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Production of a polyhedral particle in Escherichia coli from a cDNA copy of the large genomic segment of bacteriophage phi 6.

A polyhedral particle that resembles in composition and structure the procapsid of bacteriophage phi 6 was produced in Escherichia coli containing cDNA copies of the entire large genomic segment inserted into expression vector plasmids under the control of lac or tac promoters. The particles were composed of proteins P1, P2, P4, and P7 in the same stoichiometry as in the intact virion. In electron micrographs of negatively stained samples, the particles appeared as hexagons, stars, or rings of 10 knobs, which are characteristic of the five-, three-, and twofold axes of symmetry characteristic of phi 6 procapsids. Stable particles were also produced from cDNA deletions that produce only P1 and P4. Other cDNA deletions producing P1 and P7 and P1 alone resulted in unstable particles which could only be visualized in electron micrographs of thin sections of E. coli transformed by the recombinant plasmids. Our results indicate that the assembly of the phi procapsid is independent of other phage proteins and of normal phage RNA.

Bacteriophages↗

Grouping of hantaviruses by small (S) genome segment polymerase chain reaction and amplification of viral RNA from wild-caught rats.

A single pair of consensus primers in the polymerase chain reaction (PCR) amplified a conserved region of the small genome segment of twenty hantavirus isolates. Isolates tested included representatives of the four recognized hantaviruses, Hantaan, Seoul, Puumala and Prospect Hill, as well as isolates from Mus musculus (Leakey), Bandicota indica (Thailand 749), and Suncus murinus (Thottapalayam). Viruses from the Nairovirus and Phlebovirus genera yielded negative results. The amplification products were 281-nucleotide pairs (np) in length, with the exception of Thottapalayam, which had an amplification product of approximately 320 np. Products of all isolates were detected by Southern hybridization with a 32P-labeled Hantaan 76-118 amplicon, while an oligonucleotide probe to a conserved region of the amplified fragment failed to detect some isolates of Seoul and Puumala viruses. Restriction endonuclease analysis allowed three groupings: Hantaan-like viruses, Seoul-like viruses, and a diverse group of patterns for the other viruses. Differences were found within the Seoul-like virus group by this method, whereas the Hantaan-like viruses were shown to be similar. RNA extracted from tissues of seropositive and seronegative rats trapped in Baltimore showed the practical application of the test. Hantavirus-specific RNA was detected in 12 (92%) of 13 seropositive rats, but not in seronegative rats. This simple method for detecting and characterizing hantaviruses has potential for epidemiologic studies and for diagnosing human hantavirus infections.

Animals↗

Sequence analysis of genome segments S5 and S10 of Mal de Rio Cuarto virus (Fijivirus, Reoviridae).

Mal de Rio Cuarto virus (MRCV) was recently described as a new species of the genus Fijivirus, family Reoviridae. The nucleotide sequence of two MRCV genome segments was determined. MRCV S5 and S10 were predicted to encode proteins of 106.9 and 63.5 kDa respectively. The protein coded by MRCV S5 had 62.8% and 35.7% identity to fijiviruses RBSDV S5 and FDV S5 coded proteins, and contained a rarely reported type-1 C-terminal peroxisomal targeting signal. The protein coded by MRCV S10 had identity levels of 72.4% and 21.7% to the major outer capsid proteins of fijiviruses RBSDV S10 and NLRV S8.

Capsid Proteins↗

Sequence and phylogenetic analysis of genome segments S1, S2, S3 and S6 of Mal de Río Cuarto virus, a newly accepted Fijivirus species.

Mal de Río Cuarto virus (MRCV) is a newly described species of the genus Fijivirus, family Reoviridae. The nucleotide sequence of four MRCV genome segments was determined. MRCV S1, S2, S3 and S6 were predicted to encode proteins of 168.4, 134.4, 141.7 and 90 kDa, respectively. MRCV S1 encodes a basic protein that contains conserved RNA-dependent RNA polymerase motifs, and is homologous to Rice black streaked dwarf virus (RBSDV), Fiji disease virus (FDV) and Nilaparvata lugens reovirus (NLRV) polymerases as well as to corresponding proteins of members of other genera of the Reoviridae. MRCV S2 codes for a protein with intermediate homology to the ones coded by RBSDV S4 and FDV S3 'B' spike, which is presumably the B-spike protein. MRCV S3 most probably encodes the major core protein and is highly homologous to corresponding proteins of RBSDV S2 and FDV S3. MRCV S6-encoded protein has low homology to the proteins of unknown function coded by RBSDV S6 and FDV S6. The identity levels between all analyzed MRCV coded proteins and their RBSDV counterparts varied between 84.5 and 44.8%. The analysis of the reported sequences allowed a phylogenetic comparison of MRCV with other reovirus and supported its taxonomic status within the genus.

Amino Acid Sequence↗

Short sequences define genetic lineages: phylogenetic analysis of group A rotaviruses based on partial sequences of genome segments 4 and 9.

Genetic diversity in strains of human group A rotaviruses was analysed by phylogenetic methods. The study material comprised 109 serotype G1 or G4 rotavirus samples isolated in Finland during 1986-1990. Parts of the coding regions of rotaviral genome segments 4 and 9, which encode proteins with serotype specificity, the spike protein VP4 (P serotype) and the outer capsid protein VP7 (G serotype), respectively, were sequenced. As determined by analysis of segment 4 sequences all G1 strains and all except one G4 strain showed P[8] specificity, the one being of P[6] specificity. The G1P[8] strains could be further differentiated into four groups based on segment 9 sequences, while G4P[8] strains formed only one group. Type P[8] (G1P[8] and G4P[8]) strains formed two main groups based on segment 4 sequences, suggesting free segregation of segment 4 between these G strains. Most global G1, G4 and P[8] strains in GenBank/EMBL originating from the 1970s to the present co-clustered with these groups, suggesting that the groups exist as relatively stable lineages. No linear accumulation of nucleotide substitutions was detected in strains of one serotype during the study period. Also, the deduced amino acids of the antigenic regions A, B and C of VP7 were nearly conserved within the phylogenetic lineages. Interestingly, only short amino acid sequences were necessary to divide the e-types correctly into phylogenetic lineages. These amino acid signature motifs were located in aa 29-68 of VP7 and aa 121-135 of VP4 of the G1 and P[8] lineages, respectively.

Amino Acid Sequence↗

Comparison of genome segments 2, 7 and 10 of bluetongue viruses serotype 2 for differentiation between field isolates and the vaccine strain.

Bluetongue (BT) virus serotype 2 (BTV 2) was first confirmed in Tunisia in February 2000 and has since spread northward and westward, infecting several other countries and islands, including Corsica, where clinical disease was reported in October 2000. BT was again reported on the Island in July 2001, some six months after a vaccination campaign against BTV 2. The molecular relationship between isolates of the BTV 2 Corsican wild-type viruses from 2000 and 2001, and the attenuated BTV 2 vaccine were determined by comparing corresponding sequences of genome segments 2, 7 and 10 with each other and with already published sequences available in the genome database. Complete genetic stability was observed between the isolates of the Corsican BTV 2. There was some divergence between the nucleotide sequences of segment 10 obtained from the wild-type and vaccine virus strains. Based on these differences, primers were selected that could be used in RT-PCR to differentiate between the wild-type and the vaccine viruses.

Amino Acid Sequence↗

Significance of the genetic relationships deduced from partial nucleotide sequencing of infectious bursal disease virus genome segments A or B.

The rapid genomic characterization of infectious bursal disease virus (IBDV) requires determining which partial nucleotide (nt) sequences derived from IBDV segments A or B would produce phylogenetic information as significant as sequencing the whole corresponding segments. Long nt coding sequences of 27 IBDV segments A (aa 20-991) and 21 segments B (aa 7-stop codon) were retrieved from databanks and used to compute reference phylogenetic trees using Neighbor Joining (NJ) and Parsimony (P): clusters appearing in the NJ and P reference trees with a bootstrap value greater than 80% were considered as significant (Whole Segment Clusters, WSC). The sequences were then cut into overlapping regions. These were used to compute phylogenetic trees which were compared with reference ones. Of the partial sequences, the VP2 gene best represented IBDV segment A (10 out of 13 WSC were conserved), and the 5' two thirds of segment B best represented segment B (5 to 6 conserved WSC out of 6). Implementation of the Plato programme finally demonstrated that the region encoding VP2 variable domain (vVP2, segment A) is the only region of IBDV genome with a significantly different evolution rate, which result is consistent with vVP2 being subjected to a high selection pressure.

Databases, Genetic↗

Baculovirus expression of the small genome segment of Hantaan virus and potential use of the expressed nucleocapsid protein as a diagnostic antigen.

Autographa californica nuclear polyhedrosis virus (AcNPV) was used as an expression vector for the nucleocapsid protein gene of Hantaan virus. Two different cDNA clones representing the small genome segment of Hantaan virus were inserted into the transfer vector pAcYM1, and recombinants were generated by replacement of a portion of the baculovirus polyhedrin gene with the foreign, Hantaan virus gene. Recombinants containing both the first and second ATG initiation codons of the Hantaan virus gene produced nucleocapsid protein, while those containing only the second codon did not. The expressed nucleocapsid protein was evaluated as a potential diagnostic antigen with a variety of hantavirus-immune sera. The high levels of expression obtained, specific serological reactivity with immune sera and the low level of biological containment required for production of this protein all suggest a significant advantage over authentic viral antigen for diagnosis of hantavirus infection.

Antigens, Viral↗

Muscovy duck reovirus sigmaC protein is atypically encoded by the smallest genome segment.

Although muscovy duck reovirus (DRV) shares properties with the reovirus isolated from chicken, commonly named avian reovirus (ARV), the two virus species are antigenically different. Similar to the DRV sigmaB-encoded gene (1201 bp long) previously identified, the three other double-stranded RNA small genome segments of DRV have been cloned and sequenced. They were 1325, 1191 and 1124 bp long, respectively, and contained conserved terminal sequences common to ARVs. They coded for single expression products, except the smallest (S4), which contained two overlapping open reading frames (ORF1 and ORF2). BLAST analyses revealed that the proteins encoded by the 1325 and 1191 bp genes shared high identity levels with ARV sigmaA and sigmaNS, respectively, and to a lesser extent with other orthoreovirus counterparts. No homology was found for the S4 ORF1-encoded p10 protein. The 29.4 kDa product encoded by S4 ORF2 appeared to be 25% identical to ARV S1 ORF3-encoded sigmaC, a cell-attachment oligomer inducing type-specific neutralizing antibodies. Introduction of large gaps in the N-terminal part of the DRV protein was necessary to improve DRV and ARV sigmaC amino acid sequence alignments. However, a leucine zipper motif was conserved and secondary structure analyses predicted a three-stranded alpha-helical coiled-coil feature at this amino portion. Thus, despite extensive sequence divergence, DRV sigmaC was suggested to be structurally and probably functionally related to ARV sigmaC. This work provides evidence for the diversity of the polycistronic S class genes of reoviruses isolated from birds and raises the question of the relative classification of DRV in the Orthoreovirus genus.

Amino Acid Sequence↗

P2 protein encoded by genome segment S2 of rice dwarf phytoreovirus is essential for virus infection.

Loss of infectivity to insect vector cell monolayers of rice dwarf phytoreovirus (RDV) after CCl4 treatment was associated with the removal of one of the viral proteins from the virus particles. This protein, encoded by genome segment S2 and thus named P2 protein, was located at the outer capsid of the virus particle. When RDV was treated with CCl4 for various times, the reduction in the amount of P2 protein and the loss of viral infectivity to vector cell monolayers were proportional to treatment time. RDV purified using CCl4 treatment thus lacking P2 protein, lost the ability to infect vector insects through feeding and consequently failed to be transmitted to plants. These results suggest that P2 protein is essential for RDV infection of the insect cells and may be related to transmission of the virus by the vector insect.

Amino Acid Sequence↗

Expression of non-conserved regions of the S genome segments of three hantaviruses: evaluation of the expressed polypeptides for diagnosis of haemorrhagic fever with renal syndrome.

Haemorrhagic fever with renal syndrome (HFRS) is a serious and often fatal disease caused by viruses in the Hantavirus genus of the family Bunyaviridae. We expressed the entire coding region of the small (S) genome segments of three serologically distinct hantaviruses as soluble proteins in Escherichia coli and evaluated the expressed nucleocapsid proteins (NPs) as antigens for diagnosis of HFRS. We also prepared novel diagnostic antigens by expressing truncated genes from which we deleted amino acid coding regions that were highly conserved among the three viruses. These antigens were analysed for their potential to detect and differentiate between antisera to various hantaviruses by ELISA. ELISA results obtained with HFRS patient sera or with sera from naturally or experimentally infected animals indicate that homologous antigens and antisera reacted to high titre. The truncated NPs were more specific than the complete NPs in distinguishing between possible aetiological agents of HFRS. Our findings demonstrate that prokaryotic expression of portions of the NPs of specific hantaviruses can be used to generate, readily and efficiently, large quantities of antigen that is both sensitive and specific in diagnostic assays for HFRS.

Animals↗

Sequence analysis of genome segments S4 and S8 of Mal de Río Cuarto virus (MRCV): evidence that the virus should be a separate Fijivirus species.

This is the first sequence-based characterization of Mal de Río Cuarto virus (MRCV), currently classified as a variant of Maize rough dwarf virus (MRDV) and exclusively found in South America. We sequenced and analyzed genome segments S4 and S8. MRCV S4 coded for a putative 131.67 kDa protein while MRCV S8 coded for a putative 68.26 kDa protein containing an ATP/GTP-binding motif. The 5' and 3' ends of MRCV segments, were 5'AAGUUUUU3' and 5'CAGCUnnnGUC3', respectively. Prediction of secondary structure of both segments coding strands showed that terminal regions were able to form structures that are proposed to be replication and packaging signals. MRCV S4 showed identity to members of Fijivirus as well as to two other genera of the Reoviridae family. MRCV S8 revealed identity with Rice black streaked dwarf virus (RBSDV) S8, MRDV S7, Oat sterile dwarf virus (OSDV) S9 and Nilaparvata lugens reovirus (NLRV) S7. While MRDV and RBSDV segments are highly homologous between each other, MRCV identity levels with them was considerably lower. We discussed the evolutionary relationships of MRCV to other Reoviridae, and based on phylogenetic analysis we proposed that although MRCV is related to MRDV, it could be regarded as a new species of the Fijivirus genus.

Amino Acid Sequence↗

Infectious salmon anemia virus (ISAV) genomic segment 3 encodes the viral nucleoprotein (NP), an RNA-binding protein with two monopartite nuclear localization signals (NLS).

Infectious salmon anemia virus (ISAV) is the type species of the genus Isavirus belonging to the Orthomyxoviridae, and causes serious disease in Atlantic salmon (Salmo salar). This study presents the expression and functional analysis of the ISAV genome segment 3, and provides further evidence that it encodes the viral nucleoprotein (NP). The encoded protein was expressed in a baculovirus system, and Western blot analysis showed that it corresponds to the 66-71 kDa structural protein previously found in purified ISAV preparations. RNA-binding activity was established by the interaction of viral and recombinant NP with single-stranded RNA transcribed in vitro. Immunofluorescence studies of infected cells showed the ISAV NP to be an early protein. It locates to the nucleus of infected cells before it is transported to the cytoplasm prior to virus assembly. A similar localization pattern was observed in cells transfected with the NP gene, confirming that the encoded protein has an intrinsic ability to be imported into the nucleus. Two monopartite nuclear localization signals (NLS) at amino acids (230)RPKR(233) and (473)KPKK(476) were identified by computer analysis, and validated by site-directed mutagenesis. In contrast to other orthomyxovirus-NPs, that have several NLSs that function independent of each other, both NLSs had to be present for the ISAV NP protein to be transported into the nucleus, indicating that these motifs cooperate to target the protein to the nucleus.

Amino Acid Sequence↗

Coding properties of the S and the M genome segments of Sapporo rat virus: comparison to other causative agents of hemorrhagic fever with renal syndrome.

Three serologically distinct groups of hantaviruses have been associated with severe, moderate, and mild forms of hemorrhagic fever with renal syndrome (HFRS). To gain a better understanding of the genetic variation among these viruses, we cloned and sequenced the M and the S genome segments of Sapporo rat virus, an etiologic agent of moderate HFRS, and compared the predicted gene products to those of Hantaan virus, and the Hällnäs strain of Puumala virus, which are etiologic agents of severe and mild HFRS, respectively. The SR-11 S segment consisted of 1769 nucleotides and had an open reading frame (ORF) in the virus-complementary sense RNA with a coding capacity of 429 amino acids. Deduced amino acids from the SR-11 S segment ORF displayed 83% homology with those of Hantaan nucleocapsid (N) protein. Comparison of the S segment ORFs of all three viruses revealed 58% homology. No evidence for additional nonstructural protein(s) encoded by the SR-11 S segment was obtained. The SR-11 M segment consisted of 3651 nucleotides and had an ORF in the virus-complementary sense RNA with a coding capacity of 1134 amino acids. Amino acid sequences predicted from the SR-11 M segment ORF were 75% homologous with those encoding Hantaan G1 and G2 envelope glycoproteins. Comparison of the deduced amino acid sequences of the M segment ORFs of SR-11, Hantaan, and Hällnäs viruses revealed a 43% homology for amino acids constituting the G1 proteins and a 55% homology for amino acids constituting the G2 proteins of the three viruses. The envelope proteins of SR-11 virus were localized within the M segment ORF by amino-terminal sequence analysis of purified G1 and G2. G1 initiated at amino acid 17 and G2 at amino acid 647 within the ORF. Five potential asparagine-linked glycosylation sites were identified in the SR-11 G1 coding sequences, four of which were conserved between Hantaan and SR-11 viruses and three of which were conserved among all three viruses. One potential glycosylation site was identified in the SR-11 G2 coding sequences and was conserved among Hantaan, SR-11 and Hällnäs viruses. Cysteine residues were highly conserved within the M segment ORFs of all three viruses, suggesting a similar structure and function of the G1 and G2 proteins.

Amino Acid Sequence↗

Selection of genome segments following coinfection of chicken fibroblasts with avian reoviruses.

Two avian reoviruses (883 and 176) shown to have distinct growth kinetics were used to coinfect chicken embryonic fibroblasts asynchronously to generate reassortants. More than 300 plaque-derived clones were obtained from passage 3 of two separate coinfections made at different m.o.i. and time intervals between infection and superinfection. The genome electropherotype of each plaque-derived clone was determined, and a diverse group of reassortants were detected. Genome segments 883 M2 and 176 S1 were shown to be preferentially selected. The preferential selection of the 176 S1 segment was shown to be a virus growth-determined nonrandom event conferred by the function of 176 S1 segment, whereas the data suggest that a factor(s) other than viral growth properties was involved in the preferential selection of 883 M2 segment.

Animals↗

Terminal sequence conservation among the genomic segments of a group B rotavirus (IDIR strain).

Terminal nucleic acid sequences were determined for all 11 segments of the IDIR strain of group B rotavirus. Consensus sequences were defined at both ends of the (+) RNA strands as 5' GGN(A/U)NA(A/U)(A/U)(A/U)---and---(A/U)NA(A/G)N(A/C)(C/A)CC3 '. The 5' and 3' terminal sequences of the (+) strand IDIR RNA were not complementary to one another. The IDIR terminal sequences and those of group A rotaviruses (GAR) were similar in that each of the (+) strands began with "GG" and ended with "CC." Otherwise, the IDIR terminal sequences did not match the consensus sequences that have been reported for the ends of the GAR genomic segments.

Base Sequence↗

Andes virus M genome segment is not sufficient to confer the virulence associated with Andes virus in Syrian hamsters.

Sin Nombre virus (SNV) and Andes virus (ANDV), members of the genus Hantavirus, in the family Bunyaviridae, are causative agents of hantavirus pulmonary syndrome (HPS) in North and South America, respectively. Although ANDV causes a lethal HPS-like disease in hamsters, SNV, and all other HPS-associated hantaviruses that have been tested, cause asymptomatic infections of laboratory animals, including hamsters. In an effort to understand the pathogenicity of ANDV in the hamster model, we generated ANDV/SNV reassortant viruses. Plaque isolation of viruses from cell cultures infected with both parental viruses yielded only one type of stable reassortant virus: large (L) and small (S) segments of SNV and M segment of ANDV. This virus, designated SAS reassortant virus, had in vitro growth and plaque morphology characteristics similar to those of ANDV. When injected into hamsters, the SAS reassortant virus was highly infectious and elicited high-titer, ANDV-specific neutralizing antibodies; however, the virus did not cause HPS and was not lethal. These data indicate that the ANDV M genome segment is not sufficient to confer the lethal HPS phenotype associated with ANDV.

Animals↗

Molecular diversity of partial-length genomic segment 2 of human picobirnavirus.

OBJECTIVES: This study was carried out in order to evaluate the efficacy of the recently developed picobirnavirus (PBV) sets of primers and to establish the phylogenetic relationships of Argentine strains with PBV strains isolated in China and the USA. METHODS: Thirteen fecal specimens tested as positive for PBV by polyacrylamide gel electrophoresis were analyzed by reverse transcription-polymerase chain reaction assays using primers target to the genomic segments 2 of PBV strains isolated in China and the USA. The amplicons were sequenced and analyzed. RESULTS: Primers derived from the China strain produced amplicons in only 4 of the 13 specimens (30.76%). No sample was revealed as positive with the primers derived from the US strain. DNA sequencing of polymerase chain reaction products differed in nucleic acid and amino acid sequences by 13.9-42.28% and 18.1-51.1%, respectively. Despite this strain diversity, three domains of conserved nucleotide sequences as well as the amino acid motif D-S-D typical of RNA-dependent RNA polymerase gene of double-strand RNA viruses were identified. Comparatively, these conserved regions were also identified in homologous PBV strains from the USA and China. Phylogenetic analysis showed no time or geographic clustering. CONCLUSIONS: These findings provide evidence that PBV may represent an emerging heterogeneous group of viruses.

Adolescent↗