Molecular characterization of a porcine Group A rotavirus strain with G12 genotype specificity

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.

Diversity of Rotavirus Strains in Children; Results From a Community-Based Study in Nepal

Objective: The objectives of this study were to describe the incidence and genetic diversity of Rotavirus (RV) infection among children up to 3 years of age in a community in Nepal.

Methods: We investigated community-acquired cases of asymptomatic and symptomatic RV infections in children from birth to 36 months of age in a community-based birth cohort in Bhaktapur, Nepal. Monthly surveillance and diarrheal stool samples were collected from 240 children enrolled at birth, of which 238 completed the 3 years of follow-up. Samples were screened for rotavirus by Enzyme Immuno Assay (EIA). All RV screened positives were further genotyped by reverse transcription-polymerase chain reaction for the capsid genes VP7 and VP4.

Results: In total, 5,224 stool samples were collected from 238 children, followed from birth to 36 months of age. Diarrhea occurred in 92.4% (230/238) of all children in the cohort. During the 3 years study period, RV was more frequently seen in children with symptoms (7.6%) than in non-symptomatic children (0.8%). The highest RV detection rate was found in younger children between 3 and 21 months of age. Although rotavirus is known as winter diarrhea, it was detected throughout the year except in August. The highest positivity rate was observed in the months between December and March, with a peak in January. Four common G types were seen: G2 (30%), G1 (29%), G12 (19%), and G9 (16%). The most predominant genotypes seen were G2P[4] (30%), followed by G1P[8] (27.0%), G12P[6] (14.0%), G9P[8] (10%), and remaining were mixed, partial, and untyped.

Conclusion: Our study confirms that rotavirus is a common cause of gastroenteritis in young children in the community. The prevalence and pathogenicity of rotavirus infection differed by age. There was substantial variability in circulating strains in the community samples compared to samples collected from hospitals. This shows the importance of including community-based surveillance systems to monitor the diversity of circulating rotavirus strains in Nepal.

Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014

BACKGROUND

G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.

METHODS

The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.

RESULTS

The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 × 10^- 3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.

CONCLUSIONS

At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

Genomic analysis of group A rotavirus G12P[8] including a new Japanese strain revealed evidence for intergenotypic recombination in VP7 and VP4 genes

Group A rotavirus is a leading cause of severe acute gastroenteritis worldwide. In this study, the first complete coding sequences of 11 RNA segments of human group A rotavirus G12P[8] in Japan were determined by an unbiased viral metagenomics. Its genomic constellation (VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes) was identified as G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. When performing the genetic analysis, we discovered an intergenotypic recombination event in the pig group A rotavirus G12P[8] strain BUW-14-A008. The novel recombination was found between two different genotypes G12 and G3 in the VP7 gene, and P[8] and P[13] in the VP4 gene.

Diversity of rotavirus genotypes circulating in children < 5 years of age hospitalized for acute gastroenteritis in India from 2005 to 2016: analysis of temporal and regional genotype variation

Background

From 2016, the Government of India introduced the oral rotavirus vaccine into the national immunization schedule. Currently, two indigenously developed vaccines (ROTAVAC, Bharat Biotech; ROTASIIL, Serum Institute of India) are included in the Indian immunization program. We report the rotavirus disease burden and the diversity of rotavirus genotypes from 2005 to 2016 in a multi-centric surveillance study before the introduction of vaccines.

Methods

A total of 29,561 stool samples collected from 2005 to 2016 (7 sites during 2005–2009, 3 sites from 2009 to 2012, and 28 sites during 2012–2016) were included in the analysis. Stools were tested for rotavirus antigen using enzyme immunoassay (EIA). Genotyping was performed on 65.8% of the EIA positive samples using reverse transcription- polymerase chain reaction (RT-PCR) to identify the G (VP7) and P (VP4) types. Multinomial logistic regression was used to quantify the odds of detecting genotypes across the surveillance period and in particular age groups.

Results

Of the 29,561 samples tested, 10,959 (37.1%) were positive for rotavirus. There was a peak in rotavirus positivity during December to February across all sites. Of the 7215 genotyped samples, G1P[8] (38.7%) was the most common, followed by G2P[4] (12.3%), G9P[4] (5.8%), G12P[6] (4.2%), G9P[8] (4%), and G12P[8] (2.4%). Globally, G9P[4] and G12P[6] are less common genotypes, although these genotypes have been reported from India and few other countries. There was a variation in the geographic and temporal distribution of genotypes, and the emergence or re-emergence of new genotypes such as G3P[8] was seen. Over the surveillance period, there was a decline in the proportion of G2P[4], and an increase in the proportion of G9P[4]. A higher proportion of mixed and partially typed/untyped samples was also seen more in the age group 0–11 months.

Conclusions

This 11 years surveillance highlights the high burden of severe rotavirus gastroenteritis in Indian children < 5 years of age before inclusion of rotavirus vaccines in the national programme. Regional variations in rotavirus epidemiology were seen, including the emergence of G3P[8] in the latter part of the surveillance. Having pre-introduction data is important to track changing epidemiology of rotaviruses, particularly following vaccine introduction.

Detection and molecular characterization of rotavirus of pigs in Kerala, India

Group A rotaviruses (GAR) are an important cause of diarrhoea in infants and newborn animals especially pigs. In this paper, we report the detection, G and P typing and phylogenetic analysis of GAR of pigs in Kerala. A total of 100 fecal samples from diarrhoeic piglets were collected from organized farms in Wayanad, Ernakulam, Thrissur, and Palakkad districts of Kerala. The samples were tested for the presence of GAR employing reverse transcriptase polymerase chain reaction (RT-PCR) targeting VP6 gene. Positive samples were tested by G and P genotyping primers and representative amplicons were sequenced. Of the 100 samples, 12 were positive for GAR. The G and P types detected were G2, G4, G5, G6, G9, P[6] and P[19]. An untypable P type (P21-5 like) was also detected. In some of the samples more than one G type was detected. The nucleotide sequences of G2, G4 and G5 types were similar to those seen in pigs and that of G6 was similar to bovine sequences. G9, P[6] and P[19] sequences showed similarity to human rotavirus sequences. The findings of this study provide the first information on the G and P genotypes of GAR of pigs in Kerala.

Rotavirus surveillance in Pakistan during 2015-2016 reveals high prevalence of G12P[6]

The G12 rotavirus genotype has emerged globally since their first detection in 1987 from the Philippines; however it remains a rare cause of gastroenteritis in Pakistan. Rotavirus surveillance conducted during 2015-2016, assessed 3446 children <5 years hospitalized for gastroenteritis and found 802 (23.2%) positive on ELISA. Genotyping of a subset of positive samples (n = 319) revealed G12P[6] (11.28%) as the third most common G/P combination following G3P[8] (28.5%) and G1P[8] (12.5%); G2P[4] (10.65%) and G3P[6] (8.15%) were other frequently detected strains. Phylogenetic analysis of G12 strains from Pakistan revealed high genetic similarity to G12 strains from Italy, Thailand, Korea, and Great Britain as well as local strains within G12 lineage III. In conclusion, G12P[6] was a major contributor of RVA gastroenteritis in Pakistani children. Robust surveillance after the introduction of rotavirus vaccines will help determine the evolution of G12 and other circulating genotypes in the country.

Whole genome characterisation of a porcine-like human reassortant G26P[19] Rotavirus A strain detected in a child hospitalised for diarrhoea in Nepal, 2007

A rare G26 Rotavirus A strain RVA/Human-wt/NPL/07N1760/2007/G26P[19] was detected in a child hospitalised for acute diarrhoea in Kathmandu, Nepal. The complete genome of 07N1760 was determined in order to explore its evolutionary history as well as examine its relationship to a Vietnamese strain RVA/Human-wt/VNM/30378/2009/G26P[19], the only G26 strain whose complete genotype constellation is known. The genotype constellation of 07N1760 was G26-P[19]-I12-R1-C1-M1-A8-N1-T1-E1-H1, a unique constellation identical to that of the Vietnamese 30378 except the VP6 gene. Phylogenetic analysis revealed that both strains were unrelated at the lineage level despite their similar genotype constellation. The I12 VP6 gene of 07N1760 was highly divergent from the six currently deposited I12 sequences in the GenBank. Except for its NSP2 gene, the remaining genes of 07N1760 shared lineages with porcine and porcine-like human RVA genes. The NSP2 gene belonged to a human RVA N1 lineage which was distinct from typical porcine and porcine-like human lineages. In conclusion, the Nepali G26P[19] strain 07N1760 was a porcine RVA strain which derived an NSP2 gene from a human Wa-like RVA strain by intra-genotype reassortment probably after transmission to the human host.

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.

Complete genome analysis of a rare G12P[6] rotavirus isolated in Thailand in 2012 reveals a prototype strain of DS-1-like constellation

Species A rotaviruses (RVAs) are a major cause of severe diarrhea in children worldwide. G12 RVA detection is currently increasing and has been reported from many countries around the world. However, few studies have reported whole genome sequences of G12 RVAs. In the present study, the complete genome sequence of a G12P[6] RVA strain (RVA/Human-wt/THA/CMHN49-12/2012/G12P[6]) detected in a stool sample from a child with acute gastroenteritis in 2012 in Thailand was analyzed. In the CMHN49-12 strain, all genome segments had a DS-1-like backbone: G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 indicates that it is most likely the prototype strain of G12P[6] with a DS-1-like genotype constellation. Based on a Bayesian evolutionary analysis of VP7 nucleotide sequence, G12 RVA strains reported previously from Thailand during the period of 2007-2012 could be divided into 3 clusters, indicating that they originated from at least 3 different ancestral G12 strains. The evolutionary rate of G12 calculated by Bayesian Markov Chain Monte Carlo analysis indicated that the nucleotide substitution rate of G12 was 1.11×10(-3) mutations/site/year. The finding of a G12P[6] RVA possessing a DS-1-like backbone provides insights into the evolution of global G12 RVAs.

The epidemiology of rotavirus disease in under-five-year-old children hospitalized with acute diarrhea in central Uganda, 2012-2013

A cross-sectional study was undertaken during 2012-2013 to determine the prevalence, strains and factors associated with rotavirus infection among under-5-year-old children hospitalized with acute diarrhea in Uganda. Rotaviruses were detected in 37 % (263/712) of the children. The most prevalent strains were G9P[8] (27 %, 55/204) and G12P[4] (18.6 %, 38/204). Mixed infections were detected in 22.5 % (46/204) of the children. The study suggests that consumption of raw vegetables (OR = 1.45, 95 % CI = 1.03-2.03) and family ownership of dogs (OR = 1.9, 95 % CI = 1.04-3.75) increases the risk of rotavirus infection. The study findings will be used to assess the impact of RV vaccination in Uganda.

Hospital based surveillance and genetic characterization of rotavirus strains in children (<5 years) with acute gastroenteritis in Kolkata, India, revealed resurgence of G9 and G2 genotypes during 2011-2013

INTRODUCTION

India accounts for an estimated 457,000-884,000 hospitalizations and 2 million outpatient visits for diarrhea. In spite of the huge burden of rotavirus (RV) disease, RV vaccines have not been introduced in national immunization programme of India. Therefore, continuous surveillance for prevalence and monitoring of the circulating genotypes is needed to assess the disease burden prior to introduction of vaccines in this region.

METHODS

During January 2011 through December 2013, 830 and 1000 stool samples were collected from hospitalized and out-patient department (OPD) patients, respectively, in two hospitals in Kolkata, Eastern India. After primary screening, the G-P typing was done by multiplex semi-nested PCR using type specific primers followed by sequencing. Phylogenetic analysis for the VP7 gene of 25 representative strains was done.

RESULTS

Among hospitalized and OPD patients, 53.4% and 47.5% cases were positive for rotaviruses, respectively. Unlike previous studies where G1 was predominant, in hospitalized cases G9 rotavirus strains were most prevalent (40%), followed by G2 (39.6%) whereas G1 and G12 occurred at 16.4% and 5.6% frequency. In OPD cases, the most prevalent strain was G2 (40.3%), followed by G1, G9 and G12 at 25.5%, 22.8%, 9.3%, respectively. Phylogenetically the G1, G2 and G9 strains from Kolkata did not cluster with corresponding genotypes of Rotarix, RotaTeq and Rotavac (116E) vaccine strains.

CONCLUSION

The study highlights the high prevalence of RV in children with gastroenteritis in Kolkata. The circulating genotypes have changed over the time with predominance of G9 and G2 strains during 2011-2013. The current G2, G9 and G1 Kolkata strains shared low amino acid homologies with current vaccine strains. Although there is substantial evidence for cross protection of vaccines against a variety of strains, still the strain variation should be monitored post vaccine introduction to determine if it has any impact on vaccine effectiveness.

Unexpected spreading of G12P[8] rotavirus strains among young children in a small area of central Italy

Rotavirus gastroenteritis is associated mainly with the five genotypes G1,3,4,9P[8] and G2P[4] that are common worldwide, but emerging strains including G6, G8, and G12 are also reported sporadically. G12P[8] rotavirus was observed unexpectedly to spread in a limited area of Italy during the rotavirus surveillance season 2012-2013. All strains were genotyped for VP7 and VP4 and subjected to phylogenetic analysis. Amino acid sequences of antigenic regions were compared with vaccine and field strains. G12P[8] strains were detected in the stools of 52 of 69 (75%) children infected with rotavirus in the central Italian region of Umbria. All G12 strains belonged to lineage III, and presented the P[8] genotype. Sequence analysis showed close nucleotide identity of both VP4 and VP7 genes among Umbria G12P[8] strains. The VP7 gene was also similar to other G12 strains circulating in different years and countries, and the VP4 gene was closely related to other local and global P[8] strains possessing different G-types. Overall findings suggest either the introduction and evolution of a G12 VP7 gene into the local Wa-like rotavirus population or the spreading of a strain novel for the area. Comparison of the VP8* and VP7 antigenic regions showed high conservation between the amino acid sequences of Umbria G12P[8] strains, and revealed various substitutions in the VP8* antigenic regions between the Italian G12P[8] strains and RotaTeq™ and Rotarix™ vaccine strains. The sudden and unexpected emergence of G12P[8] rotavirus confirms that these strains have the potential to become a sixth common genotype across the world.

H2 genotypes of G4P[6], G5P[7], and G9[23] porcine rotaviruses show super-short RNA electropherotypes

During group A rotavirus (RVA) surveillance of pig farms in Japan, we detected three RVA strains (G4P[6], G5P[7], and G9P[23] genotypes), which showed super-short RNA patterns by polyacrylamide gel electrophoresis, in samples from a healthy eight-day-old pig and two pigs of seven and eight days old with diarrhea from three farms. Reverse transcription PCR and sequencing revealed that the full-length NSP5 gene of these strains contained 952 or 945 nucleotides, which is consistent with their super-short electropherotypes. Due to a lack of whole genome data on Japanese porcine RVAs, we performed whole genomic analyses of the three strains. The genomic segments of these RVA strains showed typical porcine RVA constellations, except for H2 NSP5 genotype, (G4,5,9-P[6,7,23]-I5-R1-C1-M1-A8-N1-T1-E1-H2 representing VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes). In phylogenetic analyses, these porcine RVA strains clustered with porcine and porcine-like human RVA strains and showed a typical porcine RVA backbone, except for the NSP5 gene; however, intra-genotype reassortment events among porcine and porcine-like human RVA strains were observed. The NSP5 gene segments of these strains were clustered within the H2b genotype with super-short human RVA strains. The H2 genotype has to date only been identified in human and lapine RVA strains. Thus, to our knowledge, this report presents the first case of H2 NSP5 genotype showing a super-short RNA pattern in porcine RVA. These data suggest the possibility of interspecies transmission between pigs and humans and imply that super-short porcine RVA strains possessing H2 genotype are circulating among both asymptomatic and diarrheic porcine populations in Japan.

Community based case-control study of rotavirus gastroenteritis among young children during 2008-2010 reveals vast genetic diversity and increased prevalence of G9 strains in Kolkata

BACKGROUND

Group A Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children (<5 years) worldwide. Although rotavirus vaccines have been successfully administered in many countries, in India the introduction of rotavirus vaccine in national immunization program was approved in 2014. Since high disease burden and large number of genetic variants have been reported from low income countries including India, monitoring of rotavirus was initiated prior to implementation of the vaccine in the region.

METHODS

A total number of 3,582 stool samples were collected from an urban slum community in Kolkata, among which 1,568 samples were obtained from children of ≤ 5 years of age, with moderate to severe diarrhoea and 2,014 samples were collected from age-sex matched healthy neighbourhood controls. Rotavirus positive samples were typed by multiplex semi-nested PCR and nucleotide sequencing. Circulating strains were phylogenetically analyzed.

RESULTS

Among 1,568 children with diarrhoea, 395 (25.2%), and among 2,014 asymptomatic children, 42 (2%) were rotavirus positive. G1P[8] was identified as the most common strain (32%) followed by G9P[8] (16.9%), G2P[4] (13.5%) and G9P[4] (10.75%). G12 strains with combinations of P[4], P[6] and P[8] comprised 11.9% of total positive strains. The rest (<10%) were rare and uncommon strains like G1P[4], G1P[6], G2P[8] and animal-like strains G4P[6], G6P[14] and G11P[25]. The 42 rotavirus positive samples from asymptomatic children revealed common genotypes like G1, G2 and G9.

CONCLUSION

This community based case-control study showed increased predominance of genotype G9 in Kolkata. It also confirmed co-circulation of a large number of genetic variants in the community. Asymptomatic rotavirus positive children though low in number can also be a source of dispersal of infection in the community. This study provides background information to the policy makers for implementation of rotavirus vaccines in this region.

Molecular characterization of group B rotavirus circulating in pigs from India: identification of a strain bearing a novel VP7 genotype, G21

The occurrence of group B rotavirus (RVB) infections in pigs has been reported from different parts of world. However, such infection in the pig population maintained in Indian farms has not been investigated as yet. A total of 187 faecal specimens were collected from pigs reared in different pig farms/pigsties located in western and northern regions of India and tested for the presence of porcine RVB by amplification of the NSP2 gene using conventional RT-PCR. Nine specimens (4.8%) were shown to contain RVB RNA. N2 and N4 genotypes of NSP2 gene were detected in three and six RVB strains respectively. VP7 (G-type) and NSP5 (H-type) genes of selected six RVB strains were characterized to identify the genotypes. Multiple G (G7, G19 and G20) and H (H4 and H5) genotypes detected in the RVB strains indicated circulation of heterogeneous population of RVB strains in pigs of India. Additionally, one strain was proposed to belong to a novel RVB genotype designated as G21 on account of <80% identity of VP7 gene sequence with its counterpart in RVB strains from 20 established genotypes. Deduced amino acid sequence of VP7 gene also displayed the presence of seven unique substitutions in the strain. The study reports for the first time the occurrence of RVB infections in Indian pig herds and provides important epidemiological data useful for better understanding of ecology and evolution of porcine RVBs.

Whole genomic analysis of human G12P[6] and G12P[8] rotavirus strains that have emerged in Kenya: identification of porcine-like NSP4 genes

G12 rotaviruses are globally emerging rotavirus strains causing severe childhood diarrhea. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed, of which only one G12P[4] and one G12P[6] are from Africa. In this study, we sequenced and characterized the complete genomes of three G12 strains (RVA/Human-tc/KEN/KDH633/2010/G12P[6], RVA/Human-tc/KEN/KDH651/2010/G12P[8], and RVA/Human-tc/KEN/KDH684/2010/G12P[6]) identified in three stool specimens from children with acute diarrhea in Kenya, Africa. On whole genomic analysis, all three Kenyan G12 strains were found to have a Wa-like genetic backbone: G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strains KDH633 and KDH684) and G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 (strain KDH651). Phylogenetic analysis showed that most genes of the three strains examined in this study were genetically related to globally circulating human G1, G9, and G12 strains. Of note is that the NSP4 genes of strains KDH633 and KDH684 appeared to be of porcine origin, suggesting the occurrence of reassortment between human and porcine strains. Furthermore, strains KDH633 and KDH684 were very closely related to each other in all the 11 gene segments, indicating derivation of the two strains from a common origin. On the other hand, strain KDH651 consistently formed distinct clusters of 10 of the 11 gene segments (VP1-2, VP4, VP6-7, and NSP1-5), indicating a distinct origin of strain KDH651 from that of strains KDH633 and KDH684. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Kenya. Our observations will provide important insights into the evolutionary dynamics of emerging G12 rotaviruses in Africa.

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.

Diversity of circulating rotavirus strains in children hospitalized with diarrhea in India, 2005-2009

BACKGROUND

India accounts for 22% of the 453,000 global rotavirus deaths among children <5 years annually. The Indian Rotavirus Strain Surveillance Network provides clinicians and public health partners with valuable rotavirus disease surveillance data. Our analysis offers policy-makers an update on rotavirus disease burden with emphasis on regional shifts in rotavirus strain epidemiology in India.

METHODS

Children <5 years requiring hospitalization for acute gastroenteritis were selected from 10 representative hospitals in 7 cities throughout India between November 2005 through June 2009. We used a modified World Health Organization protocol for rotavirus surveillance; stool specimens were collected and tested for rotavirus using enzyme immunoassay and reverse-transcription polymerase chain reaction.

RESULTS

A total of 7285 stool specimens collected were tested for rotavirus, among which 2899 (40%) were positive for rotavirus. Among the 2899 rotavirus detections, a G-type could not be determined for 662 (23%) and more than one G type was detected in 240 (8%). Of 1997 (69%) patients with only one G-type, the common types were G1 (25%), G2 (21%), G9 (13%), and G12 (10%). The proportion of rotavirus infections attributed to G12 infections rose from 8% to 39% in the Northern region and from 8% to 24% in the Western region.

CONCLUSIONS

This study highlights the large, ongoing burden of rotavirus disease in India, as well as interesting regional shifts in rotavirus strain epidemiology, including an increasing detection of G12 rotavirus strains in some regions. While broad heterotypic protection from rotavirus vaccination is expected based on pre- and post-licensure data from other settings, effectiveness assessments and rotavirus strain monitoring after vaccine introduction will be important.

Molecular characterization of a rare G9P[23] porcine rotavirus isolate from China

The fifth most important G genotype, G9 rotavirus, is recognized as an emerging genotype that is spreading around the world. Sequence analysis was completed of a rare group A rotavirus, strain G9P[23], that was designated rotavirus A pig/China/NMTL/2008/G9P[23] and abbreviated as NMTL. It was isolated from a piglet with diarrhea in China. Nucleotide sequence analysis revealed that the VP7 gene clustered within the G9 lineage VId. The VP4 gene clustered within the rare P[23] genotype. NMTL is the first porcine G9 stain reported in China. Thus, to further characterize the evolutionary diversity of the NMTL strain, all gene segments were used to draw a phylogenetic tree. Based on the new classification system of rotaviruses, the NMTL sequence revealed a G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotype with close similarity to human Wa-like and porcine strains. The results showed that (i) NSP2 and NSP4 genes of NMTL exhibited higher genetic relatedness to human group A rotaviruses than to porcine strains, (ii) the VP2 and VP4 genes clustered with porcine and porcine-like human strains, and (iii) VP1 genes clustered apart from the Wa-like human and porcine clusters. In view of rotavirus evolution, this report provides additional evidence to support the notion that the human and porcine rotavirus genomes might be related.

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.

Identification of lineage III of G12 rotavirus strains in diarrheic children in the Northern Region of Brazil between 2008 and 2010

This study reports on the surveillance for rotavirus genotypes and the identification of G12 human rotavirus in the Northern Region of Brazil. Rotavirus-positive samples were collected from children <5 years of age with acute diarrhea from January 2008 to October 2010. G2P[4] was the most prevalent genotype, accounting for 45.6% (126/303) of cases. Five rotavirus strains bearing G12P[6] genotype specificity were detected. Phylogenetic analysis of the VP7 gene showed that G12 strains clustered into lineage III. This is the first detection of G12 strains from lineage III in Latin America, broadening the current evidence for the worldwide emergence of this genotype.

Full genomic analysis of a G8P[1] rotavirus strain isolated from an asymptomatic infant in Kenya provides evidence for an artiodactyl-to-human interspecies transmission event

Group A rotavirus (GAR) G8P[1] strains, found sometimes in cattle, have been reported rarely from humans. Therefore, analysis of the full genomes of human G8P[1] strains are of significance in the context of studies on interspecies transmission of rotaviruses. However, to date, only partial-length nucleotide sequences are available for the 11 genes of a single human G8P[1] strain, while the partial sequences of two other strains have been reported. The present study reports the first complete genome sequence of a human G8P[1] strain, B12, detected from an asymptomatic infant in Kenya in 1987. By nucleotide sequence identities and phylogenetic analyses, the full-length nucleotide sequences of VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes of strain B12 were assigned to G8-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3 genotypes, respectively. Each of the 11 genes of strain B12 appeared to be more related to cognate genes of artiodactyl (ruminant and/or camelid) and/or artiodactyl-derived human GAR strains than those of most other rotaviruses. Strain B12 exhibited low levels of genetic relatedness to canonical human GAR strains, such as Wa and DS-1, ruling out the possibility of its origin from reassortment events between artiodactyl-like human and true human strains. These observations suggest that strain B12 might have been directly transmitted from artiodactyls to humans. Unhygienic conditions and close proximity of humans to livestock at the sampling site might have facilitated this rare event. This is the first report on a full genomic analysis of a rotavirus strain from Kenya. To our knowledge, strain B12 might be the oldest G8 strain characterized molecularly from the Africa continent.

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.

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].

Phylodynamic analyses of rotavirus genotypes G9 and G12 underscore their potential for swift global spread

Rotaviruses (RVs) are responsible for more than 600,000 child deaths each year. The worldwide introduction of two life oral vaccines RotaTeq and Rotarix is believed to reduce this number significantly. Before the licensing of both vaccines, two new genotypes, G9 and G12, emerged in the human population and were able to spread across the entire globe in a very short time span. To quantify the VP7 mutation rates of these G9 and G12 genotypes and to estimate their most recent common ancestors, we used a Bayesian Markov chain Monte Carlo framework. Based on 356 sequences for G9 and 140 sequences for G12, we estimated mutation rates (nt substitutions/site/year) of 1.87 × 10(-3) (1.45-2.27 × 10(-3)) for G9 and 1.66 × 10(-3) (1.13-2.32 × 10(-3)) for G12. For both the G9 and G12 strains, one particular (sub) lineage was able to disseminate and cause disease across the world. The most recent common ancestors of these particular lineages were dated back to 1989 (1986-1992) and 1995 (1992-1998) for the G9 and G12 genotypes, respectively. These estimates suggest that a single novel RV (e.g., a vaccine escape mutant) can spread worldwide in little more than a decade. These results re-emphasize the need for thorough and continued RV surveillance in order to detect such potential spreading events at an early stage.

Complete genome constellation of a caprine group A rotavirus strain reveals common evolution with ruminant and human rotavirus strains

This study reports the first complete genome sequence of a caprine group A rotavirus (GAR) strain, GO34. The VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes of strain GO34, detected in Bangladesh, were assigned to the G6-P[1]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genotypes, respectively. Strain GO34 was closely related to the VP4, VP6-7 and NSP4-5 genes of bovine GARs and the NSP1 gene of GO34 to an ovine GAR. Strain GO34 shared low nucleotide sequence identities (<90 %) with VP2-3 genes of other GARs, and was equally related to NSP3 genes of human, ruminant and camelid strains. The VP1, VP6 and NSP2 genes of strain GO34 also exhibited a close genetic relatedness to human G2, G6, G8 and G12 DS-1-like GARs, whereas the NSP1 of GO34 was also closely related to human G6P[14] strains. All these findings point to a common evolutionary origin of GO34 and bovine, ovine, antelope, guanaco and human G6P[14] GARs, although phylogenetically GO34 is not particularly closely related to any other rotavirus strains known to date.

Zoonotic aspects of rotaviruses

Rotaviruses are important enteric pathogens of humans and animals. Group A rotaviruses (GARVs) account for up to 1 million children deaths each year, chiefly in developing countries and human vaccines are now available in many countries. Rotavirus-associated enteritis is a major problem in livestock animals, notably in young calves and piglets. Early in the epidemiological GARV studies in humans, either sporadic cases or epidemics by atypical, animal-like GARV strains were described. Complete genome sequencing of human and animal GARV strains has revealed a striking genetic heterogeneity in the 11 double stranded RNA segments across different rotavirus strains and has provided evidence for frequent intersections between the evolution of human and animal rotaviruses, as a result of multiple, repeated events of interspecies transmission and subsequent adaptation.

Genetic characterization of rotavirus subtypes in Pakistan-first report of G12 genotype from Pakistan under WHO-Eastern Mediterranean region

Rotaviruses are among the major causes of gastroenteritis and diarrhea among children in developed as well as the developing countries. The rapidly evolving strain prevalence and circulation have resulted in the emergence of novel strains over the period worldwide. The introduction of G12 prototype in 1987 from Philippines and subsequently re-emergence among most of the Asian countries along with USA and Europe has provoked new research horizons to address the global distribution of rotavirus serotypes. These newly emerging subtypes and their sustenance among the population have posed tremendous challenge to the development of an effectual vaccine with heterotypic protective efficacy. In Pakistan, no data is available regarding the prevalent rotavirus serotypes; therefore, this is the first study to report the prevalence of G12 strain in Pakistan in hospitalized children with diarrhea addressing a dire need of further large-scale epidemiological surveys to resolve the underlying rotavirus isolates in both the hospitalized and the community neonatal and child population before formulating the vaccine introduction policies in the country's routine immunization program.

Full genomic analysis of a human group A rotavirus G9P[6] strain from Eastern India provides evidence for porcine-to-human interspecies transmission

Deduced amino acid sequence and phylogenetic analyses of a group A rotavirus G9P[6] strain (designated as mcs/13-07), detected from a 3-year-old child in Eastern India, revealed a VP8* closely related to porcine P[6] strains (P[6] sublineage 1D), and the VP7 clustered with G9 lineage-III strains. To our knowledge, this is the first report of human P[6] strain clustering in sublineage Id. Thus, to further characterize the evolutionary diversity of strain mcs/13-07, all gene segments were analyzed. VP6 and NSP4 exhibited genetic relatedness to Wa-like human subgroup II strains, while VP1-3, NSP1-3 and NSP5 were closely related to porcine strains. Based on the new classification system of rotaviruses, mcs/13-07 revealed a G9-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 genotype with close similarity to human Wa-like and porcine Gottfried strains. Therefore, considering the porcine-like or porcine origin of multiple gene segments, it might be tempting to assume that strain mcs/13-07 represents a rare instance of whole-virus transmission from pig to human, after which the virus evolved with time. Alternatively, it is possible that strain mcs/13-07 resulted from multiple reassortment events involving human subgroup II and porcine P[6] strains. Nevertheless, detection of strain mcs/13-07 provides further evidence for complex interspecies transmission events, which are frequent in developing countries.

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.

Emergence of G12 rotavirus strains in Delhi, India, in 2000 to 2007

The prospect that rotavirus diarrhea in children may soon be prevented by vaccines has placed a new priority on understanding the diversity of rotavirus strains and the mechanism by which these strains evolve over time. We have characterized a total of 465 rotavirus strains collected in North India from 2000 to 2007 for G and P types by reverse transcription-PCR and sequencing. The novel G12 rotavirus strains recently detected in other countries were first detected in India in 2001 and have emerged as the predominant strains in Delhi, India, during 2005 to 2007. While the VP7 sequence was highly homologous among G12 strains isolated in Delhi, suggesting recent emergence from a common ancestor, the strains had a diverse constellation of other gene segments, demonstrating substantial reassortment. For the entire period, the common rotavirus G types G1 (26%), G2 (25%), and G9 (14%) comprised 65% of the strains, and common P types, P[4] (19%), P[6] (22%), and P[8] (35%), comprised 76% of the total P types. Of note, we detected a high percentage of unusual (17%) strains and fecal specimens with mixed (12% G and 15% P) rotavirus infections having a variety of genomic constellations. For the first time, we identified two novel rotavirus strains with unusual G/P combinations, G2P[11] and G3P[11], in patients with diarrhea. The study highlights the great diversity among rotaviruses isolated from Indian children, the opportunity for genetic reassortment between strains, and the emergence of a novel G12 strain in our country. Due to the demonstrated effect of antigenic diversity on rotavirus vaccines, it will be important to continue careful monitoring of these strains as rotavirus vaccine programs are implemented in India.

Development of a microtiter plate hybridization-based PCR-enzyme-linked immunosorbent assay for identification of clinically relevant human group A rotavirus G and P genotypes

A microtiter plate hybridization-based PCR-enzyme-linked immunosorbent assay (PCR-ELISA) has been used for the detection and identification of a variety of microorganisms. Here, we report the development of a PCR-ELISA for the identification of clinically relevant human rotavirus VP7 (G1 to G6, G8 to G10, and G12) and VP4 (P[4], P[6], P[8], P[9], and P[14]) genotypes. The G and P types of reference human and animal rotavirus strains for which specific probes were available were correctly identified by the PCR-ELISA. In addition, reference strains bearing G or P genotypes for which specific probes were unavailable, such as G11, G14, P[3], P[10], and P[11], did not display any cross-reactivity to the probes. The usefulness of the assay was further evaluated by analyzing a total of 396 rotavirus-positive stool samples collected in four countries: Brazil, Ghana, Japan, and the United States. The results of this study showed that the PCR-ELISA was sensitive and easy to perform without the use of any expensive and sophisticated equipment, the reagents used are easy to obtain commercially and advantageous over multiplex PCR since more than one type-specific probe is used and the selection of probes is more flexible.

Modification of rotavirus multiplex RT-PCR for the detection of G12 strains based on characterization of emerging G12 rotavirus strains from South India

Rotaviruses are the major etiological agents of diarrhea in children less than 5 years of age. The commonest G types in humans are G1-4 and G9. G12 is a rare human rotavirus (HRV) strain first reported in the Philippines. In this study, 13 G12 strains obtained from a community-based cohort and a hospital-based surveillance system in 2005 were characterized by phylogenetic analysis of partial nucleotide sequences of VP7, VP6, and NSP4 genes. Sequence and phylogenetic analysis of VP7 gene sequences showed that these southern Indian strains had the greatest homology with G12 strains recently reported from eastern India (97-99% identity both at the nucleotide level and deduced amino acid level) and less homology with the prototype G12 strain, L26 (89-90% identity at the nucleotide level and 90-94% at the deduced amino acid level). Phylogenetic analysis of the VP6 and the NSP4 genes revealed that the Vellore G12 strains belonged to VP6 subgroup II and NSP4 genotype B. The P types associated with these strains were P[6] and P[8]. A G12 type-specific primer was designed for inclusion in an established VP7 G-typing multiplex RT PCR, and tested against a panel of known G types and untyped samples and was found to detect G12 strains in the multiplex-PCR. Close homology of the South Indian G12 strains to those from Kolkata suggests that G12 HRV strains are emerging in India. Methods for characterization of rotaviruses in epidemiological studies need to be updated frequently, particularly in developing countries.

First detection of G12 rotaviruses in newborns with neonatal rotavirus infection at all India Institute of Medical Sciences, New Delhi, India

Rotavirus genotype G12 strains were detected for the first time among newborns with asymptomatic rotavirus infection (74% of 39 rotavirus strains isolated from the infected infants were genotype G12) in the nursery of the All India Institute of Medical Sciences during a period from 2005 to 2006. Sequence analysis of the VP7 genes from these neonatal strains indicated a high level of homology to other G12 strains reported worldwide, suggesting the recent emergence of these strains in humans. Such nosocomial infections of newborns represent a potential source of introduction of novel rotavirus serotypes into the community.

Emergence of serotype G12 rotaviruses, Hungary

We describe the emergence of serotype G12 rotaviruses (67 [6.9%] of 971 specimens tested) among children hospitalized with rotavirus gastroenteritis in Hungary during 2005. These findings are consistent with recent reports of the possible global spread and increasing epidemiologic importance of these strains, which may have implications for current rotavirus vaccination strategies.

Detection of G12 human rotaviruses in Nepal

Of 731 stool specimens collected from children with diarrhea in Kathmandu, Nepal, from August 2004 through July 2005, 170 (23.3%) tested positive for rotavirus. Reverse transcription-PCR, including a revised G12-specific primer set, identified 56 (32.9%) as G2P[4] and 39 (23.0%) as G12 with P[6], P[8], or P[4].

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.