Novel porcine rotavirus of genotype P[27] shares new phylogenetic lineage with G2 porcine rotavirus strain

Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013-2016

Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted.

Zoonotic RVA: State of the Art and Distribution in the Animal World

Rotavirus species A (RVA) is a pathogen mainly affecting children under five years old and young animals. The infection produces acute diarrhea in its hosts and, in intensively reared livestock animals, can cause severe economic losses. In this study, we analyzed all RVA genomic constellations described in animal hosts. This review included animal RVA strains in humans. We compiled detection methods, hosts, genotypes and complete genomes. RVA was described in 86 animal species, with 52% (45/86) described by serology, microscopy or the hybridization method; however, strain sequences were not described. All of these reports were carried out between 1980 and 1990. In 48% (41/86) of them, 9251 strain sequences were reported, with 28% being porcine, 27% bovine, 12% equine and 33% from several other animal species. Genomic constellations were performed in 80% (32/40) of hosts. Typical constellation patterns were observed in groups such as birds, domestic animals and artiodactyls. The analysis of the constellations showed RVA's capacity to infect a broad range of species, because there are RVA genotypes (even entire constellations) from animal species which were described in other studies. This suggests that this virus could generate highly virulent variants through gene reassortments and that these strains could be transmitted to humans as a zoonotic disease, making future surveillance necessary for the prevention of future outbreaks.

Prevalence of rotavirus A infection and the detection of type G3P[11] strain in ruminants in Yobe state, Nigeria

Rotaviruses have a worldwide distribution and the infection is associated with diarrhea in young of ruminants as well as children. However, limited data exist on its prevalence and types in Yobe state, Nigeria. Detection of rotavirus A and types in ruminant population in Yobe state was the aim of the study. A total of 470 diarrheic fecal samples were collected and tested for rotavirus and types using serology and molecular techniques respectively. A prevalence rate of 2.98% (14/470) was found in the three species with specific rates of 2.9% (6/202), 3.8% (6/158), and 1.8% (2/110) in goat, sheep, and cattle respectively. The prevalence rates of 3.6% (12/331), 1.2% (1/84), and 1.8% (1/55) were for those aged < 1-3, 4-6, and 7-9 months old, respectively, while 4.9% (9/185) and 1.7% (5/285) were in males and females respectively. Rotavirus genes VP7 and VP4 were detected in 2 (14.3%) out of the 14 ELISA-positive samples while deduced amino acid sequences of the major variable regions revealed the genes to belong to types G3P[11] strain. Significant association was found between the infection and sex (P < 0.05) unlike in the species and age groups of the ruminants. The circulation of rotavirus virus in ruminants and type G3P[11] in cattle has been confirmed in the study. Hence, there is a need for continuous surveillance, awareness campaign, and assessment of the economic losses and public health implications of rotavirus infection in Nigeria.

Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011-2016

Swine are economically important food animals, but highly contagious porcine epidemic diarrhea virus (PEDV) and rotavirus can afflict pig herds and contribute significantly to piglet morbidity and mortality. While there have been studies on rotavirus group A (RVA) in Thailand, reports of rotavirus group C (RVC) are limited. Here, we aimed to identify the prevalence of RVC circulating on Thai commercial swine farms. We analyzed 769 feces and intestine mucosal contents of pigs affected with diarrhea between 2011 and 2016 using RT-PCR specific for the PEDV spike (S), rotavirus glycoprotein (G) VP7, and protease-sensitive protein (P) VP4 genes. We found that 6.6% (51/769) of samples tested positive for RVC, of which 11 samples were co-infected with RVA and four samples were co-infected with PEDV. Three samples tested positive for all three viruses. Phylogenetic analysis of the VP7 gene showed that the most frequent RVC genotype was G1, which grouped with the prototypic RVC Cowden strain. While G6 and G9 were also common, G3 was relatively rare. Analysis of the VP4 gene revealed that the most common P type was P[5], followed by P[4], P[7], and P[1]. In all, there were six G/P combinations (G6P[5], G1P[1], G1P[4], G1P[5], G9P[4], and G9P[7]), of which G6P[5] was the most predominant.

Porcine Rotaviruses: Epidemiology, Immune Responses and Control Strategies

Rotaviruses (RVs) are a major cause of acute viral gastroenteritis in young animals and children worldwide. Immunocompetent adults of different species become resistant to clinical disease due to post-infection immunity, immune system maturation and gut physiological changes. Of the 9 RV genogroups (A–I), RV A, B, and C (RVA, RVB, and RVC, respectively) are associated with diarrhea in piglets. Although discovered decades ago, porcine genogroup E RVs (RVE) are uncommon and their pathogenesis is not studied well. The presence of porcine RV H (RVH), a newly defined distinct genogroup, was recently confirmed in diarrheic pigs in Japan, Brazil, and the US. The complex epidemiology, pathogenicity and high genetic diversity of porcine RVAs are widely recognized and well-studied. More recent data show a significant genetic diversity based on the VP7 gene analysis of RVB and C strains in pigs. In this review, we will summarize previous and recent research to provide insights on historic and current prevalence and genetic diversity of porcine RVs in different geographic regions and production systems. We will also provide a brief overview of immune responses to porcine RVs, available control strategies and zoonotic potential of different RV genotypes. An improved understanding of the above parameters may lead to the development of more optimal strategies to manage RV diarrheal disease in swine and humans.

Novel G9 rotavirus strains co-circulate in children and pigs, Taiwan

Molecular epidemiologic studies collecting information of the spatiotemporal distribution of rotavirus VP7 (G) and VP4 (P) genotypes have shown evidence for the increasing global importance of genotype G9 rotaviruses in humans and pigs. Sequence comparison of the VP7 gene of G9 strains identified different lineages to prevail in the respective host species although some of these lineages appear to be shared among heterologous hosts providing evidence of interspecies transmission events. The majority of these events indicates the pig-to-human spillover, although a reverse route of transmission cannot be excluded either. In this study, new variants of G9 rotaviruses were identified in two children with diarrhea and numerous pigs in Taiwan. Whole genome sequence and phylogenetic analyses of selected strains showed close genetic relationship among porcine and human strains suggesting zoonotic origin of Taiwanese human G9 strains detected in 2014-2015. Although the identified human G9P[19] and G9P[13] rotaviruses represented minority strains, the repeated detection of porcine-like rotavirus strains in Taiwanese children over time justifies the continuation of synchronized strain surveillance in humans and domestic animals.

Epidemiology of gastroenteritis viruses in Japan: Prevalence, seasonality, and outbreak

Acute gastroenteritis has been recognized as one of the most common diseases in humans and continues to be a major public health problem worldwide. Several groups of viruses have been reported as the causative agents of acute gastroenteritis, including rotavirus, norovirus, sapovirus, human astrovirus, adenovirus, and an increasing number of others which have been reported more recently. The epidemiology, prevalence, seasonality, and outbreaks of these viruses have been reviewed in a number of studies conducted in Japan over three decades. Rotavirus and norovirus were the two most common viruses detected almost equally in children under 5 years of age who were suffering from acute gastroenteritis. Like many other countries, the main rotavirus strains circulating in pediatric patients in Japan are G1P[8], G2P[4], G3P[8], and G9P[8]. Norovirus GII.4 was involved in most outbreaks in Japan and found to be associated with the emergence of new variants Sydney_2012. The classic human astrovirus, MLB, and VA clades astroviruses were also commonly found in pediatric patients with acute diarrhea. The sapovirus and adenovirus have been identified as the minor viral causative agents for acute gastroenteritis in Japan.

The prevalence and genetic diversity of group A rotaviruses on pig farms in the Mekong Delta region of Vietnam

Group A rotaviruses (ARoVs) are a common cause of severe diarrhea among children worldwide and the cause of approximately 45% of pediatric hospitalizations for acute diarrhea in Vietnam. ARoVs are known to cause significant economic losses to livestock producers by reducing growth performance and production efficiencies, however little is known about the implications of asymptomatic endemic circulation of ARoV. We aimed to determine the prevalence and predominant circulating genotypes of ARoVs on pig farms in a southern province of Vietnam. We found overall animal-level and farm-level prevalence of 32.7% (239/730) and 74% (77/104), respectively, and identified six different G types and 4 P types in various combinations (G2, G3, G4, G5, G9, G11 and P[6], P[13], P[23], and P[34]). There was no significant association between ARoV infection and clinical disease in pigs, suggesting that endemic asymptomatic circulation of ARoV may complicate rotavirus disease attribution during outbreaks of diarrhea in swine. Sequence analysis of the detected ARoVs suggested homology to recent human clinical cases and extensive genetic diversity. The epidemiological relevance of these findings for veterinary practitioners and to ongoing pediatric ARoV vaccine initiatives in Vietnam merits further study.

Rotavirus associated gastroenteritis in Thailand

Group A rotavirus is the leading cause of severe diarrhea in infants and young children, and in young animals of many species worldwide. Rotavirus is also the major cause of deaths of children younger than 5 years of age, particularly, in developing countries in Asia and Africa. In Thailand, the burden of rotavirus infection rate in children admitted to the hospitals with acute gastroenteritis ranged from 28.4 to 44.5 %. The seasonality of rotavirus gastroenteritis in Thailand was detected all-year-round with the peak from November to April of the following year. The distributions of G genotypes in pediatric patients during twelve-year surveillances of 2000-2011 were G1, G2, G3, G4, G9, and G12. The G9 was detected as the most predominant genotype in 2000-2004 while G1 and G3 were predominated in 2005-2009 and 2009-2011, respectively. The G4 was detected only in 2001-2003 and G12 only in 2007-2009 but was not detectable in any other years of surveillances. For P genotype, P[8] was the only P genotype that always existed as the most predominant with high prevalence. The G-P combination of human rotavirus strains circulated in Thailand were G1P[8], G2P[4], G2P[8], G3P[3], G3P[8], G3P[9], G3P[10], G3P[19], G9P[8], G12P[6], and G12P[8]. The G1P[8] was the most predominant strain followed by G9P[8], G2P[4], G3P[8], G12P[8], G3P[9], G3P[10], G3P[3], G2P[8], G3P[19], and G12P[6]. The studies of animal rotaviruses were performed mainly on porcine rotaviruses and a wide variety of porcine rotavirus strains have been reported, including G2P[27], G3P[6], G3P[13], G3P[19], G3P[23], G4P[6], G4P[13], G4P[19], G4P[23], G5P[6], G5P[13], G9P[7], G9P[13], and G9P[19]. Several unusual strains of human rotaviruses that carried the genes with nucleotide sequences closely related to those of animal rotaviruses have been described in Chiang Mai, Thailand which provided evidences for interspecies transmission of rotaviruses between humans and animals, and also animals to animals are occurring in nature.

Exotic rotaviruses in animals and rotaviruses in exotic animals

Group A rotaviruses (RVA) are a major cause of viral diarrhea in the young of mammals and birds. RVA strains with certain genotype constellations or VP7-VP4 (G-P) genotype combinations are commonly found in a particular host species, whilst unusual or exotic RVAs have also been reported. In most cases, these exotic rotaviruses are derived from RVA strains common to other host species, possibly through interspecies transmission coupled with reassortment events, whilst a few other strains exhibit novel genotypes/genetic constellations rarely found in other RVAs. The epidemiology and evolutionary patterns of exotic rotaviruses in humans have been thoroughly reviewed previously. On the other hand, there is no comprehensive review article devoted to exotic rotaviruses in domestic animals and birds so far. The present review focuses on the exotic/unusual rotaviruses detected in livestock (cattle and pigs), horses and companion animals (cats and dogs). Avian rotaviruses (group D, group F and group G strains), including RVAs, which are genetically divergent from mammalian RVAs, are also discussed. Although scattered and limited studies have reported rotaviruses in several exotic animals and birds, including wildlife, these data remain to be reviewed. Therefore, a section entitled "rotaviruses in exotic animals" was included in the present review.

Hospital-based surveillance for rotavirus gastroenteritis in children younger than 5 years of age in Ethiopia: 2007-2012

BACKGROUND

Rotavirus surveillance was initiated in Ethiopia to estimate the burden of rotavirus gastroenteritis in children <5 years of age, to generate data to assist the policy-making process for new vaccine introduction and to monitor impact of vaccination on disease burden after introduction.

METHODS

Sentinel surveillance was conducted at 3 hospitals in Addis Ababa, Ethiopia using a standardized WHO surveillance protocol from August 2007 to March 2012. Children <5 years of age, hospitalized for the primary reason of treatment for acute gastroenteritis, were enrolled, stool samples were collected and tested for group A rotavirus using an enzyme immunoassay. Confirmed positive specimens were further characterized by rotavirus genotyping.

RESULTS

A total of 1841 children were enrolled and 21% were rotavirus positive. Children 6-12 months of age had the highest proportion of rotavirus (36%) followed by children <6 months of age (23%). There was no significant difference between sexes. Significant differences in clinical characteristics, such as vomiting, vomiting episodes, cases with vomiting and diarrhea among rotavirus positive cases, were observed. Rotavirus circulated year round with peak prevalence from October through January. The most prevalent detected genotypes were G1P[8] (20%), G12P[8] (17%) and G3P[6] (15%), respectively.

CONCLUSIONS

Rotavirus infection is common in Ethiopian children. A safe and effective intervention against the infection is needed to prevent severity of the disease. Rotavirus vaccine introduction is planned before the end of 2013. The established surveillance system and the data generated can be used to monitor the impact of rotavirus vaccination program on severe disease.

Phylogenetic Analysis of the Rotavirus Genotypes Originated from Children < 5 Years of Age in 16 Cities in South Korea, between 2000 and 2004

Objectives

The purpose of this study was to examine the diversity of the G and P types of human rotavirus strains isolated in South Korea during 2000 to 2004.

Methods

We selected 38 Group A rotavirus isolates among 652 fecal samples, which were collected from infants and children < 5 years of age with acute gastroenteritis or diarrhea admitted in 8 hospitals representative of five provinces of South Korea between 2000 and 2004. Rotavirus P- and G-genotypes were determined by nucleotide sequencing and phylogenetic analysis was performed.

Results

One G1P[4] consisted G1-Id-P[4]-V; one G1P[6] consisted G1-Id-P[6]-Ia; nine G1P[8] consisted G1-Ib-P[8]-Ia (n=3), G1-Ic-P[8]-Ia (n=1), and G1-Id-P[8]-Ia (n=5); 13 G2P[4] consisted G2-V-P[4]-V; two G3P[4] consisted G3-IIId-P[4]-V; five G3P[8] consisted G3-IIId-P[8]-Ia; four G4P[6] consisted G4-Ie-P[6]-Ia; two G4P[8] consisted G4-Ie-P[8]-II; one G9P[6] consisted G9-III-P[6]-Ia.

Conclusions

A considerable amount of rotavirus genotypic diversity was detected in South Korea from 2000 to 2004. These findings are important to develop the effective vaccines and to undertake epidemiologic studies.

Epidemiology and clinical features of rotavirus and norovirus infection among children in Ji'nan, China

Background

Acute gastroenteritis caused by bacteria, virus and parasite is an important cause of childhood morbidity and mortality in developing countries. Rotavirus and norovirus have been recognized as the most common pathogens causing acute gastroenteritis among children. However, there is still no valuable data about infections of rotavirus and norovirus in children in Ji’nan, an eastern city in China. The aims of the present study are to determine the incidence of rotavirus and norovirus associated acute gastroenteritis in Ji’nan among children, to characterize rotavirus and norovirus strains circulating during this period; and to provide useful epidemiological and clinical data.

Methods

Fecal specimens and clinical data were collected from 767 children (502 outpatients and 265 inpatients) under 5 years of age with acute diarrhea at Shandong University Qilu Hospital and Qilu children’s Hospital in Ji’nan, China between February 2011 and January 2012. Virus RNA was extracted, amplified, electrophoresed, sequenced and phylogenetically analyzed to determine the prevalent genotypes. Chi-square and U test were used to compare characteristics of clinical manifestation in each group.

Results

Of the 767 specimens 263 (34.3%) were positive for rotavirus and 80 (10.4%) were positive for norovirus. Among 263 rotavirus positive cases, G3 (40.7%) was the most prevalent serotype, P[8] (46.8%) was the dominant genotype and G3P[8] (31.9%) was the most common combination. All of the norovirus strains belonged to GII genogroup including GII.3, GII.4 and GII.6, of which GII.4 (61.2%) was the predominant genotype. Phylogenetic analysis of the GII.4 sequences showed that 18 GII.4 strains belonged to GII.4 2004–2006 cluster and 31 GII.4 strains were divided into GII.4 2006b cluster. A peak number of rotavirus infections was observed during the cold season from November to next January. Higher rates of norovirus infections were detected from September to November. Most patients with rotavirus and norovirus associated diarrhea experienced vomiting (88.2% and 67.5%, respectively) and fever (79.1% and 46.3%, respectively).

Conclusions

The present study showed that rotavirus and norovirus were still the important causative agents of pediatric diarrhea in Ji’nan during this period.

Detection and genetic diversity of porcine group A rotaviruses in historic (2004) and recent (2011 and 2012) swine fecal samples in Ohio: predominance of the G9P[13] genotype in nursing piglets

Epidemiological surveillance of porcine group A rotavirus (RVA) strains was conducted in five swine herds in Ohio using historical (2004) and recent (2011 to 2012) fecal samples. Of the 371 samples examined, 9.4% (35/371) were positive for RVA. The RVA detection rates increased from 5.9% in 2004 and 8.5% in 2011 to 13.8% in 2012. A total of 23 positive samples were analyzed for RVA G and P genotypes. The dominant G-P combination was G9P[13] found in 60.9% of positive samples. The other combinations were G9P[7] (8.7%), G4P[13] (8.7%), G11P[13] (4.3%), and G11P[7] (4.3%). Sequence analysis of partial VP7 genes of selected strains revealed that the G4 strains were closely related to one another (95%) and, to a lesser extent, to human (82 to 84%) and porcine (84 to 86%) G4 strains. The G11 strains detected shared identical VP7 gene sequences (100%) and were closely related to human (85 to 86%) and other porcine (83%) G11 strains. The G9 strains identified were closely related to one another and to human and other porcine strains (96 to 97%, 89 to 91%, and 89 to 91% nucleotide identities, respectively). The VP4 gene analysis revealed that P[7] strains were closely related to each other and to P[7] strains isolated from porcine, bovine, and panda samples (91 to 99%, 92 to 99% and 92 to 99%, respectively). The P[13] strains showed a higher diversity among themselves and with other porcine P[13] strains, ranging from 83% to 99% and from 82 to 97%, respectively. Our results demonstrate broad genetic heterogeneity of the RVA strains and suggest the possibility of genetic reassortment between different RVA genotypes within these farms.

Full-length genome analysis of G2, G9 and G11 porcine group A rotaviruses

Group A rotaviruses with G2 and G9 VP7 specificity are common in humans, while G11 strains have been detected only sporadically. G2, G9 and G11 rotaviruses also circulate in pigs and swine rotaviruses have been suspected of interspecies and zoonotic transmissions in numerous studies. However, the complete gene constellation of G2 and G9 porcine rotaviruses has not yet been determined. In order to start filling this gap, the genomic make up of two G2, one G9 and one G11 porcine rotavirus strains, detected in Canada in 2005-2007, was determined. With the exception of a G2P[34] strain, with E9 NSP4 type and mixed I5+I14 VP6 type, the constellation of genomic segments was rather conserved and were closely related to prototype porcine strains in the four viruses characterized (I5-R1-C1-M1-A8-N1-T7-E1-H1). Most notably, all the viruses displayed a rare NSP3 genotype, T7, which has also been identified in rare human reassortant strains and in the reference strain RVA/Cow-tc/GBR/UK/1973/G6P[5]. This study provides crucial genetic data on these complex viruses and will help understand the origin and ecological niche of gene segments and the role played by pigs in their evolution.

Genetic diversity and novel combinations of G4P[19] and G9P[19] porcine rotavirus strains in Thailand

Several epidemiological studies reported the detection of rotavirus strains bearing unusual combinations of genetic background of human and porcine rotaviruses. This observation supports the hypothesis of interspecies transmission of rotaviruses in humans and pigs. The aims of this study were to investigate the genotypes and molecular characteristics of rotaviruses in piglets with diarrhea in several farms from two provinces in Thailand. A total of 207 fecal specimens collected from diarrheic piglets were screened for the presence of groups A, B, and C rotaviruses. Group A rotaviruses were detected in 41 out of 207 (19.8%) fecal specimens tested. A wide variety of G-P combination rotavirus strains were detected in this study. The G4P[6] was identified as the most prevalent genotype (39.0%), followed by G4P[23] (12.2%), G3P[23] (7.3%), G4P[19] (7.3%), G3P[6] (4.9%), G3P[13] (4.9%), G3P[19] (4.9%), G9P[13] (4.9%), G9P[19] (4.9%), G5P[6], and G5P[13] each of 2.4%. Furthermore, G5 and G9 in combinations with P-nontypeable strains were also found at each consisting of 2.4% (n=1) of the collection. It was interesting to note that among diversified porcine rotavirus strains, novel combinations of G4P[19] and G9P[19] strains were detected for the first time in this study. Nucleotide sequences of VP4 and VP7 of these strains were closely related to human rotaviruses reported previously. The data implies that these porcine rotaviruses were probably generated in nature from the reassortment between the viruses of human and porcine origin. This study provides valuable epidemiological information and molecular characteristics of porcine rotaviruses circulating in piglets with diarrhea in northern Thailand.

Full-length genomic analysis of porcine G9P[23] and G9P[7] rotavirus strains isolated from pigs with diarrhea in South Korea

Group A rotaviruses (RVAs) are agents causing severe gastroenteritis in infants and young animals. G9 RVA strains are believed to have originated from pigs. However, this genotype has emerged as the fifth major human RVA genotype worldwide. To better understand the relationship between human and porcine RVA strains, complete RVA genome data are needed. For human RVA strains, the number of complete genome data have grown exponentially. However, there is still a lack of complete genome data on porcine RVA strains. Recently, G9 RVA strains have been identified as the third most important genotype in diarrheic pigs in South Korea in combinations with P[7] and P[23]. This study is the first report on complete genome analyses of 1 G9P[7] and 3 G9P[23] porcine RVA strains, resulting in the following genotype constellation: G9-P[7]/P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. By comparisons of these genotype constellations, it was revealed that the Korean G9P[7] and G9P[23] RVA strains possessed a typical porcine RVA backbone, similar to other known porcine RVA strains. However, detailed phylogenetic analyses revealed the presence of intra-genotype reassortments among porcine RVA strains in South Korea. Thus, our data provide genetic information of G9 RVA strains increasingly detected in both humans and pigs, and will help to establish the role of pigs as a source or reservoir for novel human RVA strains.

Genotyping of human rotaviruses circulating among children with diarrhea in Valencia, Venezuela

Rotavirus infection is the most common cause of severe gastroenteritis during childhood worldwide, especially in developing countries. Two rotavirus vaccines are available for childhood immunization programs. Evaluation of the vaccine performance will benefit from knowledge of the epidemiological features of rotavirus infection in regional settings. Limited information on the molecular characteristics of the rotavirus types circulating in Venezuela is available. Eighty seven (89.7%) of the 97 ELISA rotavirus positive stool samples collected from children with diarrhea aged <5 years during 2003 in Valencia (Carabobo State), were G-, P- and NSP4-genotyped by RT-PCR and/or automated sequencing. Four common combinations, G3P[8]/NSP4-E1, G2P[4]/NSP4-E2, G9P[8]/NSP4-E1, and G1P[8]/NSP4-E1 were responsible for 50.6%, 35.6%, 5.7%, and 1.1%, respectively of cases of rotavirus diarrhea, most of them (66%) in children ≤12 months. One uncommon G8P[14]/NSP4-E2 strain was also detected. Temporal fluctuation of genotype distribution occurred, but no differences by age, diarrhea severity score, sex, treatment type or patient medical attention were observed, except for the G3P[8]/NSP4-E1, associated with a more severe dehydration than any other type (P < 0.01). The results confirm the broad diversity among rotavirus strains circulating in Venezuela prior to vaccine implementation, showing the predominance of G3, significant proportion of G2 and moderate circulation of G9 strains. Epidemiological surveillance is needed to detect the emergence of new genotypes that could escape protection induced by vaccination.

Clinical characteristics and genotypes of rotaviruses in a neonatal intensive care unit

BACKGROUND

There are few reports on the symptoms of rotavirus infections in neonates. This study aims to describe clinical signs of rotavirus infections among neonates, with a particular focus on preterm infants, and to show the distribution of genotypes in a neonatal intensive care unit (NICU).

METHODS

A prospective observational study was conducted at a regional NICU for 1 year. Stool specimens from every infant in the NICU were collected on admission, at weekly intervals, and from infants showing symptoms. Rotavirus antigens were detected by enzyme-linked immunosorbent assay (ELISA), and genotypes were confirmed by Reverse transcription-Polymerase chain reaction (RT-PCR). The infants were divided into three groups: symptomatic preterm infants with and without rotavirus-positive stools [Preterm(rota+) and Preterm(rota-), respectively] and symptomatic full- or near-term infants with rotavirus-positive stools [FT/NT(rota+)]. Demographic and outcome data were compared among these groups.

RESULTS

A total of 702 infants were evaluated for rotaviruses and 131 infants were included in this study. The prevalence of rotavirus infections was 25.2%. Preterm(rota+) differed from Preterm(rota-) and FT/NT(rota+) with respect to frequent feeding difficulty (p = 0.047 and 0.034, respectively) and higher percentage of neutropenia (p = 0.008 and 0.011, respectively). G4P[6] was the exclusive strain in both the Preterm(rota+) (97.7%) and FT/NT(rota+) (90.2%), and it was the same for nosocomial, institutional infections, and infections acquired at home.

CONCLUSION

Systemic illness signs such as feeding difficulty and neutropenia are specific for preterm infants with rotavirus infections. G4P[6] was exclusive, regardless of preterm birth or locations of infections. This study might be helpful in developing policies for management and prevention of rotavirus infections in NICUs.

Whole genome analysis of multiple rotavirus strains from a single stool specimen using sequence-independent amplification and 454® pyrosequencing reveals evidence of intergenotype genome segment recombination

Infection of a single host cell with two or more different rotavirus strains creates conditions favourable for evolutionary mechanisms like reassortment and recombination that can generate novel strains. Despite numerous reports describing mixed rotavirus infections, whole genome characterisation of rotavirus strains in a mixed infection case has not been reported. Double-stranded RNA, exhibiting a long electropherotype pattern only, was extracted from a single human stool specimen (RVA/Human-wt/ZAF/2371WC/2008/G9P[8]). Both short and long electropherotype profiles were however detected in the sequence-independent amplified cDNA derived from the dsRNA, suggesting infection with more than one rotavirus strain. 454® pyrosequencing of the amplified cDNA revealed co-infection of at least four strains. Both genotype 1 (Wa-like) and genotype 2 (DS-1-like) were assigned to the consensus sequences obtained from the nine genome segments encoding NSP1-NSP5, VP1-VP3 and VP6. Genotypes assigned to the genome segments encoding VP4 were P[4] (DS-1-like), P[6] (ST3-like) and P[8] (Wa-like) genotypes. Since four distinct genotypes [G2 (DS-1-like), G8, G9 (Wa-like) and G12] were assigned to the four consensus nucleotide sequences obtained for genome segment 9 (VP7), it was concluded that at least four distinct rotaviruses were present in the stool. Intergenotype genome recombination events were observed in genome segments encoding NSP2, NSP4 and VP6. The close similarities of some of the genome segments encoding NSP2, VP6 and VP7 to artiodactyl rotaviruses suggest that some of the infecting strains shared common ancestry with animal strains, or that interspecies transmission occurred previously. The sequence-independent genome amplification technology coupled with 454® pyrosequencing used in this study enabled the characterisation of the whole genomes of multiple rotavirus strains in a single stool specimen that was previously assigned single genotypes, i.e. G9P[8], by sequence-dependent RT-PCR.

Comparison of the rapid methods for screening of group a rotavirus in stool samples

In this study, the sensitivity and specificity of three immunochromatography (IC) test kits for rapid detection of group A rotavirus were compared and evaluated with stool samples collected from children, who suffered from acute gastroenteritis during February to June, 2009 in Japan. A total of 86 stool samples were tested and compared with a reference RT-PCR method. The sensitivity among IP-Rota V, Dipstick Eiken ROTA and ROTA-ADENO test kits were 97.2, 95.8 and 88.7%, while the specificity were 100, 93.3 and 100%, respectively. It was demonstrated that the IC kits evaluated in this study could be used as an alternative method for the rapid screening of group A rotavirus in fecal specimens, especially during acute gastroenteritis outbreak season.

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.

Predominance of porcine P[23] genotype rotaviruses in piglets with diarrhea in northern Thailand

Of 131 stool samples collected from piglets with diarrhea in northern Thailand between July 2006 and August 2008, 14 (10.7%) were positive for group A rotavirus. Sequence analysis showed that 13 strains (92.9%) belonged to the rare P[23] genotype combination with G9 or G3 genotypes.

Rotavirus genetic diversity, disease association, and temporal change in hospitalized rural Kenyan children

BACKGROUND

The effectiveness of rotavirus vaccines will be dependent on the immunity conferred against prevalent and emergent variants causing severe diarrheal disease. Longitudinal surveillance of disease-causing strains is a prerequisite to intervention.

METHODS

Molecular characterization was conducted on rotavirus-positive stool samples from children admitted with diarrhea to a rural district hospital during 2002-2004. Extracted viral RNA was separated by polyacrylamide gel electrophoresis, and rotavirus VP4 (P types) and VP7 (G types) specificities were determined.

RESULTS

Among 558 investigated cases, the predominant genotype was P[8]G1 (42%), followed by P[8]G9 (15%), P[4]G8 (7%), P[6]G8 (6%), and P[8]G8 (4%), with 10% mixed strains. Overall, there were 6 different P types and 7 G types. No association was identified between genotype and child age, sex, or severity of diarrhea. The P and G genotypes and polyacrylamide gel electropherotypes showed significant temporal variation in frequency: P[8]G1 decreased from 51% (95% confidence interval [CI], 43%-58%) in 2002 to 30% (95% CI, 24%-37%) in 2004, and P[4]G8 increased from 2% (95% CI, 0%-5%) in 2002 to 13% (95% CI, 9%-19%). Quarterly data revealed seasonally endemic and emergence and/or decay patterns.

CONCLUSIONS

Our study of rotavirus strains causing severe diarrhea in rural Kenyan children showed a predominance of P[8]G1 and confirms the importance of G8 and G9 strains in sub-Saharan Africa. Considerable genetic diversity of rotavirus strains was observed, including substantial mixed and unusual types, coupled with significant temporal strain variation and emergence. These results warn of variable vaccine efficacy and the need for long-term surveillance of circulating rotavirus genotypes.

Identification of a G2-like porcine rotavirus bearing a novel VP4 type, P[32]

A porcine group A rotavirus (GARV) strain, 61/07/Ire, was isolated from a 4–5 week asymptomatic piglet, during an epidemiological survey of porcine herds in Southern Ireland, in 2007. The nucleotide (nt) and amino acid (aa) sequence of the full-length VP4 protein of the PoRV strain 61/07/Ire was determined. Based on the entire VP4 open reading frame (nt), strain 61/07/Ire displayed ≤ 76.5% identity to representatives of the established 31 P-types, a value far lower than the percentage identity cutoff value (80%) established by the Rotavirus Classification Working Group (RCWG) to define a novel P genotype. Strain 61/07/Ire revealed low aa identity, ranging from 57.1% to 83.6%, to the cognate sequences of representatives of the various P genotypes. The aa identity was lower in the VP8* trypsin-cleavage fragment of the VP4, which encompasses the VP4 hypervariable region, ranging from 36.9% to 75.3%. Sequence analyses of the VP7, VP6, and NSP4 genes revealed that the GARV strain 61/07/Ire possessed a G2-like VP7, an E9 NSP4 genotype and an I5 VP6 genotype. Altogether, these results indicate that the GARV strain 61/07/Ire should be considered as a prototype of a new VP4 genotype, P[32], and provide further evidence for the vast heterogeneity of group A rotaviruses.

Sequence analysis of the VP7 gene of human rotaviruses G2 and G4 isolated in Japan, China, Thailand, and Vietnam during 2001-2003

Sequence and phylogenetic analyses of the rotavirus VP7 gene were performed on 52 human G2 and G4 strains isolated in Japan, China, Thailand, and Vietnam during 2001-2003. All genotype G2 strains included in the study clustered into lineage II of the phylogenetic tree, together with the majority of global G2 strains detected since 1995. The amino acid substitution at position 96 from aspartic acid to asparagine was noted among the emerging or re-emerging G2 rotavirus strains in Japan, Thailand, and Vietnam during 2002-2003. Genotype G4 strains detected in Vietnam grouped into lineage Ia of the phylogenetic tree, whereas Japanese G4 strains clustered in lineage Ic which included emerging G4 strains from Argentina, Italy, Paraguay, and Uruguay. It is noteworthy that an insertion of asparagine was found at position 76 in all the Japanese strains and that its presence might be involved in the emergence of G4 rotavirus in Japan during 2002-2003.

Detection and characterisation of group A rotavirus in asymptomatic piglets in southern Ireland

Porcine group A rotaviruses (GARV) are causative agents of enteritis in piglets and are a large reservoir of genetic material for the diversification of human GARVs. Accumulation of information on the genetic heterogeneity of porcine viruses is pivotal for readily characterising unusual human strains. Screening of 292 fecal samples, collected from 4-5- to 8-9-week-old asymptomatic pigs from four herds in Ireland between 2005 and 2007 resulted in 19 (6.5%) samples testing positive by reverse-transcription PCR (RT-PCR) for GARV. The strains were molecularly characterized to collate data on the VP7 and partial VP4 outer capsid genes. By sequence analysis of the VP7 gene, the Irish strains were identified as G2, G4, G5, G9 and G11 viruses. The G11 strains were closely related to other human and porcine G11 strains, while the G2 strains resembled porcine G2 viruses detected recently in Europe and southern Asia. The G4 strains were distantly related to other G4 human and animal strains, constituting a separate G4 VP7 lineage. Analysis of the G5 strains revealed that they were similar to a selection of G5 human and porcine strains, while the G9 strains resembled other porcine G9 viruses. By sequence analysis of the VP8* fragment of the VP4, the Irish viruses were characterised as P[6], P[7], P[13], P[13]/[22], P[26] and P[32].

Genotypic linkages of VP4, VP6, VP7, NSP4, NSP5 genes of rotaviruses circulating among children with acute gastroenteritis in Thailand

Rotavirus is the main cause of acute viral gastroenteritis in infants and young children worldwide. Surveillance of group A rotavirus has been conducted in Chiang Mai, Thailand since 1987 up to 2004 and those studies revealed that group A rotavirus was responsible for about 20-61% of diarrheal diseases in hospitalized cases. In this study, we reported the continuing surveillance of group A rotavirus in 2005 and found that group A rotavirus was detected in 43 out of 147 (29.3%) stool samples. Five different G and P genotype combinations were detected, G1P[8] (27 strains), G2P[4] (12 strains), G9P[8] (2 strains), G3P[8] (1 strain), and G3P[10] (1 strain). In addition, analysis of their genotypic linkages of G (VP7), P (VP4), I (VP6), E (NSP4), and H (NSP5) genotypes demonstrated that the rotaviruses circulating in Chiang Mai, Thailand carried 3 unique linkage patterns. The G1P[8], G3P[8], and G9P[8] strains carried their VP6, NSP4, NSP5 genotypes of I1, E1, H1, respectively. The G2P[4] strains were linked with I2, E2, H2 genotypes, while an uncommon G3P[10] genotype carried unique genotypes of I8, E3 and H6. These findings provide the overall picture of genotypic linkage data of rotavirus strains circulating in Chiang Mai, Thailand.

Detection and genotyping of Korean porcine rotaviruses

Porcine group A rotavirus (GARV) is considered to be an important animal pathogen due to their economic impact in the swine industry and its potential to cause heterologous infections in humans. This study examined 475 fecal samples from 143 farms located in 6 provinces across South Korea. RT-PCR and nested PCR utilizing primer pairs specific for the GARV VP6 gene detected GARV-positive reactions in 182 (38.3%) diarrheic fecal samples. A total of 98 porcine GARV strains isolated from the GARV-positive feces were analyzed for G and P genotyping. Based on the sequence and phylogenetic analyses, the most predominant combination of G and P genotypes was G5P[7], found in 63 GARV strains (64.3%). The other combinations of G and P genotypes were G8P[7] (16 strains [16.3%]), G9P[7] (7 strains [7.1%]), G9P[23] (2 strains [2.0%]), and G8P[1] (1 strain [1.0%]). The counterparts of G or P genotypes were not determined in three G5, five P[7], and one P[1] strains. Interestingly, phylogenetic analysis indicated that all Korean G9 strains were more closely related to lineage VI porcine and human viruses than to other lineages (I–V) of GARVs and to Korean human G9 strains (lineage III). These results show that porcine GARV infections are common in diarrheic piglets in South Korea. The infecting strains are genetically diverse, and include homologous (G5P[7]), heterologous (G8P[1]), and reassortant (G8P[7]), as well as emerging G9 GARV strains.

Diversidade genotípica de rotavírus suínos no Estado de São Paulo

Rotavírus é uma das causas mais comuns de diarréia tanto em humanos quanto em diferentes espécies animais. Foi conduzido um estudo transversal a partir de 144 amostras fecais diarréicas colhidas de leitões, provenientes de 16 criações comerciais distribuídas por 10 municípios do Estado de São Paulo, Brasil, com o objetivo de se detectar a ocorrência de rotavírus e realizar sua caracterização molecular quanto seus genotipos G e P. Um total de 43 amostras (29,86%) foram positivas para rotavírus por Eletroforese em Gel de Poliacrilamida (PAGE) e ELISA, num esquema de triagem em paralelo. A caracterização mediante reações do tipo nested-multiplex RT-PCR demonstrou que, isoladamente, o genotipo P[6] foi o mais frequente, detectado em 25,58% das amostras, seguido pelo P[1] (11,63%) e P[7] (9,3%). Infecções concomitantes de genotipos P[6]+P[7] (9,3%), P[1]+P[6] (4,65%), P[1]+P[6]+P[7] (2,33%) foram também observadas. Analogamente, o genotipo G[5] foi detectado em 30,23% das amostras, seguido pelo G[10] (20,93%) e G[6] (4,65%) e G[5]+G[10] (18,6%). O genotipo G[5]P[6] foi o mais frequente (11,63%), porém outras combinações e amostras não tipificáveis também foram observadas. Considerando-se a diversidade de rotavírus suínos encontrada na população estudada, medidas profiláticas específicas devem levar em conta, para sua efetividade, o grau de proteção cruzada entre os genotipos presentes nas formulações vacinais e aqueles que realmente são circulantes numa região.

Sequence analysis of unusual P[7]G5 bovine rotavirus strains reveals evidence of interspecies transmission

By sequence and phylogenetic analyses, the 11 genomic segments of two bovine rotaviruses isolated from clinically infected calves were proven to be derived from the swine-like P[7]G5 genotype. This finding reinforced the hypothesis that interspecies transmission of completely heterologous strains can occur in nature.

Genotypification of bovine group A rotavirus in México

Bovine scours, frequently provoked by rotavirus infection, causes significant economic losses. Nevertheless, no information exists about the bovine rotavirus genotypes present in Mexico. This information is necessary for designing efficient vaccines. In this work, 128 samples from diarrheic calves were collected between 2005 and 2006 in 26 dairy and/or beef cattle herds located in 10 regions of Mexico, and analyzed for the presence of group A rotavirus. G and P genotypes were determined by PCR in rotavirus-positive samples (12/128). Three different genotype combinations were found, G10, P[11]; G6, P[5]; and G10, P[5]; in 67, 25 and 8% of the positive samples, respectively. Some rotavirus-positive animals had been vaccinated with an inactivated rotavirus strain of a different genotype.

Assignment of the group A rotavirus NSP4 gene into genotypes using a hemi-nested multiplex PCR assay: a rapid and reproducible assay for strain surveillance studies

The rotavirus non-structural protein NSP4 has been implicated in a number of biological functions during the rotavirus cellular cycle and pathogenesis, and has been addressed as a target for vaccine development. The NSP4 gene has been classified into six genotypes (A-F). A semi-nested triplex PCR was developed for genotyping the major human NSP4 genotypes (A-C), which are common in human rotavirus strains but are also shared among most mammalian rotavirus strains. A total of 192 previously characterized human strains representing numerous G and P type specificities (such as G1P[8], G1P[4], G2P[4], G3P[3], G3P[8], G3P[9], G4P[6], G4P[8], G6P[4], G6P[9], G6P[14], G8P[10], G8P[14], G9P[8], G9P[11], G10P[11], G12P[6] and G12P[8]) were tested for NSP4 specificity by the collaborating laboratories. An additional 35 animal strains, including the reference laboratory strains SA11 (simian, G3P[2]), NCDV (bovine, G6P[1]), K9 and CU-1 (canine, G3P[3]), together with 31 field isolates (canine, G3P[3]; feline, G3P[9]; porcine, G2P[23], G3P[6], G4P[6], G5P[6], G5P[7], G5P[26], G5P[27], G9P[6] and G9P[7]) were also successfully NSP4-typed. Four human G3P[9] strains and one feline G3P[9] strain were found to possess an NSP4 A genotype, instead of NSP4 C, suggesting a reassortment event between heterologous strains. Routine NSP4 genotyping may help to determine the genomic constellation of rotaviruses of man and livestock, and identify interspecies transmission of heterologous strains.

Rotavirus vaccine RIX4414 (Rotarix): a review of its use in the prevention of rotavirus gastroenteritis

Rotavirus vaccine RIX4414 is an oral vaccine composed of a monovalent, live, attenuated, human rotavirus strain of G1P[8] type. RIX4414 vaccination in infants aged 6-17 weeks at enrolment provided protection against rotavirus gastroenteritis (RVGE) of any severity and high-level protection against severe RVGE requiring hospitalization in large, randomized clinical trials conducted in a wide range of geographic regions. Protective efficacy was evident over the period (2 months) between the first and second doses of vaccine, and the protection afforded by the full two-dose course was sustained for at least 2 years, the limit to which efficacy was assessed. RIX4414 displayed protective efficacy against the common rotavirus G, P[8] types (G1P[8], G3P[8], G4P[8], and G9P[8]) and the fully heterotypic G2P[4] type. RIX4414 did not interfere with other common childhood injectable immunizations when administered concomitantly, suggesting that it should be possible to integrate the vaccine into most routine childhood vaccination schedules, including those still using oral poliovirus vaccine. RIX4414 was generally well tolerated and there was no evidence of an increased risk of intussusception. Although dependent on many factors, including prevalent infecting strains, efficacy rates, and vaccine costs, pharmacoeconomic analyses suggest that mass immunization with RIX4414 would be cost effective in many countries, especially when assessed from the societal perspective. Therefore, rotavirus vaccine RIX4414 offers a highly effective control strategy for reducing the burden of RVGE in infants.

Rotavirus diarrhea in bovines and other domestic animals

Rotavirus diarrhea is the major cause of death of millions of children in developing countries besides causing economically significant malady in neonates of many domestic animals. In neonates, the infection is non-viremic, have very short incubation period, and manifests profuse diarrhea and severe dehydration. Concurrent infection with secondary pathogens may augment the disease severity. Diarrhea occurs due to virus-mediated destruction of absorption efficient enterocytes, activation of enteric nervous system, or due to a rotavirus enterotoxin. Diagnosis of the infection relies on conventional techniques like isolation in MA 104 cell lines, electron microscopy, electro-pherotyping, and various serological tests. Presently, diagnosis and molecular typing is performed using serotype specific RT-PCR, sequencing or genomic hybridization techniques. As the rotaviruses are known to exhibit extreme genetic diversity and outplay disinfection procedures, eradication of the pathogen is often difficult. Hence, for prevention, good management practices coupled with vaccination of dam for protecting young ones, has to be practiced. Recently, new generation prophylactic strategies including DNA vaccines, subunit vaccines, virus-like particles (VLPs) and edible vaccines have been found to induce sufficient levels of passive immunity. Aside to the infection in animals, zoonotic significance of the animal rotaviruses has to be further unearthed. In this review, efforts have been made to highlight the importance and prevalence of the disease in bovines, its pathogenesis along with preventive measures, salient features of rotaviruses and their inter-species transmission abilities, zoonotic implications, and a concise account of the infection in various domestic animals and poultry.