Characterization of a novel P[25],G11 human group a rotavirus

Complete genome constellation of a dominant Bovine rotavirus genotype circulating in Bangladesh reveals NSP4 intragenic recombination with human strains

Rotavirus A is a leading cause of non-bacterial gastroenteritis in humans and domesticated animals. Despite the vast diversity of bovine Rotavirus A strains documented in South Asian countries, there are very few whole genomes available for phylogenetic study. A cross-sectional study identified a high prevalence of the G6P[11] genotype of bovine Rotavirus A circulating in the commercial cattle population in Bangladesh. Next-generation sequencing and downstream phylogenetic analysis unveiled all 11 complete gene segments of this strain (BD_ROTA_CVASU), classifying it under the genomic constellation G6P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3, which belongs to a classical DS-1-like genomic backbone. We found strong evidence of intragenic recombination between human and bovine strains in the Non-structural protein 4 (NSP4) gene, which encodes a multifunctional enterotoxin. Our analyses highlight frequent zoonotic transmissions of rotaviruses in diverse human-animal interfaces, which might have contributed to the evolution and pathogenesis of this dominant genotype circulating in the commercial cattle population in Bangladesh.

Genetic diversity of G9, G3, G8 and G1 rotavirus group A strains circulating among children with acute gastroenteritis in Vietnam from 2016 to 2021

Rotavirus group A (RVA) is the most common cause of severe childhood diarrhea worldwide. The introduction of rotavirus vaccination programs has contributed to a reduction in hospitalizations and mortality caused by RVA. From 2016 to 2021, we conducted surveillance to monitor RVA prevalence and genotype distribution in Nam Dinh and Thua Thien Hue (TT Hue) provinces where a pilot Rotavin-M1 vaccine (Vietnam) implementation took place from 2017 to 2020. Out of 6626 stool samples, RVA was detected in 2164 (32.6%) by ELISA. RT-PCR using type-specific primers were used to determine the G and P genotypes of RVA-positive specimens. Whole genome sequences of a subset of 52 specimens randomly selected from 2016 to 2021 were mapped using next-generation sequencing. From 2016 to 2021, the G9, G3 and G8 strains dominated, with detected frequencies of 39%, 23%, and 19%, respectively; of which, the most common genotypes identified were G9P[8], G3P[8] and G8P[8]. G1 strains re-emerged in Nam Dinh and TT Hue (29.5% and 11.9%, respectively) from 2020 to 2021. G3 prevalence decreased from 74% to 20% in TT Hue and from 21% to 13% in Nam Dinh province between 2017 and 2021. The G3 strains consisted of 52% human typical G3 (hG3) and 47% equine-like G3 (eG3). Full genome analysis showed substantial diversity among the circulating G3 strains with different backgrounds relating to equine and feline viruses. G9 prevalence decreased sharply from 2016 to 2021 in both provinces. G8 strains peaked during 2019-2020 in Nam Dinh and TT Hue provinces (68% and 46%, respectively). Most G8 and G9 strains had no genetic differences over the surveillance period with very high nucleotide similarities of 99.2-99.9% and 99.1-99.7%, respectively. The G1 strains were not derived from the RVA vaccine. Changes in the genotype distribution and substantial diversity among circulating strains were detected throughout the surveillance period and differed between the two provinces. Determining vaccine effectiveness against circulating strains over time will be important to ensure that observed changes are due to natural secular variation and not from vaccine pressure.

Phylogenetic analysis of open reading frame of 11 gene segments of novel human-bovine reassortant RVA G6P[1] strain in Pakistan

Multiple Rotavirus A (RVA) strains are linked with gastrointestinal infections in children that fall in age bracket of 0 to 60 months. However, the problem is augmented with emergence of unique strains that reassort with RVA strains of animal origin. The study describes the sequence analysis of a rare G6P[1] rotavirus strain isolated from a less than 1 year old child, during rotavirus surveillance in Rawalpindi district, Pakistan in 2010. Extracted RNA from fecal specimen was subjected to high throughput RT-PCR for structural and nonstructural gene segments. The complete rotavirus genome of one isolate RVA/Human-wt/PAK/PAK99/2010/G6P[1] was sequenced for phylogenetic analysis to elucidate the evolutionary linkages and origin. Full genome examination of novel strain RVA/Human-wt/PAK/PAK99/2010/G6P[1] revealed the unique genotype assemblage: G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H1. The evolutionary analyses of VP7, VP4, NSP1 and NSP3 gene segments revealed that PAK99 clustered with bovine, or cattle-like rotavirus strains from other closely related species, in the genotypes G6, P[1], A3 and T6 respectively. Gene segments VP6, VP1, VP2, VP3, NSP2 and NSP4 all possessed the DS-1-like bovine genotype 2 and bovine (-like) RVA strains instead of RVA strains having human origin. However, the NSP5 gene was found to cluster closely with contemporary human Wa-like rotavirus strains of H1 genotype. This is the first report on bovine-human (Wa-like reassortant) genotype constellation of G6P[1] strain from a human case in Pakistan (and the second description worldwide). Our results emphasize the significance of incessant monitoring of circulating RVA strains in humans and animals for better understanding of RV evolution.

Outbreak associated with Rotavirus G11,P[25] in Korea in 2018

We here report the first outbreak caused by rotavirus G11,P[25] in Korea in 2018, representing a case of re-assortment with pig-derived rotavirus. The genotype constellation was identical to the virus identified in Korea in 2012 as G11-P[25]-I12-R1-C1-M1-A1-N1-T1-E1-H1. The infection source was not known exactly but it must be considered infection from swine.

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.

Evidence of zoonotic transmission of VP6 and NSP4 genes into human species A rotaviruses isolated in Pakistan in 2010

Introduction of animal group A rotavirus (RVA) gene segments into the human RVA population is a major factor shaping the genetic landscape of human RVA strains. The VP6 and NSP4 genes of 74 G/P-genotyped RVA isolates collected in Rawalpindi during 2010 were analyzed, revealing the presence of VP6 genotypes I1 (60.8%) and I2 (39.2%) and NSP4 genotypes E1 (60.8%), E2 (28.3%) and E-untypable (10.8%) among the circulating human RVA strains. The typical human RVA combinations I1E1 and I2E2 were found in 59.4% and 24.3% of the cases, respectively, whereas 5.4% of the RVA strains were reassortants, i.e., either I1E2 or I2E1. The phylogeny of the NSP4 gene showed that one G2P[4] and two G1P[6] RVA strains clustered with porcine E1 RVA strains or RVA strains that were considered to be (partially) of porcine origin. In addition, the NSP4 gene segment of the unusual human G6P[1] RVA strains clustered closely with bovine E2 RVA strains, further strengthening the hypothesis of an interspecies transmission event. The study further demonstrates the role of genomic re-assortment and the involvement of interspecies transmission in the evolution of human RVA strains. The VP6 and NSP4 nucleotide sequences analyzed in the study received the GenBank accession numbers KC846908- KC846971 and KC846972-KC847037, respectively.

FIRST MOLECULAR DETECTION AND VP7 (G) GENOTYPING OF GROUP A ROTAVIRUS BY SEMI-NESTED RT-PCR FROM SEWAGE IN NIGERIA

Rotavirus is the leading cause of viral gastroenteritis worldwide, and sewage is a major source of the virus dissemination in the environment. Our aim was to detect and genotype rotaviruses from sewages in Nigeria. One hundred and ninety sewage samples were collected between June 2014 and January 2015. The two phase concentration method using PEG 6000 and dextran was used to concentrate sewage samples following WHO protocols. Molecular detection was performed by RT-PCR, and VP7 genotyping by semi-nested multiplex PCR. A total of 14.2% (n = 27) samples tested positive. Monthly distribution showed that June to September had a lower rate (3.7% to 7.4%), while October to January recorded 11% to 26%. Genotype G1 predominated followed by G8, G9, G4 and lastly G2, 7.4% (n = 2) of isolates were nontypeable. This is the first report of rotavirus detection in sewages from Nigeria. Genotype G1 remains the most prevalent genotype. This observation calls for an effort by the governmental authorities to implement a molecular surveillance, both clinical and environmental, in order to provide vital information for the control and the vaccine efficacy not only in Nigeria, but globally.

Great genetic diversity of rotaviruses detected in piglets with diarrhea in Thailand

A total of 491 fecal specimens collected from diarrheic piglets in Thailand from January 2011 to March 2014 were screened for group A rotavirus by RT-PCR assay. The G and P genotypes of the detected rotaviruses were determined by multiplex PCR or nucleotide sequencing. Group A rotaviruses were detected in 113 out of 491 (23.0 %) fecal specimens. A wide variety of G-P genotype combinations were identified, and G4P[13] was the most prevalent genotype combination (29.2 %), followed by G4P[23] (14.1 %), G5P[23] (11.5 %), G4P[6] (9.7 %), G3P[23] (7.0 %), G5P[13] (6.1 %), G3P[13] (4.4 %), G3P[6] (2.7 %), and G5P[6] (2.7 %). In addition, the other G-P combinations were also detected at a low percentage, including G3P[19], G4P[7], G9P[19], G9P[23], G9P[7], G4P[19], and G11P[13] strains. This study indicated that group A rotaviruses are a common causes of diarrhea in piglets and a great diversity of G and P genotype combinations are circulating in piglets in Thailand.

Multiplexed one-step RT-PCR VP7 and VP4 genotyping assays for rotaviruses using updated primers

The current two-step VP7 and VP4 genotyping RT-PCR assays for rotaviruses have been linked consistently to genotyping failure in an estimated 30% of RVA positive samples worldwide. We have developed a VP7 and VP4 multiplexed one-step genotyping assays using updated primers generated from contemporary VP7 and VP4 sequences. To determine assay specificity and sensitivity, 17 reference virus strains, 6 non-target gastroenteritis viruses and 725 clinical samples carrying the most common VP7 (G1, G2, G3, G4, G9, and G12) and VP4 (P[4], P[6], P[8], P[9] and P[10]) genotypes were tested in this study. All reference RVA strain targets yielded amplicons of the expected sizes and non-target genotypes and gastroenteritis viruses were not detected by either assay. Out of the 725 clinical samples tested, the VP7 and VP4 assays were able to assigned specific genotypes to 711 (98.1%) and 714 (98.5%), respectively. The remaining unassigned samples were re-tested for RVA antigen using EIA and qRT-PCR assays and all were found to be negative. The overall specificity, sensitivity and limit of detection of the VP7 assay were in the ranges of 99.0-100%, 94.0-100% and 8.6×10(1) to 8.6×10(2) copies of RNA/reaction, respectively. For the VP4 assay, the overall specificity, sensitivity and limit of detection assay were in the ranges of 100%, 94.0-100% and ≤1 to 8.6×10(2) copies of RNA/reaction, respectively. Here we report two highly robust, accurate, efficient, affordable and documentable gel-based genotyping systems which are capable of genotyping 97.8% of the six common VP7 and 98.3% of the five common VP4 genotypes of RVA strains which are responsible for approximately 88.2% of all RVA infections worldwide.

Effect of monovalent rotavirus vaccine on rotavirus disease burden and circulating rotavirus strains among children in Morocco

Rotarix(TM) vaccine was introduced into the National Program of Immunization of Morocco in October 2010, reaching quickly 87% of the target population of children nationally. The incidence of rotavirus gastroenteritis and the prevalence of circulating rotavirus strains has been monitored in three sentinel hospitals since June 2006. The average percentage of rotavirus positive cases among all children under 5 years old hospitalized for gastroenteritis during the pre-vaccine period (2006-2010) was 44%. This percentage dropped to 29%, 15% and 24% in the 3 years post vaccine introduction (2011, 2012 and 2013), which is a decline of 34%, 66%, and 45%, respectively. Declines in prevalence were greatest among children 0-1 years of age (53%) and were most prominent during the winter and autumn rotavirus season. The prevalence of the G2P[4] and G9P[8] genotype sharply increased in the post vaccine period (2011-2013) compared to the previous seasons (2006-2010). Rotavirus vaccines have reduced greatly the number of children hospitalized due to rotavirus infection at the three sentinel hospitals; it is however unclear if the predominance of G2P[4] and G9P[8] genotypes is related to the vaccine introduction, or if this is attributable to normal genotype fluctuations. Continued surveillance will be pivotal to answer this question in the future.

Genotyping and clinical factors in pediatric diarrhea caused by rotaviruses: one-year surveillance in Surabaya, Indonesia

BACKGROUND

Rotavirus infections are a major cause of diarrhea in children in both developed and developing countries. Rotavirus genetics, patient immunity, and environmental factors are thought to be related to the severity of acute diarrhea due to rotavirus in infants and young children. The objective of this study was to provide a correlation between rotavirus genotypes, clinical factors and degree of severity of acute diarrhea in children under 5 years old in Surabaya, Indonesia.

METHODS

A cross-sectional study was conducted in children aged 1-60 months with acute diarrhea hospitalized in Soetomo Hospital, Surabaya, Indonesia from April to December 2013. Rotavirus in stool specimens was identified by ELISA and genotyping (G-type and P-type) using multiplex reverse transcription PCR. Severity was measured using the Ruuska and Vesikari scoring system. The clinical factors were investigated included patient's age (months), hydration, antibiotic administration, nutritional state, co-bacterial infection and co-viral infection.

RESULTS

A total of 88 children met the criteria; 80.7% were aged 6-24 months, watery diarrhea was the most common type (77.3%) and 73.6% of the subjects were co-infected with bacteria, of which pathogenic Escherichia coli was the most common (42.5%). The predominant VP7 genotyping (G-type) was G2 (31.8%) and that of VP4 genotyping (P-type) was P[4] (31.8%). The predominant rotavirus genotype was G2P[4] (19.3%); G1P[4] and G9P[4] were uncommon with a prevalence of 4.5%. There were significant differences between the common genotype and uncommon genotype with respect to the total severity score of diarrhea (p <0.05). G3, G4 and G9 were significantly correlated with severe diarrhea (p = 0.009) in multivariate analyses and with frequency of diarrhea (>10 times a day) (p = 0.045) in univariate analyses, but there was no significant correlation between P typing and severity of diarrhea. For combination genotyping of G and P, G2P[4] was significantly correlated with severe diarrhea in multivariate analyses (p = 0.029).

CONCLUSIONS

There is a correlation between rotavirus genotype and severity of acute diarrhea in children. Genotype G2P[4] has the highest prevalence. G3, G4, G9 and G2P[4] combination genotype were found to be associated with severe diarrhea.

Complete genome analysis of a rare group A rotavirus, G11P[25], isolated from a child in Mumbai, India, reveals interspecies transmission and reassortment with human rotavirus strains

Hospital-based rotavirus surveillance was carried out in Mumbai during 2005-2009. An isolate (B08299) with a rare genotype combination (G11P[25]) was detected. The present study was undertaken to characterize the complete genome of the isolate. B08299 exhibited a G11-P[25]-I12-R1-C1-M1-A1-N1-T1-E1-H1 genotype constellation. Phylogenetic analysis of the 11 gene segments of B08299 revealed that the VP2 and NSP5 genes of B08299 had a human origin, while the VP6 gene represented an I12 genotype of obscure origin. The remaining six genes formed a lineage distinct from human and porcine rotaviruses within genotype 1. Analysis of the structural and non-structural genes suggested that B08299 has evolved by gene reassortment. Our findings provide further evidence that interspecies transmission is an important mechanism involved in the evolution and genetic diversity of human rotaviruses in nature.

Rotaviruses: is their surveillance needed?

Rotaviruses, a major cause of gastroenteritis in children worldwide accounts for around 0.5 million deaths annually. Owing to their segmented genome and frequently evolving capability, these display a wide variation in their genotypes. In addition to commonly circulating genotypes (G1, G2, G3, G4, G9, P[4] and P[8]), a number of infrequent genotypes are being continuously reported to infect humans. These viral strains exhibit variation from one geographical setting to another in their distribution. Though the introduction of vaccines (RotaTeq and Rotarix) proved to be very effective in declining rotavirus associated morbidity and mortality, the number of infections remained same. Unusual genotypes significantly contribute to the rotavirus associated diarrhoeal burden, may reduce the efficacy of the vaccines in use and hence vaccinated individuals may not be benefited. Vaccine introduction may bring about a notable impact on the distribution and prevalence of these viruses due to selection pressure. Moreover, there is a sudden emergence of G2 and G3 in Brazil and United States, respectively, during the years 2006-2008 post-vaccination introduction; G9 and G12 became predominant during the years 1986 through 1998 before the vaccine introduction and now are commonly prevalent strains; and disparity in the predominance of strains after introduction of vaccines and their natural fluctuations poses a vital question on the impact of vaccines on rotavirus strain circulation. This interplay between vaccines and rotavirus strains is yet to be explored, but it certainly enforces the need to continuously monitor these changes in strains prevalence in a particular region. Furthermore, these fluctuations should be considered while administration or development of a vaccine, if rotavirus associated mortality is ever to be controlled.

One year survey of human rotavirus strains suggests the emergence of genotype G12 in Cameroon

In this study the emergence of rotavirus A genotype G12 in children <5 years of age is reported from Cameroon during 2010/2011. A total of 135 human stool samples were P and G genotyped by reverse transcriptase PCR. Six different rotavirus VP7 genotypes were detected, including G1, G2, G3, G8, G9, and G12 in combinations with P[4], P[6] and P[8] VP4 genotypes. Genotype G12 predominated in combination with P[8] (54.1%) and P[6] (10.4%) genotypes followed by G1P[6] (8.2%), G3P[6] (6.7%), G2P[4] (5.9%), G8P[6] (3.7%), G2P[6] (0.7%), G3P[8] (0.7%), and G9P[8] (0.7%). Genotype P[6] strains in combination with various G-types represented a substantial proportion (N=44, 32.6%) of the genotyped strains. Partially typed strains included G12P[NT] (2.2%); G3P[NT] (0.7%); G(NT)P[6] (1.5%); and G(NT)P[8] (0.7%). Mixed infections were found in five specimens (3.7%) in several combinations including G1+ G12P[6], G2+ G3P[6] + P[8], G3+ G8P[6], G3 + G12P[6] + P[8], and G12P[6] +P[8]. The approximately 10% relative frequency of G12P[6] strains detected in this study suggests that this strain is emerging in Cameroon and should be monitored carefully as rotavirus vaccine is implemented in this country, as it shares neither G- nor P-type specificity with strains in the RotaTeq® and Rotarix® vaccines. These findings are consistent with other recent reports of the global spread and increasing epidemiologic importance of G12 and P[6] strains.

Epidemiology and genetic diversity of rotavirus strains in children with acute gastroenteritis in Lahore, Pakistan

Pakistan harbors high disease burden of gastro-enteric infections with majority of these caused by rotavirus. Unfortunately, lack of proper surveillance programs and laboratory facilities have resulted in scarcity of available data on rotavirus associated disease burden and epidemiological information in the country. We investigated 1306 stool samples collected over two years (2008–2009) from hospitalized children under 5 years of age for the presence of rotavirus strains and its genotypic diversity in Lahore. The prevalence rate during 2008 and 2009 was found to be 34% (n = 447 out of 1306). No significant difference was found between different age groups positive for rotavirus (p>0.05). A subset of EIA positive samples was further screened for rotavirus RNA through RT-PCR and 44 (49.43%) samples, out of total 89 EIA positive samples, were found positive. G and P type prevalence was found as follows: G1P [4] = 3(6.81%); G1P [6] = 9(20.45%); G1P [8] = 1(2.27%); G2P [4] = 21(47.72%); G2P [8] = 1(2.27%); G9P [4] = 1(2.27%); G9P [6] = 1(2.27%) and G9P [8] = 7(15.90%). Phylogenetic analysis revealed that the VP7 and VP4 sequences clustered closely with the previously detected strains in the country as well as Belgian rotaviruses. Antigenic characterization was performed by analyzing major epitopes in the immunodominant VP7 and VP4 gene segments. Although the neutralization conferring motifs were found variable between the Pakistani strains and the two recommended vaccines strains (Rotarix™ and RotaTeq™), we validate the use of rotavirus vaccine in Pakistan based on the proven and recognized vaccine efficacy across the globe. Our findings constitute the first report on rotavirus’ genotype diversity, their phylogenetic relatedness and epidemiology during the pre-vaccination era in Lahore, Pakistan and support the immediate introduction of rotavirus vaccine in the routine immunization program of the country.

Shared G12 VP7 gene among human and bovine rotaviruses detected in Cameroonian villages

Group A rotaviruses (RVA) are an important enteric pathogen in humans and livestock animals. Transmission of animal RVA strains to humans has been documented on several occasions. A reverse route of transmission of RVA under natural circumstances is anticipated, although evidence is scarce. However, experimental studies indicated that animals can be infected with human RVAs. By screening the stool samples collected from 157 cattle during 2011 in two Cameroonian villages, four samples (2.5%) were found positive for RVA. Upon sequence analysis of a 410 bp fragment of the VP7 gene, the RVA strains shared up to 100% nt identity to each other and to G12 RVAs identified in human patients living in the same geographic regions. This finding provides evidence for a human-to-animal transmission of an epidemic human rotavirus strain.

Genomic analysis of human rotavirus strains G6P[14] and G11P[25] isolated from Kolkata in 2009 reveals interspecies transmission and complex reassortment events

In a community based case-control study in Kolkata, India, in 2009, two human rotaviruses with uncommon genotypes G6P[14] and G11P[25] were identified, having bovine and porcine characteristics respectively. Strain N-1/2009 with G6P[14] and strain N-38/2009 with G11P[25] genotypes, were isolated from a 13months aged boy who was asymptomatic and a 10months old girl with severe diarrhea respectively. The remaining 9 gene segments of these two strains were analyzed to find the exact origin of these unusual rotaviruses, and the origin of these two strains from bovine/porcine rotaviruses was apparent. This study identifies zoonotic transmission and single and multiple reassortment events as mechanisms driving the diversity of human rotaviruses. This study indicates interspecies transmission between human and animal rotaviruses causes single or multiple reassortment and thus contribute to the genetic diversity of rotavirus.

Diversity of rotavirus strains circulating in children under 5 years of age admitted to hospital for acute gastroenteritis in Morocco, June 2006 to May 2009

Rotavirus vaccine was introduced in Morocco during 2010. In anticipation of introducing rotavirus vaccines, the Ministry of Health in Morocco established a rotavirus surveillance network in June 2006 at four hospitals in Morocco to obtain baseline data on rotavirus disease burden and prevalent strains. From June 2006 to May 2009, stool samples were collected from children under 5 years of age admitted for diarrhea to four sentinel hospitals serving different regions of Morocco. Rotaviruses were detected in stools using enzyme immunoassay, then genotyped by reverse-transcriptase polymerase chain reaction. Samples with adequate stool in which the P or G types could not be determined by RT-PCR were subjected to nucleotide sequence analysis. Overall, 42% (579 of 1,388) of the stools samples tested were positive for rotavirus. Genotyping of 548 (95%) samples demonstrated that G1P[8] (55%) was the most prevalent strain, followed by G9P[8] (11.3%), G2P[4] (9.1%), G4P[8] (0.9%), and G3P[8] (0.4%). Several other strains were identified including G1P[4] (0.2%), G1P[6] (0.9%), G2P[6] (4.3%), G2P[8] (0.2%), G3P[6] (0.4%), G3P[4] (0.2%), and G9P[6] (0.2%). A high prevalence of mixed infections was found (15% of all samples) of which G1G2P[8] (4%) and G1G3P[8] (3.6%) accounted for the majority. Considerable diversity of rotavirus genotypes was present among strains circulating in Morocco prior to the introduction of the vaccine. This study highlighted the need for maintaining active surveillance to monitor changes in rotavirus disease burden and strain dynamics and to detect changes over time that could impact the effectiveness of the vaccination program.

Burden and typing of rotavirus group a in children with acute gastroenteritis in shiraz, southern iran

BACKGROUND

Human Rotavirus is a significant cause of severe gastroenteritis in infants and young children worldwide. In recent years, Rotavirus genotyping by RT-PCR has provided valuable information about the diversity of Rotaviruses circulating worldwide. The purpose of the present study is to monitor the prevalence of the different G types of Rotaviruses circulating in Shiraz, Southern Iran and detect any uncommon or novel types.

METHODS

During the period from December 2007 to November 2008, a total of 138 stool samples were collected from children less than 5 years old who were hospitalized for acute gastroenteritis. Rotavirus-associated diarrhea was investigated in fecal specimens with enzyme immunoassays (EIA). Rotavirus-positive specimens were typed by the Nested RT-PCR and by using different types of specific primers.

RESULTS

Out of the 138 collected samples, 34.78% (48 cases) tested positive for Rotavirus. The frequency of G1, G2 and G4 types was 6.25%, 2.08% and 27.08%, respectively. Mixed and non-typeable infections were detected in 33.34% and 31.25% of hospitalized children with acute diarrhea, respectively. This is the first time mixed Rotavirus infections with G1/G3 have been reported in Iran.

CONCLUSION

The high frequency of Rotavirus detection indicates the severity and the burden of Rotavirus disease may be able to reduce through the implementation of an effective vaccine and continual surveillance for the detection of Rotavirus genotypes circulating in other regions of Iran. Regarding to the noticeable frequency of non-typeable and mixed infections, it is suggested to use the other specific primers and further studies to detection of other novel and unusual types.

A systematic review of rotavirus strain diversity in India, Bangladesh, and Pakistan

Of the estimated half-million deaths from rotavirus globally each year, approximately one-third (N = 160,000 deaths) occur in the Indian subcontinent (defined as India, Bangladesh, and Pakistan). Two commercial vaccines are available for use and recommended by WHO, although the prohibitive vaccine price has limited their introduction into routine childhood immunization programs. New rotavirus vaccines are in late clinical development, including two advanced candidates in India. As significant shifts in rotavirus strain diversity have occurred in the past three decades and questions remain regarding whether strain replacement may occur following introduction of rotavirus vaccines, it is important to understand the temporal and regional strain diversity profile before vaccine introduction. We reviewed 33 peer-reviewed manuscripts from the Indian subcontinent and found that the most common G-types (G1-4) and P-types (P[4] and P[8]) globally accounted for three-fourths of all strains in the subcontinent. However, strains varied by region, and temporal analysis showed the decline of G3 and G4 in recent years and the emergence of G9 and G12. Our findings underscore the large diversity of rotavirus strains in the Indian subcontinent and highlight the need to conduct surveillance on a regional scale to better understand strain diversity before and after rotavirus vaccine introduction.

Molecular characterization of group A bovine rotavirus in southeastern and central-western Brazil, 2009-2010

Rotavirus is an important cause of neonatal diarrhea in humans and several animal species, including calves. A study was conducted to examine 792 fecal samples collected from calves among 65 dairy and beef herds distributed in two of Brazil's major livestock producing regions, aiming to detect the occurrence of rotavirus and perform a molecular characterization of the rotavirus according to G and P genotypes in these regions. A total of 40 (5.05%) samples tested positive for rotavirus by the polyacrylamide gel electrophoresis (PAGE) technique. The molecular characterization was performed by multiplex semi-nested RT-PCR reactions, which indicated that the associations of genotypes circulating in herds in Brazil's southeastern region were G6P[11], G10P[11], G[-]P[5] + [11], G[-]P[6] in the state of São Paulo and G6P[11], G8P[5], G11P[11], G10P[11] in the state of Minas Gerais. In the central-western region, the genotypes G6P[5] + [11], G6P[5], G8P[-], G6P[11], G [-] P[1], G[-] P[11], and G[-] P[5] were detected in the state of Goiás, while the genotypes G6P[5], G8[P11], G6[P11], G8[P1], G8[P5], G6[P1] were circulating in herds in the state of Mato Grosso do Sul. The genotypic diversity of bovine rotavirus found in each region under study underlines the importance of characterizing the circulating samples in order to devise the most effective prophylactic measures.

A large outbreak of enteritis in goat flocks in Marmara, Turkey, by G8P[1] group A rotaviruses

Group A rotaviruses are regarded as major enteric pathogens of large ruminants, while their impact on the health of small ruminants is not well documented. We report the detection of group A rotavirus from a large outbreak of enteritis that occurred in two goat flocks in the town of Kırklareli, Marmara Region, Turkey, in 2007. The disease was observed in young kids, with high morbidity and mortality rates, but not in adult animals. Rotavirus antigen was detected in the stools of the examined animals, and rotaviruses were isolated in MA104 cells. Upon sequencing of the VP4, VP6, VP7 and NSP4 genes, the strain (RVA/goat-tc/TUR/Kirklareli/2007/G8P[1]) was characterized as G8P[1], with E2 NSP4 and VP6 I2 genotype. These findings indicate that group A rotavirus should be included in the diagnostic algorithms for enteric disease in small ruminants.

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.

Human infection with novel G3P[25] rotavirus strain in Taiwan

Genotype P[25] rotaviruses are rare and to date have been reported to occur only in a few countries of mainland Asia. Here we report the molecular characterization of a novel human rotavirus genotype combination, G3P[25], detected in a 17-month-old child hospitalized due to severe gastroenteritis during 2009 in central Taiwan. Sequencing and phylogenetic analysis of the VP4 gene demonstrated a distinct origin from other strains bearing the P[25] VP4 gene, whereas the VP7, VP6 and NSP4 gene phylogenies identified common origins with cognate genes of other, presumed human-porcine reassortment Taiwanese strains. These results suggest that interactions between human and animal strains appear to contribute to the generation of genetic and antigenic diversity of rotavirus strains, with potential public health importance in Taiwan.

Burden and typing of rotavirus group A in Latin America and the Caribbean: systematic review and meta-analysis

The efficacy of licensed rotavirus vaccines has only been shown against certain rotavirus group A (RV-A) types. It is critical to understand the burden of rotavirus gastroenteritis (RVGE) and its prevalent types to assess the potential impact of these vaccines in Latin America and the Caribbean (LA&C). We performed a systematic review and meta-analyses of all the available evidence reported from 1990 to 2009 on the burden of rotavirus disease and strains circulating in LA&C. Eligible studies--185 country-level reports, 174 951 faecal samples--were selected from MEDLINE, Cochrane Library, EMBASE, LILACS, regional Ministries of Health, PAHO, regional proceedings, doctoral theses, reference lists of included studies and consulting experts. Arc-sine transformations and DerSimonian-Laird random-effects model were used for meta-analyses. The proportion of gastroenteritis cases due to rotavirus was 24.3% (95%CI 22.3-26.4) and the incidence of RVGE was 170 per 1000 children-years (95%CI 130-210). We estimated a global annual mortality for 22 countries of 88.2 (95%CI 79.3-97.1) deaths per 100 000 under 5 years (47 000 deaths).The most common G type detected was G1 (34.2%), followed by G9 (14.6%), and G2 (14.4%). The most common P types detected were P[8] (56.2%), P[4] (22.1%) and P[1] 5.4%, and the most prevalent P-G type associations were P[8]G1 17.9%, P[4]G2 9.1% and P[8]G9 8.8%. In the last 10 years, G9 circulation increased remarkably and G5 almost disappeared. More recently, G12 appeared and P[4]G2 re-emerged. To our knowledge, this is the first meta-analysis of rotavirus infection and burden of disease in LA&C.

Molecular characterization of rotavirus diarrhea among children in South Korea: detection of an unusual G11 strain

Among 312 rotavirus-positive samples collected from eight hospitals across South Korea during 2008 and 2009, the most prevalent circulating G genotype was G1 (35.9%), followed by G3 (24.7%), G2 (17.0%), G4 (7.7%), and G9 (2.6%). Notably, one unusual G11 lineage III strain-the first hypoendemic infection case in the world-was found. Of the P genotypes, P[8] (43.9%) was the most common, followed by P[6] (29.5%), P[4] (9.3%) and P[9] (0.6%). Determining G- and P-type combinations showed that G1P[8] was the most prevalent (20.5%), followed by G2P[6] (12.8%) and G3P[8] (12.8%). These findings provide new information concerning the current prevalence and spread of the rare G11 rotavirus.

Ovine rotavirus strain LLR-85-based bovine rotavirus candidate vaccines: construction, characterization and immunogenicity evaluation

Group A bovine rotaviruses (BRVs) are the most important cause of diarrheal diseases in neonatal calves and cause significant morbidity and mortality in the young animals, and epidemiologic surveillance of bovine rotavirus G genotypes conducted in various cattle populations throughout the world has shown that approximately 90% of the bovine rotavirus isolates belong to G6 and G10. Based on the modified Jennerian approach to immunization, we constructed and characterized a reassortant rotavirus stain, which bears a single bovine rotavirus VP7 gene encoding G genotype 6 specificity while the remaining 10 genes are derived from the ovine attenuated rotavirus LLR-85. The reassortant rotavirus strain, named as R191, and its parental virus strain LLR-85 were combined as bivalent vaccine candidates to inoculate the colostrums-deprived neonatal calves for evaluation of the immunogenicity. The calves were orally inoculated with the reassortant R191 (group 1), the parental rotavirus LLR-85 (group 2), or combined the R191 and LLR-85 (group 3), and serum specimens were detected to determine the immune response of IgG and IgA antibodies. Results showed that seroconversion to positivity for IgG and IgA antibodies occurred at postinoculation day (PID) 10 in all of the inoculated calves, and the highest titers of the serum IgG (range 1:800 to 1:6400) and IgA (range 1:800 to 1:3200) antibodies were obtained at PID 21 for all calves. Meanwhile, virus shedding was detected after inoculation, showing that the inoculated virus was positive in 2 of 77 fecal specimens (2.6%) collected from the inoculated calves during the first 7 days of oral inoculation with the rotavirus vaccine candidates. The results suggested that the rotavirus strains R191 and LLR-85 are promising bivalent vaccine candidates for the prevention of bovine G6 and G10 rotavirus infection.

The global spread of rotavirus G10 strains: Detection in Ghanaian children hospitalized with diarrhea

From October 2003 through September 2004, a total of 289 stool samples were collected from children <5 years of age who had severe diarrhea at admission to or when visiting the emergency department at the Navrongo War Memorial Hospital in rural Ghana during a study on rotavirus disease burden. Rotavirus antigen was detected in 115 stool samples (39.8%) tested for rotavirus. Four rotavirus-positive samples were found to bear G10P[6] specificity by reverse-transcription polymerase chain reaction, polymerase chain reaction-enzyme-linked immunosorbent assay, and oligonucleotide microarray hybridization. Two of these strains further exhibited serotype G10 specificity by neutralization and subgroup II specificity by enzyme immunoassay and possessed long electropheretic patterns by polyacrylamide gel electrophoresis. Their VP7 genes shared a much closer nucleotide identity with other African human G10 strains (>97%) than with human G10 strain from Asia or South America (<86%) or animal strains (<85%). The VP8* genes of the Ghanaian G10 strains exhibited >94% identity to that of human P[6] virus strains and belonged to the P[6] lineage 1a. The deduced VP7 amino acid sequence showed that the Ghanaian strains were more closely related to human G10 strains than to animal G10 strains. The possession of the typical human subgroup II specificity and the P[6] specificity (frequently found in Ghana and the rest of Africa) and the marked similarity in the VP7 antigenic sites suggest that these G10 strains may have evolved through genetic reassortment between bovine and human strains.

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].

Circulating human group A rotavirus genotypes in Malaysia

This study examined the temporal distribution of rotavirus genotypes in Malaysia. Rotaviruses from children with diarrhea admitted to hospitals in 1996 (n = 93) and 2007 (n = 12) in two different regions of Peninsular (West) Malaysia were analyzed for their G and P genotypes using a hemi-nested RT-PCR assay. In the 2007 samples, the dominant strain was G9P[8]. It was identified in 42% of the samples. Different strains all possessing the G1 genotype were identified in the rest of the samples. In contrast, 81% of the samples collected in 1996 were the G1P[8] strain. No strains with G9 genotype were detected in samples collected in 1996.

Genetic variation of G4P[6] rotaviruses: evidence for novel strains circulating between the hospital and community

One hundred forty-six fecal specimens collected between 2007 and 2008 from infants with acute gastroenteritis were screened for rotavirus by ELISA with VP6-specific antibody. One hundred twenty-three of the samples (84.2%) were confirmed to be positive for group A rotavirus (community-acquired, n = 90 [73.2%] and nosocomial, n = 33 [26.8%]), and were typed subsequently using RT-PCR and sequence analysis methods. Determination of G- and P-type combinations showed that G4P[6] (78.9%) was the most common strain, followed by G3P[8] (7.3%), G1P[8] (6.5%), G2P[4] (0.8%), G2P[6] (0.8%), G1P[6] (0.8%), and G9P[8] (0.8%) strains. Of the 97 G4P[6] strains, 62 (63.8%) were responsible for community-acquired cases and 35 (36.1%) were hospital-acquired cases. Phylogenetic analysis of the VP7 gene from the G4P[6] strains revealed that both the community-acquired and nosocomial strains were segregated to the human rotaviruses circulating world-wide, including the prototype vaccinal strain, ST3, which constituted a novel sublineage in lineage 1. Owing to the recent emergence of G4P[6] rotaviruses within the hospital, as well as in the community, the findings from this study are important since they provide new information concerning the community and nosocomial spread of rotaviruses.

Reassortment of human rotavirus gene segments into G11 rotavirus strains

G11 rotaviruses are believed to be of porcine origin. However, a limited number of G11 rotaviruses have been recently isolated from humans in combination with P[25], P[8], P[6], and P[4]. To investigate the evolutionary relationships of these strains, we analyzed the complete genomes of 2 human G11P[25] strains, 2 human G11P[8] strains, and 3 porcine reference strains. Most of the 11 gene segments of these 7 strains belonged to genotype 1 (Wa-like). However, phylogenetic clustering patterns suggested that an unknown G11P[25] strain with a new I12 VP6 genotype was transmitted to the human population, in which it acquired human genotype 1 gene segments through reassortment, resulting in a human G11P[8] rotavirus strain with an entire human Wa-genogroup backbone. This Wa-like backbone is believed to have caused the worldwide spread of human G9 and G12 rotaviruses. G11 human rotavirus strains should be monitored because they may also become major human pathogens.

Surveillance of rotavirus in a rural diarrhoea treatment centre in Bangladesh, 2000-2006

Rotavirus was detected in 33% of 4519 children less than 5 years of age admitted with diarrhoea to treatment centres at Matlab in rural Bangladesh from 2000 to 2006. Highest rotavirus detection rates were in children aged 6-11 months with 56% being less than 1 year old. The peak seasonal detection was in July-September and December-February. The population-based incidence rates of rotavirus ranged from 10.8 to 19.6/1000 children less than 5 years of age. G1 serotype predominated between June 2002-May 2005 and June 2005-May 2006 the predominant type was G2 (41%) followed by G1 (22%) and G9 (22%). Rotavirus is an important cause of childhood diarrhoea in rural Bangladesh and this burden may be reduced with a rotavirus vaccination programme.

Rotavirus disease and vaccination: impact on genotype diversity

Temporal and spatial fluctuations in the genotype distribution of human rotaviruses are continuously observed in surveillance studies. New genotypes, such as G9 and G12, have emerged and spread worldwide in a very short time span. In addition, reassortment events have the potential to contribute substantially to genetic diversity among human and animal rotaviruses. With the recent introduction of the two rotavirus vaccines, RotaTeq and Rotarix, in many countries, it appears that the total number of hospitalizations due to rotavirus infections is being reduced, at least in developed countries that implemented a universal immunization program. However, continued surveillance is warranted, especially regarding the long-term effects of the vaccines. No data analyses are available to clarify whether rotavirus vaccine introduction would allow other rotavirus P and G genotypes, which are not covered by the current vaccines, to emerge into the human population and fill the apparent gap. This kind of data analysis is essential, but its interpretation is hampered by natural and cyclical genotype fluctuations.

Distribution of G (VP7) and P (VP4) genotypes of group A bovine rotaviruses from Turkish calves with diarrhea, 1997-2008

Group A rotaviruses are major enteric pathogens of calves. In order to investigate the genetic diversity of bovine rotaviruses (BRVs), a collection of 53 BRVs, detected from diarrheic calves from several Turkish geographical areas, between 1997 and 2008 was analyzed by RT-PCR for specificities of the outer capsid proteins VP7 (G type) and VP4 (P type), for the first time. Overall, G6 was the predominant G type, detected in 40/53 samples (75.4%), while P[11] was the predominant P type, detected in 52/53 samples (98.1%). The most common VP7/VP4 combinations were G6P[11] (60.3%) and G10P[11] (24.5%). Mixed infections were identified in 7/53 samples (13.2%). In the VP7 region the G6P[11] viruses were similar to other ones detected worldwide, forming an independent G6 lineage, distantly related to the G6 gene of the vaccine G6P[1] strain NCDV (90.1% amino acid identity), and suggesting that G6P[11] viruses represent a genetically stable BRV strain. The study of G and P type diversity is pivotal to understand the efficacy of the existing rotavirus vaccines and to provide the basis of future prophylaxis tools against rotaviral diarrhea of calves.

Molecular characterization of a rare, human-porcine reassortant rotavirus strain, G11P[6], from Ecuador

The Pan-American Health Organization established a rotavirus pre-vaccination disease burden and strain surveillance network in Latin America and the Caribbean in 2004. During strain surveillance in Ecuador in 2005-2006, a rare rotavirus genotype, G11P[6], was detected among common strains. Sequencing and phylogenetic analysis of this strain identified a novel lineage of the G11 VP7 gene, most closely related to A253 (91.8% nt identity), a porcine rotavirus strain identified in Venezuela. Most genes of this strain clustered with porcine, human-porcine or bovine-porcine reassortant strains; only VP6 and perhaps NSP2 genes were more closely related to cognate genes of human rotaviruses. Thus, this strain was likely generated by gene reassortment between porcine and human parental strains. Our study provides further evidence that animal rotaviruses play an important role in genetic and antigenic diversity of rotaviruses pathogenic for humans.

Characterization of full-length VP4 genes of OP354-like P[8] human rotavirus strains detected in Bangladesh representing a novel P[8] subtype

The G1 and G9 rotavirus strains MMC71 and MMC38 (subgroup II, NSP4 genogroup B), respectively, isolated from children in Bangladesh, were analyzed genetically. Full-length VP4 genes of these strains had 98.9% identity to each other and showed 83.9-89.4% identity to those of the P[4] and P[8] rotaviruses. Phylogenetic analysis of VP4 nucleotide sequences revealed that strains MMC38 and MMC71 were located in a lineage of P[8] strains. However, the cluster was highly divergent from the previously established P[8] strains. The VP8* portions of strains MMC38 and MMC71 showed more than 93.9% nucleotide sequence identity to OP354-like P[8] strains, and these strains were clustered into the same lineage. These findings indicate that the VP4 of these strains should be classified into a subtype of the P[8] genotype (P[8]b) that is distinct from that of common P[8] rotaviruses (P[8]a).

G2 strain of rotavirus among infants and children, Bangladesh

To determine G and P genotypes, we performed nested PCR on 307 rotavirus specimens collected in Dhaka, Bangladesh, during 2004–2005. G2 (43.3%) was detected at the highest frequency, followed by G4 (19.5%), G9 (13.7%), G1 (12.7%), and G3 (2.6%). P[8] was the most predominant genotype (53.2%), followed by P[4] (42.9%).

Characterization of novel VP7, VP4, and VP6 genotypes of a previously untypeable group A rotavirus

Rotavirus is the most common cause of acute gastroenteritis among infants and young children throughout the world, but rotavirus cases in developing countries account for nearly all of the approximately 600,000 annual deaths. We studied the epidemiology of rotavirus in 22 rural communities in northern coastal Ecuador over a five-year period. From 250 rotavirus positive stool specimens, the percentage that could not be RT-PCR genotyped for VP4 and VP7 was 77% and 63%, respectively. The possibility of sample degradation was considered but discounted after an experimental examination of rotavirus stability and EM visualization of rotavirus-like particles in several untypeable samples. Finally, alternate primers were used to amplify Ecu534, a sample that was untypeable using most published VP4 and VP7 primers. Characterization of the VP7, VP4, and VP6 full gene segments revealed novel genotypes and nucleotide mismatches with most published primer sequences. When considered with other findings, our results suggest that primer mismatch may be a widespread cause of genotyping failure, and might be particularly problematic in countries with greater rotavirus diversity. The novel sequences described in this study have been given GenBank accession numbers EU805775 (VP7), EU805773 (VP4), EU805774 (VP6) and the RCWG has assigned them novel genotypes G20P[28]I13, respectively.