Molecular epidemiologic analysis of group A rotaviruses in adults and children with diarrhea in Wuhan city, China, 2000-2006

Surveillance of Human Rotaviruses in Wuhan, China (2019-2022): Whole-Genome Analysis of Emerging DS-1-like G8P[8] Rotavirus

Group A rotaviruses (RVAs) are major etiologic agents of gastroenteritis in infants and young children worldwide. To study the prevalence and genetic characteristics of RVAs, a hospital-based surveillance study was conducted in Wuhan, China from June 2019 through May 2022. The detection rates of RVAs were 19.40% (142/732) and 3.51% (8/228) in children and adults, respectively. G9P[8] was the predominant genotype, followed by G8P[8] and G3P[8]. G8P[8] emerged and was dominant in the 2021-2022 epidemic season. The genome constellation of six G8P[8] strains was assigned to G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that the VP7, VP4, VP2, VP3, NSP1, NSP2, NSP3, and NSP5 genes of these G8P[8] strains clustered closely with those of the G8P[8] strains in Asia and were distant from those of the P[8] and G2P[4] strains simultaneously detected in Wuhan. In contrast, the VP1, VP6, and NSP4 genes were closely related to the typical G2P[4] rotavirus, including those of G2P[4] strains simultaneously detected in Wuhan. The detection rate of RVAs decreased in the COVID-19 pandemic era. It was deduced that the G8P[8] rotaviruses that emerged in China may be reassortants, carrying the VP6, VP1, and NSP4 genes derived from the G2P[4] rotavirus in the backbone of the neighboring DS-1-like G8P[8] strains represented by CAU17L-103.

The burden of rotavirus-associated acute gastroenteritis in the elderly: assessment of the epidemiology in the context of universal childhood vaccination programs

INTRODUCTION

Rotaviruses (RVs) cause acute gastroenteritis (AGE) in infants and young children worldwide and also in older adults (≥60 years), however the burden among this age group is not well understood. Herd immunity through pediatric RV vaccination may reduce the burden of RVGE across all ages, however the impact of pediatric vaccination on burden in older adults is poorly understood.

AREAS COVERED

This systematic review was undertaken to identify studies related to the following objectives: understand the burden of RV in older adults, RV seroprevalence, and the impact of pediatric vaccination on this burden and highlight evidence gaps to guide future research. Of studies identified, 59 studies from two databases were included in this analysis following a review by two reviewers.

EXPERT OPINION

RV is an understudied disease in older adults. We found that 0-62% of patients with AGE tested positive for RV, with results varying by setting, country, and patient age. Results also suggest that pediatric vaccination benefits older adults through herd protection. Several studies showed a reduction in RV incidence after vaccination. However, there was variety in results and lack of consistency in outcomes reported. Further studies targeting older adults are needed to better characterize RV burden.

Genotype Distribution and Evolutionary Analysis of Rotavirus Associated with Acute Diarrhea Outpatients in Hubei, China, 2013–2016

Group A human rotaviruses (RVAs) annually cause the deaths of 215,000 infants and young children. To understand the epidemiological characteristics and genetic evolution of RVAs, we performed sentinel surveillance on RVA prevalence in a rotavirus-surveillance network in Hubei, China. From 2013 to 2016, a total of 2007 fecal samples from hospital outpatients with acute gastroenteritis were collected from four cities of Hubei Province. Of the 2007 samples, 153 (7.62%) were identified positive for RVA by real-time RT-PCR. RVA infection in Hubei mainly occurred in autumn and winter. The highest detection rate of RVA infection was in 1–2 years old of outpatients (16.97%). No significant difference of RVA positive rate was observed between females and males. We performed a phylogenetic analysis of the G/P genotypes based on the partial VP7/VP4 gene sequences of RVAs. G9P[8] was the most predominant strain in all four years but the prevalence of G2P[4] genotype increased rapidly since 2014. We reconstructed the evolutionary time scale of RVAs in Hubei, and found that the evolutionary rates of the G9, G2, P[8], and P[4] genotypes of RVA were 1.069 ​× ​10⁻³, 1.029 ​× ​10⁻³, 1.283 ​× ​10⁻³ and 1.172 ​× ​10⁻³ nucleotide substitutions/site/year, respectively. Importantly, using a molecular clock model, we showed that most G9, G2, P[8], and P[4] genotype strains dated from the recent ancestor in 2005, 2005, 1993, and 2013, respectively. The finding of the distribution of RVAs in infants and young children in Hubei Province will contribute to the understanding of the epidemiological characteristics and genetic evolution of RVAs in China.

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A four-year study of sentinel surveillance program of RVAs was performed in Hubei, China.

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The key population of rotavirus infection is 1–2 years old of outpatients with acute gastroenteritis.

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G9P[8] was the most predominant strain between 2013 and 2016.

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The estimating time to the most recent common ancestor for the G9 genotype based on partial VP7 gene was 46 years.

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RVA distribution in Hubei Province contributes to the understanding of the epidemiological characteristics of RVAs in China.

Prevalence of rotavirus among older children and adults with diarrhea: A systematic review and meta-analysis

BACKGROUND

Older children and adults are susceptible to rotavirus, but the extent to which rotavirus affects this population is not fully understood, hindering accuracy of global rotavirus estimations.

OBJECTIVE

To determine what proportion of diarrhea cases are due to rotavirus among persons ≥ 5 years old and to estimate this proportion by age strata.

METHODS

We conducted a systematic review and meta-analysis using the PRISMA guidelines. We included studies that reported on conditional rotavirus prevalence (i.e., percent of diarrhea due to rotavirus) in persons ≥ 5 years old who were symptomatic with diarrhea/gastroenteritis and had laboratory confirmation for rotavirus infection. Studies on nosocomial infections and outbreak investigations were excluded. We collected age group-specific conditional rotavirus prevalence and other variables, such as study geography, study setting, and study type. We calculated pooled conditional rotavirus prevalence, corresponding 95% confidence intervals (95% CI), heterogeneity (I²) estimates, and prediction intervals (PI).

RESULTS

Sixty-six studies from 32 countries met the inclusion criteria. Conditional rotavirus prevalence ranged from 0% to 30% across the studies. The total pooled prevalence of rotavirus among persons ≥ 5 years old with diarrhea was 7.6% (95% CI: 6.2-9.2%, I² = 99.6%, PI: 0-24%). The pooled prevalence of rotavirus among older children and adolescents was 8.7% (95% CI: 6.2-11.7%, I² = 96%, PI:0-27%), among younger adults was 5.4% (95% CI: 1.4-11.8%, I² = 96%, PI:0-31%), and among older adults was 4.7% (95% CI: 2.8-7.0%, I² = 96%, PI:0-16%). Pooled conditional rotavirus prevalences did not differ by other variables.

CONCLUSION

In this systematic review and meta-analysis of rotavirus among persons ≥ 5 years old with diarrhea, we found relatively low pooled conditional rotavirus prevalence compared to what is typically reported for children < 5 years; however, results should be interpreted with caution as the wide prediction intervals suggest large heterogeneity.

Group A rotavirus prevalence and genotypes among adult outpatients with diarrhea in Beijing, China, 2011-2018

Group A rotavirus (RVA) is one of the most common causes of severe diarrhea in children worldwide. However, RVA is also an important pathogen causing adult diarrhea, with higher infection rates in older patients. To provide evidence for rotavirus epidemic control and to inform vaccine development, we analyzed the molecular epidemiology of RVA among adult outpatients with diarrhea in Beijing from 2011 to 2018. Stool specimens were collected monthly from 14 districts. RVA was detected using enzyme-linked immunosorbent assay and real-time reverse-transcription polymerase chain reaction (RT-PCR). Genotyping of rotavirus was performed using multiplex semi-nested RT-PCR. Phylogenetic analysis was performed using maximum likelihood methods implemented in MEGA software (version 6.06). Logistic regression and chi-square tests were used to assess differences among age groups, districts, years, and genotype distributions. The prevalence of rotavirus was 10.16% (1310 of 12,893) among adult outpatients with diarrhea from 2011 to 2018 in Beijing. The highest prevalence (13.74%, 600 of 4367) was observed among those aged 41 to 65 years. November, December, and January had the highest positive detection rates. In 2011, G3P[8] and G9P[8] were the dominant genotypes. Starting from 2012, G9P[8] became the dominant genotype. Most G9 strains belonged to the G9-VI clade. Most P[8] strains belonged to the P[8]-III clade. RVA is a major cause of adult diarrhea in Beijing. Continuous molecular surveillance is needed, and transmission of rotavirus between children and adults should be investigated further.

Surveillance of Human Rotavirus in Wuhan, China (2011-2019): Predominance of G9P[8] and Emergence of G12

Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. To learn the shift of genotypes and genetic characteristics of Rotavirus A (RVA) causing diarrhea in children and adults, a hospital-based surveillance of rotavirus was conducted in Wuhan, China from June 2011 through May 2019, and representative virus strains were phylogenetically analyzed. Among a total of 6733 stool specimens collected from both children and adults with acute gastroenteritis, RVA was detected in 25.5% (1125/4409) and 12.3% (285/2324) of specimens, respectively. G9P[⁸] was the most common genotype (74.5%), followed by G1P[⁸] (8.7%), G2P[⁴] (8.4%), and G3P[⁸] (7.3%), with G9P[⁸] increasing rapidly during the study period. The predominant genotype shifted from G1P[⁸] to G9P[⁸] in 2012-2013 epidemic season. G12P[⁶] strain RVA/Human-wt/CHN/Z2761/2019/G12P[⁶] was detected in April 2019 and assigned to G12-P[⁶]-I1-R1-C1-M1-A1-N1-T2-E1-H1 genotypes. Phylogenetic analysis revealed that VP7, VP4, VP6, VP3, NSP1, NSP2, and NSP5 genes of Z2761 clustered closely with those of Korean G12P[⁶] strain CAU_214, showing high nucleotide identities (98.0-98.8%). The NSP3 gene of Z2761 was closely related to those of G2P[⁴] and G12P[⁶] rotaviruses in Asia. All the eleven gene segments of Z2761 kept distance from those of cocirculating G9P[⁸], G1P[⁸], and G3P[⁸] strains detected in Wuhan during this study period. This is the first identification of G12 rotavirus in China. It is deduced that Z2761 is a reassortant having DS-1-like NSP3 gene in the background of G12P[⁶] rotavirus genetically close to CAU_214.

Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia

A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans.

Genetic diversity of species A rotaviruses detected in clinical and environmental samples, including porcine-like rotaviruses from hospitalized children in the Philippines

Rotaviruses are the major cause of severe acute diarrhea in infants and young children. Rotaviruses exhibit zoonosis and thereby infect both humans and animals. Viruses detected in urban rivers possibly reflect the presence of circulating viruses in the catchment. The present study investigates the genetic diversity of species A rotaviruses detected from river water and stool of hospitalized children with acute diarrhea in Tacloban City, the Philippines. Species A rotaviruses were detected by real-time RT-PCR and their genotypes were identified by multiplex PCR and sequencing of partial regions of VP7 and VP4. Rotaviruses were detected in 85.7% (30/35) of the river water samples and 62.7% (151/241) of the clinical samples. Genotypes of VP7 in the river water samples were G1, G2, G3, G4, G5, and G9, and those of VP4 were P[3], P[4], P[6], P[8], and P[13]. Genotypes of viruses from the clinical samples were G2P[4], G1P[8], G3P[8], G4P[6], G5P[6], and G9P[8]. Among those, G2P[4] in clinical samples (77.9%, 81/104) and P[4] of VP4 in river water samples (67.5%, 56/83)) were the most frequently detected rotavirus genotypes. However, G5 was the more frequently detected than G2 in the river water samples (42% vs. 13%) which may be originated from porcine rotavirus. Sequence analyses of eleven gene segments revealed one G5P[6] and two G4P[6] rotaviruses in the clinical samples, wherein, several gene segments were closely related to porcine rotaviruses. The constellation of these rotavirus genes suggests the emergence of reassortment between human and porcine rotavirus due to interspecies transmission. Although two commercial rotavirus vaccines are available now, these vaccines are designed to confer immunity against the major human rotaviruses. Constant monitoring of viral variety in populated areas where humans and domestic animals live in close proximity provides vital information related to the diversity of rotaviruses in a human population.

Prevalence and genotypes of group A rotavirus among outpatient children under five years old with diarrhea in Beijing, China, 2011-2016

BACKGROUND

Rotavirus is a leading cause of severe diarrheal disease, and one of the common causes of death in children aged under five years old. The dominant epidemic strains may change in different years in the same area. In order to provide evidence for rotavirus epidemic control and inform vaccine development, we analyzed epidemiological patterns and genetic characteristics of rotavirus in Beijing during 2011-2016.

METHODS

Stool specimens of outpatient children under five years old were collected from three children's hospitals on a weekly basis. Group A rotavirus antigens were detected using enzyme-linked immunosorbent assay (ELISA) kit. The partial VP4 genes and VP7 genes of rotavirus were both amplified and sequenced. Genotyping and phylogenetic analyses were performed. Logistic regression and Chi-square tests were performed to determine differences across age groups, districts and years in rotavirus prevalence and genotype distribution.

RESULTS

A total of 3668 stool specimens from children with acute diarrhea identified through hospital-based surveillance were collected from 2011 to 2016 in Beijing. A total of 762 (20.8%) specimens tested positive for rotavirus. The rotavirus-positive rate was highest among the 1-2 years old age group (29.0%, 310/1070). November, December and January were the highest rotavirus-positive rate months each year. G9 was the most common G genotype (64.4%, 461/716), and P [8] was the most common P genotype (87.0%, 623/716) among the 716 rotavirus-positive specimens. G9P [8], G3P [8] and G2P [4] were the most common strains. The rotavirus-positive rates of samples in 2012 and 2013 were higher than that in 2011, and the dominant genotype changed from G3P [8] to G9P [8] in 2012 and 2013. VP7 gene sequences of G9 strains in this study clustered into two main lineages. Most of the G9 strains exhibited the highest nucleotide similarity (99.1%~ 100.0%) to the strain found in Japan (MI1128). VP4 gene sequences of P [8] strains were almost P[8]b.

CONCLUSIONS

Rotavirus accounted for more than one fifth of childhood diarrhea in Beijing during the study period. Targeted measures such as immunization with effective rotavirus vaccines should be carried out to reduce the morbidity and mortality due to rotavirus.

Molecular characterisation and clinical correlates of rotavirus in children and adults in a tertiary care centre, Chennai, South India

AIMS

This study was undertaken to determine the rate of detection of rotavirus causing diarrhoea among children and adults, identify the common genotypes circulating and determine clinical correlates.

SETTINGS AND DESIGN

This is a cross-sectional study in a tertiary care centre.

MATERIALS AND METHODS

Stool samples were collected from adults and children, transported on ice, aliquoted and stored at - 80°C. Rotavirus antigen detection enzyme-linked immunosorbent assay was performed on all samples. Representative samples were typed by conventional hemi-nested VP7 and VP4 reverse transcription-polymerase chain reaction.

STATISTICAL ANALYSIS USED

Test of proportion, Student's t-test and Chi-square test were used for statistical analysis.

RESULTS

A total of 444 stool samples were collected and tested over 14 months. Among these, 116 were paediatric with a rate of positivity of 36.21% and 328 were adults with rate of positivity of 20.73%. Among children under 5 years (n = 90), the rate of positivity was 41.11%. Vesikari scale was used for clinical assessment. The mean ± standard deviation Vesikari score in rotavirus-infected children and rotavirus-uninfected children was 11.2 ± 3.2 and 8.9 ± 3.6, respectively, and the difference was statistically significant. Nineteen samples were genotyped in children < 5 years, 94.7% were of G1P[8] and 5.3% were of G9P[4] genotype. Genotyping of 14 adult samples, G1P[8](85.7%) was found as the predominant genotype, two samples (14.3%) were partially typed (G9PUT and G12PUT).

CONCLUSIONS

The rate of positivity of rotavirus in children under 5 years was 41.11%. G1P[8] is the most common strain circulating across all age groups.

Genomic characterization of G3P[6], G4P[6] and G4P[8] human rotaviruses from Wuhan, China: Evidence for interspecies transmission and reassortment events

We report here the whole genomic analyses of two G4P[6] (RVA/Human-wt/CHN/E931/2008/G4P[6], RVA/Human-wt/CHN/R1954/2013/G4P[6]), one G3P[6] (RVA/Human-wt/CHN/R946/2006/G3P[6]) and one G4P[8] (RVA/Human-wt/CHN/E2484/2011/G4P[8]) group A rotavirus (RVA) strains detected in sporadic cases of diarrhea in humans in the city of Wuhan, China. All the four strains displayed a Wa-like genotype constellation. Strains E931 and R1954 shared a G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 constellation, whilst the 11 gene segments of strains R946 and E2484 were assigned to G3-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 genotypes, respectively. Phylogenetically, the VP7 gene of R946, NSP3 gene of E931, and 10 of 11 gene segments of E2484 (except for VP7 gene) belonged to lineages of human RVAs. On the other hand, based on available data, it was difficult to ascertain porcine or human origin of VP3 genes of strains E931 and R946, and NSP2 genes of strains R946 and R1954. The remaining genes of E2484, E931, R946 and R1954 were close to those of porcine RVAs from China, and/or porcine-like human RVAs. Taken together, our observations suggested that strain R1954 might have been derived from porcine RVAs, whilst strains R946 and E931 might be reassortants possessing human RVA-like gene segments on a porcine RVA genetic backbone. Strain E2484 might be derived from reassortment events involving acquisition of a porcine-like VP7 gene by a Wa-like human RVA strain. The present study provided important insights into zoonotic transmission and complex reassortment events involving human and porcine RVAs, reiterating the significance of whole-genomic analysis of RVA strains.

Analysis of human rotaviruses from a single location over an 18-year time span suggests that protein coadaption influences gene constellations

Rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses that cause severe gastroenteritis in children. In addition to an error-prone genome replication mechanism, RVs can increase their genetic diversity by reassorting genes during host coinfection. Such exchanges allow RVs to acquire advantageous genes and adapt in the face of selective pressures. However, reassortment may also impose fitness costs if it unlinks genes/proteins that have accumulated compensatory, coadaptive mutations and that operate best when kept together. To better understand human RV evolutionary dynamics, we analyzed the genome sequences of 135 strains (genotype G1/G3/G4-P[8]-I1-C1-R1-A1-N1-T1-E1-H1) that were collected at a single location in Washington, DC, during the years 1974 to 1991. Intragenotypic phylogenetic trees were constructed for each viral gene using the nucleotide sequences, thereby defining novel allele level gene constellations (GCs) and illuminating putative reassortment events. The results showed that RVs with distinct GCs cocirculated during the vast majority of the collection years and that some of these GCs persisted in the community unchanged by reassortment. To investigate the influence of protein coadaptation on GC maintenance, we performed a mutual information-based analysis of the concatenated amino acid sequences and identified an extensive covariance network. Unexpectedly, amino acid covariation was highest between VP4 and VP2, which are structural components of the RV virion that are not thought to directly interact. These results suggest that GCs may be influenced by the selective constraints placed on functionally coadapted, albeit noninteracting, viral proteins. This work raises important questions about mutation-reassortment interplay and its impact on human RV evolution.

IMPORTANCE

Rotaviruses are devastating human pathogens that cause severe diarrhea and kill >450,000 children each year. The virus can evolve by accumulating mutations and by acquiring new genes from other strains via a process called reassortment. However, little is known about the relationship between mutation accumulation and gene reassortment for rotaviruses and how it impacts viral evolution. In this study, we analyzed the genome sequences of human strains found in clinical fecal specimens that were collected at a single hospital over an 18-year time span. We found that many rotaviruses did not reassort their genes but instead maintained them as specific sets (i.e., constellations). By analyzing the encoded proteins, we discovered concurrent amino acid changes among them, which suggests that they are functionally coadapted to operate best when kept together. This study increases our understanding of how rotaviruses evolve over time in the human population.

Molecular epidemiology and genetic evolution of the whole genome of G3P[8] human rotavirus in Wuhan, China, from 2000 through 2013

BACKGROUND

Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. Since the latter of the 1990s, G3 human rotaviruses referred to as "new variant G3" have emerged and spread in China, being a dominant genotype until 2010, although their genomic evolution has not yet been well investigated.

METHODS

The complete genomes of 33 G3P[8] human rotavirus strains detected in Wuhan, China, from 2000 through 2013 were analyzed. Phylogenetic trees of concatenated sequences of all the RNA segments and individual genes were constructed together with published rotavirus sequences.

RESULTS

Genotypes of 11 gene segments of all the 33 strains were assigned to G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, belonging to Wa genogroup. Phylogenetic analysis of the concatenated full genome sequences indicated that all the modern G3P[8] strains were assigned to Cluster 2 containing only one clade of G3P[8] strains in the US detected in the 1970s, which was distinct from Cluster 1 comprising most of old G3P[8] strains. While main lineages of all the 11 gene segments persisted during the study period, different lineages appeared occasionally in RNA segments encoding VP1, VP4, VP6, and NSP1-NSP5, exhibiting various allele constellations. In contrast, only a single lineage was detected for VP7, VP2, and VP3 genes. Remarkable lineage shift was observed for NSP1 gene; lineage A1-2 emerged in 2007 and became dominant in 2008-2009 epidemic season, while lineage A1-1 persisted throughout the study period.

CONCLUSION

Chinese G3P[8] rotavirus strains have evolved since 2000 by intra-genogroup reassortment with co-circulating strains, accumulating more reassorted genes over the years. This is the first large-scale whole genome-based study to assess the long-term evolution of common human rotaviruses (G3P[8]) in an Asian country.

Rotavirus in adults, Brazil, 2004–2011: G2P[4] dominance and potential impact on vaccination

Objectives

The aim of this study was to monitor rotavirus (RV) infections in adults >18 years with acute gastroenteritis during 2004–2011 national Brazilian RV surveillance. In addition, to characterize the RV group A (RVA) strains in order to gain insight into the supposed vaccine selective pressure imposed to Brazilian children population.

Methods

A total of 2102 convenient fecal specimens were investigated by ELISA, PAGE, and RT-PCR.

Results

RV was detected in 203 (9.6%) of 2102 specimens, and showed a marked peak of detection in September. RVA infection was detected in 9.4% (197/2102) and RV group C (RVC) in 0.3% (6/2102). The most frequent genotypes detected in 2004 and 2005 were G9P[8] (38.5%; 5/13) and G1P[8] (54.5%; 6/11), respectively. The dominant genotype identified from 2006 to 2011 was G2P[4] (64.4%; 116/180). Detection rate varied during the 8-year period of the study from 0.7% to 12.9%.

Conclusion

The high detection rate of G2P[4] in adults provides further evidence that its dominance reflects the seasonality of RVA strains instead of the supposed selective advantage created by vaccination program. It also can be suggested that adult infections may serve as a reservoir to maintain RVA strains in childhood gastroenteritis. Considering the detection rate, the evident reduction of RVA frequency observed in children after vaccine introduction was not present in adults.

Global seasonality of rotavirus disease

BACKGROUND

A substantial number of surveillance studies have documented rotavirus prevalence among children admitted for dehydrating diarrhea. We sought to establish global seasonal patterns of rotavirus disease before the introduction of widespread vaccination.

METHODS

We reviewed studies of rotavirus detection in children with diarrhea published since 1995. We assessed potential relationships between seasonal prevalence and locality by plotting the average monthly proportion of diarrhea cases positive for rotavirus according to geography, country development and latitude. We used linear regression to identify variables that were potentially associated with the seasonal intensity of rotavirus.

RESULTS

Among a total of 99 studies representing all 6 geographic regions of the world, patterns of year-round disease were more evident in low- and low-middle income countries compared with upper-middle and high-income countries where disease was more likely to be seasonal. The level of country development was a stronger predictor of strength of seasonality (P = 0.001) than geographic location or climate. However, the observation of distinctly different seasonal patterns of rotavirus disease in some countries with similar geographic location, climate and level of development indicate that a single unifying explanation for variation in seasonality of rotavirus disease is unlikely.

CONCLUSION

While no unifying explanation emerged for varying rotavirus seasonality globally, the country income level was somewhat more predictive of the likelihood of having seasonal disease than other factors. Future evaluation of the effect of rotavirus vaccination on seasonal patterns of disease in different settings may help understand factors that drive the global seasonality of rotavirus disease.

Rotavirus infection and its genetic characterization in non-hospitalized adults with acute gastroenteritis in Shanghai, China

Rotavirus is a major cause of acute gastroenteritis in infants and young children, while its role as a pathogen in adults has long been underappreciated. In order to describe the epidemiological patterns and genetic characteristics of rotavirus causing sporadic acute gastroenteritis in adults, hospital-based surveillance of rotavirus infections was conducted in Shanghai, China, between June 2010 and May 2011. Stool specimens were collected from outpatients with acute gastroenteritis admitted to three local hospitals. Rotavirus was detected using a colloidal gold test device. G and P genotyping were performed by multiplex PCR assays, and the VP7 gene of G9 strains were sequenced for further genetic characterization. Of 1,479 adult diarrheal stool samples examined during the 1-year surveillance period, 138 (9.3 %) were found to be rotavirus positive. G1 appeared to be the predominant genotype (35.5 %), suggesting a shift from genotype G3 to G1 in the study population in Shanghai. Meanwhile, a high frequency of genotype G9 (27.5 %) was also observed, and G9 was also predominant (38.1 %) in the small number of children (n=123) involved in the present study. Other specificities detected in adults were G2 (12.3 %) and G3 (13.8 %). For P genotyping, only two types, P[8] and P[4], were detected. P[8] was dominant in both children and adults. Sequence and phylogenetic analysis revealed that these strains could be divided into two different groups, with clustering within G9 lineage 3 and the subcluster of Japanese and Chinese G9 strains, respectively. In comparison to the previous data, G9 strains established themselves in a short time span as an important genotype in Shanghai, China.

Whole genomic analysis of human G1P[8] rotavirus strains from different age groups in China

G1P[8] rotaviruses are an important cause of diarrhea in humans in China. To date, there are no reports on the whole genomic analysis of the Chinese G1P[8] rotaviruses. To determine the origin and overall genetic makeup of the recent Chinese G1P[8] strains, the whole genomes of three strains, RVA/Human-wt/CHN/E1911/2009/G1P[8], RVA/Human-tc/CHN/R588/2005/G1P[8] and RVA/Human-tc/CHN/Y128/2004/G1P[8], detected in an infant, a child and an adult, respectively, were analyzed. Strains E1911, R588 and Y128 exhibited a typical Wa-like genotype constellation. Except for the NSP3 gene of E1911, the whole genomes of strains E1911, R588 and Y128 were found to be more closely related to those of the recent Wa-like common human strains from different countries than those of the prototype G1P[8] strain, or other old strains. On the other hand, the NSP3 gene of E1911 was genetically distinct from those of Y128, R588, or other Wa-like common human strains, and appeared to share a common origin with those of the porcine-like human G9 strains, providing evidence for intergenotype reassortment events. Comparisons of the amino acid residues defining the VP7 and VP4 antigenic domains revealed several mismatches between these Chinese G1P[8] strains and the G1 and P[8] strains contained in the currently licensed rotavirus vaccines Rotarix(TM )and RotaTeq(TM).

Molecular epidemiology of noroviruses in children and adults with acute gastroenteritis in Wuhan, China, 2007-2010

To study epidemiological features and genetic characteristics of noroviruses in children and adults with acute gastroenteritis, fecal specimens were collected in three hospitals from Jan. 2007 to May 2010 in Wuhan, China. Noroviruses were detected in 25.9 % (286/1103) and 24.6 % (202/822) of the specimens from children and adults, respectively, with genogroup II (GII) being predominant (99.2 %). The most frequent genotype among GII strains was GII.4 (2006b variant) (77.3 %) (72.0 % in children and 87.9 % in adults), followed by GII.3 (15.0 %) and GII.6 (3.4 %). Potential recombinant genotypes (polymerase/capsid) were detected in 51 GII strains (15.9 %), including the most frequent type, GII.12/GII.3 (28 strains), and GII.16/GII.2, detected for the first time in China, which were found in only children. The results indicated that genetically similar noroviruses were circulating among children and adults as a cause of gastroenteritis, except for some recombinant genotypes.

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

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

Burden of rotavirus gastroenteritis and distribution of rotavirus strains in Asia: a systematic review

BACKGROUND

Rotavirus is the leading cause of severe diarrhea in children worldwide. We systematically reviewed the burden of rotavirus gastroenteritis (RVGE) and distribution of rotavirus strains in Asia.

METHODS

We searched MEDLINE, EMBASE and the World Health Organization (WHO) website for the term "rotavirus" and the name of each country. We included studies that were conducted in children between 2000 and 2011 and that examined the epidemiology, health and/or economic burden of RVGE, and G and P-type distribution in Eastern, South East, Southern and Central Asia. Random effects models were used to pool the proportions of RVGE. We also estimated child mortality due to RVGE using the updated WHO and United Nations Children's Fund's mortality estimates in 2008.

RESULTS

The search identified 113 eligible articles. The incidence rates of rotavirus-related hospitalizations in children under 5 years of age ranged from 2.1 to 20.0 cases per 1000 children per year with the highest rates reported in Bangladesh, South Korea, Taiwan, Thailand, and Vietnam. Rotavirus accounted for 37.5% of year-round hospitalized gastroenteritis cases, with higher proportions reported in South East Asia. Rotavirus was associated with approximately 145,000 deaths every year in Asia, with the greatest numbers occurring in India, Pakistan, and Indonesia. The highest annual societal costs of treating RVGE were reported in China (US$365 million), followed by Japan (US$254 million) and India (US$41-72 million). A diversity of rotavirus G and P-types was observed across Asia and the distribution of strains differed by country and year. The most common strains were G1P[8] (23.6%), G2P[4] (11.8%), G3P[8] (18.9%), and G9P[8] (7.4%).

CONCLUSIONS

Rotavirus is associated with substantial hospitalizations and deaths among children and causes large healthcare expenditures throughout Asia. Safe and effective rotavirus vaccines could substantially reduce the burden of disease.

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.

Co-dominance of G1 and emerging G3 rotaviruses in Hong Kong: a three-year surveillance in three major hospitals

BACKGROUND

The World Health Organization recommends rotavirus vaccines be included in all national immunization programs as part of a strategy to control diarrhoeal diseases. Sentinel surveillance is advised to monitor impact post-vaccine introduction and to document changes in genotype distribution.

OBJECTIVES

To determine the molecular epidemiology of circulating rotaviruses in Hong Kong prior to implementation of universal rotavirus vaccination.

STUDY DESIGN

From December 2004 through December 2007, 830 rotavirus-positive stool samples from subjects admitted for acute diarrhea to three major hospitals in Hong Kong were examined. The electropherotypes, and the G and P genotypes of these rotaviruses were determined. Phylogenetic analysis of the VP7 gene was performed.

RESULTS

G3P[8] was the dominant genotype (46.1%), followed by G1P[8] (36.5%) and G9P[8] (9.2%). A total of 35 electropherotypes were identified. The G3 and G1 strains had high sequence similarities among themselves and were clustered with strains from Asia particularly mainland China. The G9 strains were clustered with the globally spreading strains. G12 and G4 were not found. The prevalence of rotavirus infection peaked in winter season when temperature was low, atmospheric pressure was high, relative humidity was low and rainfall was negligible.

CONCLUSIONS

Genotype G3 and G1 were the dominant rotaviruses circulating in Hong Kong between 2004 and 2007. Strains were mainly related with those from mainland China. Ongoing surveillance of circulating genotypes should continue in anticipation of universal rotavirus vaccine introduction.

Full genomic analysis of a porcine-bovine reassortant G4P[6] rotavirus strain R479 isolated from an infant in China

During the 2004 surveillance of rotaviruses in Wuhan, China, a G4P[6] rotavirus strain R479 was isolated from a stool specimen collected from a 2-year-old child with diarrhea. The strain R479 had an uncommon subgroup specificity I + II, and analysis of the VP6 gene suggested that it was related to porcine rotaviruses. In the present study, full-length nucleotide sequences of all the RNA segments of R479 were determined and analyzed phylogenetically to identify the origin of individual RNA segments. According to the rotavirus genotyping system based on 11 RNA segments, the genotype of R479 was expressed as G4-P[6]-I5-R1-C1-M1-A1-N1-T7-E1-H1. This genotype includes the porcine-like VP6 genotype (I5) and bovine-like NSP3 genotype (T7). Phylogenetic analysis revealed that R479 genes encoding VP1, VP2, VP3, VP6, VP7, VP8*, NSP1, NSP4, and NSP5 were more closely related to those of porcine rotaviruses than human or other animal rotaviruses. In contrast, it was remarkable that the NSP3 gene of R479 was genetically closely related to only a bovine rotavirus strain UK. The NSP2 gene of R479 was also unique and clustered with only the G5P[8] human strain IAL28 and G3P[24] simian strain TUCH. These results suggested that R479 may be a reassortant virus having the NSP3 gene from a bovine rotavirus in the genetic background of a porcine rotavirus, with an NSP2 gene related to the porcine-human reassortant strain IAL28. To our knowledge, R479 is the first porcine-bovine reassortant rotavirus isolated from a human.

Genetic characterization of rotavirus in children in South Korea from 2007 to 2009

Rotavirus is the most important etiological agent in children with acute gastroenteritis (AGE). The recent implementation of a rotavirus vaccine in Korea requires the monitoring of prevailing rotavirus strains in order to control the infection. One hundred thirty-nine rotavirus strains were detected in children hospitalized with AGE in Seoul, Korea from 2007 to 2009. The most frequent combination of genotypes was G9P[8] (32.1%), followed by G1P[8] (20.7%) and G3P[8] (11.7%). Mixed G-types were detected in 14 samples (10.0%), and mixed P-types were found in six samples (4.3%). G9 genotypes were predominant from 2007 to 2008, whereas G1 and G3 genotypes were predominant from 2008 to 2009. G1 strains clustered mostly in the Id lineage, and some clustered in the Ic, IId, and Ia lineages. G2 strains clustered in the IV and V lineages. G3 and G9 strains clustered in the IIId and Id lineages, respectively. This study shows a rapid change of the prevalent genotype from G9 to G1 and G3 genotypes, suggesting that continuous surveillance of rotavirus strains is important for rotavirus vaccination.

A novel multiplex RT-PCR for identification of VP6 subgroups of human and porcine rotaviruses

VP6 protein antigens allow classification of rotaviruses into at least four subgroups, depending on the presence or absence of SG-specific epitopes: SG I, SG II, SG (I+II), and SG non-(I+II). However, MAbs against epitopes on the VP6 protein of human and porcine rotaviruses, sometimes, do not recognize SG-specific epitopes or recognize irrelevant-SG epitopes and therefore result in the incorrect assignment of subgroups. In order to solve this problem, a novel multiplex RT-PCR was developed as an alternative tool to identify VP6 genogroups using newly designed primers which are specific for genogroup I or II. The sensitivity and specificity of the newly developed multiplex RT-PCR method was evaluated by testing with human and porcine rotaviruses of known SG I, SG II, SG (I+II), and SG non-(I+II) strains in comparison with monoplex RT-PCR and VP6 sequence analysis. The results show that the genogroups of both human and porcine rotaviruses as determined by the new multiplex RT-PCR method were in 100% agreement with those determined by monoplex RT-PCR and VP6 sequence analysis. The method was shown to be specific, sensitive, less-time consuming, and successful in genogrouping clinical isolates of rotaviruses circulating in children and piglets with acute diarrhea.

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

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

Characterization of group A rotavirus infections in adolescents and adults from Pune, India: 1993-1996 and 2004-2007

A total of 1,591 fecal specimens were collected in 1993-1996 and 2004-2007 from adolescents and adults with acute gastroenteritis in Pune, India for detection and characterization of rotavirus. At the two time points, group A rotavirus was detected in 8.6% and 16.2% of the adolescents and 5.2% and 17.2% of the adults, respectively. Reverse transcription-PCR with consensus primers followed by multiplex genotyping PCR detected common strains G1P[8], G2P[4], G3P[8], and G4P[8] in a total of 53.1% of the samples from 1993 to 1996, while the only prevalent strain identified in 2004-2007 was G2P[4] (23.5% of total). Uncommon rotavirus strains (G1P[4], G2P[8] G9P[6]/P[4]) increased from 7.8% (1993-1996) to 41.2% (2004-2007), while the prevalence of mixed rotavirus infections was high (39%/35%) at both time points. Mixed infections detected by multiplex PCR were confirmed by sequencing two or more individual genotype-specific PCR products of the VP7 and VP4 genes from the same sample. Phylogenetic analysis of the sequences showed circulation of a heterogeneous rotavirus strain population comprising genotypes G1 (lineages I and IIb), G2 (lineages I and IIb), G4 (lineage Ia), P[4] (lineages P[4]-5 and P[4]-1), P[8] (lineages P[8]-II and P[8]-III), and P[6] (M37-like lineage). The VP6 gene sequences of the nontypeable strains were most homologous to animal strains. This study documents the molecular epidemiology of rotavirus strains in adolescents and adults in India, and suggests that it may be important to monitor these strains over time for the potential impact on rotavirus vaccines under development for use in the Indian population. J. Med. Virol. 82:519-527, 2010. (c) 2010 Wiley-Liss, Inc.

Novel light-upon-extension real-time PCR assay for simultaneous detection, quantification, and genogrouping of group A rotavirus

We have developed a light-upon-extension (LUX) real-time PCR assay for detection, quantification, and genogrouping of group A rotavirus (RV), the most common cause of acute gastroenteritis in children. The LUX system uses a fluorophore attached to one primer and having a self-quenching hairpin structure, making it cost-effective and specific. We designed genogroup-specific primers having different fluorophores, making it possible to differentiate between the two main genogroups of human group A RVs. The assay was applied on clinical stool specimens from Sweden and Central America (n=196) and compared to immunological and conventional PCR assays. The genogrouping ability was further validated against a subset of clinical specimens, which had been genogrouped using monoclonal antibodies. Our real-time PCR assay detected and quantified all positive specimens (n=145) and exhibited higher sensitivity than immunological assays and conventional PCR. The assay exhibited a wide dynamic range, detecting from 5 to >10(7) genes per PCR, resulting in a theoretical lower detection limit of <10,000 viruses per gram of stool. No cross-reaction was observed with specimens containing norovirus, sapovirus, astrovirus, or adenovirus. In total, 22 (15%) of the positive clinical specimens were identified as genogroup I, 122 (84%) were identified as genogroup II, and 1 specimen was found to contain a mix of both genogroups. All genogroup I-positive specimens were associated with capsid glycoprotein 2 (G2). No significant difference in viral load was found between genogroups or geographic region. The detection and quantification, combined with the genogrouping ability, make this assay a valuable tool both for diagnostics and for molecular epidemiological investigations.

Analysis of genetic diversity and molecular evolution of human group B rotaviruses based on whole genome segments

Group B rotavirus (GBR) is a rare enteric pathogen that causes severe diarrhoea, primarily in adults. Nearly full-length sequences of all 11 RNA segments were determined for human GBRs detected recently in India (IDH-084 in 2007, IC-008 in 2008), Bangladesh (Bang117 in 2003) and Myanmar (MMR-B1 in 2007), and analysed phylogenetically with the sequence data of GBRs reported previously. All RNA segments of GBR strains from India, Bangladesh and Myanmar showed >95 % nucleotide sequence identities. Among the 11 RNA segments, the VP6 and NSP2 genes showed the highest identities (>98 %), whilst the lowest identities were observed in the NSP4 gene (96.1 %), NSP5 gene (95.6 %) and VP8*-encoding region of the VP4 gene (95.9 %). Divergent or conserved regions in the deduced amino acid sequences of GBR VP1-VP4 and NSP1-NSP5 were similar to those in group A rotaviruses (GARs), and the functionally important motifs and structural characteristics in viral proteins known for GAR were conserved in all of the human GBRs. These findings suggest that, whilst the degree of genetic evolution may be dependent on each RNA segment, human GBR may have been evolving in a similar manner to GAR, associated with the similar functional roles of individual viral proteins.

Clinical and molecular epidemiology of rotavirus in children with community-acquired and hospital-acquired diarrhea in Shanghai, China

A hospital-based investigation was conducted to understand the epidemiologic profile of rotavirus diarrhea due to community-acquired and hospital-acquired infection among children >28 days of age, between November 2006 and January 2008 in Shanghai. Rotavirus infection was related to 37.2% of clinic visit and 48.1% of ward admission attributable to community-acquired noninvasive bacterial diarrhea among Shanghainese children. Rotavirus was responsible for 54.8% of nosocomial diarrhea. G3P[8] (56.8%) was the most prevalent, followed by G1P[8] (15.8%), G2P[4] (3.0%), and G9P[8] (2.3%).

First molecular detection of group A rotaviruses in drinking water sources in Beijing, China

The most prevalent group A rotavirus found in the diarrheic children was also determined in drinking water sources including raw water, treated water and tap water in Beijing, and then the possible contamination contributions to tap water for human consumption were discussed in this study. A total of 26 raw water samples, 77 treated water samples and 143 tap water samples in Beijing were collected for analysis of group A rotavirus from April 2006 to August 2007. According to the results, it was shown that group A rotaviruses occurred in 9 raw water samples (34.6%), 9 treated water samples (11.7%) and 32 tap water samples (22.4%) during the sampling period, and low disinfectant residuals or a vulnerability of the distribution system to pressure transients, in addition to raw water, may account for the group A rotaviruses contamination to tap water. The rotavirus contamination observed in this study may highlight a potential public health risk and illustrate the importance of including routine virological analysis of drinking water supplies during winter time in Beijing.

Phylogenetic analysis of rotaviruses with predominant G3 and emerging G9 genotypes from adults and children in Wuhan, China

Prevalence and phylogenetic relatedness of rotaviruses causing diarrheal diseases in children and adults were analyzed in Wuhan, China. During a period between June 2006 and February 2008, group A rotavirus was identified in 24.9% (280/1126) and 7.6% (83/1088) of specimens taken from children and adults, respectively. G3P[8] was the most frequent genotype in both children (66.3%) and adults (62.7%), followed by G1P[8] (20.3% and 26.2%, respectively). G9 was detected in specimens from six children (2.0%) and seven adults (5.6%). The VP7 genes of G3P[8] rotaviruses from children and adults showed extremely high sequence identities to each other (98.9-100%) and also to those of G3 viruses isolated in Wuhan in 2003-2004. In the phylogenetic analysis of the VP7 gene, the G3P[8] rotaviruses in Wuhan were clustered into a single lineage with some G3 viruses, which had been referred to as "the new variant G3" rotaviruses, reported recently in East Asia and Southeast Asia. Similar to G3P[8] rotaviruses, extremely high sequence identities between children and adults were observed for VP7 genes of G1 and G9 rotaviruses. The G9 viruses were clustered in the lineage of globally spreading strains, while G1 viruses were genetically close to those reported previously in China and Japan. These findings indicated the persistence of the variant G3 rotaviruses and spread of G9 rotaviruses derived from the global G9 lineage in Wuhan, and suggested that the rotaviruses were circulating among children and adults, irrelevant to the G types.

Emerging G9 rotavirus strains in the northwest of China

Although G9 rotaviruses have become one of the important rotavirus genotypes worldwide, they have been uncommon in China. Recently, we reported G9 rotaviruses as a highly prevalent genotype in Xinjiang, the northwest part of China [Yang, X., Matthijnssens, J., Sun, H., Muhamaiti, J., Zhang, B., Nahar, S., Van Ranst, M., Rahman, M., 2008. Temporal changes of rotavirus strain distribution in a northwest city of China, 1996-2005. Int. J. Infect. Dis., June (Epub ahead of print)]. Here we report the genetic variations of the Xinjiang-G9 rotaviruses isolated between 1999 and 2005. Sequence analysis of the VP7 genes of Xinjiang-G9 strains indicated that they were more closely related to the contemporary global G9 strains than to the prototype Chinese G9 strains. However, their VP4 genes were most similar to those from the locally circulating G1P[8], G2P[4], G3P[6] and G3P[8] strains. This indicates that reassortment rather than antigenic drift might be the preferred evolutionary mechanism for the emergence of the G9 rotaviruses in Xinjiang. These findings will be of major significance for understanding the emergence of newly introduced rotavirus strains.

Viral diversity and dynamics in an infant gut

Metagenomic sequencing of DNA viruses from the feces of a healthy week-old infant revealed a viral community with extremely low diversity. The identifiable sequences were dominated by phages, which likely influence the diversity and abundance of co-occurring microbes. The most abundant fecal viral sequences did not originate from breast milk or formula, suggesting a non-dietary initial source of viruses. Certain sequences were stable in the infant's gut over the first 3 months of life, but microarray experiments demonstrated that the overall viral community composition changed dramatically between 1 and 2 weeks of age.

Phylogenetic analysis of porcine rotavirus in Argentina: Increasing diversity of G4 strains and evidence of interspecies transmission

Group A rotaviruses are one of the most frequently detected viral agents associated with neonatal diarrhea in piglets. In order to characterize rotavirus (RV) strains circulating in Argentinean swine, four porcine production farms located in Buenos Aires were studied. RV strains genotyped as P[6]G4, P[6]G8 and P[1]G6 were found in piglets under 30 days of age, without diarrhea. Phylogenetic and sequence analysis of the VP7 gene from G4 strains available in databases, reveals five porcine new lineages (III-VII) and three sublineages (VIIa-VIIc). The G4 porcine Argentinean strains were grouped with a porcine RV strain isolated in Brazil and another RV strain isolated from a child with diarrhea in Mexico, constituting an American lineage (VII). On the other hand, porcine G6 and G8 were closely related to RV's circulating in Argentinean cattle and South-American camelids, respectively. The fact that G4 porcine lineages were epidemiologically related to human strains, and G6 and G8 Argentinean porcine strains were found related to bovine and South-American camelids, respectively, suggests that pigs might play a crucial role as reservoir and generator of newly adapted emerging RV strains for human and other species.