Molecular characterization of a rare G3P[3] human rotavirus reassortant strain reveals evidence for multiple human-animal interspecies transmissions

An unusual strain of human rotavirus G3P[3] (CMH222), bearing simian-like VP7 and caprine-like VP4 genes, was isolated from a 2-year-old child patient during the epidemiological survey of rotavirus in Chiang Mai, Thailand in 2000-2001. The rotavirus strain was characterized by molecular analysis of its VP4, VP6, VP7, and NSP4 gene segments. The VP4 sequence of CMH222 shared the greatest homology with those of caprine P[3] (GRV strain) at 90.6% nucleotide and 96.4% amino acid sequence identities. Interestingly, the VP7 sequence revealed highest identity with those of simian G3 rotavirus (RRV strain) at 88% nucleotide and 98.1% amino acid sequence identities. In contrast, percent sequence identities of both the VP4 and VP7 genes were lower when compared with those of human rotavirus G3P[3] reference strains (Ro1845 and HCR3). Analyses of VP6 and NSP4 sequences showed a close relationship with simian VP6 SG I and caprine NSP4 genotype C, respectively. Phylogenetic analysis of VP4, VP6, VP7, and NSP4 genes of CMH222 revealed a common evolutionary lineage with simian and caprine rotavirus strains. These findings strongly suggest multiple interspecies transmission events of rotavirus strains among caprine, simian, and human in nature and provide convincing evidence that evolution of human rotaviruses is tightly intermingled with the evolution of animal rotaviruses.     

Molecular characterization of rare G3P[9] rotavirus strains isolated from children hospitalized with acute gastroenteritis

In 2004, an epidemiological survey of human rotavirus infection in Chiang Mai, Thailand detected two uncommon human rotavirus strains (CMH120/04 and CMH134/04) bearing AU-1-like G3P[9] genotypes in 1 year old children hospitalized with acute gastroenteritis. The CMH120/04 and CMH134/04 rotavirus strains were characterized by molecular analyses of their VP6, VP7, VP8*, and NSP4 gene segments as well as the determination of RNA patterns by polyacrylamide gel electrophoresis (PAGE). Analysis of the VP8* gene revealed a high level of amino acid sequence identities with those of P[9] rotavirus reference strains, ranging from 94.9% to 98.3%. The highest identities were shared with the human rotavirus AU-1 strain at 97.8% and 98.3% for CMH120/04 and CMH134/04 strains, respectively. Analysis of the VP7 gene sequence revealed the highest identities with G3 human rotavirus strain KC814 at 96.6% and 96.2% for CMH120/04 and CMH134/04 strains, respectively. Based on the analyses of VP7 and VP8* genes, CMH120/04 and CMH134/04 belonged to G3P[9] genotypes. In addition, analyses of VP6 and NSP4 sequences revealed a VP6 subgroup (SG) I, with NSP4 genetic group C specificities. Moreover, both strains displayed a long RNA electrophoretic pattern. The finding of uncommon G3P[9] rotaviruses in pediatric patients provided additional evidence of the genetic/antigenic diversities of human group A rotaviruses in the Chiang Mai area of Thailand.     

Sequence Analysis of the VP4, VP6, VP7, and NSP4 Gene Products ofthe Bovine Rotavirus WC3

The bovine rotavirus (BRV) WC3 serves as the background strain in the development of a multivalent reassortant vaccine against rotavirus gastroenteritis in infants. The genes encoding the outer capsid spike protein VP4, the inner capsid protein VP6, the outer capsid glycoprotein VP7, and the viral enterotoxin NSP4 of BRV WC3 were sequenced. Comparative analysis of the deduced amino acids of the sequenced genes indicated that the BRV WC3 strain shares a high degree of amino acid identity with serotype P7[5] VP4 (93–96%), serotype G6 VP7 (91–97%), subgroup (SG) I VP6 (96–99%), and NSP4 genogroup A (96–98%) BRV strains. Our results confirm and extend previous studies which suggested that the VP4 of BRV WC3 was closely related to that of the P7[5] prototype, BRV UK. In addition, the VP6 and VP7 of BRV WC3 were very similar to the VP6 and VP7 of both SG I and G6 BRV NCDV and UK strains. However, the NSP4 of BRV WC3 was more closely related to that BRV NCDV, the P6[1] prototype, than to that of BRV UK.     

Molecular characterization of the VP4, VP6, VP7, and NSP4 genes of lapine rotaviruses identified in italy: emergence of a novel VP4 genotype

The genes encoding the glycoprotein VP7, the VP8* trypsin-cleavage product of the protein VP4, a fragment of the protein VP6 associated with subgroup (SG) specificity, and the enterotoxin NSP4 of rotavirus strains identified in diarrheic fecal samples of rabbits in Italy were sequenced. The Italian lapine rotavirus (LRV) strains possessed a G3 VP7, SG I VP6, and KUN-like NSP4, a gene constellation typical of LRVs. One LRV strain (30/96), isolated in 1996, shared the closest amino acid (aa) identity (87-96%) with the P[14] genotype, composed of human and LRV strains. Conversely, three LRV strains (160/01, 229/01, and 308/01), identified in 2001, were highly identical (90-95%) among each other, but showed low aa identity (34-77%) to the VP8* genotype-specific sequences of representative rotavirus strains of all remaining P genotypes. This report confirms the worldwide genetic constellations of LRVs and identifies a novel VP4 genotype in rabbits, tentatively proposed as genotype P[22].     

Diverse origin of P[19] rotaviruses in children with acute diarrhea in Taiwan: Detection of novel lineages of the G3, G5, and G9 VP7 genes

We previously reported the detection of genotype P[19] rotavirus strains from children hospitalized with acute dehydrating diarrhea during a 5-year surveillance period in Taiwan. The characterization of five P[19] strains (0.4% of all typed), including three G3P[19], a novel G5P[19], and a unique G9P[19] genotype is described in this study. Phylogenetic analysis of the VP4, VP7, VP6, and NSP4 genes was performed, which demonstrated novel lineages for respective genotypes of the VP4 and the VP7 genes. The sequence similarities of the P[19] VP4 gene among Taiwanese human strains was higher (nt, 91.5-96.2%; aa, 93.7-97.6%) than to other P[19] strains (nt, 83.5-86.6%; aa, 89.4-94.1%) from different regions of the world. The VP7 gene of the three G3P[19] Taiwanese strains shared up to 93.4% nt and 97.5% aa identity to each other but had lower similarity to reference strain sequences available in GenBank (nt, <90.1%; aa, <95.6%). Similarly, the VP7 gene of the novel G5P[19] strain was only moderately related to the VP7 gene of reference G5 strains (nt, 82.2-87.3%; aa, 87.0-93.1%), while the VP7 gene of the single G9P[19] strain was genetically distinct from other known human and animal G9 rotavirus strains (nt, ≤ 92.0%; aa, ≤ 95.7%). Together, these findings suggest that the Taiwanese P[19] strains originated by independent interspecies transmission events. Synchronized surveillance of human and animal rotaviruses in Taiwan should identify possible hosts of these uncommon human rotavirus strains.     

Genomic characterization of a novel group A lamb rotavirus isolated in Zaragoza, Spain

An ovine rotavirus (OVR) strain, 762, was isolated from a 30-day-old lamb affected with severe gastroenteritis, in Zaragoza, Spain, and the VP4, VP7, VP6, NSP4, and NSP5/NSP6 genes were subsequently characterized molecularly. Strain OVR762 was classified as a P[14] rotavirus, as the VP4 and VP8* trypsin-cleavage product of the VP4 protein revealed the highest amino acid (aa) identity (94% and 97%, respectively) with that of the P11[14] human rotavirus (HRV) strain PA169, isolated in Italy. Analysis of the VP7 gene product revealed that OVR762 possessed G8 serotype specificity, a type common in ruminants, with the highest degree of aa identity (95-98%) shared with serotype G8 HRV, bovine rotavirus, and guanaco (Lama guanicoe) rotavirus strains. Moreover, strain OVR762 displayed a bovine-like NSP4 (genotype E2) and NSP5/NSP6 (genotype H3), and a VP6 genotype I2, as well as a long electropherotype pattern. This is the first report of a lamb rotavirus with P[14] and G8 specificities, providing additional evidence for the wide genetic and antigenic diversity of group A rotaviruses.     

Molecular characterization of G11P[25] and G3P[3] human rotavirus strains associated with asymptomatic infection in South India

Rotaviruses are the major etiological agents of diarrhea in children less than 5 years of age. Two unusual rotavirus strains not previously reported in India, G11P[25] (CRI 10795) and G3P[3] (CRI 33594) were isolated from faecal samples of asymptomatic children in India. The strains were characterized by sequence analysis of the genes encoding the VP7, VP4, VP6, and NSP4. The G11P[25] strain was closely related to the human G11P[25] strains from Bangladesh (with 98% identity at the nucleotide [nt] level and the amino acid [aa] level for the VP7 gene and 96% identity at the nt and 98% at the aa level for the VP4 gene). The G3P[3] strain was found to be related to a G3P[3] strain isolated in Thailand (CMH222; 88% identity at the nt level and 97% at aa level for the VP7 gene and 84% identity at the nt level and 90% at the aa level for the VP4 gene). Phylogenetic analysis of the VP6 and the NSP4 genes revealed that the Vellore G11P[25] strain was of VP6 subgroup II and NSP4 genotype B. The G3P[3] strain was identified as NSP4 genotype C and the VP6 gene showed 97% identity at the deduced amino acid level with strain CMH222 (Thailand) strain but did not cluster with sequences of SGI, SGII, SGI+II or SG-nonI/nonII. Both strains had gene segments of animal rotavirus origin suggesting inter-species transmission of rotavirus, and in the case of G11P[25] possibly underwent reassortment subsequently with human strains resulting in an animal-human hybrid strain.     

Genetic characterization of group C rotavirus isolated from a child hospitalized with acute gastroenteritis in Chiang Mai,Thailand

During an epidemiological survey of human rotavirus infection in Chiang Mai, Thailand, from 2002 to 2004, in which 263 stool specimens tested, one isolate of group C rotavirus was detected from a two-year-old child admitted to hospital with acute gastroenteritis. The human group C rotavirus, named CMH004/03, was characterized further by molecular analyses of its VP4, VP6, and VP7 gene segments as well as determination of RNA pattern by polyacrylamide gel electrophoresis (PAGE). Molecular characterization of VP4, VP6, and VP7 genes by sequence analyses showed high levels of sequence identities with those of human group C rotavirus reference strains isolated worldwide at 95.2% to 99.4% on nucleotide and 97.5% to 100% on amino acid levels. In contrast, the CMH004/03 strain exhibited far lesser nucleotide and amino acid sequence identities at 67.7% to 84.1% and 68.7% to 91.3%, respectively, when compared with those of porcine and bovine group C rotaviruses. Phylogenetic analyses of VP4, VP6, and VP7 genes clearly confirmed that the CMH004/03 strain clustered in a monophyletic branch with other human group C rotavirus reference strains and distantly related to the clusters of animal group C rotavirus strains. In addition, the RNA electrophoretic migration pattern of CMH004/03 showed a typical pattern (4-3-2-2) of group C rotavirus. To our knowledge, this study is the second report of group C rotavirus infection in pediatric patients in Thailand after it was reported for the first time about two decades ago.     

Genetic variation of prevalent G1P[8] human rotaviruses in South Korea

The human rotavirus G1P[8] strain is one of the most common rotaviruses worldwide, including Korea. Six Korean G1P[8] human rotaviruses, isolated using cell culture techniques, were characterized on the basis of sequence differences in VP7, VP4, VP6, and NSP4 genes to elucidate the evolutionary relationships in the community. All strains had a long RNA electropherotype, supported by VP6 gene analysis, clearly associated with subgroup II specificity. The phylogenetic analysis of VP7 gene sequences showed that they all clustered into lineage I, as reported for G1 strains in Japan, China, Vietnam, and Thailand. In addition, phylogenetic analysis of the VP4 gene showed that they belong to two distinct lineages, P[8]‐II and P[8]‐III. With respect to the NSP4 gene, all strains belonged to genotype B. An understanding of the ecology and molecular evolution of rotaviruses circulating in the country is very important for the development of vaccines and vaccination strategies. This study provides new information concerning the genetic variability of the rotavirus strain G1P[8] occurring most commonly as a vaccine candidate. J. Med. Virol. 82: 886–896, 2010. © 2010 Wiley‐Liss, Inc.     

Emergence of human G9 rotavirus with an exceptionally high frequency in children admitted to hospital with diarrhea in Chiang Mai, Thailand

Among 315 fecal specimens collected from children hospitalized with diarrhea in Chiang Mai, Thailand, in 2000-2001, group A rotavirus was detected in 107 (34.0%). Of these, 98 (91.6%) were G9, 6 (5.6%) were G3 and 3 (2.8%) were G2, respectively. Identification of their P-types demonstrated that 103 (96.3%) were P[8], 3 (2.8%) were P[4], and 1 (0.9%) was P[3] genotypes. Determination of G- and P-type combination revealed that all of G9 isolates were associated with P[8]. G9P[8] was the most predominant genotype and accounted for the majority (91.6%) of rotaviruses detected in this study. Molecular characterization of these G9 isolates demonstrated that all had long electropherotype, 96 of 98 (98.0%) belonged to subgroup II, one belonged to subgroup I and the other one was subgroup unidentifiable. All of G9 isolates possessed NSP4 genetic group B except for one isolate that showed dual genetic group specificities, B and C. The full-length VP7 gene nucleotide sequences among 15 representatives of these G9 strains were found to be highly homologous with percent identities of 99.3%-100%. Comparison with other G9 strains recently isolated showed that their nucleotide sequences were closely related to those of the US strain, US1205 (98.7%-99.0%) and Thai strain, 97CM108 (98.1%-99.0%). Interestingly, they were most closely related to the Japanese strain, 00-SG2509VP7, isolated in the same epidemic season, with percent nucleotide sequence identity of 99.4%-99.8%. The data imply that G9 strains isolated in this study and a G9 strain isolated in Japan in the year 2000 might have descended from the same ancestor.     

Molecular analysis of the VP7, VP4, VP6, NSP4, and NSP5/6 genes of a buffalo rotavirus strain: identification of the rare P[3] rhesus rotavirus-like VP4 gene allele

We report the detection and molecular characterization of a rotavirus strain, 10733, isolated from the feces of a buffalo calf affected with diarrhea in Italy. Strain 10733 was classified as a P[3] rotavirus, as the VP8* trypsin cleavage product of the VP4 protein revealed a high amino acid identity (96.2%) with that of rhesus rotavirus strain RRV (P5B[3]), used as the recipient virus in the human-simian reassortant vaccine. Analysis of the VP7 gene product revealed that strain 10733 possessed G6 serotype specificity, a type common in ruminants, with an amino acid identity to G6 rotavirus strains ranging from 88 to 98%, to Venezuelan bovine strain BRV033, and Hungarian human strain Hun4. Phylogenetic analysis based on the VP7 gene of G6 rotaviruses identified at least four lineages and an apparent linkage between each lineage and the VP4 specificity, suggesting the occurrence of repeated interspecies transmissions and genetic reassortment events between ruminant and human rotaviruses. Moreover, strain 10733 displayed a bovine-like NSP4 and NSP5/6 and a subgroup I VP6 specificity, as well as a long electropherotype pattern. The detection of the rare P[3] genotype in ruminants provides additional evidence for the wide genetic and antigenic diversity of group A rotaviruses.     

Characterization of human rotavirus serotype G9 isolated in Japan and Thailand from 1995 to 1997.

Serotyping of human rotavirus was conducted in 396 Japanese and 100 Thai rotavirus-positive fecal specimens collected from 1995 to 1997. Serotype G9 was found to be the third most common serotype with frequency of 16.2% in Thailand from 1996 to 1997. It was also detected in Japan with a low frequency (0.7%) in this year. The genetic analyses of VP4 and NSP4 genes of these G9 strains showed that 1 strain from Japan possessed P[8] genotype and NSP4 Wa-group with long electropherotype (e-type). In contrast, 5 strains from Thailand belonged to P[6] and 1 strain belonged to P[4]. All of the Thai strains were in the NSP4 KUN-group with a short e-type. Sequence analysis of their VP7 gene revealed that there was the highest homology among fecal G9 strains (> 96.3%, amino acid identity) and a relatively high degree of homology to standard viruses, F45 from Japan (95.4-96.3%, amino acid identity) and 116E from India (92-92.3%, amino acid identity). However, immunological analysis using G9 specific monoclonal antibodies (Mabs) against VP7 protein showed that the G9 strains isolated from the two countries had different antigenic specificity. It was confirmed further by intraserotypical phylogenetic analysis of VP7 amino acid. These results indicated that the prevalence of G9 rotavirus in 1996-1997 in Thailand was relative to the continuing recent emergence of it on a worldwide basis, while the Japanese G9 strain isolated in this survey was identified to have progenitors common to the F45 strain that was prevalent in 1985 in Japan. Phylogenetic analysis of VP7 amino acid of G1-14 prototype rotavirus showed that the G9 strains were most closely related to the equine G14 rotavirus FI23 strain but G3 strains, interserotypically. These findings suggest that G9 rotaviruses might be divided into two or more subtypes.     

Sequence Analysis of the NSP4 Gene from Human Rotavirus Strains Isolated in the United States

Two major and one minor genotype of the rotavirus NSP4 gene have been described. The sequences of 29 NSP4 genes from rotavirus isolates obtained in the United States during the 1996–1997 rotavirus season (types P[8]G1, P[8]G9, P[4]G2 and P[6]G9) and 10 strains isolated during previous rotavirus seasons (types P[8]G1 and P[4]G2) were determined. All NSP4 genes from strains with short E types (6 P[4]G2, 4 P[6]G9) belonged to genotype NSP4A, whereas all 19 strains with long E types (16 P[8]G1, 3 P[8]G9) had NSP4 genes of genotype NSP4B. Genetic variation within genotypes was low (2.3% for both NSP4A and NSP4B), confirming that the NSP4 genes are highly conserved. Nonetheless, at least two distinct sub-lineages could be detected within each genotype: strains isolated in the same year, regardless of geographic location, were more closely related or even identical at the deduced amino acid level; strains isolated in different years were more distinct. Thus, geographic distance did not affect genetic distance. Northern hybridization analysis with NSP4A and NSP4B total gene probes failed to detect any unusual combinations of the VP6 and NSP4 genes in 31 additional isolates from the 1996–1997 rotavirus season.     

Relationships among porcine and human P[6] rotaviruses: evidence that the different human P[6] lineages have originated from multiple interspecies transmission events

Porcine rotavirus strains (PoRVs) bearing human-like VP4 P[6] gene alleles were identified. Genetic characterization with either PCR genotyping or sequence analysis allowed to determine the VP7 specificity of the PoRVs as G3, G4, G5 and G9, and the VP6 as genogroup I, that is predictive of a subgroup I specificity. Sequence analysis of the VP8* trypsin-cleavage product of VP4 allowed PoRVs to be characterized further into genetic lineages within the P[6] genotype. Unexpectedly, the strains displayed significantly higher similarity (up to 94.6% and 92.5% at aa and nt level, respectively) to human M37-like P[6] strains (lineage I), serologically classifiable as P2A, or to the atypical Hungarian P[6] human strains (HRVs), designated as lineage V (up to 97.0% aa and 96.1% nt), than to the porcine P[6] strain Gottfried, lineage II (<85.1% aa and 82.2 nt), which is serologically classified as P2B. Interestingly, no P[6] PoRV resembling the original prototype porcine strain, Gottfried, was detected, while Japanase P[6] PoRV clustered with the atypical Japanase G1 human strain AU19. By analysis of the 10th and 11th genome segments, all the strains revealed a NSP4B genogroup (Wa-like) and a NSP5/6 gene of porcine origin. These findings strongly suggest interspecies transmission of rotavirus strains and/or genes, and may indicate the occurrence of at least 3 separate rotavirus transmission events between pigs and humans, providing convincing evidence that evolution of human rotaviruses is tightly intermingled with the evolution of animal rotaviruses.     

Molecular analysis of VP4, VP7, and NSP4 genes of P[6]G2 rotavirus genotype strains recovered from neonates admitted to hospital in Belém, Brazil

This investigation describes the molecular characterization of P[6]G2 rotavirus strains from hospitalized neonates with community-acquired diarrhea (CAD), nosocomial diarrhea (ND), and asymptomatic nosocomial infection (ANI) in Belém, Brazil. Twenty-six rotavirus strains with P[6]G2 genotype were sequenced to genes coding for VP4, VP7, and NSP4 proteins. Phylogenetic analysis of the VP4 gene, including prototype strains RV3, ST3, M37, and U1205, showed that local P[6]G2 strains clustered forming a distinct lineage (bootstrap of 99%). Brazilian P[6]G2 strains had the highest homology (ranging from 96.0%-98.3%) with the African strain GR1107, G4P[6]. Phylogenetic tree for VP7 gene was constructed including old and new G2 African strains SA3958GR/97, SA356PT/96, SA514GR/87, SA4476PT/97, BF3676/99, GH1803/99, and representative strains of G1, G3, G4, G5, G8, and G9 genotypes. The Brazilian P[6]G2 samples fell into a distinct group (bootstrap value of 97%) and showed homology rates ranging from 92.1% to 93.5% with P[6]G2 African strains BF3676/99, GH1803/99, and SA3958GR/97. Nucleotide sequence analysis of the NSP4 gene, including human prototype strains S2, KUN, DS-1, RV5, RV3 and ST3, and animal prototype OSU, showed that all neonatal isolates fell into genotype A and clustered with a bootstrap value of 100%, with in-group similarities ranging from 99.3% to 100%. In this study no significant differences in nucleotide sequences of the VP4, VP7, and NSP4 genes could be observed when comparing diarrheic (CAD and ND) and non-diarrheic (ANI) babies. Monitoring of rotavirus strains in hospital environments is of particular importance, since it is claimed currently that an efficacious rotavirus vaccine, when available for routine use, will determine an impact on hospital-acquired rotavirus disease.     

Characterization of inter-genogroup reassortant rotavirus strains detected in hospitalized children in Italy

Analysis of archival stool collections provides an invaluable source of virus strains and genetic material that may be exploited for molecular, epidemiological, and biological studies. The aim of this study was the molecular characterization of unusual human rotavirus (HRV) strains displaying atypical combinations of electropherotype (e-type) and VP4 and/or VP7 genotypes. Analysis of a panel of archival stools collected in northern Italy revealed continual circulation of P[8]G1 HRVs during 1987-1990 and the onset of P[6] + P[8]G1 strains after 1989. Interestingly, nine G1 strains, associated with either P[8], P[4] + P[8], P[6] + P[8], or untypeable VP4 genes, and two P[4]G1 + G2 strains, displayed short RNA e-type. The genetic constellation of the unusual strains was investigated by analysis of the VP4, VP6, VP7, and NSP4 genes. All the G1 strains with short e-type were subgroup (SG)II or SGI + SGII, and possessed a NSP4 of genogroup B or A + B. Conversely, the P[4]G1 + G2 strains were SGI and possessed a genogroup A NSP4. Sequence analysis of the VP7 and VP4 genes revealed that the unusual P[8]G1 and P[4]G1 + G2 viruses emerged by reassortment of strains circulating locally, rather than by introduction of new strains.     

Identification of a novel VP4 genotype carried by a serotype G5 porcine rotavirus strain

Rotavirus genome segment 4, encoding the spike outer capsid VP4 protein, of a porcine rotavirus (PoRV) strain, 134/04-15, identified in Italy was sequenced, and the predicted amino acid (aa) sequence was compared to those of all known VP4 (P) genotypes. The aa sequence of the full-length VP4 protein of the PoRV strain 134/04-15 showed aa identity values ranging from 59.7% (bovine strain KK3, P8[11]) to 86.09% (porcine strain A46, P[13]) with those of the remaining 25 P genotypes. Moreover, aa sequence analysis of the corresponding VP8* trypsin cleavage fragment revealed that the PoRV strain 134/04-15 shared low identity, ranging from 37.52% (bovine strain 993/83, P[17]) to 73.6% (porcine strain MDR-13, P[13]), with those of the remaining 25 P genotypes. Phylogenetic relationships showed that the VP4 of the PoRV strain 134/04-15 shares a common evolutionary origin with porcine P[13] and lapine P[22] rotavirus strains. Additional sequence analyses of the VP7, VP6, and NSP4 genes of the PoRV strain 134/04-15 revealed the highest VP7 aa identity (95.9%) to G5 porcine strains, a porcine-like VP6 within VP6 genogroup I, and a Wa-like (genotype B) NSP4, respectively. Altogether, these results indicate that the PoRV strain 134/04-15 should be considered as prototype of a new VP4 genotype, P[26], and provide further evidence for the vast genetic and antigenic diversity of group A rotaviruses.     

Molecular characterization of rare bovine group A rotavirus G15P[11] and G15P[21] strains from eastern India: identification of simian SA11-like VP6 genes in G15P[21] strains

During a surveillance study (November 2001-March 2005), one rare G15P[11] and two rare G15P[21] bovine group A rotavirus strains were detected in diarrhoeic calves in Eastern India. Sequence analysis of the VP8*, VP6, NSP4 and NSP5 genes of the G15P[11] strain confirmed its bovine origin. Although the NSP4 and NSP5 genes of the two G15P[21] strains were of bovine origin, their VP6 genes shared higher nucleotide and amino acid identities with simian strain SA11 (92.5-93.1% and 98.5-98.7%) than bovine strains (88.5-88.9% and 97-97.2%), and by phylogenetic analysis, exhibited clustering with SA11, distantly related to bovine strains. All these pointed towards a possible reassortment event of VP6 gene between bovine and simian (SA11-like) strains. Therefore, the present study provided molecular evidence for bovine origin of G15 strains and revealed a rare instance of genetic diversity in the bovine VP6 gene, otherwise conserved in group A rotavirus strains from cattle.     

Detection of a porcine rotavirus strain with VP4, VP7 and NSP4 genes of different animal origins

A new rotavirus strain, sh0902, was detected in diarrheic piglets on a farm in Shanghai, China, and its genotype was characterized as G1P[7]. Analysis of the VP4, VP7 and NSP4 genes demonstrated VP4 homology to bovine and swine rotavirus strains; the nucleotide (nt) and amino acid (aa) identities were 99.7% and 99.5%, respectively. The VP7 gene was highly homologous to that of a giant panda rotavirus strain, with 98.5% similarity at the nt level and 99% similarity at the aa level. The nucleotide sequence of the NSP4 gene displayed high homology to human rotavirus strain R479, with 99.7% identity at the nt level and 99.3% identity at the aa level. This is the first report of an unusual porcine rotavirus strain with VP4, VP7 and NSP4 genes that are highly homologous to bovine, swine, giant panda and human strains isolated at geographically distant sites (South Korea, China and India). Our data indicate that rotaviruses have circulated among humans and animals and undergone genome reassortment.     

Detection of rare G3P[19] porcine rotavirus strains in Chiang Mai, Thailand, provides evidence for origin of the VP4 genes of Mc323 and Mc345 human rotaviruses

Among 175 fecal specimens collected from diarrheic piglets during a surveillance of porcine rotavirus (PoRV) strains in Chiang Mai, Thailand, 39 (22.3%) were positive for group A rotaviruses. Of these, 33.3% (13 of 39) belonged to G3P[19], which was a rare P genotype seldom reported. Interestingly, their VP4 nucleotide sequences were most closely related to human P[19] strains (Mc323 and Mc345) isolated in 1989 from the same geographical area where these PoRV strains were isolated. These P[19] PoRV strains were also closely related to another human P[19] strain (RMC321), isolated from India in 1990. The VP4 sequence identities with human P[19] were 95.4% to 97.4%, while those to a porcine P[19] strain (4F) were only 87.6 to 89.1%. Phylogenetic analysis of the VP4 gene revealed that PoRV P[19] strains clustered with human P[19] strains in a monophyletic branch separated from strain 4F. Analysis of the VP7 gene confirmed that these strains belonged to the G3 genotype and shared 97.7% to 98.3% nucleotide identities with other G3 PoRV strains circulating in the regions. This close genetic relationship was also reflected in the phylogenetic analysis of their VP7 genes. Altogether, the findings provided peculiar evidence that supported the porcine origin of VP4 genes of Mc323 and Mc345 human rotaviruses.