Molecular characterization of serotype G9 rotavirus strains from a global collection

Molecular characterization of porcine rotavirus A from India revealing zooanthroponotic transmission

Rotaviruses A (RVA) are leading causes of diarrhea and dehydration in piglets and imply great economic loss to the pig farming community. In this study, the porcine RVA genotypes circulating in western and northern parts of India were determined by screening 214 fecal samples from diarrheic (n = 144) and non-diarrheic (n = 70) pigs. Subsequently, the structural (VP4 and VP7) and nonstructural (NSP3, and NSP4) genes were amplified, sequenced, and genetically characterized. The RVA positivity percentage was 7.94% (17/214) by RNA-PAGE and 10.28% (22/214) by RT-PCR. Higher RVA positivity was observed in samples from Uttar Pradesh (24.07%) followed by Maharashtra (6.77%) and Goa (2.38%). The sequence and automated genotyping software analysis confirmed the circulation of G4P[6] and G9P[13] RVA strains in porcine population. To note, the sequence similarity of the VP7 gene of Porcine/INDIA/RVA/PK-13 IVRI/Maharashtra/G4 and Porcine/INDIA/RVA/P-8/IVRI/U.P./G9 strain showed a relationship of 96.83 and 98.89% at the nucleotide level with human RVA strains indicating inter-species transmission. Additionally, the NSP3 (T1) and NSP4 (E1) genes (genotypes) also showed genetic relatedness with human RVA strains. Overall, the nucleotide sequences of VP7, NSP3, and NSP4 genes of porcine RVA indicate zooanthroponotic transmission. Further, we report the detection of G9P[13] RVA strain in porcine for the first time from India.HIGHLIGHTSRVA positivity was 7.94% (17/214) by RNA-PAGE and 10.28% (22/214) by RT-PCRThe RVA strain G9P[13] reported for the first time in Indian pigletsVP7, NSP3 and NSP4 genes analysis of porcine RVA showed genetic relatedness with human strains indicating evidence of zooanthroponotic transmission.

Reverse Genetics Approach for Developing Rotavirus Vaccine Candidates Carrying VP4 and VP7 Genes Cloned from Clinical Isolates of Human Rotavirus

Species A rotaviruses (RVs) are a leading cause of severe acute gastroenteritis in infants and children younger than 5 years. Currently available RV vaccines were adapted from wild-type RV strains by serial passage of cultured cells or by reassortment between human and animal RV strains. These traditional methods require large-scale screening and genotyping to obtain vaccine candidates. Reverse genetics is a tractable, rapid, and reproducible approach to generating recombinant RV vaccine candidates carrying any VP4 and VP7 genes that provide selected antigenicity. Here, we developed a vaccine platform by generating recombinant RVs carrying VP4 (P[4] and P[8]), VP7 (G1, G2, G3, G8, and G9), and/or VP6 genes cloned from human RV clinical samples using the simian RV SA11 strain (G3P[2]) as a backbone. Neutralization assays using monoclonal antibodies and murine antisera revealed that recombinant VP4 and VP7 monoreassortant viruses exhibited altered antigenicity. However, replication of VP4 monoreassortant viruses was severely impaired. Generation of recombinant RVs harboring a chimeric VP4 protein for SA11 and human RV gene components revealed that the VP8* fragment was responsible for efficient infectivity of recombinant RVs. Although this system must be improved because the yield of vaccine viruses directly affects vaccine manufacturing costs, reverse genetics requires less time than traditional methods and enables rapid production of safe and effective vaccine candidates.IMPORTANCE Although vaccines have reduced global RV-associated hospitalization and mortality over the past decade, the multisegmented genome of RVs allows reassortment of VP4 and VP7 genes from different RV species and strains. The evolutionary dynamics of novel RV genotypes and their constellations have led to great genomic and antigenic diversity. The reverse genetics system is a powerful tool for manipulating RV genes, thereby controlling viral antigenicity, growth capacity, and pathogenicity. Here, we generated recombinant simian RVs (strain SA11) carrying heterologous VP4 and VP7 genes cloned from clinical isolates and showed that VP4- or VP7-substituted chimeric viruses can be used for antigenic characterization of RV outer capsid proteins and as improved seed viruses for vaccine production.

Characterization of a G9 group A rotavirus reassortant strain detected in Jinzhou, China, in 2018-2019

A novel rotavirus A (RVA) strain (JZ) was detected in RVA-positive stool specimens from three pediatric patients in Jinzhou, Liaoning Province, in 2018-2019. The electrophoresis pattern of the JZ strain showed a long electropherotype. The genomic constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 was detected, suggesting that a new inter-genogroup reassortment had occurred. Whole-genome sequencing showed that the JZ isolates were identical to each other. Phylogenetic analysis revealed that VP7 and VP4 clustered in lineages G9-VI and P[8]-3, respectively. JZ strain-specific amino acid substitutions were detected in VP7, VP4 and NSP4. This study provides information on the epidemiology and characteristics of G9 strains circulating in China.

Molecular characterization of emerging G9P[4] rotavirus strains possessing a rare E6 NSP4 or T1 NSP3 genotype on a genogroup-2 backbone using a refined classification framework

Rotavirus infections associated with unusual strains are an emerging concern in rotavirus vaccination programmes. Recently, an increase in circulation of unusual G9P[4] strains was reported from different regions of India, placing this genotype in third position, after G1P[8] and G2P[4], of the most common rotavirus strains. The aim of the present study was to analyse the complete genomic constellation of three G9P[4] strains (RV09, RV10 and RV11), determine their genetic relatedness to other genogroup-2 strains and understand the evolution of a rare E6 and other NSP4 genotypes. All strains revealed the presence of a genogroup-2 backbone, with RV09 constituting the NSP3 T1 genotype and RV10 and RV11 bearing the NSP4 E6 genotype. A refined criterion adopted to classify the nine internal gene segments of G2P[4] and non-G2P[4] strains with the genogroup-2 backbone into lineages and sub-lineages indicated divergence of >8 % (except NSP1: >5.5 %) for lineages and >3 % for sub-lineages. The VP1 and/or VP3 genes of study strains showed close relationships with animal-like human rotaviruses. The estimated evolutionary rate for the NSP4 E6 genotype was marginally higher (3.78×10-3 substitutions per site per year) than that of genotypes E1 (2.6×10-3 substitutions per site per year) and E2 (3.06×10-3 substitutions per site per year), suggesting a step towards adaptation of E6 on a genogroup-2 backbone. The time and origin of the most recent common ancestor of E6 genotype were estimated to be 1981 and South Asia, respectively. Full-genome and evolutionary analyses performed in this study for G9P[4] strains will help better understand the extent of gene reassortment and origin in unusual rotavirus strains that may remain viable and cause infections in humans.

Increased detection of G3P[9] and G6P[9] rotavirus strains in hospitalized children with acute diarrhea in Bulgaria

Rotavirus severe disease in children is now vaccine-preventable and the roll-out of vaccination programs globally is expected to make a significant impact in the reduction of morbidity and mortality in children <5 years of age. Rotavirus is also a pathogen of other mammals and birds, and its segmented RNA genome can lead to the emergence of new or unusual strains in human population via interspecies transmission and reassortment events. Despite the efficacy and impact of rotavirus vaccine in preventing severe diarrhea, the correlates of protection remain largely unknown. Therefore, rotavirus strain surveillance before, during and after the introduction of immunization programs remains a crucial for monitoring rotavirus vaccine efficacy and impact. In this context, molecular characterization of 1323 Bulgarian rotavirus strains collected between June 2010 and May 2013 was performed. A total of 17 strains of interest were analyzed by partial sequence analysis. Twelve strains were characterized as G3P[9] and G6P[9] of potential animal origin. Phylogenetic analysis and comparisons with the same specificity strains detected sporadically between 2006 and 2010 revealed the constant circulation of these unusual human strains in Bulgaria, although in low prevalence, and their increased potential for person-to-person spread.

Genetic diversity of porcine group A rotavirus strains in the UK

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This is the first study of rotavirus genotypes circulating in UK pigs.

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Rotavirus transmission between pigs and humans is not thought to be common in the UK.

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Human rotavirus genotype P[8] found in a UK pig.

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The uncommon rotavirus genotype P[32] is widespread in UK pig herds.

Rotavirus is endemic in pig farms where it causes a loss in production. This study is the first to characterise porcine rotavirus circulating in UK pigs. Samples from diarrheic pigs with rotavirus enteritis obtained between 2010 and 2012 were genotyped in order to determine the diversity of group A rotavirus (GARV) in UK pigs. A wide range of rotavirus genotypes were identified in UK pigs: six G types (VP7); G2, G3, G4, G5, G9 and G11 and six P types (VP4); P[6], P[7], P[8], P[13], P[23], and P[32]. With the exception of a single P[8] isolate, there was less than 95% nucleotide identity between sequences from this study and any available rotavirus sequences.

The G9 and P[6] genotypes are capable of infecting both humans and pigs, but showed no species cross-over within the UK as they were shown to be genetically distinct, which suggested zoonotic transmission is rare within the UK. We identified the P[8] genotype in one isolate, this genotype is almost exclusively found in humans. The P[8] was linked to a human Irish rotavirus isolate in the same year. The discovery of human genotype P[8] rotavirus in a UK pig confirms this common human genotype can infect pigs and also highlights the necessity of surveillance of porcine rotavirus genotypes to safeguard human as well as porcine health.

Prevalence of human rotavirus genotypes in Wuhan, China, during 2008-2011: changing trend of predominant genotypes and emergence of strains with the P[8]b subtype of the VP4 gene

Hospital-based surveillance of rotavirus genotypes was conducted in Wuhan, China, between March 2008 and May 2011. The detection rates of group A rotavirus were 24.6% (458/1859) and 12.1% (96/795) in children and adults, respectively, with diarrhea. Among the 554 positive specimens, the most frequent genotype was G3P[8] (57.9%), followed by G1P[8] (29.4%). Compared with previous studies in Wuhan (2000-2008), the relative frequency of G3P[8] has been decreasing year by year, while the predominant genotype G3 shifted to G1 in 2011. In the present study, a rare P[8]b subtype of the VP4 gene (OP354-like P[8]) was identified in nine strains. Full-length sequences of VP7, VP4, VP6 and NSP4 genes of two G9P[8]b strains (RVA/Human-wt/CHN/E1545/2009/G9P[8]b and RVA/Human-wt/CHN/Z1108/2008/G9P[8]b) were determined for phylogenetic analysis. The four genes of these strains were closely related to one another, and the G9-VP7 genes of these strains belonged to lineage III, which contains globally spreading G9 rotaviruses. The full-length sequence of VP4 gene segments of the P[8]b strains in Wuhan clustered with those of P[8]b strains in Vietnam, Russia and Belgium, while they were distinct from those of the OP354 strain from Malawi and Bangladeshi strains. The VP6 and NSP4 genes of two P[8]b strains belonged to the I1 and E1 genotype, respectively, and clustered with those of strains belonging to Wa-like human rotaviruses from various Asian countries. These findings indicate the changing epidemiologic trend of rotavirus genotypes in Wuhan, i.e., the shift of the predominant type from G3 to G1 and the emergence of P[8]b strains genetically related to those distributed in other Asian countries.

Whole-genomic analysis of rotavirus strains: current status and future prospects

Studies on genetic diversity of rotaviruses have been primarily based on the genes encoding the antigenically significant VP7 and VP4 proteins. Since the rotavirus genome has 11 segments of RNA that are vulnerable to reassortment events, analyses of the VP7 and VP4 genes may not be sufficient to obtain conclusive data on the overall genetic diversity, or true origin of strains. In the last few years following the advent of the whole-genome-based genotype classification system, the whole genomes of at least 167 human group A rotavirus strains have been analyzed, providing a plethora of new and important information on the complex origin of strains, inter- and intra-genogroup reassortment events, animal–human reassortment events, zoonosis, and genetic linkages involving different group A rotavirus gene segments. In addition, the whole genomes of a limited number of human group B, C and novel group rotavirus strains have been analyzed. This article briefly reviews the available data on whole-genomic analysis of human rotavirus strains. The significance and future prospects of whole-genome-based studies are also discussed.

Emergence of G9 as a predominant genotype of human rotaviruses in Cuba

To study human rotaviruses in Cuban children up to 5 years old with acute diarrhea, a total of 64 faecal samples from two pediatric hospitals between 2006 and 2008 were analyzed. Thirty-nine samples (60.9%) were found positive for rotaviruses by enzyme-linked immunosorbent assay (ELISA) and polyacrylamide gel electrophoresis (PAGE), while four (6.2%) exhibited discordant results (ELISA positives/PAGE negatives). All the positive samples were genotyped by a reverse transcription-polymerase chain reaction (RT-PCR). The most prevalent G and P types were G1 (60.5%) and P[8] (90.6%), respectively. Among the rotaviruses detected, two long RNA patterns were identified by PAGE (L/A and L/B). The predominant genotype in 2006 and 2007 was G1/P[8] with detection rates 71.4% and 80%, respectively. In contrast, G9/P[8] was found at the highest rate (78.5%) in 2008. The phylogenetic analysis of VP7 genes of the ten representative strains indicated that Cuban G1/P[8] rotaviruses were close to those reported in the Americas, and G9/P[8] rotaviruses were located in the lineage of the emerging G9 strains spreading worldwide. This is the first molecular epidemiologic study of rotaviruses in Cuba, highlighting the current increase of the G9 rotavirus which has been recognized globally as an emerging genotype. The study reinforces the need for a systematic surveillance of the molecular epidemiology of rotaviruses.

Emergence of human rotavirus genotype G9 in metropolitan Detroit between 2007 and 2009

Between January 2007 and April 2009, rotavirus (RV)-positive stool samples from 238 children with acute gastroenteritis, seen at Children's Hospital of Michigan in Detroit, USA, were collected and RV genotyping was performed. G and P genotypes were determined by RT-PCR and nucleotide sequencing was conducted on selected G9 and P[6] strains. Correlation between the severity of gastroenteritis episode and the infecting G genotype was done using a 14-point scoring system. The predominant G genotype was G9 (39.5 %), followed by G1 (35.3 %) and G4 (15.5 %), while P[8] was the most prevalent P genotype (66.5 %), followed by P[4] (21.9 %) and P[6] (11.2 %). The gene combinations G1P[8] and G9P[8] were the most prevalent (21.4 % and 20.6 %, respectively), followed by G4P[8] (13 %) and G9P[6] (8.8 %). Immunization data showed that only 17/238 (7.1 %) children received ≥one dose of RV vaccine (the pentavalent vaccine RotaTeq or the monovalent vaccine Rotarix) and that 10/17 were infected with G4P[8] strains. Severity of RV gastroenteritis episodes was not related to the infecting G genotype. Our results suggest a high proportion of genotype G9 strains in combination with P[8], P[6] and P[4] specificity circulating in the metropolitan Detroit area. While the protective efficacy of the RV vaccines has been demonstrated against G9P[8] strains, the level of cross-protection offered by the vaccines against G9 strains with P[6] and P[4] genotypes in the Detroit paediatric population remains to be determined.

Molecular epidemiology of group A rotavirus in Buenos Aires, Argentina 2004-2007: reemergence of G2P[4] and emergence of G9P[8] strains

Detection and characterization of group A rotavirus in Buenos Aires, Argentina, was conducted on 710 fecal samples from children 0-15 years old collected between 2004 and 2007. Rotavirus was detected in 140 (19.7%) samples with G9P[8] (30.0%) and G2P[4] (21.4%) as the most common genotypes. Mixed (G and/or P) infections accounted for 17.9% of the samples and the emerging G12 strain was detected during 2004 (3.5%) and 2007 (2.5%). Genotype G2 was the most prevalent during 2004 (43.9%) and 2007 (57.5%) and G9 during 2005 (58.0%) and 2006 (61.5%). Analysis of genotype prevalences from studies performed since 1996 in the same area showed striking natural fluctuations in G and P genotype frequencies. In particular, G2P[4] strains disappeared after 1999 and reemerged in 2004 to become the predominant strain by 2007 with a concomitant major decrease in G1P[8] prevalence. The VP7 genes from Argentinian G9 and G2 strains were sequenced and phylogenetic analysis was conducted in order to compare with sequences from strains isolated in regional countries reported previously. Several changes in the deduced amino acid sequence in antigenic regions of the VP7 protein from Argentinian and Brazilian strains were identified compared to vaccine strains. Overall, this study revealed relationships in the circulation of rotavirus strains in South American countries and major replacements in dominant genotypes, including the virtual disappearance of G1P[8] strains in a non-vaccinated population. High numbers of mixed infections speeding up evolution, circulation of rare serotypes, and antigenic drift could, eventually, become challenges for new vaccines.

History of rotavirus research in children in Malawi: the pursuit of a killer

Rotavirus gastroenteritis is a major health problem among Malawian children. Studies spanning 20 years have described the importance, epidemiology and viral characteristics of rotavirus infections in the country. Despite a wide diversity of circulating rotavirus strains causing severe disease in young infants, a clinical trial of a human rotavirus vaccine clearly demonstrated the potential for rotavirus vaccination to greatly reduce the morbidity and mortality due to rotavirus diarrhoea in Malawi. This new enteric vaccine initiative represents a major opportunity to improve the health and survival of Malawian children.

Detection and genotyping of Korean porcine rotaviruses

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

[Evolution of group A Rotavirus strains circulating in Tunisia over a 3-year period (2005-2007)]

BACKGROUND

Rotaviruses are the most frequent agents associated with diarrhoea in children worldwide. Analysis of mobility of the 11 segments of genomic RNA by polyacrylamide gel electrophoresis (PAGE) yields a pattern which is characteristic for a particular rotavirus isolate. The group A rotaviruses can be further characterized by analysis of VP7 and VP4 genes specificities, responsible for rotavirus classification into G and P genotypes, respectively. The aim of the present study was to determine the evolution of group A Rotavirus strains circulating in Tunisia over a 3-year period (2005-2007).

MATERIAL AND METHODS

A total of 1503 stool samples collected from children less than five years old, consulting or hospitalised in Tunisia for diarrhoea between 2005 and 2007, were screened for the presence of group A Rotaviruses. Rotavirus-positive specimens were further analyzed by PAGE and G/P-genotyped by multiplex semi-nested RT-PCR.

RESULTS

Rotaviruses were detected in 323 stool samples over 1503 (21 %). Long electropherotypes predominated in Tunisia during the whole period of study (N=158 vs N=82 short electropherotypes). VP7 genotyping showed the cocirculation of five different genotypes: G1, G2, G3, G4 and G9. VP4 typing detected four different P-genotypes: P[8], P[4], P[6] and P[11]. Rotavirus strains with G3P[8] specificity were predominating in Tunisia in 2005 and 2006, replaced by G2P[4] strains in 2007.

[Post vaccination rotavirus surveillance in Hungary, in 2007]

Vaccination is the main strategy to control severe dehydrating gastroenteritis caused by rotaviruses in early childhood. The availability of new generation rotavirus vaccines has led to an intensification of strain surveillance worldwide, in part, to gauge the impact of the possible vaccine-driven immune selection of wild-type rotavirus strains. In the present study, authors describe the strain prevalence data obtained in 2007, with the involvement of different regions of Hungary. Genomic RNA was extracted from rotavirus-positive stool samples collected mainly from children and then subjected to genotyping using multiplex RT-PCR assay. Type-specific primers targeted G1 to G4, G6, G8 to G10, and G12 VP7 specificities, and P[4], P[6], and P[8] to P[11] VP4 specificities were used. Out of 489 rotavirus-positive specimens, collected from 482 patients, 466 and 474 were successfully G and P typed, respectively, and both G and P type specificities could be assigned for 457 strains. Prevalence data showed the predominance of G4P[8] (31.5%) strains, followed by G1P[8] (28.3%), G2P[4] (19.3%), and G9P[8] (10.2%). Minority strains were G1P[4] (0.4%), G2P[8] (1.3%), G3P[9] (0.2%), G4P[6] (0.7%), G6P[9] (0.4%), G8P[8] (0.2%), G9P[4] (0.2%), G9P[6] (0.8%), and G12P[8] (0.4%). Mixed infections were found in 1.2% of the samples, while 4.9% remained partially or fully non-typified. Our data indicate that the antigen specificities of medically important rotavirus strains identified in this 1-year study are well represented in the vaccines available in the pharmaceutical private market in Hungary. Depending on the vaccination coverage achievable in the forthcoming years, the post-vaccination rotavirus strain surveillance may allow us to gain comprehensive information on the impact of rotavirus vaccines on the prevalence of circulating rotavirus strains.

Characterization ofVP7andVP4genes of rotavirus strains: 1990–1994 and 2000–2002

A total of 90 rotavirus-positive faecal specimens collected from patients hospitalized with diarrhoea in 1990–1994 (n=77) and 2000–2002 (n=13) were investigated for VP7 and VP4 genotypes. The specimens included 21 typable and 69 non-reactive or multireactive rotavirus strains as monitored by monoclonal antibody-based serotyping ELISA. Genotyping was carried out by multiplex PCR/sequencing using primers specific for bothVP7andVP4genes. The contribution of common genotypes (G1P[8], G2P[4], G3P[8], G4P[8]) in causing rotavirus diarrhoea was 79·2% and 92·3% in the years 1990–1994 and 2000–2002, respectively, while G9P[8] infections were detected at lower levels (1·3% and 7·7%) at both time-points. There was a predominance of G1P[8] in 1990–1994 and of G2P[4] in 2000–2002. The detection of unusual rotavirus strains (G1P[6], G1P[4], G1P[19], G2P[8], G3P[4], G4P[6]) in 19·5% of the patients indicated a significant contribution of reassortants in causing diarrhoea in western India.

Phylogeny of G9 rotavirus genotype: a possible explanation of its origin and evolution

BACKGROUND

G9 rotavirus genotype was isolated in the 1980s and re-emerged without a clear explanation in the mid-1990s as one of the most frequently occurring genotypes with distinct genetic and molecular characteristics.

OBJECTIVES

To study the G9 genotype sequence polymorphisms in Spain and compare them with the human and porcine G9 VP7 genes from the rest of the world. Complete phylogenetic analyses have been done to better characterize G9 genotypes, their relationships and evolution.

STUDY DESIGN

Twelve G9 VP7 genes from Spanish patients were sequenced and compared with 240 G genotype sequences. Nucleotide and amino acid sequence similarity percentages and neighbour-joining dendrograms were used to establish a new phylogenetic analysis.

RESULTS

Eight of the 12 Spanish sequenced samples had different nucleotide translated region sequences, which yielded only five different proteins. New nucleotide and amino acid sequence comparisons were made that differed from previously described results.

CONCLUSIONS

Spanish G9 genotype sequences have similar structure of those belonging to lineage III as the majority of the G9 sequences and share amino acid motifs with other sequences. The phylogenetic analyses of G9 genotypes confirmed the existence of 6 lineages, but did not confirm the 11 sublineages previously reported.

Group A human rotavirus genomics: evidence that gene constellations are influenced by viral protein interactions

Group A human rotaviruses (HRVs) are the major cause of severe viral gastroenteritis in infants and young children. To gain insight into the level of genetic variation among HRVs, we determined the genome sequences for 10 strains belonging to different VP7 serotypes (G types). The HRVs chosen for this study, D, DS-1, P, ST3, IAL28, Se584, 69M, WI61, A64, and L26, were isolated from infected persons and adapted to cell culture to use as serotype references. Our sequencing results revealed that most of the individual proteins from each HRV belong to one of three genotypes (1, 2, or 3) based on their similarities to proteins of genogroup strains (Wa, DS-1, or AU-1, respectively). Strains D, P, ST3, IAL28, and WI61 encode genotype 1 (Wa-like) proteins, whereas strains DS-1 and 69M encode genotype 2 (DS-1-like) proteins. Of the 10 HRVs sequenced, 3 of them (Se584, A64, and L26) encode proteins belonging to more than one genotype, indicating that they are intergenogroup reassortants. We used amino acid sequence alignments to identify residues that distinguish proteins belonging to HRV genotype 1, 2, or 3. These genotype-specific changes cluster in definitive regions within each viral protein, many of which are sites of known protein-protein interactions. For the intermediate viral capsid protein (VP6), the changes map onto the atomic structure at the VP2-VP6, VP4-VP6, and VP7-VP6 interfaces. The results of this study provide evidence that group A HRV gene constellations exist and may be influenced by interactions among viral proteins during replication.

The VP7 genes of two G9 rotaviruses isolated in 1980 from diarrheal stool samples collected in Washington, DC, are unique molecularly and serotypically

In a retrospective study of archival diarrheal stool samples collected from 1974 to 1991 at Children's Hospital National Medical Center, Washington, DC, we detected three genotype G9P[8] viruses in specimens collected in 1980, which represented the earliest human G9 viruses ever isolated. The VP7 genes of two culture-adapted 1980 G9 viruses were phylogenetically related closely to the lineage 2 G9 virus VP7 gene. Unexpectedly, however, the VP7s of the 1980 G9 viruses were more closely related serotypically to lineage 3 VP7s than to lineage 2 VP7, which may be supported by amino acid sequence analyses of the VP7 proteins.

Diversity of group A rotavirus strains circulating in Paraguay from 2002 to 2005: Detection of an atypical G1 in South America

BACKGROUND

Group A rotaviruses are the main cause of severe gastroenteritis in children worldwide.

OBJECTIVES

To survey human rotavirus strains circulating in Paraguay.

STUDY DESIGN

One hundred ninety-six rotavirus-positive fecal samples collected from children up to 5 years old, from 2002 to 2005, were characterized.

RESULTS

The most common G genotype detected was G9 (36.2%), followed by G1 (34.2%), G2 (11.7%) and G4 (8.7%). Changes in the G genotype frequency were observed from year to year. The G4 genotype was predominant in 2002; G1 in 2003; and G9 from 2004 to 2005. Sequence and phylogenetic analysis of the VP7 gene from Paraguayan G1 strains suggested that the high frequency of G1 in 2003 could be due to the introduction of an atypical sub-lineage. In addition, there were amino acid changes in the variable/antigenic regions of the VP7 gene from G4 and G9 strains detected in different years.

CONCLUSIONS

This study further indicates that antigenic pressure can drive the evolution of rotaviruses, and also suggests that a vaccine that protects against the most prevalent strains and its variants, will be necessary to elicit a protective immune response against the range of rotavirus types currently circulating in Paraguay.

Characterization of inter-genogroup reassortant rotavirus strains detected in hospitalized children in Italy

Analysis of archival stool collections provides an invaluable source of virus strains and genetic material that may be exploited for molecular, epidemiological, and biological studies. The aim of this study was the molecular characterization of unusual human rotavirus (HRV) strains displaying atypical combinations of electropherotype (e-type) and VP4 and/or VP7 genotypes. Analysis of a panel of archival stools collected in northern Italy revealed continual circulation of P[8]G1 HRVs during 1987-1990 and the onset of P[6] + P[8]G1 strains after 1989. Interestingly, nine G1 strains, associated with either P[8], P[4] + P[8], P[6] + P[8], or untypeable VP4 genes, and two P[4]G1 + G2 strains, displayed short RNA e-type. The genetic constellation of the unusual strains was investigated by analysis of the VP4, VP6, VP7, and NSP4 genes. All the G1 strains with short e-type were subgroup (SG)II or SGI + SGII, and possessed a NSP4 of genogroup B or A + B. Conversely, the P[4]G1 + G2 strains were SGI and possessed a genogroup A NSP4. Sequence analysis of the VP7 and VP4 genes revealed that the unusual P[8]G1 and P[4]G1 + G2 viruses emerged by reassortment of strains circulating locally, rather than by introduction of new strains.

Group A rotavirus strains circulating in the eastern center of Tunisia during a ten-year period (1995-2004)

An epidemiological survey investigating rotavirus infections in children was undertaken in the Eastern Center of Tunisia between January 1995 and December 2004. A total of 982 faecal specimens collected from children less than 5 years in age were screened by enzyme-linked immunosorbent assay (ELISA) or latex agglutination assay for the presence of group A rotavirus antigen. Rotavirus-positive samples were used for G and P typing by multiplex semi-nested reverse transcription-PCR. Rotaviruses were detected in 22% (n = 220) of stools. Of these, 164 were typed for VP7: G genotypes found were G1 (59%), G2 (2%), G3 (9%), G4 (10%), G8 (1%), and G9 (1%). Sixteen specimens (9%) showed mixed G profiles. A total of 119 specimens were typed for VP4. P genotypes detected were P[8] (32%), P[6] (15%), and P[4] (13%). Mixed P profiles were also detected (6%). Although the distribution of the detected genotypes appeared to change annually, G1P[8] rotavirus strains always predominated during the 10-year period of study. This is the first report of rotaviruses in Tunisia with unconventional VP7 serotypes such as G8 and G9, highlighting the need for continual surveillance of emerging strains in Northern Africa. Indeed, the new commercial vaccines only contain the VP7 genes that dictate G1 or G1 to G4 specificities. These vaccines may protect less well against unusual strains circulating in countries planning to implement a rotavirus vaccine strategy.

Detection and molecular characterization of human group C rotaviruses in Okayama Prefecture, Japan, between 1986 and 2005

A survey of human group C rotaviruses (CHRVs) was conducted in Okayama Prefecture, Japan, over a period of 19 years between 1986 and 2005. The presence of CHRVs was screened by enzyme-linked immunosorbent assay using CHRV-specific monoclonal antibodies and confirmed by reverse transcription-PCR. Of the 3,722 fecal specimens from sporadic cases of gastroenteritis, 44 specimens (1.2%) were positive for CHRV. The CHRV isolates were detected periodically but continuously, and the rates of positivity changed from one rotavirus season to the next. Moreover, the isolates were mainly detected in April and May, and the mean age of the patients infected with CHRV was 5.27 years. The genome electropherotypes (E types) of the isolates were classified into three patterns, and the dominant pattern changed from year to year. Nucleotide sequences of the VP7 and VP4 genes of 16 strains, which were representatives of 70 isolates from sporadic cases and outbreaks, were determined and analyzed. Although the VP7 and VP4 genes of the strains were closely related to each other, a phylogenetic analysis suggested that each of the VP7 and VP4 genes of the strains were grouped into three genetic lineages. Moreover, the strains could be divided into five types based on the combination of the E type and the genetic lineages of the VP7 and VP4 genes. These results indicate that CHRVs generally exist in Okayama Prefecture and that CHRVs with various genomic backgrounds prevailed in a limited area.

Detection of human rotavirus G9P[8] strains circulating in Argentina: phylogenetic analysis of VP7 and NSP4 genes

During the surveillance of rotavirus strains that were circulating in Argentinean children from 2000 to 2004, seven rotaviruses were detected bearing the genotype combination G9P[8]. The molecular characterization of the VP7 and NSP4 genes and the RNA migration patterns support the hypothesis that rotaviruses G9 could have been reintroduced into Argentina as a novel G9P[8] strain, rather than represent VP7 gene reassortants from G9P[6] strains that had been circulating previously in this country.

Symptomatic and subclinical infection with rotavirus P[8]G9, rural Ecuador

Prevalence of this genotype is increasing.

During the past decade, rotavirus genotype G9 has spread throughout the world, adding to and sometimes supplanting the common genotypes G1–G4. We report evidence of this spread in a population sample within rural Ecuador. A total of 1,656 stool samples were collected from both patients with diarrhea and asymptomatic residents in 22 remote communities in northwestern Ecuador from August 2003 through February 2006. Rotavirus was detected in 23.4% of case-patients and 3.2% of controls. From these 136 rotavirus-positive samples, a subset of 47 were genotyped; 72% were of genotype G9, and 62% were genotype P[8]G9. As a comparison, 29 rotavirus-positive stool samples were collected from a hospital in Quito during March 2006 and genotyped; 86% were of genotype P[8]G9. Few countries have reported P[8]G9 rotavirus detection rates as high as those of the current study. This growing prevalence may require changes to current vaccination programs to include coverage for this genotype.

Molecular epidemiology of rotavirus in Central and Southeastern Europe

A surveillance network was implemented by the Istituto Superiore di Sanità of Rome in collaboration with laboratories of virology in Czech Republic, Slovenia, Croatia, Albania, and Bulgaria. About 1,500 rotavirus-positive stool samples were collected from children with severe gastroenteritis admitted to hospitals or outpatient wards between 2004 and 2006. The G and P genotypes were determined by reverse transcription-nested PCR. Significant differences were found in the geographical distributions of rotavirus genotypes between countries participating in the study. The prevalence of "common" G/P combinations, G1P[8], G3P[8], G4P[8], and G2P[4], ranged between 50 and 85%. The G9 genotype, which is emerging worldwide, was identified in 2 to 35% of all samples depending on the country. Unusual combinations, such as G1 or G4 associated with P[4] or G2 with P[8], which may have arisen by reassortment between human strains, were found in samples from 3 to 20% of patients. The uncommon genotypes G8P[8] and G10P[6], which may have an animal origin, were also identified. Double infections with two rotavirus strains were observed in between 1.7 and 14% of cases studied. Our findings might implicate challenges for rotavirus vaccine implementation in a wide geographic area of the Balkans and Central-Eastern Europe and underscore the importance of extensive strain surveillance for success in vaccine development.

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.

Molecular epidemiology of G9 rotaviruses in Taiwan between 2000 and 2002

Since the mid-1990s, novel G9 rotaviruses have been detected in many countries, suggesting that G9 is a globally important serotype. The molecular epidemiology of G9 rotaviruses in Taiwan from 2000 to 2002 was investigated in this study. G9 rotavirus first appeared in 2000 with 4 cases and constituted 33.8% and 54.8% of the rotavirus-positive samples in 2001 and 2002, respectively. These G9 strains belonged to P[8]G9, subgroup II, and long electropherotype, except one belonged to P[4]G9, subgroup II, and short electropherotype. Nucleotide sequencing and phylogenetic analysis of 52 Taiwanese G9 rotaviruses showed that the VP7 genes shared a high degree of identity to overseas G9 rotaviruses detected after 1993 and that the VP8* portions of the VP4 genes were more closely related to those of local rotaviruses of other G types. The two P[8]G9 strains with high nucleotide identities in the VP7 and the partial VP4 genes, 01TW591 of Taiwan from 2001 and 95H115 of Japan from 1995, varied in four genes, genes 2, 3, 7, and 8, which was revealed by RNA-RNA hybridization. Representative strains for different RNA patterns were also analyzed in the partial VP2 and VP3 genes; the nucleotide identities were high between Taiwanese G9 strains and local G3 or G2 strains. These results suggested that Taiwanese G9 rotaviruses possibly had evolved through reassortment between overseas G9 strains and circulating rotaviruses of other G types.

Molecular characterization of rotavirus gastroenteritis strains, Iraqi Kurdistan

Of 260 children with acute diarrhea in Erbil, Iraqi Kurdistan, 96 (37%) were infected with rotavirus. Reverse transcription-polymerase chain reaction identified G1, G4, G2, G9, P[8], P[6], and P[4] as the most common genotypes. Eight G/P combinations were found, but P[8]G1 and P[4]G2 accounted for >50% of the strains.

Rotavirus Serotype G9 Is Associated with More‐Severe Disease in Latin America

The association between rotavirus serotypes and severity is not well established. Analysis of a clinical trial conducted in Latin America points at more-severe disease associated with serotype G9. Thus, demonstration of efficacy against G9 will be an important asset of any rotavirus vaccine to be introduced into a Latin American country or any country where G9 has been shown to be prevalent.

Full genomic analysis of human rotavirus strain B4106 and lapine rotavirus strain 30/96 provides evidence for interspecies transmission

The Belgian rotavirus strain B4106, isolated from a child with gastroenteritis, was previously found to have VP7 (G3), VP4 (P[14]), and NSP4 (A genotype) genes closely related to those of lapine rotaviruses, suggesting a possible lapine origin or natural reassortment of strain B4106. To investigate the origin of this unusual strain, the gene sequences encoding VP1, VP2, VP3, VP6, NSP1, NSP2, NSP3, and NSP5/6 were also determined. To allow comparison to a lapine strain, the 11 double-stranded RNA segments of a European G3P[14] rabbit rotavirus strain 30/96 were also determined. The complete genome similarity between strains B4106 and 30/96 was 93.4% at the nucleotide level and 96.9% at the amino acid level. All 11 genome segments of strain B4106 were closely related to those of lapine rotaviruses and clustered with the lapine strains in phylogenetic analyses. In addition, sequence analyses of the NSP5 gene of strain B4106 revealed that the altered electrophoretic mobility of NSP5, resulting in a super-short pattern, was due to a gene rearrangement (head-to-tail partial duplication, combined with two short insertions and a deletion). Altogether, these findings confirm that a rotavirus strain with an entirely lapine genome complement was able to infect and cause severe disease in a human child.

A Rotavirus Vaccine for Infants: The Asian Experience

Introduction: Severe rotavirus gastroenteritis in children causes significant morbidity world- wide and substantial deaths in developing countries. Hence, a live attenuated vaccine Rotarix™ was developed with human strain RIX4414 of G1P1A P[8] specificity. RIX4414 trials in infants have begun in developed and developing countries worldwide. An overview of RIX4414 in developed and developing countries and prospects with this vaccine in Asia are presented. Methods: Completed RIX4414 trials have been reviewed. Results: Two oral doses of RIX4414 were well tolerated with a reactogenicity profile similar to placebo. RIX4414 was also highly immunogenic, e.g., in a dose-ranging study conducted in Singapore, 98.8% to100% of infants had a vaccine take after 2 doses. RIX4414 did not affect the immune response of simultaneously administered routine infant vaccines. RIX4414 significantly reduced severe rotavirus gastroen- teritis in settings where multiple serotypes including the emerging G9 type co-circulated. Conclusion: These encouraging results warrant further evaluation of the vaccine worldwide and especially in developing countries with the highest need. Therefore, evaluation of the Rotarix™ vaccine is continuing in large phase III trials in Asia and worldwide. Key words: Asia, Attenuated, Developing countries, Gastroenteritis, RIX4414

Rotavirus types in Europe and their significance for vaccination

The degree of diversity of cocirculating human rotavirus wild-type strains is high. This article reviews the occurrence and frequency of rotavirus types in European children younger than 5 years of age during the past 10-15 years. To enable greater understanding of the overall epidemiologic situation, rotavirus types found in animals in Europe are described. In addition, rotavirus types occurring in children outside Europe are considered. Taken together, these data provide an essential background to the development of rotavirus vaccines. The different concepts of immunization with the 2 main rotavirus candidate vaccines are briefly discussed, and their potential impact on the epidemiology of cocirculating rotavirus wild-type viruses is considered. A case is made for comprehensive surveillance of cocirculating human rotavirus types in Europe after the implementation of rotavirus vaccination.

Genetic variation ofNSP1 andNSP4 genes among serotype G9 rotaviruses causing hospitalization of children in Melbourne, Australia, 1997–2002

Serotype G9 rotaviruses have emerged as one of the leading causes of gastroenteritis in children worldwide. We examined 29 representative G9 rotavirus isolates from a 6-year collection (1997-2002) and determined the level of variation in genes encoding non-structural proteins, NSP1 and NSP4. Northern hybridization analysis with a whole genome probe derived from the prototype G9 strain, F45, revealed that the NSP1 gene (gene 5) of two isolates (R1 and R14) did not exhibit significant homology. Complementary DNA probes of R1 and R14 genes 5 were used in Northern blot hybridization and indicated the presence of at least two gene 5 alleles among Melbourne G9 rotaviruses. Nucleotide sequence analysis revealed that isolates carrying the R14 gene 5 shared 94-98% sequence identities with one another, while sequence identity to R1 was 78%. Surprisingly, R1 displayed 96% nucleotide identity with the prototype serotype G1 strain, Wa. The detection of different alleles of NSP1 genes prompted us to investigate the level of variation in another non-structural protein, NSP4, a multifunctional protein and the first viral-encoded enterotoxin. Phylogenetic analysis indicated that while all isolates clustered into one group containing the Wa NSP4 allele (genotype 1), isolate R1 was most closely related to Wa. This study reveals new information about the diversity of non-structural proteins of G9 rotaviruses.