Search

Full genome sequencing of six feline Rotavirus A (RVA) strains isolated in Japan in the 1990s revealed three genotype constellations, one of which had a unique constellation of G3-P[3]-I3-R3-C3-M3-A15-N3-T3-E3-H6. Genotype A15, carried by RVA/Cat-tc/JPN/FRV348/1994/G3P[3], is a rare NSP1 genotype, and only one human and one canine RVA strains have thus far been reported to carry this genotype. The other three G3P[3] strains (FRV72, FRV73, and FRV303) possessed a constellation of I3-R3-C2-M3-A9-N2-T3-E3-H6, whereas two G3P[9] strains (FRV317 and FRV384) possessed a constellation of I3-R3-C3-M3-A3-N3-T3-E3-H3.

Chikungunya virus (CHIKV) has reemerged recently as an important pathogen, causing several large epidemics worldwide. This necessitates the development of better reagents to understand its biology and to establish effective and safe control measures. The present study describes the development and characterization of polyclonal antibodies (pAbs) against synthetic peptides of CHIKV non-structural proteins (nsPs; nsP1, nsP3 and nsP4). The reactivity of these pAbs was demonstrated by ELISA and Western blot. Additionally, in vitro infection studies in a mammalian system confirmed that these pAbs are highly sensitive and specific for CHIKV nsPs, as these proteins were detected very early during viral replication. Homology analysis of the selected epitope sequences revealed that they are conserved among all of the CHIKV strains of different genotypes, while comparison with other alphavirus sequences showed that none of them are 100% identical to the epitope sequences (except Onyong-nyong and Igbo Ora viruses, which show 100% identity to the nsP4 epitope). Interestingly, two different forms of CHIKV nsP1 and three different forms of nsP3 were detected in Western blot analysis during infection; however, further experimental investigations are required to confirm their identity. Also, the use of these antibodies demonstrated faster and enhanced expression profiles of all CHIKV nsPs in 2006 Indian outbreak strains when compared to the CHIKV prototype strain, suggesting the epidemic potential of the 2006 isolate. Accordingly, it can be suggested that the pAbs reported in this study can be used as sensitive and specific tools for experimental investigations of CHIKV replication and infection.

Studies on bovine group B rotaviruses (GBRs) are limited. To date, only the VP6 gene of a single bovine GBR strain and the VP7 and NSP5 genes of a few bovine GBR strains have been sequenced and analyzed. In the present study, using a single-primer amplification method, we have determined the full-length nucleotide sequences of the VP1, VP2, VP4, VP6, NSP1 and NSP2 genes of three bovine GBR strains from eastern India. In all six of these genes, the bovine GBR strains shared high genetic relatedness among themselves but exhibited high genetic diversity with cognate genes of human, murine and ovine GBRs. Interestingly, as with group A rotaviruses, the bovine GBR VP1, VP2, VP6 and NSP2 genes appeared to be more conserved than the VP4 and NSP1 genes among strains of different species. The present study provides important insights into the genetic makeup and diversity of bovine GBRs, and also identifies a novel GBR VP4 genotype.

An infectious clone (pBR-XJ160) was constructed using the full-length cDNA of the Sindbis-like XJ-160 virus. Two nucleotide mutations, causing amino acid changes at residue 169 from Lys to Arg and at residue 173 from Thr to Ile in the nonstructural protein (nsP) 1 coding region, strongly influenced the infectivity of in vitro-synthesized RNA. We used site-directed mutagenesis to obtain clones encoding a change to Arg at residue 169 of nsP1 (pBR-169), a change to Ile at residue 173 (pBR-173), or both changes (pBR-6973). Infectivity of RNA from pBR-169 was abolished, but viral forms BR-173 and BR-6973 were obtained from pBR-173 and pBR-6973, respectively. Further, BR-173 exhibited higher propagation than BR-XJ160 in cell culture and higher neurovirulence in a suckling mouse model. BR-6973 possessed an intermediate phenotype. BR-173 and BR-6973 showed increased sensitivity to 3-deazaadenosine (3-DZA), which inhibits S-adenosylhomocysteine hydrolase. Thus, mutagenesis at residue 169 in the nsP1 region of XJ-160 is lethal, but mutation at residue 173 from Thr to Ile enhances viral infectivity and neurovirulence and suppresses the lethal effect of the mutation at residue 169. These mutations might be associated with the RNA methyltransferase (MTase) activity of nsP1.

Long electropherotype with Subgroup I specificity is a common feature of animal rotaviruses. In an epidemic of infantile gastroenteritis in Manipur, India, long but SG I strains predominated in the outbreak in the year 1987-88. One such strain isolated from that region, following the outbreak had G9P [19] specificity. As this is a rare combination, the gene sequences encoding VP4, VP6, VP7, NSP1, NSP2, NSP3, NSP4 and NSP5 of this strain were analyzed. All these genes except VP7 were closely related to porcine rotaviruses (95-99% identity at amino acid level) and clustered with the porcine strains in phylogenetic analysis. In addition, it had subgroup I nature and belonged to NSP4 genotype B which is characteristic of animal rotaviruses. This is the first report of a rotavirus with VP6 and NSP4, two crucial proteins thought to be involved in host range restriction and pathogenicity, were of porcine origin and caused diarrhoea in a human host. Among the genes of this strain sequenced so far, only VP7 had highest identity to human strains at amino acid level. This study suggests reassortment may be occurring between human and other animal strains and some of the reassortant viruses may be virulent to humans.

We detected two viruses, Japanese encephalitis virus (JEV)/Kochi/01/2005 and Getah virus (GETV)/Kochi/01/2005 in the same culture supernatant obtained by inoculation of Vero cells with a swine serum sample and subsequent passaging of the supernatant in Vero cells. Phylogenetic analysis using the nucleotide sequences of the complete genome and the E2 region of GETV indicated that GETV/Kochi/01/2005 is most similar to a Mongolian strain. In contrast, a partial sequence of the nsP1 protein coding region of GETV/Kochi/01/2005 showed that it was similar to Japanese strains isolated in the 1980s. Alignment of the nucleotide sequence of the E region of JEV showed that JEV/Kochi/01/2005 has the highest similarity to a Japanese strain. We also examined the changes in the amount of JEV/Kochi/01/2005 and GETV/Kochi/01/2005 present after passaging in Vero cells. The RNA copy number and infectious titer of JEV/Kochi/01/2005 decreased, whereas those of GETV/Kochi/01/2005 increased, following repeated passages in Vero cells. Our results provide evidence for coinfection with JEV and GETV in the Kochi/01/2005 pig. This is the first report of incidental confection with JEV and GETV in a domestic animal.

In an epidemiological study of symptomatic human rotaviruses in Mysore, India during 1993 and 1994, isolates MP409 and MP480 were isolated from two children suffering from severe, acute dehydrating diarrhea. Both isolates exhibited 'long' RNA pattern and subgroup I specificity suggesting the likelihood of their animal origin. Both isolates did not react with monoclonal antibodies (MAbs) specific for serotypes G1 to G6 as well as G10. To determine the genetic origin of these isolates, complete nucleotide sequences of genes encoding the outer capsid proteins VP4 and VP7, nonstructural proteins NSP1 and NSP3 and viral enterotoxin protein NSP4 from MP409 and partial sequences of genes from MP480 were determined. Comparison of the 5' and 3' terminal sequences of 250 nucleotides revealed complete identity of the gene sequences in both strains suggesting that MP409 and MP480 are two different isolates of a single strain. Comparison of the nucleotide and deduced amino acid sequences of VP4, VP7, NSP1 and NSP3 of MP409 with published sequences of strains belonging to different serotypes revealed that both outer capsid proteins VP4 and VP7 and NSPI are highly related to the respective proteins from the P6[1], G8 type bovine rotavirus A5 isolated from a calf with diarrhoea in Thailand and that the NSP3 is highly homologous to that of bovine rotaviruses. The NSP4 protein showed greatest sequence identity with NSP4s belonging to the KUN genetic group to which NSP4s from human G2 type strains and bovine rotaviruses belong. MP409 and MP480 likely signify interspecies transmission of P6[1], G8 type strains from cattle to humans and represent the first P6[1] type rotaviruses isolated in humans. These and our previous studies on the asymptomatic neonatal strain 1321 are of evolutionary and epidemiological significance in the context of close association of majority of the Indian population with cattle.

Function of rotavirus NSP1 was analyzed by using single-NSP1 gene-substitution reassortants, SKF, SDF, and SNF which have the NSP1 gene derived from human rotaviruses KU, DS-1, and canine rotavirus K9, respectively, in the genetic background of simian rotavirus SAff11. The NSP1 genes from KU, DS-1, K9, and SAff11 exhibited 58–76% nucleotide sequence identity to one another. No substantial difference in viral growth was observed among the reassortants and SAff11. However, production of NSP1 was not detected in SNF when viral proteins were labelled with 35S-methionine during replication in MAff104 cells, in contrast to SAff11, SKF and SDF which exhibited evident expression of NSP1. Difference in reassortant formation was examined among the reassortant clones generated between human rotavirus strain 69M and either of SAff11, SKF or SNF. Although reassortant formation rate was significantly lower in the cross 69M × SNF than the other crosses, selection rates of RNA segments from parent strain 69M in the resultant reassortants was similar among the crosses. Selectivity of homolog- ous and heterologous NSP1 genes in SAff11 background was also analyzed by mixed infection and multiple passages among the single-NSP1 gene-reassortants and/or SAff11. KU NSP1 gene was selected most frequently, whereas homologous (SAff11) NSP1 gene was least efficiently segregated. These results indicated that viral growth and genome segment reassortment with other viruses may not be influenced by the presence of heterologous NSP1 and its expression level, while genomic diversity of NSP1 genes might have been associated with the relative adaptability to the genetic background of SAff11.

Rotavirus clones Aff5–10 and Aff5–16 isolated from a bovine rotavirus strain Aff5 possess NSP1 gene which has a point mutation generating a nonsense codon and a 500 base-deletion, respectively. As a result, the two Aff5 clones encode truncated NSP1 product which lacks cysteine-rich region forming zinc finger motif. In order to analyze reassortment of these mutated NSP1 gene with RNA segments from heterologous strains, we investigated a number of reassortant clones derived from coinfection with either Aff5–10, Aff5–16 or a reference strain Aff5–13 (possessing intact NSP1 gene) and either simian rotavirus SAff11 or human rotavirus KU. In coinfection with SAff11 and Aff5–13, selection rates of Aff5–13 segments in reassortants ranged approximately from 20 to 70% (46% for NSP1 gene). In contrast, in the reassortment between SAff11 and Aff5–10 or between SAff11 and Aff5–16, selection rates of NSP1 gene from Aff5–10 and Aff5–16 were only 1% (one clone) and 0%, respectively. In reassortants from crosses KU × Aff5-clones, selection rate of Aff5–13 NSP1 gene decreased to 15%, while 11 reassortants with Aff5–10 NSP1 gene (31%) and one reassortant with Aff5–16 NSP1 gene (2%) were isolated. Reassortants with Aff5–10 NSP1 possessed a single gene (segment 9 or 11) from KU in the genetic background of Aff5–10. One reassortant clone (cl-55) with Aff5–16 NSP1 gene possessed KU gene segments 3, 4, and 8–11. When single-step growth curves were compared, the reassortant cl-55 showed almost identical growth curve to that of KU, while KU showed a better replication than Aff5–16. These results indicated that although Aff5–10 or Aff5–16 NSP1 gene encoding the truncated NSP1 is selected into reassortants much less efficiently than normal NSP1 gene, the reassortants with the mutated NSP1 gene and RNA segments from heterologous strains normally replicated in cultured cells. Thus, cysteine-rich region of NSP1 was not considered essential for genome segment reassortment with heterologous virus.

We previously found the preferential selection of VP7 gene from a parent rotavirus strain SA11 with G serotype 3 (G3) in the sequential passages after mixed infection of simian rotavirus SA11 and SA11-human rotavirus single-VP7 gene-substitution reassortants with G1, G2, or G4 specificity. However, it has not been known whether or not VP7 genes derived from other strains with G3 specificity (G3-VP7 gene) are preferentially selected in the genetic background of SA11. To address this question, mixed infections followed by multiple passages were performed with a reassortant SA11-L2/KU-R1 (SKR1) (which possesses VP7 gene derived from G1 human rotavirus KU and other 10 genes of SA11 origin) and one of the five G3-rotaviruses, RRV, K9, YO, AK35, and S3. After the 10th passage, selection rates of SA11-L2/KU-R1 gene 9 (G1-VP7 gene) and gene 5 (NSP1 gene) reduced considerably (0 to 20.4%) in the clones obtained from all the coinfection experiments, while all or some of other segments were preferentially selected from SKR1 depending on the pairs of coinfection. When viral growth kinetics was examined, SKR1 exhibited better growth and reached a higher titer than any G3 viruses. Although the generated reassortants with VP7 gene and NSP1 gene derived from G3 viruses showed almost similar growth kinetics to that of SKR1 during the first 20 h of replication, the titers of these reassortants were higher than that of SKR1 after 36 h postinfection. The results obtained in this study suggested that G3-VP7 gene is functionally more adapted to the genetic background of SA11.

We have sequenced gene 5 encoding NSP1 for three human, two porcine, two bovine, one feline, and five equine rotavirus strains, and compared the nucleotide and deduced amino acid sequences with the published sequences for other various strains. Subgroup I human strains L26, 69M, and DS-1 were found to have a similar NSP1 sequence despite their different G serotypes, VP4 genotypes, and RNA patterns. The NSP1 sequence of the human strain K8 showed a high degree of homology to those of porcine strains OSU and YM. A high degree of homology was found among three equine strains (H2, FI-14, and FI23), but they differed from the other equine strains L338 and H1. The strain H1 was similar to the porcine strains. The feline strain Cat2 showed a high homology to bovine strains UK, RF, and A44. Thus, species-specific and interspecies relatedness of NSP1 sequences among human, porcine, bovine, feline and equine rotaviruses was found. Overall genomic relatedness of strains L26 and YM to various human and animal strains was also examined by RNA-RNA hybridization assay. The present and previous hybridization results showed that there is a good correlation in most strains between overall genomic property (or genogroup) and NSP1 sequence homology.

The role of the rotavirus non-structural proteins NSP1 and NSP3 in regulating cellular and viral mRNA translation has been investigated by examining the effect of added recombinant NSP3 on protein translation in a T7-based in vitro coupled transcription-translation system. Addition of purified NSP3 to assays primed solely with cellular mRNA was found to have no effect on the translation efficiency of the mRNA. However, as expected, the addition of viral mRNA to such assays competitively inhibited the synthesis of cellular protein, and interestingly, this inhibition was enhanced by the addition of NSP3. Treatment of NSP3 with antisera raised against the purified protein abrogated its function, but only when used prior to mixing the protein with viral mRNA. Addition of partially purified NSP1 to the coupled system was able to alleviate the enhancement of the inhibition of cellular mRNA translation caused by NSP3. The role of NSP1 in this process appears to be to modulate the impact of the NSP3-based inhibition of cellular translation by binding to the 5′ end of viral mRNAs.

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.

The nonstructural rotavirus protein NSP1 binds specifically to viral mRNAs and to interferon regulatory factor 3 (IRF3), inducing IRF3 degradation through a proteasome-dependent pathway. By using a vaccinia virus expression system in mammalian cells, we found that the yield of NSP1 was 8- and 13-fold lower than the viral proteins VP2 or NSP3, respectively; while in the presence of proteasome inhibitors such difference could be reduced to 2- to 2.5-fold, respectively. The susceptibility of NSP1 to proteasome degradation was fully reversed in a dose-dependent manner by transfection with the full complement of 11 molecules of translation-competent rotavirus mRNAs, but this effect was abrogated by the protein synthesis inhibitor cycloheximide. These results demonstrate that NSP1 is degraded through a proteasome-dependent pathway, and viral proteins, alone or in combination with viral mRNAs, interfere with such degradation.

Reassortment is one of the major evolutionary mechanisms of the rotavirus genome. Preferential selection (assortment) of the NSP1 gene segment from either of the parental viruses after coinfection of these viruses has been reported as a notable finding in reassortment. To analyze genetic factors which are associated with preferential selection of the rotavirus NSP1 gene segment into progeny viruses, mixed infection and multiple passages were performed using two panels of rotaviruses, i.e., bovine rotavirus A5 clones, and simian rotavirus SA11 and five strains of SA11-based single NSP1 gene-substitution reassortants. In the first experiment, three A5 clones (A5-10, A5-13, and A5-16) that had genetically distinct NSP1 genes in the same genetic background were used. In coinfection of these A5 clones, it was noted that the A5-10 NSP1 gene, which encodes an incomplete protein product due to presence of a nonsense codon at an unusual position, was selected more preferentially than the A5-13 NSP1 gene with intact length and structure. The A5-16 NSP1 gene, with a deletion of 500 bp, was least efficiently selected. In the second experiment, we prepared two reassortants, SOF and SRF, which have NSP1 genes from rotavirus strains OSU and RRV, respectively, in the genetic background of SA11, which were used together with previously prepared reassortants SKF, SDF, and SNF, which had NSP1 genes from strains KU, DS1, and K9, respectively. Among the 6 NSP1 genes analyzed, the NSP1 gene from SKF was most preferentially selected, followed by SNF, SOF, SDF, SA11, and SRF, in that order. Although SOF exhibited less growth efficacy than SA11, the growth rates of other reassortants were similar to that of SA11. These findings suggest that for the occurrence of preferential selection of the NSP1 gene, production of the intact NSP1 protein may not be involved, but the presence of intact length of the NSP1 gene may be required. Furthermore, it was also found that genetic similarity based on primary structure of this gene is not related to the selectivity of the NSP1 gene.

The rotavirus genome encodes six nonstructural (NS) proteins, five of which (NSP1, NSP2, NSP3, NSP5, and NSP6) have been suggested to be involved in a variety of events, such as genome replication, regulation of gene expression, and gene assortment. These NS proteins have been found to be associated with replication complexes that are precursors of the viral core, however, little information is available about the intermolecular interactions that may exist among them. Using the yeast two-hybrid system, which allows the detection of protein-protein interactions in vivo, all possible combinations among the rotavirus NS proteins were tested, and several interactions were observed. NSP1 interacted with the other four proteins tested; NSP3 associated with itself; and NSP5 was found to form homodimers and to interact with NSP6. Co-immunoprecipitation of proteins from rotavirus-infected cells, using hyperimmune sera monospecific for the NS proteins, showed the same interactions for NSP1 as those observed in yeast. Immunofluorescence co-localization analysis of virus-infected epithelial cells revealed that the intracellular distribution of proteins that were seen to interact in yeast had patterns of distribution that would allow such intermolecular interactions to occur. These findings should contribute to the understanding of the role these proteins play in different aspects of the virus replication cycle.