adapted rotaviruses by enzyme immunoassay (EIA). Generally, approximately 70% of rotaviruses in stool samples are typable by VP7 EIA, an inexpensive and practical method. Variations in antigenic regions between strains within human rotavirus serotypes 1, 2, 4, and 9 have been recorded. These have been termed monotypes because they are detected with N-MAbs. The molecular basis for monotypes has been determined by mapping mutations selected in N-MAb-resistant antigenic variants, and by sequence analysis of the gene encoding VP7 in newly recognized monotypes. Antigenic regions A, B and C in VP7 are involved. In order to detect all members of a particular VP7 serotype, it is necessary to type with a panel of N-MAbs specific for that serotype. N-MAbs to VP4 of human rotavirus are difficult to raise and few have proven suitable for VP4 serotyping by EIA. The specificity of the assay for each P type is highest when the VP7 serotype specificity of the capture antiserum is matched to the G type of the rotavirus in the test sample. The VP4 EIA gives similar typing rates to the VP7 typing EIA. N-MAbs directed to VP8, the smaller subunit of VP4 generated by proteolytic cleavage, are more likely to show serotype specificity. Some N-MAbs that select mutations in the putative fusion region of VP5, the larger subunit of VP4, show cross-reactivity with extracts of normal, uninfected MA 104 cells and with fetal bovine serum. These N-MAbs also give elevated EIA OD readings with rotavirus-positive, but previously non-reactive fecal samples which have been frozen and thawed repeatedly. Overall, VP8-reactive N-MAbs appear most suitable for VP4 typing by EIA.

Serological and genomic characterization of equine rotavirus VP4 proteins identifies three different P serotypes

A series of viral reassortants was prepared between equine rotaviruses H1 (G5), H2 (G3), and L338 (G13) and human rotavirus ST3 (G4). All contained the VP4 cognate gene segment 4 from the equine parental virus and the VP7 cognate gene segment 9 from ST3. Using these viruses and antisera prepared to them, it was shown that each of the three equine viruses possessed a serologically distinct VP4 or P serotype with a > or = 16-fold difference in reciprocal cross-neutralization titers. H1 VP4 was closely related to that of porcine virus OSU, i.e., P7. L338 gene 4 was sequenced, and the sequence and serological data indicated that it constituted a novel P serotype L338. P serotype H2 was predominant among our cell culture-adapted equine rotavirus strains, but showed some serological cross-reactivity.

Sequences of the N and M genes of the sigma virus of Drosophila and evolutionary comparison

The genome of the sigma rhabdovirus of Drosophila melanogaster consists of six genes in the order 3' N-2-3-4-G-L 5'. The nucleotide sequences of the N and of the fourth genes were determined from cDNA clones. Each gene contained a single long open reading frame encoding polypeptides with predicted MW of 50 and 25 kDa, respectively. Evidence that these genes encode the nucleocapsid N and the matrix M proteins were obtained using antibodies raised against recombinant proteins derived from the cloned genes and expressed in Escherichia coli. The M and N predicted amino acid sequences were compared with those of other rhabdoviruses. The M protein of sigma virus shared a similar domain arrangement to the other M proteins, but it showed very little sequence conservation. The N protein of sigma virus showed no significant homology with its counterpart in SYNV or IHNV and VSHV; it did, however, show sequence homology with the N of four vesiculoviruses and two lyssaviruses. The extent of amino acid identity suggests that sigma virus occupies an intermediate evolutionary position between these two genera. Some conserved motifs in the M and N proteins were deduced from the comparisons.

Nucleotide sequence of gene 6 of avian-like group A rotavirus 993/83

Two cDNA clones, which hybridized in Northern blots to RNA segment 6 of the homologous avian-like group A rotavirus (RV) 993/83 and pigeon RV PO-13, but not to mammalian group A rotaviruses, were sequenced. The gene 6 sequence contained a single long open reading frame encoding a protein of 397 amino acids (total MW 44,460). Comparison of the deduced amino acid sequence with VP6 protein from mammalian group A RV revealed 72 to 74.3% of amino acid identity. These values are surprisingly low in view of the high homology levels described up to now for group A RV. Avian-like RV 993/83 is however not a missing link between group A and C RV as it is as distantly related to group C RV as group A mammalian RV to group C RV. The evolutionary implications of these observations are briefly discussed.

Glycosylation of the major outer capsid protein of bluetongue viruses

The major outer capsid protein, VP5, of five US bluetongue viruses, was found to be glycosylated. Enzymatic removal of the carbohydrate moiety did not affect the electrophoretic mobility of VP5 in SDS-PAGE, indicating the presence of only short and possibly unbranched oligosaccharide chains. The surface accessibilities and immunogenic specificities of two conformational-dependent antigenic epitopes on VP5 of BTV were not affected by deglycosylation. Selective binding of those lectins which have well-defined sugar specificities suggests that the potential short N-linked carbohydrate chain present on BTV VP5 might be composed of sialic acid alpha(2-6)-N-acetylgalactosamine-beta(1-3)-galactose-beta(1-4)-N- acetylglucosamine-beta(1-2)-mannose-N-acetylglucosamine-Asn. In accordance with the standard nomenclature, BTV-VP5 should now be termed GP5 due to the presence of the carbohydrate moiety.

The nucleotide sequence of the coat protein genes and 3' non-coding regions of two resistance-breaking tobamoviruses in pepper shows that they are different viruses

The nucleotide sequence of the coat protein genes and 3' non-coding regions of two different resistance-breaking tobamoviruses in pepper have been determined. The deduced coat protein of an Italian isolate of pepper mild mottle virus (PMMV-I) consists of 156 amino acids and its 3' non-coding region is 198 nucleotides long. They have been found to be very similar in sequence and structure to those previously reported for a Spanish isolate (PMMV-S). In contrast, a Dutch isolate termed P 11 codes for a coat protein of 160 amino acids and its 3' non-coding region is 291 nucleotides long, which may have arisen by duplication. The nucleotide and the predicted coat protein amino acid sequence analysis show that this isolate should be considered as a new virus within the tobamovirus group. The term paprika mild mottle virus (PaMMV) is proposed.

[The systematization of the nuclear polyhedrosis viruses by their morphological traits]

The results of studies on submicroscopic organization of nuclear polyhedrosis viruses (NPV) isolated from different species and populations of insects are presented. The following morphological criteria are proposed for NPV identification: the frequency of occurrence of polygenomic virions with definite number of nucleocapsids, the presence of electron-dense membrane on the surface of suprapolyvirion capsids (SPVC); total number of nucleocapsids inside one average SPVC of NPV. Analyses of morphometric maps of NPV infecting different species and populations of the same species of insects are presented.

The nucleotide sequence of RNA-2 of raspberry ringspot nepovirus

The nucleotide sequence of raspberry ringspot nepovirus (RRV) RNA-2 consists of 3928 nucleotides and a poly(A) tract at the 3' end. RNA-2 contains one open reading frame which encodes a polypeptide of M(r) 123508 (123K). Edman degradation located the N terminus of the coat protein 514 residues from the C-terminal end of the 123K protein, which suggests that the coat protein is released from the polyprotein by cleavage of a C-A bond. The RRV coat protein has some sequence similarities with the coat proteins of other nepoviruses, but is no more like any one nepovirus than another. In contrast, the portion of the 123K protein to the N-terminal side of the coat protein is similar in sequence to the corresponding parts of the polyproteins of tomato black ring and grapevine chrome mosaic nepoviruses, though not to those of other nepoviruses.

Identification of four VP4 serological types (P serotypes) of bovine rotavirus using viral reassortants

A series of five reassortant viruses each containing the VP4 gene of a distinct bovine rotavirus and the VP7 gene of human rotavirus strain ST3 was prepared, and antisera to these were produced in rabbits. In neutralization tests, these antisera allowed the differentiation of the five original strains (from three different VP7 or G serotypes) into three or possibly four VP4 or P serotypes. All of a further seven bovine rotavirus strains adapted to cell culture were successfully typed by these antisera. There was a degree of cross-reaction between antiserum to the fourth bovine rotavirus P serotype and the predominant human rotavirus serotype. However, antisera raised in guinea-pigs to recombinant VP4 from this serotype showed the bovine serotype to be distinct. There was no significant serological relationship between these four bovine rotavirus P serotypes and previously described P serotypes from rotaviruses isolated from man and non-bovine animals. The predominant bovine rotavirus VP7 serotypes G6 and G10 tended to have distinct P serotypes also.

Evolution of the capsid protein genes of foot-and-mouth disease virus: antigenic variation without accumulation of amino acid substitutions over six decades

The genetic diversification of foot-and-mouth disease virus (FMDV) of serotype C over a 6-decade period was studied by comparing nucleotide sequences of the capsid protein-coding regions of viruses isolated in Europe, South America, and The Philippines. Phylogenetic trees were derived for VP1 and P1 (VP1, VP2, VP3, and VP4) RNAs by using the least-squares method. Confidence intervals of the derived phylogeny (significance levels of nodes and standard deviations of branch lengths) were placed by application of the bootstrap resampling method. These procedures defined six highly significant major evolutionary lineages and a complex network of sublines for the isolates from South America. In contrast, European isolates are considerably more homogeneous, probably because of the vaccine origin of several of them. The phylogenetic analysis suggests that FMDV CGC Ger/26 (one of the earliest FMDV isolates available) belonged to an evolutionary line which is now apparently extinct. Attempts to date the origin (ancestor) of the FMDVs analyzed met with considerable uncertainty, mainly owing to the stasis noted in European viruses. Remarkably, the evolution of the capsid genes of FMDV was essentially associated with linear accumulation of silent mutations but continuous accumulation of amino acid substitutions was not observed. Thus, the antigenic variation attained by FMDV type C over 6 decades was due to fluctuations among limited combinations of amino acid residues without net accumulation of amino acid replacements over time.

Localization of group-specific epitopes on the major capsid protein of group A rotavirus

Chemical cleavage of the VP6 protein of bovine rotavirus showed that VP6-specific monoclonal antibodies (MAbs) reacted with the amino acid sequence between glycine 48 and asparagine 107. Furthermore, three synthetic peptides (amino acids 48 to 64, 60 to 75 and 91 to 108) containing part of this sequence and 22 consecutive overlapping heptapeptides corresponding to the region between amino acids 48 and 75 were analysed for their immunoreactivity using group-specific MAbs. The MAbs recognized peptides 48-64 and/or 60-75, and a set of overlapping heptapeptides located between residues 53 (asparagine) and 67 (glycine), which have two short sequences in common: IRNW (residues 56 to 59), recognized by MAb RV-133, and (NW)NFD (residues 58/60 to 62), recognized by MAbs RV-50, -1026 and -443. These results indicate that the sequence between amino acid residues 48 and 75 is present in one of the immunodominant sites of VP6.

Comparisons of rotavirus VP7-typing monoclonal antibodies by competition binding assay

Three sets of neutralizing monoclonal antibodies (MAbs) used to type the outer capsid protein VP7 of four group A rotavirus serotypes (1 through 4) were compared in competition immunoassays. Reciprocal competition was observed for each of the VP7 type 2-, 3-, and 4-specific MAbs. The VP7 type 1 MAbs exhibited variable competition patterns with other VP7 type 1 MAbs. MAb RV4:3, which has been used to recognize antigenic variants within VP7 type 1 strains, showed reciprocal competition with the four VP7 type 3 MAbs (RV3:1, YO-1E2, 4F8, and 159) using a VP7 type 3 virus (SA11) as antigen. MAb 2C9, also prepared against VP7 type 1, reacted with VP7 type 3 strains and competed with a VP7 type 3 MAb, 159, using RRV as antigen. Use of the different sets of VP7 type-specific MAbs in the enzyme-linked immunosorbent assay permitted the recognition of six antigenic variants within VP7 types 1, 2, and 3 among specimens whose VP7 type could not be determined previously with only one set of typing MAbs. These results demonstrate differences of typing ability among these VP7-specific MAbs and emphasize the need to improve the sensitivity of typing systems by incorporating panels of MAbs reacting with several neutralizing epitopes.

Coat protein phylogeny and systematics of potyviruses

The feasibility of applying molecular phylogenetic methods of analysis to aligned coat-protein sequences and other molecular data derived from coat proteins or genomic sequences of members of the proposed taxonomic family of Potyviridae, is discussed. We show that comparative sequence analysis of whole coat-protein sequences may be used reliably to differentiate between sequences of closely related strains, and to show groupings of more distantly related viruses; that coat proteins of putative Potyviridae cluster according to the proposed generic divisions, and, even if some are only very distantly related, the members of the family form a cluster distinct from coat proteins of other filamentous and rod-shaped viruses. Taxonomic revisions based on perceived evolutionary relationships, and the lack of feasibility of erecting higher taxa for these viruses, are discussed.