Detection of rotavirus types G8 and G10 among Brazilian children with diarrhea

Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone

Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a "Distinct" VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale.

Rotaviruses A and C in dairy cattle in the state of Rio de Janeiro, Brazil

Stool samples were collected from calves from nine family-based small dairy farms in the state of Rio de Janeiro, for detection and characterization of rotavirus (RV) species A, B, and C (RVA, RVB, and RVC, respectively) by reverse transcription polymerase chain reaction. Twenty-six samples (27.7%) were positive for at least one of the species: 22 (23.4%) samples were positive only for RVA, 3 (3.2%) were positive for RVC, and one sample (1.1%) had co-infection of RVA and RVC. RVB was not detected. Seven (21.9%; n = 32) animals with diarrhea and 19 (30.1% n = 62) asymptomatic animals were positive, with no significant difference in positivity (p = 0.3677). RV was detected in all properties studied, at rates between 14.3 and 80%, demonstrating the widespread circulation of RV in four of the seven geographic regions of the state of Rio de Janeiro. Infection was more prevalent among animals ≤ 6 months of age. Sequence analysis of a portion of the RVA VP6-encoding gene identified the I2 genotype. RVC was also detected; to our knowledge, this is the first description of this agent in cattle in Brazil. The data presented here should add knowledge regarding the importance and prevalence of RV in our national territory, and may facilitate the planning and implementation of control and prevention measures for bovine rotavirus infections in Brazil.

High prevalence of circulating DS-1-like human rotavirus A and genotype diversity in children with acute gastroenteritis in Thailand from 2016 to 2019

Background

Human rotavirus A (RVA) infection is the primary cause of acute gastroenteritis (AGE) in infants and young children worldwide, especially in children under 5 years of age and is a major public health problem causing severe diarrhea in children in Thailand. This study aimed to investigate the prevalence, genotype diversity, and molecular characterization of rotavirus infection circulating in children under 15 years of age diagnosed with AGE in Thailand from January 2016 to December 2019.

Methods

A total of 2,001 stool samples were collected from children with gastroenteritis (neonates to children <15 years of age) and tested for RVA by real-time polymerase chain reaction (RT-PCR). Amplified products were sequenced and submitted to an online genotyping tool for analysis.

Results

Overall, 301 (15.0%) stool samples were positive for RVA. RVA occurred most frequently among children aged 0-24 months. The seasonal incidence of rotavirus infection occurred typically in Thailand during the winter months (December-March). The G3P[8] genotype was identified as the most prevalent genotype (33.2%, 100/301), followed by G8P[8] (10.6%, 32/301), G9P[8] (6.3%, 19/301), G2P[4] (6.0%, 18/301), and G1P[6] (5.3%, 16/301). Uncommon G and P combinations such as G9P[4], G2P[8], G3P[4] and G3P[9] were also detected at low frequencies. In terms of genetic backbone, the unusual DS-1-like G3P[8] was the most frequently detected (28.2%, 85/301), and the phylogenetic analysis demonstrated high nucleotide identity with unusual DS-1-like G3P[8] detected in Thailand and several countries.

Conclusions

A genetic association between RVA isolates from Thailand and other countries ought to be investigated given the local and global dissemination of rotavirus as it is crucial for controlling viral gastroenteritis, and implications for the national vaccination programs.

Genotype constellation of a rotavirus A field strain with an uncommon G8P[11] genotype combination in a rotavirus-vaccinated dairy cattle herd

In this report we describe the genotype constellation of a bovine rotavirus A (RVA) strain with an uncommon G8P[11] genotype combination. The RVA/Cow-wt/BRA/Y136/2017/G8P[11] strain was classified as G8-P[11]-I2-R5-C2-M2-A3-N2-T9-E2-H3. Phylogenetic analysis based on the VP7 gene showed that the Y136 strain and a human G8P[1] strain comprise a putative new (VII) lineage for the G8 genotype. In addition, two other genotypes, R5 (VP1) and T9 (NSP3), were identified in the constellation of Y136 that are rarely found in RVA strains of bovine origin. The immunological pressure caused by regular vaccination of cows might be responsible for the selection of heterologous RVA strains.

Emergence of Rare Bovine-Human Reassortant DS-1-Like Rotavirus A Strains with G8P[8] Genotype in Human Patients in the Czech Republic

Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016–2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine–human DS-1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology.

G26P[19] rotavirus A strain causing acute gastroenteritis in the American continent

In Brazil, the rotavirus A genotype G26 was first identified in suckling piglets, while the P[19] genotype has not been identified in any animal species so far. This report details the genetic characterisation of a G26P[19] RVA strain detected from an eight year-old child, vaccinated with Rotarix^®, hospitalised with acute diarrhoeal disease in Rio de Janeiro in 2015. Most likely, the genome constellation (I5-R1-C1-M1-A8-N1-T1-E1-H1) observed in the G26P[19] Brazilian strain was a result of interspecies transmission events between humans and pigs. In addition, a rearrangement in the NSP5 gene was observed downstream of the 3’ non-coding region.

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.

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.

Rotarix™ (RIX4414): an oral human rotavirus vaccine

Rotavirus is the most common cause of severe gastroenteritis in children younger than 3 years of age worldwide. New rotavirus vaccine candidates were required to confer early protection against the most common rotavirus serotypes and to be well tolerated and not associated with intussusception. RIX4414 is a human-attenuated G1(P8) oral rotavirus vaccine administered in two doses at approximately 6-24 weeks of age. The first dose may be administered from the age of 6 weeks. There should be an interval of at least 4 weeks between doses and the vaccination course should preferably be given before 16 weeks of age and must be completed, according to the manufacturer, by the age of 24 weeks. In a worldwide development program involving more than 70,000 children in six Phase I-III field trials, this vaccine proved to be nonreactogenic, well tolerated and not associated with intussusception. The vaccine provides over 85-96% protection against moderate-to-severe gastroenteritis caused by G1 and non-G1 serotypes, as demonstrated in Latin American and European clinical trial settings, respectively; and reduces gastroenteritis-related hospitalizations by more than 40% in Latin America and by 75% in European settings.

Update of rotavirus strains circulating in Africa from 2007 through 2011

BACKGROUND

The African Rotavirus Surveillance Network has been detecting and documenting rotavirus genotypes in the subcontinent since 1998, largely based on intercountry workshops conducted at Rotavirus Regional Reference Laboratories. This article reports on rotavirus genotypes generated at Regional Reference Laboratories, South Africa between 2007 and 2011 from 16 African countries.

METHODS

Stool samples were collected from <5-year-old children with diarrhea following World Health Organization criteria of hospital-based rotavirus surveillance. Enzyme immunoassay (EIA) was performed by National Laboratories. Regional Reference Laboratories retested 10% of randomly selected EIA positives and 10% of EIA negatives from each country as part of quality control. At least 50 rotavirus EIA positives from each country per year were subjected to reverse transcriptase polymerase chain reaction based on G-/P-types. Sequencing was conducted in 5-10% of each representative G or P genotype to confirm the genotype, as well as to type some of the samples that could not be genotyped with reverse transcriptase polymerase chain reaction-based methods.

RESULTS

A total of 2555 of rotavirus EIA positives were genotyped. G1 was the most predominant (28.8%), followed by G9 (17.3%), G2 (16.8%), G8 (8.2%), G12 (6.2%) and G3 (5.9%). Similarly, the P[8] strain was the most prevalent (40.6%), followed by P[6] (30.9%) and P[4] (13.9%). The top G/P combinations detected were G1P[8] (18.4%), G9P[8] (11.7%), G2P[4] (8.6%), G2P[6] (6.2%), G1P[6] (4.9%), G3P[6] (4.3%), G8P[6] (3.8%) and G12P[8] (3.1%).

CONCLUSIONS

There is high genetic diversity of rotavirus strains circulating in the subcontinent. Understanding the strain diversity pre- and postvaccine introduction are important in Africa to understand the broader impact of the rotavirus vaccines on regionally circulating strains.

G8P[6] rotaviruses isolated from Amerindian children in Mato Grosso do Sul, Brazil, during 2009: close relationship of the G and P genes with those of bovine and bat strains

During the 2009 national group A rotavirus (RVA) surveillance, five unusual strains of the human G8P[6] genotype were detected in Brazilian indian children with acute gastroenteritis. The aim of this study was to carry out sequence analysis of the two outer capsid proteins (VP4 and VP7) and the inner capsid protein (VP6) of the G8P[6] strains detected in order to provide further information on the genetic relationship between human and animal RVA. A total of 68 stool samples, collected in Mato Grosso do Sul during 2009, were tested for RVA using ELISA, following by reverse transcriptase-PCR and sequencing. RVA infection was detected in 7.3% of samples (5/68). The IAL-RN376 G8 sequence shares a clade with bovine and human strains, displaying highest nucleotide identity to African human strains DRC86 and DRC88, followed by African bovine strain NGRBg8. IAL-RN376 and IAL-RN377 P[6] sequences showed highest identity to human strain R330 from Ireland, and a close genetic relationship to African fruit bat RVA strain KE4852/07. Strains IAL-RN376 and IAL-RN377 display genogroup I VP6 specificity and the I2 genotype, and share high nucleotide identities with human strains B1711, 272-BF and 06-242, and moderate identities with bovine (RUBV81, 86 and KJ9-1) and porcine (HP140) strains. This study suggested that a reassortment between bovine and bat RVA strains could have occurred in animal host(s) preceding the transmission to humans. In the indigenous population, zoonotic transmission is probably fairly frequent as the inhabitants live in close contact with animals under conditions of poor hygiene.

Distribution of Human Rotaviruses, Especially G9 Strains, in Japan from 1996 to 2000

A 4-year (1996-2000) survey of rotavirus infection involving 2,218 diarrheal fecal specimens of children collected from five regions of Japan was conducted. A total of 642 (28.9%) specimens were found to be rotavirus positive. A changed prevalence pattern of rotavirus G serotype was found with an increase of G9 and G2 and a decrease of G1, although G1 remained the prevailing serotype. Serotype G9 was unexpectedly determined to be the prevailing serotype in Sapporo (62.5%) and Tokyo (52.9%) in 1998-1999, and in Saga (78.4%) in 1999-2000. G9 strains isolated from 1998-1999 belonged to the P[8]-NSP4-Wa-group with long RNA pattern, while, G9 strains isolated from 1999-2000 belonged to three groups, the P[8]-NSP4-Wa-group with long RNA pattern, the P[4]-NSP4-KUN-group with short RNA pattern and a mixed-type group (P[4]/P[8]-NSP4-KUN/Wa-group with long RNA pattern). Both sequence and immunological analysis of VP7 revealed that the G9 strains from 1999-2000 were much more closely related to the G9 strains isolated worldwide in the 1990s, including G9 strains found in Thailand in 1997. However, the G9 strains from 1998-1999 were distinct from these and more closely related to the G9 prototype strains F45, AU32 and WI61 discovered in Japan and the US in the 1980s. Thus the G9 strains isolated in 1998-1999 had progenitors common to the G9 prototype strains, while the strains isolated in 1999-2000 did not directly evolve from them but were related to global G9 strains that have emerged in recent years. These data supported our previous report that G9 rotavirus might exist as two or more subtypes with diverse RNA patterns, P-genotype and NSP4 genogroup combinations (Y.M. Zhou et al., J. Med. Virol. 65: 619-628, 2001) and suggested that G9 rotavirus prevalent in Japan during two successive years belonged to different subtypes. The nucleotide sequences presented in this paper were submitted to DDBJ, EMBL and GenBank nucleotide sequence databases. The accession numbers are: 00-Ad2863VP7 (AB091746), 00-OS2986VP7 (AB091747), 00-SG2509VP7 (AB091748), 00-SG2518VP7 (AB091749), 00-SG2541 (AB091750), 00-SG2864 (AB091751), 00-SP2737VP7 (AB091752), 99-SP1542VP7 (AB091753), 99-SP1904VP7 (AB091754), 99-TK2082VP7 (AB091755) and 99-TK2091VP7 (AB091756).

Full-genome characterization of a G8P[8] rotavirus that emerged among children with diarrhea in Croatia in 2006

The whole genome of a G8P[8] rotavirus from the 2006 epidemic in Croatia was sequenced and showed a Wa-like genotype constellation. Its VP7 gene clustered with DS-1-like G8 African rotaviruses and a G8P[4] German strain. Remaining genes clustered with contemporary Belgian G1P[8] rotaviruses, suggesting reassortment between human G8 and G1P[8] rotaviruses in Croatia or other European countries.

First report of human rotavirus G8P[4] gastroenteritis in India: evidence of ruminants-to-human zoonotic transmission

Group A rotaviruses are the major cause of childhood gastroenteritis worldwide. Due to close proximity of human and cattle in rural areas of developing countries like India, interspecies transmission or zoonotic transmission is a major source of rapid generation of reassortants and genetic or antigenic variants. Previously, many human group A rotaviruses were found with porcine or bovine characteristics from eastern and north-eastern India. In this study, four unusual human G8P[4] strains were identified which had artiodactyl-like origins. During an ongoing community based surveillance for epidemiological profiling of diarrheal pathogens, these unusual human group A rotavirus G8P[4] strains were detected from the stool samples of 3-14 months old children with acute diarrhea in Sonarpur, eastern India. Analysis of eleven complete and/or partial gene segments of these unusual G8P[4] strains were done by reverse transcription-PCR (RT-PCR) followed by nucleotide sequencing and phylogenetic analysis. The VP7 nucleotide sequences revealed a close phylogenetic relationship to the G8P[7] porcine strain D-1 and bovine strain KJ59-2 from South Korea. Whereas the VP4 gene segments were also related closely to human rotavirus prototype strain DS-1. Other nine gene segments of these G8P[4] rotaviruses were related closely to either animal or animal-derived rotavirus members of the DS-1-like family. These results suggest that origin of these G8P[4] strains might have been resulted from multiple reassortment events between artiodactyls and ruminant-derived reassortant human rotaviruses. To date, this is the first report of G8P[4] rotavirus from India and the first genomic analysis of G8P[4] strains from Asian continent.

Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch

Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A) and Iturriza‐Gomara and colleagues (Set B) on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2%) were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.

Prevalence and molecular genotyping of group a rotaviruses in Iranian children

Rotavirus is the leading cause of acute gastroenteritis in worldwide young children. Effective vaccines to prevent rotavirus infection are currently available, although their clinical use is still limited, and rotavirus still causes many episodes of infantile gastroenteritis, mainly during the winter season. The aim of this study was to evaluate the prevalence of rotavirus infection in children aged <5-years-old who were hospitalised for gastroenteritis. One hundred and sixty-three stool samples from hospitalised children (<5-years-old) complicated with severe diarrhoea, in two hospitals in Jahrom City, Iran were collected from 2009 to 2010. Antigenic prevalence of rotavirus group A was distinguished by enzyme immunoassay. The antigen of group A rotavirus was diagnosed by EIA in 75 of 163 collected samples. The genotype of EIA-positive samples was determined by nested RT-PCR. The frequency of rotavirus genotypes G1, G2, G3, G4 and G9 was 17.33, 13.34, 2.67, 30.66 and 2.67 %, respectively. Also, the frequency of mixed and non-typable genotypes was detected in 2.67 and 30.66 %, respectively. G1/G8 mixed infection was the first of these rotavirus genotypes to be reported in Iran. Detection of high prevalence of group A rotavirus infection in hospitalised children with diarrhoea, and determination of circulating rotavirus genotypes in this region of Iran, provide useful data for formulating effective vaccines; especially for infants less than 5-years-old.

Increased prevalence of rotavirus among children associated gastroenteritis in Riyadh Saudi Arabia

The aim of this study is to assess the epidemiology along with the molecular structure of rotavirus causing pediatric diarrhea among Saudi patients. However, in this report we sited the epidemiological reflect coming from our project.

Genetic diversity of group A rotaviruses associated with repeated outbreaks of diarrhea in a farrow-to-finish farm: identification of a porcine rotavirus strain bearing a novel VP7 genotype, G26

Group A rotaviruses (GARs) are one of the most common causes of diarrhea in suckling pigs. Although a number of G and P genotypes have been identified in porcine GARs, few attempts have been made to study the molecular epidemiology of these viruses associated with diarrhea outbreaks within a farm over an extended period of time. Here, we investigated the molecular characteristics of GARs that caused four outbreaks of diarrhea among suckling pigs in a farrow-to-finish farm over the course of a year. G and P genotyping of GARs detected at each outbreak demonstrated genetic diversity in this farm as follows: G9P[23] was detected at the first outbreak, G9P[13]/[22] and G9P[23] at the second, G3P[7] at the third, and G9P[23], G5P[13]/[22], and P[7] combined with an untypeable G genotype at the fourth. Sequence analysis of the detected GARs revealed that such genetic diversity could have resulted not only from the introduction of new GAR strains, but also from gene reassortment between GAR strains within the farm. Further, the GAR strain carrying the untypeable G genotype was shown to be a novel porcine GAR bearing a new G26 genotype, as confirmed by the Rotavirus Classification Working Group.

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.

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.

Multiple-gene characterization of rotavirus strains: evidence of genetic linkage among the VP7-, VP4-, VP6-, and NSP4-encoding genes

A total of 162 rotavirus strains detected between 1996 and 2006 among individuals with diarrhea in Rio de Janeiro, Brazil, were analyzed by multiple-gene genotyping. Characterization of strains was done by RT-PCR assay for amplification and typing of the VP7-, VP4-, VP6-, and NSP4-encoding genes. Overall, 139 (85.8%) strains belonged to the common group A rotavirus combinations: 67 (41.4%) belonged to genotype G1-P[8]-I1-E1; 18 (11.1%) were G2-P[4]-I2-E2; 11 (6.8%) were G3-P[8]-I1-E1; 12 (7.4%) were G4-P[8]-I1-E1; and 31 (19.1%) were G9-P[8]-I1-E1. Two samples presented mixed genotypes (G1 + G3-P[8]-I1-E1 and G1 + G9-P[9]-I1-E1) and rare combinations, such as G2-P[6]-I2-E2 and G9-P[6]-I2-E2, were detected in six (3.7%) strains. The results suggest a linkage among all four genes. Genotypes G1/G3/G4/G5/G9-P[8] were correlated strongly to I1-E1 genotypes and G2-P[4]/P[6] were correlated to I2-E2 genotypes. Unusual combinations of genes, such as G3-P[9]-I2-E2, G9-P[9]-I1-E2, and G3-P[9]-I3-E3, were observed in 15 (9.3%) strains. The characterization of multiple genes allows a more complete analysis of the rotavirus isolates and provides evidence of natural reassortment of strains.

Rotavirus genotypes co-circulating in Europe between 2006 and 2009 as determined by EuroRotaNet, a pan-European collaborative strain surveillance network

EuroRotaNet, a laboratory network, was established in order to determine the diversity of co-circulating rotavirus strains in Europe over three or more rotavirus seasons from 2006/2007 and currently includes 16 countries. This report highlights the tremendous diversity of rotavirus strains co-circulating in the European population during three years of surveillance since 2006/2007 and points to the possible origins of these strains including genetic reassortment and interspecies transmission. Furthermore, the ability of the network to identify strains circulating with an incidence of ≥1% allowed the identification of possible emerging strains such as G8 and G12 since the beginning of the study; analysis of recent data indicates their increased incidence. The introduction of universal rotavirus vaccination in at least two of the participating countries, and partial vaccine coverage in some others may provide data on diversity driven by vaccine introduction and possible strain replacement in Europe.

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

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

Diversidade genotípica de rotavírus suínos no Estado de São Paulo

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

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.

Emergence of unusual human rotavirus strains in Salento, Italy, during 2006-2007

BACKGROUND

In recent years, rotavirus genotyping by RT-PCR has provided valuable information about the diversity of rotaviruses (RV) circulating throughout the world.The purpose of the present study was to monitor the prevalence of the different G and P genotypes of rotaviruses circulating in Salento and detect any uncommon or novel types.

METHODS

During the period from January 2006 to December 2007, a total of 243 rotavirus positive stool samples were collected from children with diarrhoea admitted to four Hospitals in the province of Lecce (Copertino, Galatina, Gallipoli and Tricase).All the specimens were tested for RV by real time PCR and genotyped for VP7 (G-type) and VP4 (P-type) gene by reverse transcription (RT) and multiplex PCR using different type specific primers.

RESULTS

In course of this study we identified 4 common G&P combinations viz. G2P[8], G1P[8], G2P[4] and G9P[8] amongst 59.8% of the typeable rotavirus positives.Rotavirus G2P[8] was recognized as the most widespread genotype during the sentinel-based survey in Salento.The detection of other novel and unusual strains, such as G2P[10], G4P[10], G8P[4], G9P[11] and G10P[8] is noteworthy.Furthermore, a significant number of mixed infections were observed during the survey period but G3P[8] rotaviruses were not detected.

CONCLUSION

This study highlights the genetic diversity among rotaviruses isolated from children in Salento and the emergence of some novel strains. Therefore, it is highly essential to continuously monitor for these strains so as to assess the impact of vaccines on RV strains circulating in Salento and understand the effect of strain variation on efficacy of presently available vaccines.

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.

New oligonucleotide primers for P-typing of rotavirus strains: Strategies for typing previously untypeable strains

BACKGROUND

The use of molecular methods for rotavirus characterisation provides increased sensitivity for typing, and allows the identification of putative reassortant strains. However, due to the constant accumulation of point mutations through genetic drift; and to the emergence of novel genotypes; and possibly zoonotic transmission and subsequent reassortment, the reagents and methods used for genotyping require close monitoring and updating.

OBJECTIVES

To design and evaluate a new VP4 consensus oligonucleotide primer pair that provides increased sensitivity and allows typing of strains that were untypeable using available methods.

STUDY DESIGN

A total of 489 rotavirus-positive faecal specimens from studies conducted between 1996 and 2006 were used for the evaluation of the new VP4 primers which was performed in the WHO Rotavirus Collaborating and Reference centres in the US, Australia, South Africa and the UK.

RESULTS

The new primer pair allowed P-typing of rotavirus strains and provided increased sensitivity, allowing typing of a significant number of strains that previously could not be P-typed.

CONCLUSIONS

This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses.

Changing profile of rotavirus in Ireland: predominance of P[8] and emergence of P[6] and P[9] in mixed infections

Six hundred and thirty three fecal specimens were collected from patients under 6 years, suffering from non-bacterial, putative viral gastroenteritis in the south of Ireland, between 2003 and 2006. Following laboratory identification of rotavirus as the aetiological agent in 558 specimens, reverse transcriptase polymerase chain reaction was employed to amplify the VP7 and VP4 gene segments of 249 and 245 samples, respectively. G and P typing was subsequently carried out on these amplicons. G1 (65.1%), and G3 (16.1%) were found to be the most prevalent circulating G types over the course of the study. Both G2 (1.2%) and G9 (3.6%), were also found to be circulating, however, these types were less frequently detected. Mixed G type infections were found to account for 41 samples (14%). P typing was carried out on 245 samples. P[8] was the most commonly detected P type over the course of the study (93.5%). Both P[6] and P[9], which had not previously been detected in the Irish population, were detected during this investigation. P[6] was detected in both single and mixed P type infections, while P[9] was detected as part of mixed infections only. The key findings of this study were the emergence of P[6] and P[9] as epidemiologically important rotavirus strains in the Irish population. The profile of rotavirus is changing continuously in Ireland, and continued surveillance of the circulating strains is needed to detect the appearance of new strains, or new variants which could escape immune protection induced by an outdated vaccine.

Genetic diversity of the VP4 and VP7 genes affects the genotyping of rotaviruses: analysis of Paraguayan strains

The introduction of different multiplex RT-PCR strategies for the characterization of field rotavirus strains has led to improvements of surveillance systems worldwide. Nevertheless, the failure or incorrect characterization of rotavirus strains by these PCR strategies, mainly due to accumulation of point mutations in the VP4 and VP7 genes, has been reported. In this work, sequence analyses of the VP4 and VP7 genes from Paraguayan G1P[8] and G4P[8] strains revealed that the high degree of similarity with the primers pNCDV and ET10 could lead to the incorrect characterization of these strains as P[1] and G10 types. Moreover, the nucleotide diversity of the VP4 gene at the 1T-1 primer binding site could be one, although not the only, reason of the failure of the P[8] typing. Therefore, the typing methods utilized by surveillance programs should be constantly evaluated and sequencing of atypical strains should become a current practice in order to confirm their real nature.

Sequence analysis of the VP7 gene of human rotavirus G1 isolated in Japan, China, Thailand, and Vietnam in the context of changing distribution of rotavirus G-types

Over the last decade, rotavirus G1 has represented the most common genotype worldwide. Since 2000, the prevalence of rotavirus G1 has decreased in some countries such as Japan and China. To monitor the trend of the VP7 encoding gene of rotavirus G1, we performed a sequence analysis of 74 G1 rotavirus strains isolated in Japan, China, Thailand, and Vietnam during the period from 2002 to 2005. The phylogenetic tree showed that all of the studied G1 strains from the four countries clustered into lineage III, the same as the majority of the G1 strains isolated in China and Japan in 1990 and 1991. Examination of the deduced amino acid sequences of the G1 strains from China and Japan revealed an amino acid substitution at position 91 (Asn instead of Thr) in antigenic region A when compared to the G1 strains isolated in China and Japan in 1990, 1991, and global reference strains. For the G1 strains from Thailand and Vietnam, there were three amino acid substitutions, not belonging to any antigenic regions. The study showed that there have been no considerable changes of human rotavirus G1 isolated in Japan, China, Thailand, and Vietnam. Further studies need to be carried out for a better understanding of why such changes in the prevalence of rotavirus G1 occur in these countries.

Genetic distribution of group A human rotavirus types isolated in Gyunggi province of Korea, 1999–2002

BACKGROUND

Human rotavirus genotypes G1-G4 and G9 are the major etiological agents of infantile gastroenteritis. G1 was the most prevalent in Korea during the 10-year period prior to 1997. However, between 1998 and 1999, G4 was the predominant type in Korea, as it was in other Asian countries.

OBJECTIVES

The circulating pattern and genetic variability of group A human rotavirus in Gyunggi, Korea, 1999-2002, were examined in 189 stool specimens.

STUDY DESIGN

Stool samples were collected from children with diarrhea, and group A human rotavirus type was determined using multiplex RT-PCR in those specimens found to be positive for rotavirus by ELISA. Each genotype was sequenced, and phylogenetic analysis was performed on the sequences.

RESULT

We found significant variability from year to year in the prevalence of different G and P types of rotavirus. We also found relatively high prevalence rates for types normally considered to be uncommon. Furthermore, we found that the most prevalent combination of G and P types changed from year to year. Although the combination of G and P types changed every year, the sequence of G genotypes showed a high level of similarity (>97%) compared to those of strains from other Asian countries.

CONCLUSION

We report the types of rotavirus circulating in Gyunggi province, Korea from 1999 to 2002. This information on rotavirus diversity has important implications for rotavirus vaccine efficacy and future vaccine development.

Anticipating rotavirus vaccines in Brazil: Detection and molecular characterization of emerging rotavirus serotypes G8 and G9 among children with diarrhoea in Recife, Brazil

In 2006, Brazil will initiate universal immunization of its 4-million infants with a live attenuated serotype G1P[8] human rotavirus vaccine. In anticipation of the national immunization program, this study was undertaken to characterize rotavirus strains circulating among children in Recife, one of the largest cities in the northeast region of Brazil. Group A rotaviruses were detected in 102 (35%) of 290 faecal specimens collected from children under 5 years of age who presented with acute diarrhoea during a 1-year period between May 2004 and April 2005. In addition to the globally common G1P[8] serotype that accounted for 49% of strains, emerging rotavirus serotypes G8P[6] and G9P[8] represented 2% and 29% of strains, respectively. Following cell culture adaptation, RNA-RNA hybridization demonstrated that two Brazilian G8P[6] rotavirus strains shared a high level of genomic RNA homology with Malawian G8P[6] strains, and a Brazilian G9P[8] strain was related most closely to a G9P[8] strain from India. The results suggest that certain rotavirus strains have a much wider global circulation than generally appreciated. Continued global spread of such strains might challenge the efficacy of current rotavirus vaccines.

Brazilian P[8],G1, P[8],G5, P[8],G9, and P[4],G2 rotavirus strains: Nucleotide sequence and phylogenetic analysis

Rotavirus epidemiological surveys with molecular analysis of strains are required for gastroenteritis control and prevention. Twenty-nine human rotavirus strains detected in Rio de Janeiro, Brazil, from 1986 to 2004 were characterized as P[8],G1, P[8],G5, P[8],G9, and P[4],G2 genotypes. The VP7 genes were sequenced and phylogenetic analysis was performed. Strains of genotype G1 revealed two distinct lineages, G1-3 and G1-4; strains of genotype G2 grouped in lineage G2-1; G5 strains clustered with other Brazilians G5 strains and G9 strains were closely related to each other in lineage G9-3, distinct from the original G9 strains detected in 1980s. The VP4 genes were analyzed and P[8] strains fell into two major genetic lineages, P[8]-2 and P[8]-3. Our findings document an intragenotype diversity represented by lineages and sublineages within rotavirus circulating in Rio de Janeiro from 1986 to 2004, before application of a vaccine (Rotarix) in Brazil. This report emphasizes the importance of continuing monitor genotypes to verify if uncommon strains or newly strains are emerging to be specifically addressed in future vaccine trials.

Amino acid substitutions in the VP7 protein of human rotavirus G3 isolated in China, Russia, Thailand, and Vietnam during 2001–2004

The distribution of rotavirus G-types in the world appears to be changing, especially with the emergence of G3 and G9 in many countries. Sequence analysis of the VP7 gene was performed on the 27 human G3 rotavirus strains isolated in China, Russia, Thailand, and Vietnam during 2001-2004. All the strains studied were clustered into the same branch of the phylogenetic tree. The comparison of the G3 deduced amino acid sequences between the studied Chinese strains and the strains circulating in China during 1986-1992 showed a wide range of amino acid substitutions (up to 13 amino acids in the VP7 antigenic regions). The two considerable changes both from aspartic acid to asparagine were located at positions 96 in antigenic region A and 213 in antigenic region C. Those amino acid substitutions of the Chinese G3 strains might involve in the emergence of G3 rotavirus in China during 2001-2003.

Diversity in Indian equine rotaviruses: identification of genotype G10,P6[1] and G1 strains and a new VP7 genotype (G16) strain in specimens from diarrheic foals in India

Rotaviruses causing severe diarrhea in foals in two organized farms in northern India, during the period from 2003 to 2005, were characterized by electropherotyping, serotyping, and sequence analysis of the genes encoding the outer capsid proteins. Of 137 specimens, 47 (34.31%) were positive for rotavirus and exhibited at least five different electropherotypes (E), E1 to E5. Strains belonging to different electropherotypes exhibited either a different serotype/genotype specificity or a lack of reactivity to typing monoclonal antibodies (MAbs) used in this study. Strains belonging to E1, E2, and E5 exhibited genotype G10,P6[1], G3, and G1 specificities and accounted for 19.0, 42.9, and 9.5% of the isolates, respectively. Though they possessed G10-type VP7, the E1 strains exhibited high reactivity with the G6-specific MAb, suggesting that the uncommon combination of the outer capsid proteins altered the specificity of the conformation-dependent antigenic epitopes on VP7. E3 and E4 strains accounted for 28.6% of the isolates and were untypeable. Sequence analysis of VP7 from E4 strains (Erv92 and Erv99) revealed that they represent a new VP7 genotype, G16. The detection of unexpected bovine rotavirus-derived G10,P6[1] reassortants, G1 serotype strains, and a new genotype (G16) strain in two distant farms reveals an interesting epidemiological situation and diversity of equine rotaviruses in India.