Eight-year survey of human rotavirus strains demonstrates circulation of unusual G and P types in Hungary

Next-generation sequencing of a human-animal reassortant G6P[14] rotavirus A strain from a child hospitalized with diarrhoea

We previously reported the VP4 and the VP7 genotypes of the first G6P[14] rotavirus strain (RVA/Human-wt/GHA/M0084/2010/G6P[14]) from the stool of an infant with diarrhoea in Ghana. In the current study, we obtained the complete genome sequences using Illumina MiSeq next-generation sequencing to enable us to determine the host species origin of the genes by phylogenetic analysis. The genotype constellation was G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3. Phylogenetic analysis showed that M0084 was a reassortant strain from RVAs of both artiodactyl and human host species origin. The level of sequence identity of the individual genes of M0084 to other sequences in the GenBank ranged from 95.2 to 99.5%; however, there was no single strain from the GenBank database with a complete genome sequence that was highly similar to that of M0084. To help trace the source of such unique gene pools being introduced into human RVAs, it will be useful to examine RVA sequences from potential reservoirs such as sheep and goats, which are common domestic animals in this locality.

Distribution of rotavirus genotypes in three Croatian regions among children ≤5 years of age (2012-2014)

OBJECTIVES

Rotavirus is the major cause of severe diarrhea in young children worldwide. In countries like Croatia, where rotavirus vaccine has not been introduced in the national immunization program, prospective surveillance is necessary to establish the diversity of rotavirus strains. The aim of this study was to describe the prevalence and geographical distribution of rotavirus strains in Croatia and to detect the possible emergence of novel strains.

METHODS

The study was conducted among children ≤5 years of age with acute gastroenteritis at three hospitals located in different geographical regions of Croatia, during the years 2012 to 2014. Rotavirus was detected in stools using an immunochromatographic assay and then sent for further molecular analysis.

RESULTS

Genotyping of 822 rotaviruses showed that the predominant circulating strain was G1P[8] (61.9%), followed by G2P[4] (19.5%), G1P[4] (3.9%), and G3P[8] (2.9%). A high prevalence of reassortants among common human rotavirus genotypes was detected (7.7%). Possible zoonotic reassortants were found, including G8 and G6 strains. The latter is described for the first time in Croatia.

CONCLUSIONS

This study represents pre-vaccination data that are important for decisions regarding immunization strategies in Croatia. The high prevalence of 'common' rotavirus strains circulating in Croatia may advocate for rotavirus vaccine introduction, but further surveillance is necessary to monitor the possible emergence of novel genotypes.

Whole genome sequencing of a rare rotavirus from archived stool sample demonstrates independent zoonotic origin of human G8P[14] strains in Hungary

Genotype P[14] rotaviruses in humans are thought to be zoonotic strains originating from bovine or ovine host species. Over the past 30 years only few genotype P[14] strains were identified in Hungary totaling<0.1% of all human rotaviruses whose genotype had been determined. In this study we report the genome sequence and phylogenetic analysis of a human genotype G8P[14] strain, RVA/Human-wt/HUN/182-02/2001/G8P[14]. The whole genome constellation (G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) of this strain was shared with another Hungarian zoonotic G8P[14] strain, RVA/Human-wt/HUN/BP1062/2004/G8P[14], although phylogenetic analyses revealed the two rotaviruses likely had different progenitors. Overall, our findings indicate that human G8P[14] rotavirus detected in Hungary in the past originated from independent zoonotic events. Further studies are needed to assess the public health risk associated with infections by various animal rotavirus strains.

Whole Genomic Analysis of an Unusual Human G6P[14] Rotavirus Strain Isolated from a Child with Diarrhea in Thailand: Evidence for Bovine-To-Human Interspecies Transmission and Reassortment Events

An unusual rotavirus strain, SKT-27, with the G6P[14] genotypes (RVA/Human-wt/THA/SKT-27/2012/G6P[14]), was identified in a stool specimen from a hospitalized child aged eight months with severe diarrhea. In this study, we sequenced and characterized the complete genome of strain SKT-27. On whole genomic analysis, strain SKT-27 was found to have a unique genotype constellation: G6-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The non-G/P genotype constellation of this strain (I2-R2-C2-M2-A3-N2-T6-E2-H3) is commonly shared with rotavirus strains from artiodactyls such as cattle. Phylogenetic analysis indicated that nine of the 11 genes of strain SKT-27 (VP7, VP4, VP6, VP2-3, NSP1, NSP3-5) appeared to be of artiodactyl (likely bovine) origin, while the remaining VP1 and NSP2 genes were assumed to be of human origin. Thus, strain SKT-27 was found to have a bovine rotavirus genetic backbone, and thus is likely to be of bovine origin. Furthermore, strain SKT-27 appeared to be derived through interspecies transmission and reassortment events involving bovine and human rotavirus strains. Of note is that the VP7 gene of strain SKT-27 was located in G6 lineage-5 together with those of bovine rotavirus strains, away from the clusters comprising other G6P[14] strains in G6 lineages-2/6, suggesting the occurrence of independent bovine-to-human interspecies transmission events. To our knowledge, this is the first report on full genome-based characterization of human G6P[14] strains that have emerged in Southeast Asia. Our observations will provide important insights into the origin of G6P[14] strains, and into dynamic interactions between human and bovine rotavirus strains.

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.

Large-scale whole genome sequencing identifies country-wide spread of an emerging G9P[8] rotavirus strain in Hungary, 2012

With the availability of rotavirus vaccines routine strain surveillance has been launched or continued in many countries worldwide. In this study relevant information is provided from Hungary in order to extend knowledge about circulating rotavirus strains. Direct sequencing of the RT-PCR products obtained by VP7 and VP4 genes specific primer sets was utilized as routine laboratory method. In addition we explored the advantage of random primed RT-PCR and semiconductor sequencing of the whole genome of selected strains. During the study year, 2012, we identified an increase in the prevalence of G9P[8] strains across the country. This genotype combination predominated in seven out of nine study sites (detection rates, 45-83%). In addition to G9P[8]s, epidemiologically major strains included genotypes G1P[8] (34.2%), G2P[4] (13.5%), and G4P[8] (7.4%), whereas unusual and rare strains were G3P[8] (1%), G2P[8] (0.5%), G1P[4] (0.2%), G3P[4] (0.2%), and G3P[9] (0.2%). Whole genome analysis of 125 Hungarian human rotaviruses identified nine major genotype constellations and uncovered both intra- and intergenogroup reassortment events in circulating strains. Intergenogroup reassortment resulted in several unusual genotype constellations, including mono-reassortant G1P[8] and G9P[8] strains whose genotype 1 (Wa-like) backbone gene constellations contained DS1-like NSP2 and VP3 genes, respectively, as well as, a putative bovine-feline G3P[9] reassortant strain. The conserved genomic constellations of epidemiologically major genotypes suggested the clonal spread of the re-emerging G9P[8] genotype and several co-circulating strains (e.g., G1P[8] and G2P[4]) in many study sites during 2012. Of interest, medically important G2P[4] strains carried bovine-like VP1 and VP6 genes in their genotype constellation. No evidence for vaccine associated selection, or, interaction between wild-type and vaccine strains was obtained. In conclusion, this study reports the reemergence of G9P[8] strains across the country and indicates the robustness of whole genome sequencing in routine rotavirus strain surveillance.

Zoonotic transmission of reassortant porcine G4P[6] rotaviruses in Hungarian pediatric patients identified sporadically over a 15 year period

Genotype G4P[6] Rotavirus A (RVA) strains collected from children admitted to hospital with gastroenteritis over a 15 year period in the pre rotavirus vaccine era in Hungary were characterized in this study. Whole genome sequencing and phylogenetic analysis was performed on eight G4P[6] RVA strains. All these RVA strains shared a fairly conservative genomic configuration (G4-P[6]-I1/I5-R1-C1-M1-A1/A8-N1-T1/T7-E1-H1) and showed striking similarities to porcine and porcine-derived human RVA strains collected worldwide, although genetic relatedness to some common human RVA strains was also seen. The resolution of phylogenetic relationship between porcine and human RVA genes was occasionally low, making the evaluation of host species origin of individual genes sometimes difficult. Yet the whole genome constellations and overall phylogenetic analyses indicated that these eight Hungarian G4P[6] RVA strains may have originated by independent zoonotic transmission, probably from pigs. Future surveillance studies of human and animal RVA should go parallel to enable the distinction between direct interspecies transmission events and those that are coupled with reassortment of cognate genes.

Surveillance of human rotaviruses in 2007-2011, Hungary: exploring the genetic relatedness between vaccine and field strains

BACKGROUND

The availability of rotavirus vaccines has resulted in an intensification of post vaccine strain surveillance efforts worldwide to gain information on the impact of vaccines on prevalence of circulating rotavirus strains.

OBJECTIVES

In this study, the distribution of human rotavirus G and P types in Hungary is reported. In addition, the VP4 and VP7 genes of G1P[8] strains were sequenced to monitor if vaccine-derived strains were introduced and/or some strains/lineages were selected against.

STUDY DESIGN

The study was conducted in 8 geographic areas of Hungary between 2007 and 2011. Rotavirus positive stool samples were collected from diarrheic patients mostly <5 years of age. Viral RNA was amplified by multiplex genotyping RT-PCR assay, targeting the medically most important G and P types. When needed, sequencing of the VP7 and VP4 genes was performed.

RESULTS

In total, 2380 strains were genotyped. During the 5-year surveillance we observed the dominating prevalence of genotype G1P[8] (44.87%) strains, followed by G4P[8] (23.4%), G2P[4] (14.75%) and G9P[8] (6.81%) genotypes. Uncommon strains were identified in a low percentage of samples (4.12%). Phylogenetic analysis of 318 G1P[8] strains identified 55 strains similar to the Rotarix strain (nt sequence identities; VP7, up to 97.9%; VP4, up to 98.5%) although their vaccine origin was unlikely.

CONCLUSIONS

Current vaccines would have protected against the majority of identified rotavirus genotypes. A better understanding of the potential long-term effect of vaccine use on epidemiology and evolutionary dynamics of co-circulating wild type strains requires continuous strain surveillance.

Molecular characterization of G and P-types bovine rotavirus strains from Goiás, Brazil: high frequency of mixed P-type infections

In this study, 331 samples from calves less than one month old from a dairy herd in the district of Piracanjuba, state of Goiás, Brazil were tested for rotavirus. Thirty-three samples (9.9%) tested positive for rotavirus. Out of those, 31 were submitted to G and P characterization by reverse transcription followed by semi-nested polymerase chain reaction. Two samples were characterized as G6P[1], three as G10P[11] and five as G6P[11]. The majority of the samples (51.6%) displayed multiple P genotypes (P-genotype mixtures), including typical human genotypes P[4] and P[6M], suggesting the occurrence of co-infections and genetic reassortment. Also, the detection of human genotypes in bovine samples may be considered evidence of the zoonotic potential of rotaviruses. To our knowledge, this is the first report of such a high frequency of P genotype mixtures in bovine rotavirus samples. It also increases data on G and P rotavirus genotypes circulating in dairy herds in Brazil and can help in the development of more efficient immunization approaches, thereby controlling infection and reducing economical losses.

Burden of rotavirus gastroenteritis in the pediatric population in Central and Eastern Europe: serotype distribution and burden of illness

BACKGROUND

Rotaviral gastroenteritis (RVGE) is the leading cause of severe diarrhea in children under five years of age worldwide. This comprehensive review aims to estimate the burden of RVGE among children in Central and Eastern Europe.

METHODS

An extensive search of the biomedical literature (1999-2009) was conducted in major databases. Studies pertaining to the epidemiology and burden of rotavirus in Central and Eastern Europe were captured and data from each country was systematically extracted and compared.

RESULTS

This literature search captured 38 studies pertaining to RVGE infection in the region. Among children under 15 years of age, RVGE accounted for between 22.0% and 55.3% of all cases of acute gastroenteritis per year. For most countries RVGE was most common in the winter months, although it was reported year round in Bulgaria. Geographical comparison of genotyping data revealed that three genotype combinations, G1P[8], G4P[8], and G2P[4] were present in all countries for which full genotyping data was available. Genotype predominance varied on a season to season basis within each country. Only limited data was available for healthcare resource utilization, and economic burden for this region.

CONCLUSIONS

RVGE is a common disease associated with significant morbidity, and mortality. While three genotype combinations currently predominate in the region, the dominance of a certain serotype can change dramatically from year to year and from country to country. A vaccination program with broad serotype coverage may help to decrease the burden of RVGE in Central and Eastern Europe.

Human rotavirus genotypes circulating in Brazil before and after a nationwide rotavirus vaccination program established in 2006

Accounting for an estimated 600,000 deaths worldwide each year, rotaviruses are recognized as the most important etiologic agents causing severe acute gastroenteritis among children under the age of five years. In Brazil, until rotavirus vaccination was established in the public health system in 2006, acute gastroenteritis striking children under five years and caused by these viruses was clearly associated with 3.5 million episodes of diarrhea, 650,000 visits to outpatient health care facilities, 92,000 hospitalizations, and 850 deaths each year. After the introduction of the rotavirus vaccine in Brazil in March 2006, studies all over the country have been comparing rotavirus genotypes circulating in the recent pre- and postvaccination era. Most of these studies have reported a high prevalence of the G2P[4] genotype and also a decrease in rotavirus detection all over Brazil after the introduction of the vaccine. So far, these are preliminary studies, as a longer period of time is necessary to establish if this high prevalence of G2P[4] is due to selective pressure by the vaccine on the circulating viruses or to a normal genotype fluctuation, and if it will have any impact on vaccine efficacy in the future. This review describes results from the most recent studies addressing this issue and on rotavirus genotypic variability in Brazil.

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

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

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

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

Rotavirus disease and vaccination: impact on genotype diversity

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

[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.

The ever-changing landscape of rotavirus serotypes

Rotavirus is a double-stranded RNA virus that is characterized by substantial genetic diversity. The various serotypes of rotavirus have been determined by the presence of neutralizing epitopes on the outer capsid of the protein shell. At present, 5 rotavirus serotypes (G1, G2, G3, G4, G9) are the predominant circulating strains, accounting for approximately 95% of strains worldwide, although there is considerable geographic variability. Incidence rates for various serotypes also vary temporally with seasonal and year-to-year fluctuations. Unusual serotypes are generally uncommon, but new serotypes can emerge. In particular, G9[P8], a reassortment virus, was first identified in 1983 and in the last 10 to 15 years has become widely distributed worldwide. Indeed, G9[P8] has become highly prevalent in many countries in Europe and Australia, with somewhat lower incidence rates in South America, Africa, and Asia. The heterogeneity and ever-changing epidemiology of rotavirus underscores the need for continued surveillance to ensure that vaccination programs provide optimal protection.

[Detection of a rotavirus G9P[8] outbreak causing gastroenteritis in a geriatric nursing home]

INTRODUCTION

The aim of this study was to describe an outbreak of gastroenteritis due to rotavirus in a geriatric nursing home.

METHOD

Stool samples from 8 patients were studied. Antigen detection was carried out by ELISA, and molecular typing was performed by RT-PCR.

RESULTS

Rotavirus antigen was detected in 6 patients. Typing demonstrated a common genotype (G9P[8]).

CONCLUSION

The outbreak detected in elderly persons suggests a loss of immunity with age or a lack of protection against an emergent genotype.

Prospective study of the burden of acute gastroenteritis and rotavirus gastroenteritis in children less than 5 years of age, in Padova, Italy

BACKGROUND

Data on the burden of rotavirus gastroenteritis in Europe are needed to help understand the potential impact of introducing new rotavirus vaccines.

MATERIALS AND METHODS

As part of prospective observational study (Rotavirus gastroenteritis Epidemiology and Viral types in Europe Accounting for Losses in Public Health and Society Study, REVEAL) conducted in 2004--2005 in seven European countries, we studied, the characteristics of acute gastroenteritis and rotavirus gastroenteritis in children less than 5 years in primary care, emergency room and hospital settings (Padova, Italy).

RESULTS

A total of 757 children with acute gastroenteritis were included and enzyme-linked immunoabsorbent assay (ELISA) results were available for 725 cases. The overall estimated annual incidence for rotavirus gastroenteritis was 4.7%. Overall, rotavirus gastroenteritis was estimated to account for 43.6% of acute gastroenteritis cases. Among children with acute gastroenteritis (AGE) aged 6-23 months, 61.2% were rotavirus positive. Rotavirus gastroenteritis (RVGE) was responsible for 68.8% of hospitalizations, 61% of emergency consultations, and 33% of primary care consultations. The most prevalent serotype was G9 (84.4%) followed by G1 (11.8%). The relative risk for rotavirus gastroenteritis of being referred to hospital after an initial consultation in primary care was 3.37 (95% CI: 1.77-6.43) and 3.38 (95% CI: 2.28-5.01) for emergency room referral. Children with rotavirus gastroenteritis generally had more severe disease than children with rotavirus-negative gastroenteritis.

CONCLUSION

Rotavirus accounts for a significant proportion of acute gastroenteritis cases in children less than 5 years in Italy, many of whom require frequent primary care consultations, or care in emergency room or hospital settings.

Occurrence of group A rotavirus mixed P genotypes infections in children living in Goiânia-Goiás, Brazil

Group A rotaviruses (RVA) are the main causing agents of acute gastroenteritis worldwide, having a great impact on childhood mortality in developing countries. The objective of this study was to identify RVA-positive fecal samples with mixed P genotypes by hemi-nested reverse transcriptase-polymerase chain reaction (RT-PCR), followed by sequencing confirmation. Our results showed that, from the 81 RVA-positive samples, 25 were positive for more than one P genotype by hemi-nested RT-PCR. Of these 25 samples, 12 (48%) had their mixed P genotypes confirmed by sequencing and, from these, 10 were identified as P[6]P[8], one as P[4]P[6], and one as P[4]P[6]P[8]. Our results confirm the occurrence of RVA mixed infections among children in Brazil and reinforce the importance of the constant monitoring of RVA circulating strains for the efficacy of control/prevention against these agents.

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

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

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

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

EuroRotaNet – European rotavirus strain surveillance network has been established

Az A-csoportú rotavírusok világszerte a gyermekkori súlyos gasztroenteritiszek leggyakoribb okai. A rotavírusok szero- és genotípusainak különböző földrajzi területeken észlelt megoszlása ugyanabban a szezonban és az egymást követő években egyaránt változik. Jellemző ezenkívül a genetikailag egymástól eltérő törzsek együttes előfordulása, akárcsak az adott típuson belüli variabilitás bármely területen és időben. A rotavírus elleni vakcinák széles körű alkalmazását feltételezve a közeljövőben a természetes rotavírus-fertőzések átfogó surveillance-a alapvető fontosságú lesz. Az EuroRotaNet mindenekelőtt azért jött létre, hogy átfogó információt gyűjtsön az Európában keringő rotavírusok szero- és genotípusairól. A megfogalmazott feladatok közül a legfontosabbak a következők: (i) a rotavírustörzsek hatékony tipizálási és jellemzési módszerének és algoritmusok kifejlesztése; (ii) a rotavírus-fertőzések molekuláris epidemiológiájának részletes leírása Európában; (iii) a jelenlegi genotipizálási módszerek hatékonyságának felmérése és a genetikai sodródás (drift) és váltás (shift) okozta változásokra történő reagálás; és (iv) az új törzsek európai felbukkanásának rögzítése és terjedésük nyomon követése. Mindez megfelelő alapot nyújthat a jövőbeli surveillance-tevékenységekhez, és talán lehetőséget kínál majd olyan alvizsgálatok elvégzésére, amelyekkel értékelni lehet az oltóanyagnak a leggyakoribb rotavírustörzsek által okozott fertőzések számára gyakorolt hatását az általános populációban, ki lehet szűrni azokat a genotípusokat, amelyek a vakcináció hatására létrejött ellenanyagválasz kikerülésével válnak fontossá a populációban, valamint azonosíthatók lesznek azok az új reasszoránsok, amelyek a vakcinatörzsek és a vad típusú törzsek keveredéséből jönnek létre.

Rotavírus A em crianças de até três anos de idade, hospitalizadas com gastroenterite aguda em Campo Grande, Estado do Mato Grosso do Sul

Através da eletroforese em gel de poliacrilamida e do ensaio imunenzimático combinado para rotavírus e adenovirus, foram analisadas 380 amostras fecais de crianças com até 3 anos, hospitalizadas com diarréia aguda, entre maio de 2000 e janeiro de 2004, em Campo Grande, MS. Do total de amostras, 88 (23,2%) foram positivas para Rotavirus A. Dentre essas, 81 (92%) tiveram padrão eletroferotípico definido, sendo 77 (87,5%) de padrão longo e quatro (4,5%) de padrão curto. A caracterização genotípica G e P foi feita por RT-Nested-PCR para 85 amostras, sendo 56 (65,9%) genotipáveis para genótipo G. Dentre essas, 49 (87,5%) foram G1, cinco (8,9%) G4, uma (1,8%) G3 e uma (1,8%) G9. Considerando a genotipagem P, 37 (43,5%) foram genotipáveis e todas eram P[8]. A associação G e P mais observada foi G1P[8], 33 (89,2%) amostras; seguida de G4P[8], duas (5,4%) amostras; G3P[8], uma (2,7%) amostra; e G9P[8], uma (2,7%) amostra.

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.

Genotypic characterization of rotaviruses and prevalence of serotype-specific serum antibodies in children in Kuwait

There are no data on the serotypes of rotaviruses prevalent in Kuwait, which has a large expatriate population and hence a focal point for transmission of pathogens. The serotype information will contribute to the fund of knowledge on the world epidemiology of rotavirus serotypes and will predict the outcome of vaccination in Kuwait. Of the 75 rotavirus-positive samples from 172 children (aged <5 years) with severe diarrhoea, 69 were genotyped. The distribution of genotypes was G1 (63.8%) followed by G9 (10.2%), G2 (7.3%), G4 (7.3%) and G3 (4.4%). Among the P types, P[8] was the most common type found across all G types. By fluorescent focus neutralization test, serum antibodies to genotypes G1 (94%), G4 (68%) and G9 (46%) were found in 120 other children. These results show that G1 is the predominant serotype in Kuwait and that a vaccine that contains G1 will be most effective.

Analysis of human rotavirus G1P[8] strains by RFLP reveals higher genetic drift in the VP7 than the VP4 gene during a 4-year period in Mexico

Several studies have demonstrated that rotaviruses of the G1P[8] genotype are among the most important worldwide. Sequence analysis of G1P[8] strains has revealed high genetic variability of VP4 and VP7 genes. The aim of this study was to investigate by restriction fragment length polymorphism (RFLP) analysis the genetic variability of the VP7 and VP4 genes within rotaviruses of the G1P[8] genotype. A total of 60 rotavirus-positive fecal samples genotyped as G1P[8], were collected from children with acute diarrhea under 5 years of age, between October 1995 and October 1998. The VP7 and VP4 genes were amplified by RT/PCR, using the Beg9/End9 primer pair and the Con3 and Con2 primers, respectively. VP7 amplicons were digested with three restriction enzymes Hae III, Taq I and Rsa I in separate reactions and VP4 amplicons were digested similarly with endonucleases Hinf I, Sau96 I and Rsa I. Analysis of the digested VP7 and VP4 amplicons showed a higher genetic drift for the VP7 gene (18 RFLPs) compared to the VP4 gene (9 RFLPs). The combination of profiles for both VP7 and VP4 amplicons, showed 27 different patterns, none of them similar to the Wa-1 strain. Furthermore, RFLP analysis of these G1P[8] strains, clearly differentiated the viruses into two main clusters, both of them sharing the same restriction pattern for the VP4 gene, and a different one for the VP7 gene.

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.

Serotype diversity and reassortment between human and animal rotavirus strains: implications for rotavirus vaccine programs

The development of rotavirus vaccines that are based on heterotypic or serotype-specific immunity has prompted many countries to establish programs to assess the disease burden associated with rotavirus infection and the distribution of rotavirus strains. Strain surveillance helps to determine whether the most prevalent local strains are likely to be covered by the serotype antigens found in current vaccines. After introduction of a vaccine, this surveillance could detect which strains might not be covered by the vaccine. Almost 2 decades ago, studies demonstrated that 4 globally common rotavirus serotypes (G1-G4) represent >90% of the rotavirus strains in circulation. Subsequently, these 4 serotypes were used in the development of reassortant vaccines predicated on serotype-specific immunity. More recently, the application of reverse-transcription polymerase chain reaction genotyping, nucleotide sequencing, and antigenic characterization methods has confirmed the importance of the 4 globally common types, but a much greater strain diversity has also been identified (we now recognize strains with at least 42 P-G combinations). These studies also identified globally (G9) or regionally (G5, G8, and P2A[6]) common serotype antigens not covered by the reassortant vaccines that have undergone efficacy trials. The enormous diversity and capacity of human rotaviruses for change suggest that rotavirus vaccines must provide good heterotypic protection to be optimally effective.

Genetic variability among serotype G4 Italian human rotaviruses

A total of 254 serotype GH rotavirus strains were detected in Palermo, Italy, from 1985 to 2003. Out of 38 serotype G4 strains selected for genetic analysis, 14 were recognized by genotyping as type G9. Strains confirmed to belong to the G4 type showed temporal patterns of genetic evolution in their VP7 and VP4 gene sequences, and the latest Italian G4 strains were distantly related to the reference vaccinal ST3 strain.

Global distribution of rotavirus serotypes/genotypes and its implication for the development and implementation of an effective rotavirus vaccine

A safe and effective rotavirus vaccine is urgently needed, particularly in developing countries. Critical to vaccine development and implementation is a knowledge base concerning the epidemiology of rotavirus G and P serotypes/genotypes throughout the world. The temporal and geographical distribution of human rotavirus G and P types was reviewed by analysing a total of 45571 strains collected globally from 124 studies reported from 52 countries on five continents published between 1989 and 2004. Four common G types (G1, G2, G3 and G4) in conjunction with P[8] or P[4] represented over 88% of the strains analysed worldwide. In addition, serotype G9 viruses associated with P[8] or P[6] were shown to have emerged as the fourth globally important G type with the relative frequency of 4.1%. When the global G and/or P type distributions were divided into five continents/subcontinents, several characteristic features emerged. For example, the P[8]G1 represented over 70% of rotavirus infections in North America, Europe and Australia, but only about 30% of the infections in South America and Asia, and 23% in Africa. In addition, in Africa (i) the relative frequency of G8 was as high as that of the globally common G3 or G4, (ii) P[6] represented almost one-third of all P types identified and (iii) 27% of the infections were associated with rotavirus strains bearing unusual combinations such as P[6]G8 or P[4]G8. Furthermore, in South America, uncommon G5 virus appeared to increase its epidemiological importance among children with diarrhea. Such findings have (i) confirmed the importance of continued active rotavirus strain surveillance in a variety of geographical settings and (ii) provided important considerations for the development and implementation of an effective rotavirus vaccine (e.g. a geographical P-G type adjustment in the formulation of next generation multivalent vaccines).

Dominating prevalence of P[8],G1 and P[8],G9 rotavirus strains among children admitted to hospital between 2000 and 2003 in Budapest, Hungary

Group A rotaviruses are the main cause of acute dehydrating diarrhea in children, responsible for high mortality in developing countries and a significant socio-economic burden associated with treating the disease in developed countries. Two rotavirus vaccine candidates predicated on either homotypic or heterotypic protection have undergone clinical trials recently and await licensure for routine use. In anticipation of a future vaccination campaign in Hungary, the diversity of rotaviruses collected from Budapest between 2000 and 2003 were analyzed by polyacrylamide gel electrophoresis (PAGE) of the viral genome and by serotyping and genotyping of the outer capsid genes, VP7 and VP4. Among 2,763 rotavirus positive specimens available for analysis, we were able to determine the electropherotype of 2,227, and, of these, 1,517 (68.1%) were subjected to G typing and 1,173 (52.7%) were subjected to P typing. We successfully G typed 1,481 (97.6%) and P typed 1,130 (96.3%) strains, respectively. A total of six G types (G1, 50.2%; G2, 2.2%; G3, 1.7%; G4, 5.8%; G6, 0.6%; and G9, 34.4%) and four P types (P[4], 3.0%; P[6], 0.7%; P[8], 89.9%; and P[9], 1.7%) were identified in nine individual combinations (P[8],G1; P[4],G2; P[8],G3; P[8],G4; P[8],G9; P[6],G4; P[4],G1; P[9],G3; and P[9],G6). The prevalence of VP7 and VP4 specificities varied from year to year. In this regard, a shift in serotype predominance from G1 in 2000-2001 (61.8%) and 2001-2002 (69.7%) to G9 in 2002-2003 (51.3%) was an intriguing observation that has been reported recently in some other countries, as well. The emergence of serotype G9 rotaviruses in Hungary and other parts of the world may have implications for future vaccine development and use, particularly, if current vaccine candidates cannot confer adequate homotypic or heterotypic protection against these strains.

Emergence of G3 and G9 rotavirus and increased incidence of mixed infections in the southern region of Ireland 2001-2004

Two hundred and thirty fecal specimens were collected from children (up to 5 years of age) admitted with suspected rotaviral gastroenteritis at four Irish hospitals (Cork University Hospital, Mercy Hospital, Cork, Waterford Regional Hospital, and Kerry General Hospital) in the southern region of Ireland, between 2001 and 2004. Following laboratory confirmation of the aetiological agent, the rotavirus G-type was determined in all positive samples by reverse transcriptase-polymerase chain reaction (RT-PCR). The distribution of the G-types (n=230) over the 3 year period was G1 (31%), G9 (21.8%), G3 (8.7%), G4 (6.5%), and G2 (3.5%). There were many mixed infections which accounted for 28.5% of the collection. G9 emerged as the most prevalent G type (30.1%) in 2001-2002, whilst G3 first emerged in 2002-2003 and accounted for 15.8% of the collection. Notably, G2 strains were present at a very low frequency (3.5%) during 2001-2004, compared to an earlier study (1997-1999), where they accounted for 28.5% of the specimens. A smaller subset of the study collection was similarly P-typed (n=139). P[8]-type was identified as the most prevalent P-type, accounting for 97.4% (n=186), while P[4] accounted for just 2.6% (n=5) of the collection. The low frequency of P[4] coincided with the decrease in G2 strains in circulation. The key finding in this study was the emergence of G3- and G9-serotypes as epidemiologically important rotavirus strains since 1999, and the low prevalence of the previously common G2 strains in Ireland. The profile of rotavirus is changing continuously in Ireland and the implications for a successful vaccination program are discussed.

Culture adaptation of serotype G6 human rotavirus strains from hospitalized diarrhea patients in India

During serotyping of fecal specimens positive for rotavirus from hospitalized diarrhea patients in Pune, India, about 10% showed multireactivity in enzyme immunoassay with monoclonal antibodies specific for serotypes G1-4, 6, 8, and 10. In order to characterize some of these, three fecal specimens from children and one from adult were culture adapted. All the isolates showed long RNA pattern, but three out of four isolates belonged to subgroup I and II and one, to subgroup I. The isolates were confirmed as G6 by neutralization assay and polymerase chain reaction. Nucleotide sequences of cDNA derived from the gene encoding the outer capsid protein, VP7 of two strains indicated >94% identity with G6, the serotype, generally associated with cattle. The isolates were more close to G6 RF strain, which is a bovine rotavirus, reported from France. This is a first report of isolation of bovine serotype, G6 from children as well as adults from India.

Sequencing and phylogenetic analysis of human genotype P[6] rotavirus strains detected in Hungary provides evidence for genetic heterogeneity within the P[6] VP4 gene

Although rotavirus genotype P[6] is one of the three most common VP4 specificities associated with human infection, the relatively few sequence data available in public databases suggest that the genetic variability within P[6] might be presently unexplored. Thus far, two human P[6] lineages (M37-like and AU19-like) and a single porcine P[6] lineage (Gottfried-like) have been identified by phylogenetic analysis. Serologic studies demonstrated that these three lineages are antigenically distinct from each other, a finding based on which they were classified into three subtypes, P2A[6] (M37-like), P2B[6] (Gottfried-like), and P2C[6] (AU19-like). To study heterogeneity within this genotype, we selected for molecular characterization a total of six P[6] strains detected during an ongoing surveillance in Hungary. The variable region of the VP4 gene was subjected to sequencing and phylogenetic analysis. Our data indicated that these six strains fell into two phylogenetic lineages distinguishable from the human lineages M37-like and AU19-like and from the porcine lineage Gottfried-like. Further studies are needed to understand whether these two novel lineages are genuine human strains or might have originated from animal strains and to evaluate the antigenic relationship of the novel Hungarian P[6] strains to the three established subtypes.