Amino acid sequence similarity of the VP7 protein of human rotavirus HCR3 to that of canine and feline rotaviruses

Rotavirus genotypes and the indigenous children of Brazilian midwest in the vaccine era, 2008-2012: Footprints of animal genome

World group A rotavirus (RVA) surveillance data provides useful estimates of the disease burden, however, indigenous population might require special consideration. The aim of this study was to describe the results of G- and P-types from Brazilian native children ≤ 3 years. Furthermore, selected strains have been analyzed for the VP7, VP6, VP4, and NSP4 encoding genes in order to gain insight into genetic variability of Brazilian strains. A total of 149 samples, collected during 2008-2012, were tested for RVA using ELISA and PAGE, following by RT-PCR and sequencing. RVA infection was detected in 8.7% of samples (13/149). Genotype G2P[4] was detected in 2008 and 2010, G8P[6] in 2009, and G3P[8] in 2011. The phylogenetic analysis of the VP7 and VP4 genes grouped the Brazilian G2P[4] and G3P[8] strains within the lineages currently circulating in humans worldwide. However, the phylogenetic analysis of the VP6 and NSP4 from the Brazilian G2P[4] strains, and the VP7 and NSP4 from the Brazilian G3P[8] strains suggest a distant common ancestor with different animal strains (bovine, caprine, and porcine). The epidemiological and genetic information obtained in the present study is expected to provide an updated understanding of RVA genotypes circulating in the native infant population, and to formulate policies for the use of RVA vaccines in indigenous Brazilian people. Moreover, these results highlight the great diversity of human RVA strains circulating in Brazil, and an in-depth surveillance of human and animal RVA will lead to a better understanding of the complex dynamics of RVA evolution.

Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans

Rotaviruses, the major causative agents of infantile diarrhea worldwide, are, in general, highly species-specific. Interspecies virus transmission is thought to be one of the important contributors involved in the evolution and diversity of rotaviruses in nature. Human rotavirus (HRV) G3P[3] strains Ro1845 and HCR3A have been reported to be closely related genetically to certain canine and feline rotaviruses (RVs). Whole genome sequence and phylogenetic analyses of each of these 2 HRVs as well as 3 canine RVs (CU-1, K9 and A79-10, each with G3P[3] specificity) and 2 feline RVs (Cat97 with G3P[3] specificity and Cat2 with G3P[9] specificity) revealed that (i) each of 11 genes of the Ro1845 and HCR3A was of canine/feline origin; (ii) canine and feline rotaviruses with G3P[3] specificity bore highly conserved species-specific genomes; and (iii) the Cat2 strain may have evolved via multiple reassortment events involving canine, feline, human and bovine rotaviruses.

Molecular characterization of bovine group A rotavirus G3P[3] strains

During a surveillance study, four of 130 group A rotavirus strains, detected from diarrheic calves in Eastern India, exhibited G3P[3] specificities. Molecular characterization of VP7 and VP8(*) genes of one such strain [named as RUBV3 (RU: ruminant and BV: bovine)] revealed genetic relatedness to a G3P[3] simian strain, RRV, and RRV-related caprine strain GRV. Strain RUBV3 had VP6, NSP4 and NSP5 genes of bovine origin. Therefore, the present study provides evidence for multiple reassortment events involving ruminant and simian strains and, to our knowledge, is the first report of detection of bovine group A rotavirus strains with G3P[3] specificities.

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.

Global distribution of rotavirus serotypes/genotypes and its implication for the development and implementation of an effective rotavirus vaccine

A safe and effective rotavirus vaccine is urgently needed, particularly in developing countries. Critical to vaccine development and implementation is a knowledge base concerning the epidemiology of rotavirus G and P serotypes/genotypes throughout the world. The temporal and geographical distribution of human rotavirus G and P types was reviewed by analysing a total of 45571 strains collected globally from 124 studies reported from 52 countries on five continents published between 1989 and 2004. Four common G types (G1, G2, G3 and G4) in conjunction with P[8] or P[4] represented over 88% of the strains analysed worldwide. In addition, serotype G9 viruses associated with P[8] or P[6] were shown to have emerged as the fourth globally important G type with the relative frequency of 4.1%. When the global G and/or P type distributions were divided into five continents/subcontinents, several characteristic features emerged. For example, the P[8]G1 represented over 70% of rotavirus infections in North America, Europe and Australia, but only about 30% of the infections in South America and Asia, and 23% in Africa. In addition, in Africa (i) the relative frequency of G8 was as high as that of the globally common G3 or G4, (ii) P[6] represented almost one-third of all P types identified and (iii) 27% of the infections were associated with rotavirus strains bearing unusual combinations such as P[6]G8 or P[4]G8. Furthermore, in South America, uncommon G5 virus appeared to increase its epidemiological importance among children with diarrhea. Such findings have (i) confirmed the importance of continued active rotavirus strain surveillance in a variety of geographical settings and (ii) provided important considerations for the development and implementation of an effective rotavirus vaccine (e.g. a geographical P-G type adjustment in the formulation of next generation multivalent vaccines).

Human infection with a P[14], G3 lapine rotavirus

Group A rotaviruses are the main cause of severe diarrhoea in humans and animals throughout the world. We report the first description of a clinically apparent infection with a P[14], G3 rotavirus (strain B4106) in a hospitalized 6-year-old child. The VP7 gene of the B4106 strain had the closest sequence similarity (94% and 97% on the nucleotide and amino acid level, respectively) with strain 30/96 (P[14], G3), a lapine rotavirus isolated in an Italian rabbit in 1996 while the VP4 gene had the closest similarity with strain 30/96 on the nucleotide level (96%), and with lapine strains C-11 (P[14], G3) and Alabama (P[14], G3), isolated in the United States in the 1980s on the amino acid level (99%). The host restriction determinant gene NSP4 of B4106 was also most similar to lapine strain Alabama (95% nt identity and 97% aa identity). Phylogenetic analysis showed that the VP4, VP7, and NSP4 genes of the B4106 strain share a common evolutionary lineage with those of lapine rotavirus strains. We therefore hypothesize that a lapine rotavirus was able to cross the host species barrier and caused disease in a new host. The increasing detection of strains in humans that were previously believed to be restricted to animals raises questions whether interspecies transmission of rotaviruses is a common event in nature.

Genetic analysis of Group A rotaviruses: evidence for interspecies transmission of rotavirus genes

Rotaviruses are the major cause of severe gastroenteritis in young children and animals. The rotavirus genome is composed of eleven segments of double-stranded RNA and can undergo genetic reassortment during mixed infections, leading to progeny viruses with novel or atypical phenotypes. There are numerous descriptions of rotavirus strains isolated from human and animals that share genetic and antigenic features of viruses from heterologous species. In many cases, genetic analysis by hybridization has clearly demonstrated the genetic relatedness of gene segments to those from viruses isolated from different species. Together with the observation that some virus strains appear to have been transmitted to a different species as a whole genome constellation, these data suggest that interspecies transmission occurs naturally, albeit at low frequencies. Although interspecies transmission has not been documented directly, there is an increasing number of reports of atypical rotaviruses that are apparently derived from transmission between: humans, cats and dogs; humans and cattle; humans and pigs; pigs and cattle; and pigs and horses. Interspecies evolutionary relationships are supported by phylogenetic analysis of rotavirus genes from different species. The emergence of novel strains derived from interspecies transmission has implications for the design and implementation of successful human rotavirus vaccine strategies.

Rotavirus cross-species pathogenicity: molecular characterization of a bovine rotavirus pathogenic for pigs

Rotaviruses which cause disease in heterologous animal species have been reported but the molecular basis of cross-species infectivity and disease is not established. We report the molecular characterization of a cloned rotavirus, PP-1, which was originally obtained from cattle and which had been biologically characterized in vivo in two target animal species, gnotobiotic pigs and calves. In pigs, PP-1 caused severe clinical disease but in experimental calves it replicated subclinically. PP-1 was characterized as a G3 reassortant with a porcine VP4 and NSP4 but a bovine NSP1. The PP-1 VP4 had 96 to 97% deduced amino acid identity to P[7] porcine rotaviruses and P[7] specificity was confirmed with VP4-specific monoclonal antibodies. Sequence analysis of the PP-1 NSP1 showed 94 to 99.6% deduced amino acid identity to bovine rotaviruses but the NSP4 protein had 94 to 98% identity to the NSP4 genotype B porcine rotaviruses. G-typing PCR initially classified PP-1 as a G10 rotavirus but sequence analysis revealed 92 to 96% identity of the PP-1 VP7 with porcine, simian, and human G3 rotaviruses. These results, combined with the in vivo properties of PP-1 in the two target species, supported the concept that species-specific VP4 and NSP4, but not NSP1, are required to induce rotavirus disease, at least in calves and pigs. The results illustrate experimentally that rotaviruses circulating in one animal species can pose a risk to another by the emergence of a pathogenic reassortant rotavirus under appropriate conditions.

Isolation and genetic characterization of two G3P5A[3] canine rotavirus strains in Italy

Two strains of canine rotavirus were isolated from pups with clinical signs of gastroenteritis. Both strains were identified by polymerase chain reaction (PCR) as G3P5A[3], although restriction endonuclease analysis of the PCR amplicons revealed a genetic difference between the two isolates in the VP7 gene. The isolation in Italy of canine rotaviruses displaying the same VP7 and VP4 specificities as in the USA and in Japan, suggests that the G3 and P5A[3] types are highly conserved among canine rotavirus strains.

Nucleotide sequence variation of the VP7 gene of two G3-type rotaviruses isolated from dogs

The sequence of the VP7 gene of two rotaviruses isolated from dogs in southern Italy was determined and the inferred amino acid sequence was compared with that of other rotavirus strains. There was very high nucleotide and amino acid identity between canine strain RV198/95 and other canine strains, and to the human strain HCR3A. Strain RV52/96, however, was found to have about 95% identity to the G3 serotype canine strains K9, A79-10 and CU-1 and 96% identity to strain RV198/95 and to the simian strain RRV. Therefore both of the canine strains belong to the G3 serotype. Nevertheless, detailed analysis of the VP7 variable regions revealed that RV52/96 possesses amino acid substitutions uncommon to the other canine isolates. In addition, strain RV52/96 exhibited a nucleotide divergence greater than 16% from all the other canine strains studied; however, it revealed the closest identity (90.4%) to the simian strain RRV. With only a few exceptions, phylogenetic analysis allowed clear differentiation of the G3 rotaviruses on the basis of the species of origin. The nucleotide and amino acid variations observed in strain RV52/96 could account for the existence of a canine rotavirus G3 sub-type.

Rotavirus-specific cytotoxic T lymphocytes recognize overlapping epitopes in the amino-terminal region of the VP7 glycoprotein

Rotavirus-specific cytotoxic T lymphocytes (CTL) play an important role in the resolution of rotavirus infection. The outer capsid glycoprotein, VP7, elicits a class I MHC-restricted CTL response. Vaccinia virus recombinants expressing the VP7 genes from simian rotavirus SA11 (serotype G3) and from the RF strain of bovine rotavirus (serotype G6) were used to analyze the CTL activity to this antigen in BALB/c (H-2(d)) and C57BL/6 (H-2(b)) mice neonatally infected with homologous and heterologous rotaviruses. A vaccinia virus recombinant expressing the first amino-terminal 88 amino acids of VP7 was constructed and used to search for cross-reactive CTL against this region of the protein. By using synthetic Kb, Db, and Kd motif-fitting peptides two overlapping CTL epitopes have been identified located in the first hydrophobic domain (H1) of VP7. Splenocytes obtained from rotavirus SA11-infected C57BL/6 mice induced the strongest CTL response against target cells sensitized with a peptide containing a Kb-restricted CTL epitope (amino acids 8-16). A second Kd-restricted epitope (residues 5-13) was recognized by splenocytes derived from rotavirus-infected BALB/c mice. These findings reveal the existence of CTL epitopes in the H1 signal sequence of the VP7 glycoprotein that coexist with a CTL epitope (residues 31-40) previously described within the H2 region.

Relationship among serotype G3P5A rotavirus strains isolated from different host species

The relationship among G3P5A rotavirus strains was analysed by restriction endonuclease assay of the VP4, VP6 and VP7 encoding genes, neutralization assay and phylogenetic analysis. The restriction patterns of the capsid encoding genes were species specific allowing the differentiation among the strains of different origin. The VP7 profiles differentiated human from animal strains more efficiently. The phylogenetic analysis of the VP4 gene demonstrated that HCR3A and K9 are closer related to each other than to other P5A strains. The same occurs to strains Ro1845 and Cat 97. The CU-1 virus appears to be an ancestor of the P5A strains by neutralization and phylogenetic analysis. The results placed the RRV strain definitely in a separate VP4 serotype and genotype from that of P5A strains. Restriction endonuclease assay of the capsid encoding genes seems to be a useful tool to identify the host species of rotavirus strains belonging to the same serotype and/or genotype.

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

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

Comparative nucleotide and deduced amino acid sequence analysis of VP7 gene of the NCDV Cody (I-801) strain of group A bovine rotavirus

The prevalent G serotypes of group A bovine rotavirus (BRV) reported are G6, G10, and less commonly, G8. Neonatal Calf Diarrhea Virus (NCDV), Lincoln and Cody strains were first isolated from diarrheic calves in Nebraska. The NCDV Lincoln strain is the currently used U.S. vaccine strain and has a G6 serotype. In this study, the complete nucleotide sequence of the VP7 gene of NCDV Cody (I-801 strain) was determined using the primer extension method. The VP7 gene nucleotide sequence homologies between Cody I-801 and established G8 rotaviruses, A5 (Thailand BRV), 678 (UK BRV), B37 (human RV) and 69M (human RV) were 84.7%, 86.4%, 84.7% and 85.9%, respectively. The deduced VP7 amino acid sequence of Cody I-801 was similar to that of A5, 678, B37 and 69M (93.6%, 95.7%, 92.6% and 95.1%, respectively). The VP7 gene nucleic acid sequence homologies between NCDV Cody (I-801) and NCDV Lincoln or B223 (G10) was 76.2% and the deduced VP7 amino acid sequence homologies between Cody I-801 and NCDV Lincoln or B223 were 82.5% and 81.3%, respectively. Thus, our sequence data suggests that the VP7 gene of Cody I-801 strain of BRV is genetically most similar to G8 rotaviruses and unrelated to the NCDV Lincoln G6 rotavirus strain.

Rotavirus serotype G5 associated with diarrhea in Brazilian children

Rotavirus serotype G5 in fecal specimens of 38 Brazilian children with diarrhea was identified by PCR and enzyme immunoassays. The strains exhibited long RNA electropherotypes and either subgroup II or nonsubgroup I-nonsubgroup II specificities. Serotype G5 has been found in piglets and horses but not yet in humans.

VP4 typing of bovine and porcine group A rotaviruses by PCR

A PCR typing assay was developed to identify rotavirus P types (VP4 specificity) of bovine NCDV, UK, and B223 strains and porcine OSU and Gottfried strains. Thirty-nine human and animal strains representing all known, and some undefined, rotavirus P types were used to develop and evaluate the specificity of the method. No cross-amplification was observed. The PCR results agreed with previous characterizations by monoclonal antibodies, sequence analysis, and hybridization assays, except for the Gottfried strain, which showed a P type distinct from the human asymptomatic strains. Analysis of a small number of field specimens suggested a high level of VP4 polymorphism among porcine strains. The assay should be of value in typing field isolates and tracing interspecies infections.