Human group C rotavirus: completion of the genome sequence and gene coding assignments of a non-cultivatable rotavirus

Evolution of rotavirus C in humans and several domestic animal species

Rotavirus C (RVC) causes enteric disease in multiple species, including humans, swine, bovines, and canines. To date, the evolutionary relationships of RVC populations circulating in different host species are poorly understood, owing to the low availability of genetic sequence data. To address this gap, we sequenced 45 RVC complete genomes from swine samples collected in the United States and Mexico. A phylogenetic analysis of each genome segment indicates that RVC populations have been evolving independently in human, swine, canine, and bovine hosts for at least the last century, with inter-species transmission events occurring deep in the phylogenetic tree, and none in the last 100 years. Bovine and canine RVC populations clustered together nine of the 11 gene segments, indicating a shared common ancestor centuries ago. The evolutionary relationships of RVC in humans and swine were more complex, due to the extensive genetic diversity and multiple RVC clades identified in pigs, which were not structured geographically. Topological differences between trees inferred for different genome segments occurred frequently, including at nodes deep in the tree, indicating that RVC's evolutionary history includes multiple reassortment events that occurred a long time ago. Overall, we find that RVC is evolving within host-defined lineages, but the evolutionary history of RVC is more complex than previously recognized due to the high genetic diversity of RVC in swine, with a common ancestor dating back centuries. Pigs may act as a reservoir host for RVC, and a source of the lineages identified in other species, including humans, but additional sequencing is needed to understand the full diversity of this understudied pathogen across multiple host species.

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere's viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detected by conventional reverse transcription-quantitative PCR (qRT-PCR). The simultaneous presence of diverse rotavirus signatures in wastewater indicated the potential for zoonotic infections in the area and suggested runoff from pig farms as a possible origin of these viruses. Our results show that viromics can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided appropriate and rigorous controls are included. IMPORTANCE Enteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from origin to the point where they are a threat to human health, informing reference-based detection methods and water quality management.

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere's viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detected by conventional reverse transcription-quantitative PCR (qRT-PCR). The simultaneous presence of diverse rotavirus signatures in wastewater indicated the potential for zoonotic infections in the area and suggested runoff from pig farms as a possible origin of these viruses. Our results show that viromics can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided appropriate and rigorous controls are included. IMPORTANCE Enteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from origin to the point where they are a threat to human health, informing reference-based detection methods and water quality management.

Genetic analysis of human rotavirus C: The appearance of Indian-Bangladeshi strain in Far East Asian countries

Rotaviruses C (RVCs) circulate worldwide as an enteric pathogen in both humans and animals. Most studies of their genetic diversity focus on the VP7 and VP4 genes, but the complete genomes of 18 human RVCs have been described in independent studies. The genetic background of the Far East Asian RVCs is different than other human RVCs that were found in India and Bangladesh. Recently, a RVC detected in 2010 in South Korea had genetic background similar to the Indian-Bangladeshi RVCs. This study was undertaken to determine the whole genome of eight Japanese RVCs detected in 2005-2012, and to compare them with other human and animal global RVCs to better understand the genetic background of contemporary Far East Asian RVC. By phylogenetic analysis, the human RVCs appeared to be distinct from animal RVCs. Among human RVCs, three lineage constellations had prolonged circulation. The genetic background of the Far East Asian RVC was distinguished from Indian-Bangladeshi RVC as reported earlier. However, we found one Japanese RVC in 2012 that carried the genetic background of Indian-Bangladeshi RVC, whereas the remaining seven Japanese RVCs carried the typical genetic background of Far East Asian RVC. This is the first report of the Indian-Bangladeshi RVC in Japan. With that observation and the reassortment event of human RVCs in Hungary, our study indicates that the RVCs are spreading from one region to another.

Canine rotavirus C strain detected in Hungary shows marked genotype diversity

Species C rotaviruses (RVC) have been identified in humans and animals, including pigs, cows and ferrets. In dogs, RVC strains have been reported anecdotally on the basis of visualization of rotavirus-like virions by electron microscopy combined with specific electrophoretic migration patterns of the genomic RNA segments. However, no further molecular characterization of these viruses was performed. Here, we report the detection of a canine RVC in the stool of a dog with enteritis. Analysis of the complete viral genome uncovered distinctive genetic features of the identified RVC strain. The genes encoding VP7, VP4 and VP6 were distantly related to those of other RVC strains and were putatively classified as G10, P8 and I8, respectively. The new strain was named RVC/Dog-wt/HUN/KE174/2012/G10P[8]. Phylogenetic analyses revealed that canine RVC was most closely related to bovine RVC strains with the exception of the NSP4 gene, which clustered together with porcine RVC strains. These findings provide further evidence for the genetic diversity of RVC strains.

Analysis of genetic divergence among strains of porcine rotavirus C, with focus on VP4 and VP7 genotypes in Japan

Porcine rotavirus C (RVC) has been often detected in sporadic cases or outbreaks of diarrhoea in suckling and weaned pigs. Surveillance studies of RVCs have demonstrated high prevalence in the United States, and Japan, and some other countries. To date, the zoonotic impact and pathogenicity of RVCs are not well understood, and only a few complete sequences of RVCs are available. The aim of this study was to perform sequence and phylogenetic analyses for the VP4 and VP7 genes of the 22 porcine RVCs identified in Japan from 2002 to 2010. The genetic classification of the VP4 genes of the 22 porcine RVCs revealed the presence of six clusters including one cluster each from human and bovine RVCs with a cut-off value of 80%. In addition, VP7 genes of the 22 porcine RVCs were grouped into four of the seven known clusters on the basis of cut-off values of 85% at the nucleotide level reported previously. The data presented here demonstrate that multiple porcine RVC strains with distinctive genotypes based on a combination of the VP4 and VP7 genes are widely distributed and circulated among farms throughout Japan. According to establishment of dual genetic classification for VP4 and VP7 genotypes of porcine RVCs, furthermore, we discovered a possible event of gene reassortment between different rotavirus strains from the same farm. Our findings should advance the understanding of the evolution and pathogenicity of RVCs.

Whole-genome analysis of bovine rotavirus species C isolates obtained in Yamagata, Japan, 2003–2010

An epidemic of diarrhoea in adult cows occurred at a total of 105 dairy farms in Yamagata Prefecture, Japan, between 2003 and 2010. Reverse transcription-PCR diagnostic tests revealed the presence of bovine rotavirus species C (RVCs) in samples from each of six farms (5.7 %). In this study, we determined the full-length nucleotide sequences of 11 RNA segments from six bovine RVC strains and investigated genetic diversity among them, including two bovine RVC strains identified in a previous study. Comparisons of all segmental nucleotide and the deduced amino acid sequences among bovine RVCs indicated high identities across all genes except for the VP4 gene. Phylogenetic analysis of each gene revealed that the six bovine RVCs belonged to a bovine cluster distinct from human and porcine RVCs. Bovine RVC strains could be clearly divided into two lineages of the VP4 genes. The nucleotide sequence identity for VP4 genes between lineage I and II was 83.7–84.8 %. Moreover, bovine RVC strains belonging to lineage I exhibited one amino acid deletion and three amino acid insertions, which differed for those strains belonging to lineage II. Our data suggest that multiple bovine RVCs originated from a common ancestor, but had different genetic backgrounds, not only in Yamagata Prefecture but also in the rest of Japan.

Whole-genome analysis of two bovine rotavirus C strains: Shintoku and Toyama

Rotavirus C (RVC) has been detected frequently in epidemic cases and/or outbreaks of diarrhoea in humans and animals worldwide. Because it is difficult to cultivate RVCs serially in cell culture, the sequence data available for RVCs are limited, despite their potential economical and epidemiological impact. Although whole-genome sequences of one porcine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nucleotide sequences for five as-yet underresearched genes, including the NSP4 gene, from a cultivable bovine RVC, the Shintoku strain, identified in Hokkaido Prefecture, Japan, in 1991. In addition, we elucidated the ORF sequences of all segments from another bovine RVC, the Toyama strain, detected in Toyama Prefecture, Japan, in 2010, in order to investigate genetic divergence among bovine RVCs. Comparison of segmental nucleotide and deduced amino acid sequences among RVCs indicates high identity among bovine RVCs and low identity between human and porcine RVCs. Phylogenetic analysis of each gene showed that the two bovine RVCs belong to a cluster distinct from human and porcine RVCs. These data demonstrate that RVCs can be classified into different genotypes according to host species. Moreover, RVC NSP1, NSP2 and VP1 amino acid sequences contain a unique motif that is highly conserved among rotavirus A (RVA) strains and, hence, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.

Rotavirus RNA polymerases resolve into two phylogenetically distinct classes that differ in their mechanism of template recognition

Rotaviruses (RVs) are segmented double-stranded RNA viruses that cause gastroenteritis in mammals and birds. Within the RV genus, eight species (RVA-RVH) have been proposed. Here, we report the first RVF and RVG sequences for the viral RNA polymerase (VP1)-encoding segments and compare them to those of other RV species. Phylogenetic analyses indicate that the VP1 RNA segments and proteins resolve into two major clades, with RVA, RVC, RVD and RVF in clade A, and RVB, RVG and RVH in clade B. Plus-strand RNA of clade A viruses, and not clade B viruses, contain a 3'-proximal UGUG cassette that serves as the VP1 recognition signal. VP1 structures for a representative of each RV species were predicted using homology modeling. Structural elements involved in interactions with the UGUG cassette were conserved among VP1 of clade A, suggesting a conserved mechanism of viral RNA recognition for these viruses.

Mutational analysis of residues involved in nucleotide and divalent cation stabilization in the rotavirus RNA-dependent RNA polymerase catalytic pocket

The rotavirus RNA-dependent RNA polymerase (RdRp), VP1, contains canonical RdRp motifs and a priming loop that is hypothesized to undergo conformational rearrangements during RNA synthesis. In the absence of viral core shell protein VP2, VP1 fails to interact stably with divalent cations or nucleotides and has a retracted priming loop. To identify residues of potential import to nucleotide and divalent cation stabilization, we aligned VP1 of divergent rotaviruses and the structural homolog reovirus λ3. VP1 mutants were engineered and characterized for RNA synthetic capacity in vitro. Conserved aspartic acids in RdRp motifs A and C and arginines in motif F that likely stabilize divalent cations and nucleotides were required for efficient RNA synthesis. Mutation of individual priming loop residues diminished or enhanced RNA synthesis efficiency without obviating the need for VP2, which suggests that this structure serves as a dynamic regulatory element that links RdRp activity to particle assembly.

Whole-genomic analysis of rotavirus strains: current status and future prospects

Studies on genetic diversity of rotaviruses have been primarily based on the genes encoding the antigenically significant VP7 and VP4 proteins. Since the rotavirus genome has 11 segments of RNA that are vulnerable to reassortment events, analyses of the VP7 and VP4 genes may not be sufficient to obtain conclusive data on the overall genetic diversity, or true origin of strains. In the last few years following the advent of the whole-genome-based genotype classification system, the whole genomes of at least 167 human group A rotavirus strains have been analyzed, providing a plethora of new and important information on the complex origin of strains, inter- and intra-genogroup reassortment events, animal–human reassortment events, zoonosis, and genetic linkages involving different group A rotavirus gene segments. In addition, the whole genomes of a limited number of human group B, C and novel group rotavirus strains have been analyzed. This article briefly reviews the available data on whole-genomic analysis of human rotavirus strains. The significance and future prospects of whole-genome-based studies are also discussed.

Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)

In April 2008, a nucleotide-sequence-based, complete genome classification system was developed for group A rotaviruses (RVs). This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff values. Using this approach, the genome of individual RV strains are given the complete descriptor of Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx. The Rotavirus Classification Working Group (RCWG) was formed by scientists in the field to maintain, evaluate and develop the RV genotype classification system, in particular to aid in the designation of new genotypes. Since its conception, the group has ratified 51 new genotypes: as of April 2011, new genotypes for VP7 (G20-G27), VP4 (P[28]-P[35]), VP6 (I12-I16), VP1 (R5-R9), VP2 (C6-C9), VP3 (M7-M8), NSP1 (A15-A16), NSP2 (N6-N9), NSP3 (T8-T12), NSP4 (E12-E14) and NSP5/6 (H7-H11) have been defined for RV strains recovered from humans, cows, pigs, horses, mice, South American camelids (guanaco), chickens, turkeys, pheasants, bats and a sugar glider. With increasing numbers of complete RV genome sequences becoming available, a standardized RV strain nomenclature system is needed, and the RCWG proposes that individual RV strains are named as follows: RV group/species of origin/country of identification/common name/year of identification/G- and P-type. In collaboration with the National Center for Biotechnology Information (NCBI), the RCWG is also working on developing a RV-specific resource for the deposition of nucleotide sequences. This resource will provide useful information regarding RV strains, including, but not limited to, the individual gene genotypes and epidemiological and clinical information. Together, the proposed nomenclature system and the NCBI RV resource will offer highly useful tools for investigators to search for, retrieve, and analyze the ever-growing volume of RV genomic data.

Whole-genome characterization of human group C rotaviruses: identification of two lineages in the VP3 gene

Group C rotavirus (GCRV) is distributed worldwide as an enteric pathogen in humans and animals. However, to date, whole-genome sequences are available only for a human strain (Bristol) and a porcine strain (Cowden). To investigate the genetic diversity of human GCRVs, nearly full-length sequences of all 11 RNA segments were determined for human GCRVs detected recently in India (v508), Bangladesh (BS347), China (Wu82 and YNR001) and Japan (OH567 and BK0830) and analysed phylogenetically with sequence data for GCRVs published previously. All the RNA segments of human GCRV strains except for the VP3 gene showed high levels of conservation (>93 % nucleotide sequence identity, >92 % amino acid sequence identity), belonging to a single genetic cluster distinct from those of animal GCRVs. In contrast, the VP3 genes of human GCRVs could be discriminated into two clusters, designated M2 and M3, that were distinguished phylogenetically from those of porcine and bovine GCRVs (clusters M1 and M4, respectively). Between M2 and M3, amino acid sequence identity of the VP3 gene was 84.1-84.7 %, whereas high identities were observed within each cluster (92.3-97.6 % for M2, 98.2-99.3 % for M3). Sequence divergence among the four VP3 clusters was observed throughout the amino acid sequence except for conserved motifs, including those possibly related to enzyme functions of VP3. The presence of obvious genetic diversity only in the VP3 gene among human GCRVs suggested that either the M2 or M3 VP3 gene of human GCRVs might have been derived through reassortment from an animal GCRV or from an unidentified human GCRV strain belonging to a novel genogroup.

Optimized approaches for the sequence determination of double-stranded RNA templates

Double-stranded RNA (dsRNA) is in many cases the only available template for molecular and diagnostic studies of RNA viruses. A novel mycovirus with a five dsRNAs segmented-genome served as a model system for the amplification and cloning of dsRNA segments using several PCR-based methods. Sequences obtained by the classical method; random PCR (rPCR) with a single primer assembled into 4 contigs out of the 5 segments. Moreover, using a modified single primer amplification technique (SPAT) resulted in the amplification of all or part of the dsRNA segments in one RT-PCR. Introducing such modifications into the FLAC method (full-length amplification of cDNA) resulted in amplicons comparable to those of the SPAT method. Full-length PCR products representing the five genomic segments were cloned and sequenced. The optimized conditions for each method are presented and discussed. In another approach, purified dsRNA segments were cloned directly into the blunt end pJET1.2 or the pGEM(®)-T cloning vectors with low efficiency though. This led to several sequences up to 2.2kb in length, which could constitute a starting material for other methods like primer walking or as probes for diagnosis.

Genomic evolution, host-species barrier, reassortment and classification of rotaviruses

Evaluation of: Yamamoto D, Ghosh S, Ganesh B et al.: Analysis on genetic diversity and molecular evolution of human group B rotaviruses based on whole genome segments. J. Gen. Virol. 91(Pt 7), 1772–1781 (2010). Rotaviruses are members of the Reoviridae family, causing severe diarrheal illness and death in humans and animals. They have been subdivided into at least seven serological groups (A–G), and, recently, a new rotavirus known as ‘new adult diarrhea virus’ or ADRV-N was discovered. Only in group A rotaviruses have a substantial number of strains been analyzed completely on the molecular level. For groups B, C and ADRV-N rotaviruses a very limited number of complete genomes are available, and for group D, E and F no sequence data are available at all. Here, Yamamoto and colleagues describe the full genomic characterization of four human group B rotaviruses isolated in India, Bangladesh and Myanmar. These four strains were analyzed phylogenetically and individual gene segments were compared with their group A and C counterparts, indicating that functionally important motifs and structural characteristics were conserved. This study, together with others, highlights the need for complete genome analysis of rotaviruses, in order to study their genetic evolution, the occurrence of reassortments, crossing of the host-species barrier and their classification. Upcoming new mass sequencing technologies are expected to speed up the process of filling in the gaps in our data.

Shared and group-specific features of the rotavirus RNA polymerase reveal potential determinants of gene reassortment restriction

Rotaviruses (RVs) are nonenveloped, 11-segmented, double-stranded RNA viruses that are major pathogens associated with acute gastroenteritis. Group A, B, and C RVs have been isolated from humans; however, intergroup gene reassortment does not occur for reasons that remain unclear. This restriction might reflect the failure of the viral RNA-dependent RNA polymerase (RdRp; VP1) to recognize and replicate the RNA of a different group. To address this possibility, we contrasted the sequences, structures, and functions of RdRps belonging to RV groups A, B, and C (A-VP1, B-VP1, and C-VP1, respectively). We found that conserved amino acid residues are located within the hollow center of VP1 near the active site, whereas variable, group-specific residues are mostly surface exposed. By creating a three-dimensional homology model of C-VP1 with the A-VP1 crystallographic data, we provide evidence that these RV RdRps are nearly identical in their tertiary folds and that they have the same RNA template recognition mechanism that differs from that of B-VP1. Consistent with the structural data, recombinant A-VP1 and C-VP1 are capable of replicating one another's RNA templates in vitro. Nonetheless, the activity of both RdRps is strictly dependent upon the presence of cognate RV core shell protein A-VP2 or C-VP2, respectively. Together, the results of this study provide unprecedented insight into the structure and function of RV RdRps and support the notion that VP1 interactions may influence the emergence of reassortant viral strains.

Molecular characterization of a novel adult diarrhoea rotavirus strain J19 isolated in China and its significance for the evolution and origin of group B rotaviruses

The complete genome of a novel adult diarrhoea rotavirus strain J19 was cloned and sequenced using an improved single-primer sequence-independent method. The complete genome is 17,961 bp and is AU-rich (66.49 %). Northern blot analysis and genomic sequence analysis indicated that segments 1-11 encode 11 viral proteins, respectively. Protein alignments with the corresponding proteins of J19 with B219, and groups A, B and C rotaviruses, produced higher per cent sequence identities to B219. Among groups A, B and C rotaviruses, 10 proteins from group B rotaviruses exhibited slightly higher amino acid sequence identity to the J19 proteins, but proteins of J19 showed low amino acid sequence identity with groups A and C rotaviruses. Construction of unrooted phylogenetic trees using a set of known proteins and representatives of three known rotavirus groups revealed that six structural proteins were positioned close to B219 and the basal nodes of groups A, B and C lineages, although with a preferred association with group B lineages. Phylogenetic analysis of the five non-structural proteins showed a similar trend. The results of the serological analysis, protein sequence analysis and phylogenetic analysis suggested that J19 would be a novel rotavirus strain with great significance to the evolution and origin of group B rotaviruses.

Virus discovery by sequence-independent genome amplification

Genome sequences from several blood borne and respiratory viruses have recently been recovered directly from clinical specimens by variants of a technique known as sequence‐independent single primer amplification. This and related methods are increasingly being used to search for the causes of diseases of presumed infectious aetiology, but for which no agent has yet been found. Other methods that do not require prior knowledge of the genome sequence of any virus that may be present in the patient specimen include whole genome amplification, random PCR and subtractive hybridisation and differential display. This review considers the development and application of these techniques. Copyright © 2006 John Wiley & Sons, Ltd.

Structure-function analysis of rotavirus NSP2 octamer by using a novel complementation system

Viral inclusion bodies, or viroplasms, that form in rotavirus-infected cells direct replication and packaging of the segmented double-stranded RNA (dsRNA) genome. NSP2, one of two rotavirus proteins needed for viroplasm assembly, possesses NTPase, RNA-binding, and helix-unwinding activities. NSP2 of the rotavirus group causing endemic infantile diarrhea (group A) was shown to self-assemble into large doughnut-shaped octamers with circumferential grooves and deep clefts containing nucleotide-binding histidine triad (HIT)-like motifs. Here, we demonstrate that NSP2 of group C rotavirus, a group that fails to reassort with group A viruses, retains the unique architecture of the group A octamer but differs in surface charge distribution. By using an NSP2-dependent complementation system, we show that the HIT-dependent NTPase activity of NSP2 is necessary for dsRNA synthesis, but not for viroplasm formation. The complementation system also showed that despite the retention of the octamer structure and the HIT-like fold, group C NSP2 failed to rescue replication and viroplasm formation in NSP2-deficient cells infected with group A rotavirus. The distinct differences in the surface charges on the Bristol and SA11 NSP2 octamers suggest that charge complementarity of the viroplasm-forming proteins guides the specificity of viroplasm formation and, possibly, reassortment restriction between rotavirus groups.

Coupling of Rotavirus Genome Replication and Capsid Assembly

The Reoviridae family represents a diverse collection of viruses with segmented double-stranded (ds)RNA genomes, including some that are significant causes of disease in humans, livestock, and plants. The genome segments of these viruses are never detected free in the infected cell but are transcribed and replicated within viral cores by RNA-dependent RNA polymerase (RdRP). Insight into the replication mechanism has been provided from studies on Rotavirus, a member of the Reoviridae whose RdRP can specifically recognize viral plus (+) strand RNAs and catalyze their replication to dsRNAs in vitro. These analyses have revealed that although the rotavirus RdRP can interact with recognition signals in (+) strand RNAs in the absence of other proteins, the conversion of this complex to one that can support initiation of dsRNA synthesis requires the presence and partial assembly of the core capsid protein. By this mechanism, the viral polymerase can carry out dsRNA synthesis only when capsid protein is available to package its newly made product. By preventing the accumulation of naked dsRNA within the cell, the virus avoids triggering dsRNA-dependent interferon signaling pathways that can induce expression and activation of antiviral host proteins.

Cloning of complete genome sets of six dsRNA viruses using an improved cloning method for large dsRNA genes

Cloning full-length large (>3 kb) dsRNA genome segments from small amounts of dsRNA has thus far remained problematic. Here, a single-primer amplification sequence-independent dsRNA cloning procedure was perfected for large genes and tailored for routine use to clone complete genome sets or individual genes. Nine complete viral genome sets were amplified by PCR, namely those of two human rotaviruses, two African horsesickness viruses (AHSV), two equine encephalosis viruses (EEV), one bluetongue virus (BTV), one reovirus and bacteriophage Phi12. Of these amplified genomes, six complete genome sets were cloned for viruses with genes ranging in size from 0.8 to 6.8 kb. Rotavirus dsRNA was extracted directly from stool samples. Co-expressed EEV VP3 and VP7 assembled into core-like particles that have typical orbivirus capsomeres. This work presents the first EEV sequence data and establishes that EEV genes have the same conserved termini (5' GUU and UAC 3') and coding assignment as AHSV and BTV. To clone complete genome sets, one-tube reactions were developed for oligo-ligation, cDNA synthesis and PCR amplification. The method is simple and efficient compared to other methods. Complete genomes can be cloned from as little as 1 ng dsRNA and a considerably reduced number of PCR cycles (22-30 cycles compared to 30-35 of other methods). This progress with cloning large dsRNA genes is important for recombinant vaccine development and determination of the role of terminal sequences for replication and gene expression.