Genetic characterization of a novel, naturally occurring recombinant human G6P[6] rotavirus

Immunogenicity of a Rotavirus VP8* Multivalent Subunit Vaccine in Mice

Rotavirus remains a significant public health threat, especially in low-income countries, where it is the leading cause of severe acute childhood gastroenteritis, contributing to over 128,500 deaths annually. Although the introduction of the Rotarix and RotaTeq vaccines in 2006 marked a milestone in reducing mortality rates, approximately 83,158 preventable deaths persisted, showing ongoing challenges in vaccine accessibility and effectiveness. To address these issues, a novel subcutaneous vaccine formulation targeting multiple rotavirus genotypes has been developed. This vaccine consists of nine VP8* proteins from nine distinct rotavirus genotypes and sub-genotypes (P[4], P[6], P[8]LI, P[8]LIII, P[8]LIV, P[9], P[11], P[14], and P[25]) expressed in E. coli. Two groups of mice were immunized either with a single immunogen, the VP8* from the rotavirus Wa strain (P[8]LI), or with the nonavalent formulation. Preliminary results from mouse immunization studies showed promising outcomes, eliciting antibody responses against six of the nine immunogens. Notably, significantly higher antibody titers against VP8* P[8]LI were observed in the group immunized with the nonavalent vaccine compared to mice specifically immunized against this genotype alone. Overall, the development of parenteral vaccines targeting multiple rotavirus genotypes represents a promising strategy in mitigating the global burden of rotavirus-related morbidity and mortality, offering new avenues for disease prevention and control.

Factors associated with dehydrating rotavirus diarrhea in children under five in Bangladesh: An urban-rural comparison

Introduction

Rotavirus is the leading cause of dehydrating diarrhea in young children worldwide. This study aimed to identify the factors associated with dehydrating rotavirus diarrhea in children under five years of age in urban and rural Bangladesh.

Methods

The study analyzed data from 7,758 children under five who presented with rotavirus diarrhea to Dhaka (urban) and Matlab (rural) hospital of icddr,b during 2009–2018, and were enrolled in the Diarrheal Disease Surveillance System. Cases were defined as children having rotavirus isolated in stool specimens presented with dehydrating diarrhea. Controls were children infected with rotavirus have no dehydration. Multivariable logistic regression models were built to identify the factors associated with dehydrating diarrhea.

Results

Among the rotavirus-infected children, 1,784 (34%) in Dhaka and 160 (6%) in Matlab had diarrhea with some or severe dehydration. The female children and age group 24–59 months age was found to be at higher risk of dehydration compared to 6–11 months age. In the multivariable logistic regression model, maternal illiteracy, vomiting, the onset of diarrhea less than 24 hours prior to presenting to the hospital, monsoon months, stunting, and wasting were significantly associated with dehydrating rotavirus diarrhea among children aged 0–59 months in Dhaka. In Matlab, monthly income, duration less than 24 hours prior to attending the hospital, and wasting had an independent significant association with dehydrating rotavirus diarrhea episodes.

Conclusions

Considering factors diversity, educating parents and proper counselling by health care personnel during diarrhea, could lessen the severity of dehydration and the number of hospital visits later on by eliminating the modifiable risk factors among the children, which needs further studies.

Isolation and whole protein characterization of species A and B bovine rotaviruses from Chinese calves

Rotaviruses (RVs) account for severe diarrhea in children and young animals globally. In the current study, the fecal samples of diarrheic calves from a beef farm in Inner Mongolia were screened for RVA by ELISA and RT-PCR, followed by culture of three positive RVA samples in the MA-104 cell line. After 10 blind passages, cytopathic effects (CPE) appeared as detachment, granulation, and clustering of the inoculated cells. The virus isolates were identified by RT-PCR (VP6 gene RVA) and ESI-LC-MS/MS for whole protein sequencing. The protein sequences demonstrated the presence of two strains from species A rotavirus and one RVB strain; RVA/Cow-tc/CHN/35333/2019/G6P[5] was mixed with one RVB strain (RVB/Cow-tc/CHN/35334/2019/G5P[3]) in two samples, and RVA/Cow-tc/CHN/10927/2019/G8P[7] was found in one sample. They are of genotype constellations (G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3), (G8-P[7]-I5-R1-C1- M2-A1-N1-T1-E1-H1), and (G5-P[3]-I3-R5-C5-A5-N4-H5), respectively. Besides, phylogenetic analysis of the obtained sequences demonstrated viral evolution.

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

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

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.

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.

A Multiplex PCR/LDR Assay for Viral Agents of Diarrhea with the Capacity to Genotype Rotavirus

Rotavirus and noroviruses are major causes of diarrhea. Variable rotavirus vaccination efficacy in Africa and Asia is multifactorial, including the diversity of circulating strains and viral co-infection. We describe a multiplexed assay that detects and genotypes viruses from stool specimens. It includes a one-step reverse transcriptase PCR reaction, a ligase detection reaction (LDR), then hybridization of fluorescent products to micro-beads. In clinical samples it detects rotavirus, caliciviruses (sapovirus and norovirus), mixed infections, and genotypes or genogroups of rotaviruses and noroviruses, respectively. The assay also has the capacity to detect hepatitis A. The assay was validated on reference isolates and 296 stool specimens from the US and Ghana. The assay was 97% sensitive and 100% specific. The genogroup was concordant in 100% of norovirus, and the genotype in 91% and 89% of rotavirus G- and P-types, respectively. Two rare rotavirus strains, G6P[6] and G6P[8], were detected in stool specimens from Ghana. The high-throughput assay is sensitive, specific, and may be of utility in the epidemiological surveillance for rare and emerging viral strains post-rotavirus vaccine implementation.

Rotavirus and norovirus in children with severe diarrhea in Burkina Faso before rotavirus vaccine introduction

Burkina Faso introduced rotavirus vaccine (RotaTeq) to the national immunization program in November 2013. This study describes the detection rates, clinical profiles, and molecular epidemiology of rotavirus and norovirus (NoV) infections among children <5 years hospitalized (n = 154) because of acute diarrhea in Ouagadougou, Burkina Faso, from December 2012 to November 2013, just before the start of vaccination. Overall, 44% and 23% of fecal samples were positive for rotavirus and NoV, respectively, most of them detected during the cold dry season (December-March). The predominant G/P combinations were G12P[8] (47%) and G6P[6] (30%). G2P[4] (n = 3), G12P[6] (n = 3), and G6P[8] (n = 1) were also detected. Nearly all (94%) successfully genotyped NoV strains belonged to genotype GII.4. The predominance of rotavirus and NoV was noteworthy in the age group ≤6 months, with 67% rotavirus and 22% NoV, respectively. Vomiting was significantly more common among rotavirus-infected children. To conclude, this study shows high detection rates of both rotavirus and NoV in children with severe diarrhea in Burkina Faso just before the introduction of rotavirus group A vaccination. The results can be used for estimating the impact of rotavirus group A vaccination, which started in the end of 2013. Furthermore, this study shows that the G6P[6] rotavirus strains emerging in Burkina Faso in 2010 is now established as a regionally important genotype.

Whole-genome sequencing and analyses identify high genetic heterogeneity, diversity and endemicity of rotavirus genotype P[6] strains circulating in Africa

Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P[6] VP4 full-length sequences downloaded from GenBank. The strength of association between the phenotypic features and the phylogeny was also determined. A number of reassortment and mixed infections of RVA genotype P[6] strains were observed in this study. Phylogenetic analyses demostrated the extensive genetic diversity that exists among human P[6] strains, porcine-like strains, their concomitant clades/subclades and estimated that P[6] VP4 gene has a higher substitution rate with the mean of 1.05E-3 substitutions/site/year. Further, the phylogenetic analyses indicated that genotype P[6] strains were endemic in Africa, characterised by an extensive genetic diversity and long-time local evolution of the viruses. This was also supported by phylogeographic clustering and G-genotype clustering of the P[6] strains when Bayesian Tip-association Significance testing (BaTS) was applied, clearly supporting that the viruses evolved locally in Africa instead of spatial mixing among different regions. Overall, the results demonstrated that multiple mechanisms such as reassortment events, various mutations and possibly interspecies transmission account for the enormous diversity of genotype P[6] strains in Africa. These findings highlight the need for continued global surveillance of rotavirus diversity.

Burden and Risk Factors of Antimicrobial Use in Children Less Than 5 Years of Age with Diarrheal Illness in Rural Bangladesh

Antimicrobial overuse contributes to antimicrobial resistance. Empiric use of antimicrobials for diarrheal illness is warranted only in a minority of cases, because of its self-limiting nature and multifactorial etiology. This study aims to describe the factors contributing to antimicrobial overuse for diarrheal disease among children less than 5 years of age in rural Bangladesh. A total of 3,570 children less than 5 years of age presenting with diarrhea in a tertiary level hospital were enrolled in the study. The rate of antimicrobial use at home was 1,395 (39%), compared with 2,084 (89%) during a hospital visit. In a multivariate analysis, factors associated with antimicrobial use at home included residence located more than 5 miles from a hospital; use of zinc and oral rehydration salts at home; vomiting; greater than 10 stools per 24 hours; diarrheal duration greater than 3 days; and rotavirus diarrhea (P < 0.05 for all). Characteristics of children more likely to be given antimicrobials in a health-care setting included greater than 10 stools per 24 hours; duration of diarrhea greater than 3 days; use of antimicrobials before hospital presentation; fever (≥ 37.8°C); rectal straining; and Shigella infection (P < 0.05 for all). The most commonly used drugs in rotavirus diarrhea were azithromycin and erythromycin, both before hospital presentation and during hospital admission. Our study underscores the importance of diligent vigilance on the rationale use of antimicrobials both at home and in health-care facilities with a special concern for children less than 5 years of age living in rural Bangladesh.

Long-term impact of changing childhood malnutrition on rotavirus diarrhoea: Two decades of adjusted association with climate and socio-demographic factors from urban Bangladesh

Background

There is strong association between childhood rotavirus, diarrhoea, climate factors and malnutrition. Conversely, a significant nutritional transition (reduced under-nutrition) with a concurrent increasing trend of rotavirus infection in last decade was also observed among under 5 children, especially in developing countries including Bangladesh. Considering the pathophysiology of rotavirus, there might be an interaction of this nutrition transition which plays a pivotal role in increasing rotavirus infection in addition to climate and other man-made factors in urban areas such as Dhaka, Bangladesh.

Methods

Relevant monthly data from 1993–2012 were extracted from the archive of the Diarrhoeal Disease Surveillance System of icddr, b and linked with data collected from the Dhaka station of the Bangladesh Meteorological Department (mean temperature, rainfall, sea level pressure and humidity). Seasonal autoregressive integrated moving average time series models were deployed to determine the association between the monthly proportion of rotavirus infection and underweight, stunting and wasting adjusting for climate, socio-demographic and sanitation factors.

Finding

The proportion of rotavirus cases among all causes diarrhoea increased from 20% in 1993 to 43% in 2012 (Chi squared for trend p = 0.010). In contrast, underweight, stunting and wasting decreased from 59%-29% (p<0.001); 53%-21% (p<0.001) and 32%-22% (p<0.001) respectively over the same period. Mean ambient temperature increased from 25.76°C-26.62°C (p = 0.07); mean rainfall, sea level pressure and mean humidity decreased from 234.92–111.75 mm (p = 0.5), 1008.30–1006.61 mm of hg (p = 0.02) and 76.63%-70.26% (p<0.001), respectively. In the adjusted model, a decrease in monthly proportion of underweight [coef.: -0.189 (95% CI:-0.376, -0.003)] and wasting [-0.265 (-0.455, -0.075)] were significantly and inversely associated with rotavirus infection. However, an inverse but insignificant association was observed for stunting [-0.070 (-0.249, 0.109)].

Interpretation

The reduction of acute childhood malnutrition is significantly associated with increasing rotavirus diarrhoea among under-5 children. Thus mass vaccination in addition to interventions directed at man-made modifiable predictors for prevention and control is warranted.

Clinical severity and molecular characteristics of circulating and emerging rotaviruses in young children attending hospital emergency departments in France

Group A rotavirus (RVA) is the leading cause of acute gastroenteritis in young children worldwide. A prospective surveillance network has been set up to investigate the virological and clinical features of RVA infections and to detect the emergence of potentially epidemic strains in France. From 2009 to 2014, RVA-positive stool samples were collected from 4800 children <5 years old attending the paediatric emergency units of 16 large hospitals. Rotaviruses were then genotyped by RT-PCR with regard to their outer capsid proteins VP4 and VP7. Genotyping of 4708 RVA showed that G1P[8] strains (62.2%) were predominant. The incidence of G9P[8] (11.5%), G3P[8] (10.4%) and G2P[4] (6.6%) strains varied considerably, whereas G4P[8] (2.7%) strains were circulating mostly locally. Of note, G12P[8] (1.6%) strains emerged during the seasons 2011-12 and 2012-13 with 4.1% and 3.0% prevalence, respectively. Overall, 40 possible zoonotic reassortants, such as G6 (33.3%) and G8 (15.4%) strains, were detected, and were mostly associated with P[6] (67.5%). Analysis of clinical records of 624 hospitalized children and severity scores from 282 of them showed no difference in clinical manifestations or severity in relation to the genotype. The relative stability of RVA genotypes currently co-circulating and the large predominance of P[8] type strains may ensure vaccine effectiveness in France. The surveillance will continue to monitor the emergence of new reassortants that might not respond to current vaccines, all the more so as all genotypes can cause severe infections in infants.

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.

Molecular epidemiology of enteric viruses and genotyping of rotavirus A, adenovirus and astrovirus among children under 5 years old in Gabon

OBJECTIVES

This study aimed to determine the prevalence of enteric viruses causing gastroenteritis, and the circulating stains, in Gabonese children under five years old who visited health centers between March 2010 and June 2011.

METHODS

Stool specimens were collected and sent for analysis to CIRMF (Centre International de Recherches Médicales de Franceville). Stools were screened for six enteric viruses (rotavirus, adenovirus, norovirus I and II, sapovirus, human astrovirus) by means of a multiplex real-time reverse transcription polymerase chain reaction, and Rotavirus A, Adenovirus and Astrovirus were genotyped.

RESULTS

Among the 317 specimens analyzed, 193 (60.9%) were positive for at least one enteric virus. Rotavirus A (RVA) (27.1%) was the most frequently detected virus, followed by human Adenovirus (HAdV) (19.6%), Norovirus II (NoVs-II) (13.9%), Norovirus I (NoVs-I) (9.1%), Sapovirus (SaV) (9.5%) and human Astrovirus (HAstV) (6.3%). One-third of the 193 positive samples contained more than one virus. The most common Rotavirus A genotype was G6P[6]. Various HAdV serotypes were found. HAstV-1 was identified.

CONCLUSIONS

These findings improve our knowledge of circulating enteric viruses in Gabon. The emergence of unusual G6P[6] strain of rotavirus A, predominant, suggested a particular epidemiological surveillance of circulating rotavirus strains during the introduction of vaccination in Gabon.

Determinants of percent expenditure of household income due to childhood diarrhoea in rural Bangladesh

There is limited information on percent expenditure of household income due to childhood diarrhoea especially in rural Bangladesh. A total of 4205 children aged <5 years with acute diarrhoea were studied. Percent expenditure was calculated as total expenditure for the diarrhoeal episode divided by monthly family income, multiplied by 100. Overall median percent expenditure was 3·04 (range 0·01-94·35). For Vibrio cholerae it was 6·42 (range 0·52-82·85), for enterotoxigenic Escherichia coli 3·10 (range 0·22-91·87), for Shigella 3·17 (range 0·06-77·80), and for rotavirus 3·08 (range 0·06-48·00). In a multinomial logistic regression model, for the upper tertile of percent expenditure, significant higher odds were found for male sex, travelling a longer distance to reach hospital (⩾median of 4 miles), seeking care elsewhere before attending hospital, vomiting, higher frequency of purging (⩾10 times/day), some or severe dehydration and stunting. V. cholerae was the highest and rotavirus was the least responsible pathogen for percent expenditure of household income due to childhood diarrhoea.

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

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

Community based case-control study of rotavirus gastroenteritis among young children during 2008-2010 reveals vast genetic diversity and increased prevalence of G9 strains in Kolkata

BACKGROUND

Group A Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children (<5 years) worldwide. Although rotavirus vaccines have been successfully administered in many countries, in India the introduction of rotavirus vaccine in national immunization program was approved in 2014. Since high disease burden and large number of genetic variants have been reported from low income countries including India, monitoring of rotavirus was initiated prior to implementation of the vaccine in the region.

METHODS

A total number of 3,582 stool samples were collected from an urban slum community in Kolkata, among which 1,568 samples were obtained from children of ≤ 5 years of age, with moderate to severe diarrhoea and 2,014 samples were collected from age-sex matched healthy neighbourhood controls. Rotavirus positive samples were typed by multiplex semi-nested PCR and nucleotide sequencing. Circulating strains were phylogenetically analyzed.

RESULTS

Among 1,568 children with diarrhoea, 395 (25.2%), and among 2,014 asymptomatic children, 42 (2%) were rotavirus positive. G1P[8] was identified as the most common strain (32%) followed by G9P[8] (16.9%), G2P[4] (13.5%) and G9P[4] (10.75%). G12 strains with combinations of P[4], P[6] and P[8] comprised 11.9% of total positive strains. The rest (<10%) were rare and uncommon strains like G1P[4], G1P[6], G2P[8] and animal-like strains G4P[6], G6P[14] and G11P[25]. The 42 rotavirus positive samples from asymptomatic children revealed common genotypes like G1, G2 and G9.

CONCLUSION

This community based case-control study showed increased predominance of genotype G9 in Kolkata. It also confirmed co-circulation of a large number of genetic variants in the community. Asymptomatic rotavirus positive children though low in number can also be a source of dispersal of infection in the community. This study provides background information to the policy makers for implementation of rotavirus vaccines in this region.

Aetiologies of diarrhoea in adults from urban and rural treatment facilities in Bangladesh

The objective of our analysis was to describe the aetiology, clinical features, and socio-demographic background of adults with diarrhoea attending different urban and rural diarrhoeal disease hospitals in Bangladesh. Between January 2010 and December 2011, a total of 5054 adult diarrhoeal patients aged ⩾20 years were enrolled into the Diarrhoeal Disease Surveillance Systems at four different hospitals (two rural and two urban) of Bangladesh. Middle-aged [adjusted odds ratio (aOR) 0·28, 95% confidence interval (CI) 0·23-0·35, P < 0·001] and elderly (aOR 0·15, 95% CI 0·11-0·20, P < 0·001) patients were more likely to present to rural diarrhoeal disease facilities than urban ones. Vibrio cholerae was the most commonly isolated pathogen (16%) of the four pathogens tested followed by rotavirus (5%), enterotoxigenic Escherichia coli (ETEC) (4%), and Shigella (4%). Of these pathogens, V. cholerae (19% vs. 11%, P < 0·001), ETEC (9% vs. 4%, P < 0·001), and rotavirus (5% vs. 3%, P = 0·013) were more commonly detected from patients presenting to urban hospitals than rural hospitals, but Shigella was more frequently isolated from patients presenting to rural hospitals than urban hospitals (7% vs. 2%, P < 0·001). The isolation rate of Shigella was higher in the elderly than in younger adults (8% vs. 3%, P < 0·001). Some or severe dehydration was higher in urban adults than rural adults (P < 0·001). Our findings indicate that despite economic and other progress made, conditions facilitating transmission of V. cholerae and Shigella prevail in adults with diarrhoea in Bangladesh and further efforts are needed to control these infections.

Gastroenteritis due to typhoidal Salmonella: a decade of observation at an urban and a rural diarrheal disease hospital in Bangladesh

Background

The study aimed to compare the socio-demographic, host and clinical characteristics, seasonality and antimicrobial susceptibility of Typhoidal Salmonella (Salmonella enterica serovar Typhi and Paratyphi) (TS) with diarrhea between urban and rural Bangladesh.

Methods

Relevant information of 77/25,767 (0.30%) and 290/17,622 (1.65%) patients positive with TS (in stool) were extracted from the data archive of Diarrheal Disease Surveillance System of icddr,b (urban Dhaka and rural Matlab Hospitals respectively) during 2000–2012. Comparison group (diarrhea patients negative for TS) was randomly selected from the database (1:3 ratio). Two poisson regression models were investigated for modelling seasonal effects on the number of cases.

Results

Salmonella Typhi was more frequently isolated in Dhaka than Matlab (57% vs. 5%, p < 0.001); while Salmonella Paratyphi was more frequent in Matlab than Dhaka (96% vs. 43%; p < 0.001). Fever [adj. OR-5.86 (95% CI: 2.16, 15.94)], antimicrobial use at home [5.08 (2.60, 9.90)], and fecal red blood cells [2.53 (1.38, 4.64)] were significantly associated with detection of TS in stool of patient from Dhaka. For Matlab, the correlates were, vomiting [1.88 (1.35, 2.64)], fecal macrophage [1.89 (1.29, 2.74)] in addition to fever and duration of diarrhea and antimicrobial use. At Dhaka, all Salmonella Typhi isolates were susceptible to ceftriaxone; while in Dhaka and Matlab however, for ciprofloxacin it was 45% and 91%, respectively. Susceptibility to chloramphenicol, ampicillin, trimethoprim-sulphamethoxazole and nalidixic acid ranged from 12%-58%. Salmonella Paratyphi were susceptible to ceftriaxone (99%). A significant seasonal trend and year difference (before and after 2007) for Matlab was observed (p < 0.001 for all effects). Dhaka does not show significant year or seasonal effects (p = 0.07 for years and p = 0.81 and p = 0.18 for the cos and sin components, respectively). While not significant, two seasonal peaks were observed in Dhaka (January-February and September-November); while a single peak (August-November) was observed in Matlab.

Conclusions

Proportion of serovar distribution of TS and their clinical characteristics, antimicrobial susceptibility and seasonal pattern were different among diarrhea patients in urban Dhaka and rural Matlab of Bangladesh.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2334-14-435) contains supplementary material, which is available to authorized users.

Rotavirus surveillance in Kisangani, the Democratic Republic of the Congo, reveals a high number of unusual genotypes and gene segments of animal origin in non-vaccinated symptomatic children

Group A rotavirus (RVA) infections form a major public health problem, especially in low-income countries like the Democratic Republic of the Congo (COD). However, limited data on RVA diversity is available from sub-Saharan Africa in general and the COD in particular. Therefore, the first aim of this study was to determine the genetic diversity of 99 RVAs detected during 2007–2010 in Kisangani, COD. The predominant G-type was G1 (39%) and the most predominant P-type was P[6] (53%). A total of eight different G/P-combinations were found: G1P[8] (28%), G8P[6] (26%), G2P[4] (14%), G12P[6] (13%), G1P[6] (11%), G9P[8] (4%), G4P[6] (2%) and G8P[4] (1%). The second aim of this study was to gain insight into the diversity of P[6] RVA strains in the COD. Therefore, we selected five P[6] RVA strains in combination with the G1, G4, G8 (2x) or G12 genotype for complete genome analysis. Complete genome analysis showed that the genetic background of the G1P[6] and G12P[6] strains was entirely composed of genotype 1 (Wa-like), while the segments of the two G8P[6] strains were identified as genotype 2 (DS-1-like). Interestingly, all four strains possessed a NSP4 gene of animal origin. The analyzed G4P[6] RVA strain was found to possess the unusual G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1 constellation. Although the majority of its genes (if not all), were presumably of porcine origin, this strain was able to cause gastro-enteritis in humans. The high prevalence of unusual RVA strains in the COD highlights the need for continued surveillance of RVA diversity in the COD. These results also underline the importance of complete genetic characterization of RVA strains and indicate that reassortments and interspecies transmission among human and animal RVAs strains occur regularly. Based on these data, RVA vaccines will be challenged with a wide variety of different RVA strain types in the COD.

Aetiology and clinical features of dysentery in children aged <5 years in rural Bangladesh

The study identified the common aetiological agents and prominent clinical features of dysentery cases in children aged <5 years and compared this to non-dysentery diarrhoeal cases from the same population. From January 2010 to December 2011, 2324 children aged <5 years received treatment at Kumudini Hospital, of which 682 (29%) presented with dysentery. Of the dysenteric children, aetiology could not be determined for over half (61%). Shigella spp. accounted for 32% of dysentery cases. Significant associations were found between presence of blood in stool and: child age (24-59 months) [odds ratio (OR) 2.21, 95% confidence interval (CI) 1.49-3.27], no treatment of drinking water at home (OR 2.00, 95% CI 1.09-3.67), vomiting (OR 0.19, 95% CI 0.14-0.25), abdominal pain (OR 4.68, 95% CI 3.24-6.77), straining (OR 16.45, 95% CI 11.92-22.69), wasting (OR 1.66, 95% CI 1.15-2.41), and presence of Shigella in stool (OR 6.25, 95% CI 4.20-9.29) after controlling for confounders. This study makes it clear that appropriate public health strategies are needed to reduce the burden of dysentery in Bangladesh.

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

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

Clinical characteristics, etiology and antimicrobial susceptibility among overweight and obese individuals with diarrhea: observed at a large diarrheal disease hospital, Bangladesh

BACKGROUND

The present study aimed to determine the clinical characteristics and etiology of overweight and obese (OO) individuals with diarrhea attending an urban Dhaka Hospital, International Centre for Diarrheal Disease Research (icddr,b), Bangladesh.

METHODS

Total of 508 under-5 children, 96 individuals of 5-19 years and 1331 of >19 years were identified as OO from the Diarrheal Disease Surveillance System (DDSS) between 1993-2011. Two comparison groups such as well-nourished and malnourished individuals from respective age stratums were selected.

RESULTS

Isolation rate of rotavirus was higher among OO under-5 children compared to malnourished group (46% vs. 28%). Rotavirus infection among OO individuals aged 5-19 years (9% vs. 3%) (9% vs. 3%) and >19 years (6% vs. 4%) (6% vs. 3%) was higher compared to well-nourished and malnourished children. Conversely, Vibrio cholerae was lower among all OO age groups compared to well-nourished and malnourished ones. Shigella (4% vs. 6%) (4% vs. 8%), and Campylobacter (3% vs. 5%) (3% vs. 5%) were lower only among OO in >19 years individuals compared to their counterparts of the same age stratum. Salmonella was similarly isolated in all age strata and nutritional groups. In multinomial logistic regression among under-5 children, significant association was observed only with use of antimicrobials at home [OR-1.97] and duration of hospital stay [OR-0.68]. For individuals aged 5-19 years, use of antimicrobials at home (OR-1.83), some or severe dehydration (OR-3.12), having received intravenous saline (OR-0.46) and rotavirus diarrhea (OR-2.96) were found to be associated with OO respectively. Moreover, significant associations were also found for duration of diarrhea before coming to hospital (>24 hours) (OR-1.24), Shigella (OR-0.46), and Campylobacter (OR-0.58) among >19 years OO individuals along with other associated co-variates in 5-19 years group (all p<0.05).

CONCLUSION AND SIGNIFICANCE

Higher proportion of OO were infected with rotavirus and a greater proportion of them used antimicrobials before coming to the hospital.

Genetic characterization of a rare bovine-like human VP4 mono-reassortant G6P[8] rotavirus strain detected from an infant in Bangladesh

During an ongoing diarrhea etiology surveillance in Mirzapur, Bangladesh, a rare human G6P[8] RVA strain (RVA/Human-wt/BGD/KH2288/2011/G6P[8]) was detected in a stool sample of a 7-month-old infant with acute diarrhea. Complete genotype analyses revealed that KH2288 possessed the G6-P[8]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genotype constellation. Sequence analysis of the VP7 gene revealed a close phylogenetic relationship with bovine G6 strains from India, whereas, the VP4 gene segment was nearly identical to typical human P[8] strain circulating in Bangladesh and the rest of the world. Phylogenetic analysis of the remaining nine gene segments revealed a close relatedness to either animal or animal derived human RVA strain. We speculated that, strain KH2288 was a monoreassortant between a human RVA strain and a RVA strain typically infecting member of the Artiodactyla, such as cattle, goat or sheep. To our knowledge, this is the first complete genotyping report of a naturally occurring G6P[8] RVA strain, worldwide.

Severity of diarrhea and malnutrition among under five-year-old children in rural Bangladesh

Enteric pathogens are commonly associated with diarrhea among malnourished children. This study aimed to determine the association between the severity of diarrheal illnesses and malnutrition among under 5-year-old children. During 2010 and 2011, we studied 2,324 under 5-year-old diarrheal children with mild disease (MD) and moderate-to-severe disease (MSD) attending a hospital in Bangladesh. Children with MSD were more likely to be malnourished compared with children with MD (35% versus 24%, P < 0.001). In multivariate analysis, malnutrition (odds ratio [95% confidence interval] = 1.53 [1.22, 1.92]), age of the child (24-59 months; 1.67 [1.28, 2.19]), fever (1.65 [1.28, 2.12]), abdominal pain (1.87 [1.48, 2.37]), straining (5.93 [4.80, 7.33]), and infection with Shigella (3.26 [2.38, 4.46]) and Vibrio cholerae (2.21 [1.07, 4.58]) were shown to be significantly associated with MSD. Factors significantly associated with malnutrition were disease severity (1.56 [1.24, 1.95]), age (24-59 months; 1.75 [1.38, 2.22]), mother's schooling (1.54 [1.16, 2.04]), and monthly household income (1.71 [1.42, 2.07]). Childhood malnutrition was associated with dysentery and dehydrating diarrhea.

Characteristics of diarrheal illnesses in non-breast fed infants attending a large urban diarrheal disease hospital in Bangladesh

Background

Lack of breast feeding is associated with higher morbidity and case-fatality from both bacterial and viral etiologic diarrheas. However, there is very limited data on the characteristics of non–breastfed infants attending hospital with diarrheal illnesses caused by common bacterial and viral pathogens. Our objective was to assess the impact of lack of breast feeding on diarrheal illnesses in infants living in urban Bangladesh.

Methods

We extracted data of infants (0–11 months) for analyses from the data archive of Diarrheal Disease Surveillance System (DDSS) of the Dhaka Hospital of icddr,b for the period 2008–2011.

Results

The prevalence of breastfeeding in infants attending the hospital with diarrhea reduced from 31% in 2008 to 17% in 2011, with corresponding increase in the prevalence of non-breastfed (chi square for trend <0.001). Among breastfed infants, the incidence of rotavirus infections was higher (43%) among the 0–5 months age group than infants aged 9–11 months (18%). On the other hand, among non-breastfed infants, the incidence of rotavirus infections was much higher (82%) among 9–11 months old infants compared to those in 0–5 months age group (57%) (chi square for trend <0.001). Very similar trends were also observed in the incidence of cholera and ETEC diarrheas among different age groups of breastfed and non-breastfed infants (chi square for trend 0.020 and 0.001 respectively). However, for shigellosis, the statistical difference remained unchanged among both the groups (chi square for trend 0.240).

Conclusion and Significance

We observed protective role of breastfeeding in infantile diarrhea caused by the major viral and common bacterial agents. These findings underscore the importance of promotion and expansion of breastfeeding campaigns in Bangladesh and elsewhere.

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

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

Complete genetic characterization of human G2P[6] and G3P[6] rotavirus strains

During the 2008-2009 rotavirus season, 10 G3P[6] rotavirus strains were isolated for the first time in Belgium, while an outbreak of G2P[6] strains occurred in the USA in 2005-2006. Partial sequencing of the 11 genome segments of the 10 Belgian G3P[6] strains revealed a clonal origin. Two of these strains, and a G2P[6] strain representative of the American outbreak, were selected and sequenced completely to analyze their evolutionary relationships. Genetic analysis revealed that all strains possessed a DS-1-like genotype constellation. The 2 Belgian G3P[6] strains showed >99% sequence identity at the nucleotide level and the American G2P[6] strain was phylogenetically closely related to the Belgian P[6] strains. These data suggest that reassortment(s) involving VP7 occurred recently, and that the prevalence of DS-1-like P[6] rotavirus strains need to be closely monitored because the currently licensed RVA vaccines contain neither the P[6] genotype nor strains with a complete human DS-1 genotype constellation.

Rotavirus in diarrheal children in rural Burkina Faso: high prevalence of genotype G6P[6]

Group A rotavirus (RVA) is the most common cause of severe gastroenteritis in young children globally, and responsible for a significant number of deaths in African countries. While vaccines are available, trials have shown a lesser efficacy in Africa. One of the reasons could be the prevalence and/or emergence of unusual or novel RVA strains, as many strains detected in African countries remain uncharacterized. In this study, we characterized RVA positive specimens from two remote rural areas in Burkina Faso, West Africa. In total 56 RVA positive specimens were subgrouped by their VP6 gene, and G-and P typed by PCR and/or sequencing of the VP7 and VP4 genes, respectively. Notably, we found a high prevalence of the unusual G6P[6]SGI strains (23%). It was the second most common constellation after G9P[8]SGII (32%); and followed by G1P[8]SGII (20%) and G2P[4]SGI (9%). We also detected a G8P[6]SGI strain, for the first time in Burkina Faso. The intra-genetic diversity was high for the VP4 gene with two subclusters within the P[8] genotype and three subclusters within the P[6] genotype which were each associated with a specific G-type, thereby suggesting a genetic linkage. The G6P[6]SGI and other SGI RVA strains infected younger children as compared to SGII strains (p<0.05). To conclude, in this study we observed the emergence of unusual RVA strains and high genetic diversity of RVA in remote rural areas of Burkina Faso. The results highlight the complexity of RVA epidemiology which may have implication for the introduction of rotavirus vaccines currently being evaluated in many African countries.

Emergence of unusual G6P[6] rotaviruses in children, Burkina Faso, 2009-2010

High incidence highlights the need for long-term surveillance of rotavirus strains.

To obtain more information about rotavirus (ROTAV) genotypes in Burkina Faso, we characterized 100 ROTAVs isolated from fecal samples of children with acute gastroenteritis in the capital city of Ouagadougou, during December 2009–March 2010. Of note, 13% of the ROTAV-positive samples, including those with mixed infections, were positive for the unusual G6 genotype ROTAV strain. The genotypes identified were G9P[8], G6P[6], G1P[6], G3P[6], G1P[8], and G2P[4]. G9P[8] subgroup (SG)II strains dominated during the beginning of the ROTAV season, but later in the season, other G types associated with P[6] and SGI specificity emerged. This emergence was related to a shift in the overall age of infected children; ROTAV SGII infected younger children and induced more severe symptoms. The finding of a high incidence of G6P[6] strains highlights the need for long-term surveillance of ROTAV strains in Burkina Faso, especially when ROTAV vaccination is being considered in several African countries.

Burden of rotavirus and other enteropathogens among children with diarrhea in Burkina Faso

OBJECTIVE

There is limited information available regarding the etiology of gastrointestinal infections in Burkina Faso. The aim of this study was to investigate the prevalence and epidemiology of enteric pathogens causing gastroenteritis in young children, with a focus on rotavirus, and to investigate the levels of malnutrition and other clinical factors in association with the severity of diarrhea.

METHODS

A prospective study was undertaken from May 2009 to March 2010, covering the rainy and dry seasons, at the Saint Camille Medical Center in Ouagadougou, Burkina Faso. A total of 309 children less than 5 years of age with diarrhea were enrolled and examined for rotavirus, bacterial, and parasitic infections, as well as clinico-epidemiological aspects.

RESULTS

At least one enteropathogen was detected in 57.9% (n=179) of the children. Of these, 32.4% had rotavirus infections, 16.8% bacterial infections (enteropathogenic Escherichia coli 9.7%, Shigella spp 5.8%, and Salmonella spp 2.3%), and 18.8% parasitic infections (Giardia lamblia 11.3%, Trichomonas intestinalis 6.8%, Entamoeba histolytica/dispar 1.3%). During the cold dry period from December 2009 to February 2010, we observed a large increase in diarrhea cases, which was mainly attributed to rotavirus infections, as 63.8% of these diarrhea cases were positive for rotavirus. In contrast, no rotavirus infection was observed during the rainy season (June-September 2009), when the frequency of parasitic infections was high. Rotavirus and parasitic infections were age-related, with rotavirus being more prevalent in young children (<12 months) and parasites more common in older children (>12 months), while bacteria were equally prevalent among all age groups. Rotavirus infections exhibited more severe symptoms compared to bacteria and parasites, and were associated with fever, vomiting, and severe dehydration. Malnutrition, especially acute malnutrition (wasting), was significantly associated with more severe symptoms in rotavirus-induced diarrhea. The undernourished children also exhibited a prolonged duration of diarrheal episodes.

CONCLUSION

This study demonstrates rotavirus as the main etiological agent in pediatric diarrhea in Burkina Faso, and further shows the great severity of rotavirus-induced diarrhea in undernourished children in Burkina Faso.

Detection of the first G6P[14] human rotavirus strain from a child with diarrhea in Egypt

We report the first detection of a G6P[14] rotavirus strain in Egypt from the stool of a child participating in a hospital-based diarrhea surveillance study conducted throughout the year 2004. Rotavirus infection was initially detected using a rotavirus group A VP6 enzyme immunoassay; the P (VP4) and G (VP7) genotypes of the strain were identified by RT-PCR. We sequenced the VP7 gene and the VP8* portion of the VP4 gene and the strain displayed the strongest identity to the VP7 [>94% nucleotides (nt), >97% amino acids (aa)] and VP4 (>93% nt, >98% aa) sequences of PA169, a novel G6P[14] strain first isolated from a child in Italy during the winter of 1987. Additional sequencing and analysis of the other remaining structural (VP1-VP3, VP6) and non-structural (NSP1-NSP5) proteins support this animal-to-human reassortment theory. According to the full genome classification system, the G6P[14] strain (EGY3399) was assigned to G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genotypes. The greatest similarity of EGY3399 NSP4 and NSP5 gene sequences were to those of ovine and simian origin, respectively. Coupled with other observations, our results suggest G6P[14] isolates rarely cause severe diarrhea in Egyptian children, and support other studies that indicate animal rotavirus contribute to the genetic diversity of rotavirus detected from humans through interspecies transmission and single or multiple segments reassortment.

Molecular and clinical characterization of rotavirus from diarrheal infants admitted to pediatric emergency units in france

BACKGROUND

rotaviruses are the major cause of acute gastroenteritis in young children worldwide, and require careful surveillance, especially in the context of vaccination programs. Prospective surveillance is required to monitor and characterize rotavirus infections, including viral and clinical data, and to detect the emergence of potentially epidemic strains.

METHODS

between 2006 and 2009, stool samples and clinical records were collected from 2044 children with acute diarrhea admitted to the pediatric emergency units of 13 French university hospitals. Rotaviruses were detected in stools, then genotyped by reverse transcription-polymerase chain reaction with regard to their outer capsid proteins VP4 and VP7.

RESULTS

the genotyping of 1947 rotaviruses showed that G1 (61.7%) and G9 (27.4%) strains were predominant and stable, followed by G2 (6.5%), G3 (4.0%), and G4 (2.5%) strains. Most strains were associated with P[8] (92.9%). Overall, 31 uncommon strains and possible zoonotic reassortants were detected including G12 and G8 strains, some being closely related to bovine strains. No difference in clinical presentation and severity was found among genotypes.

CONCLUSIONS

the relative stability of rotavirus genotypes currently cocirculating in France may ensure vaccine effectiveness in the short and medium term. However, the likely emergence of G12 and G8 strains should be monitored during ongoing and future vaccination programs, especially as all genotypes can cause severe infections. Special attention should be paid to the emergence of new rotavirus reassortants not included in current rotavirus vaccines.

Full genomic analyses of human rotavirus G4P[4], G4P[6], G9P[19] and G10P[6] strains from North-eastern India: evidence for interspecies transmission and complex reassortment events

In hospitalized patients with acute gastroenteritis in Manipur, India, four rotavirus strains were found to possess VP7 and/or VP4 genes with porcine or bovine characteristics. Considering the animal-like nature of these strains, the remaining eight gene segments were analysed to decipher their exact origin. Analyses of full genome of these strains exhibited their origin from porcine/bovine rotaviruses. This study suggests single or multiple events of reassortment involving multiple gene segments of more than one host type among the strains and emphasizes the significance of complete genetic characterization of unusual strains in regions with high incidence and mortality rates.

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.

A case of meningoencephalitis associated with G1P[8] rotavirus infection in a Japanese child

We report the case of a 2-y, 11-month-old boy with G1P[8] rotavirus infection accompanied by acute meningoencephalitis. Substitutions in both the VP4 and VP7 genes were found in the identified strain. A commonly circulating G1P[8] rotavirus with such mutations might be associated with the pathogenesis of CNS complications, including meningoencephalitis.

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

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

Full genomic analysis of a human group A rotavirus G9P[6] strain from Eastern India provides evidence for porcine-to-human interspecies transmission

Deduced amino acid sequence and phylogenetic analyses of a group A rotavirus G9P[6] strain (designated as mcs/13-07), detected from a 3-year-old child in Eastern India, revealed a VP8* closely related to porcine P[6] strains (P[6] sublineage 1D), and the VP7 clustered with G9 lineage-III strains. To our knowledge, this is the first report of human P[6] strain clustering in sublineage Id. Thus, to further characterize the evolutionary diversity of strain mcs/13-07, all gene segments were analyzed. VP6 and NSP4 exhibited genetic relatedness to Wa-like human subgroup II strains, while VP1-3, NSP1-3 and NSP5 were closely related to porcine strains. Based on the new classification system of rotaviruses, mcs/13-07 revealed a G9-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 genotype with close similarity to human Wa-like and porcine Gottfried strains. Therefore, considering the porcine-like or porcine origin of multiple gene segments, it might be tempting to assume that strain mcs/13-07 represents a rare instance of whole-virus transmission from pig to human, after which the virus evolved with time. Alternatively, it is possible that strain mcs/13-07 resulted from multiple reassortment events involving human subgroup II and porcine P[6] strains. Nevertheless, detection of strain mcs/13-07 provides further evidence for complex interspecies transmission events, which are frequent in developing countries.

Unexpected substitution of dominant rotavirus G genotypes in French hospitalized children over five consecutive seasons

The study was designed to evaluate the circulation of group A rotaviruses in French hospitalized children, and to detect unusual strains. This prospective study was conducted from 2001 to 2006 in children consulting for acute diarrhea at the pediatric emergency department in three French University Hospitals. The rotaviruses were detected by rapid test and genotyped by RT-PCR on the basis of their outer capsid proteins VP4 (P-type) and VP7 (G-type). The stools from 757 children were analyzed. G1P[8] strains were predominant (44.0%), followed by G9P[8] (17.7%), G3P[8] 13.1%, G4P[8] (9.5%), and G2P[4] (1.8%); mixed rotavirus infections occurred in 2.3%. G9 rotaviruses emerged during the 2004-2005 season (73.4%) and remained the second most prevalent strains. Few unusual strains, G6, G8, G12 and P[6]-types, were detected. The monitoring of rotavirus infections should be maintained to document strain distribution and to assess the emergence of new reassortants that may not respond to current rotavirus vaccines.

Two out of the 11 genes of an unusual human G6P[6] rotavirus isolate are of bovine origin

In 2003, we described the first human G6P[6] rotavirus strain (B1711). To investigate further the molecular origin of this strain and to determine the possible reassortments leading to this new gene constellation, the complete genome of strain B1711 was sequenced. SimPlot analyses were conducted to compare strain B1711 with other known rotavirus gene segments, and phylogenetic dendrograms were constructed to analyse the origin of the eleven genome segments of strain B1711. Our analysis indicated that strain B1711 acquired its VP1-, VP2-, VP4-, VP6- and NSP1–5-encoding gene segments from human DS-1-like P[6] rotavirus strains, and its VP3 and VP7 gene segments from a bovine rotavirus strain through reassortment. The introduction of animal–human reassortant strains, which might arise in either of the hosts, into the human rotavirus population is an important mechanism for the generation of rotavirus diversity, and might be a challenge for the current rotavirus vaccines and vaccines under development.

Molecular characterization of VP4 and NSP4 genes from rotavirus strains infecting neonates and young children in Belém, Brazil

Several reports have identified P[6] specificities in humans and in animals in different countries of the world, but few sequence data are available in public databases. In this work we have characterized the VP4 strains bearing P[6] specificity and NSP4 genotypes among diarrheic young children and diarrheic and non-diarrheic neonates from three studies previously conducted in Belém, Northern region of Brazil. As the to VP8* fragment, we observed a close relationship to both human prototypes of lineage P[6]-Ia (bootstrap of 99%) and porcine sublineages Ib and Ic (89.2-98.1% aa similarity and mean of 95%). With regards to the NSP4, the samples clustered into genotypes A and B. Of note, of the 27 P[6] strains analyzed in the present study and classified as genotype B, 8 (29.6%) were more similar to porcine prototypes when VP8* and NSP4 genes are compared, and were recovered, one from a neonate and seven from diarrheic children. These preliminary findings reinforce that further investigations are needed to assess the relative frequencies of P[6] strains in our region, as well as to investigate the potential for interspecies transmission involving humans and animals, particularly pigs.

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.

Molecular characterization of bovine rotavirus circulating in beef and dairy herds in Argentina during a 10-year period (1994-2003)

Group A bovine rotavirus (BRV) is one of the main causes of neonatal calf diarrhea. The present study reports the incidence of rotavirus diarrhea and the genotypes of BRV strains circulating in beef and dairy herds from Argentina, during a 10-year period (1994-2003). Group A BRV was detected in 62.5% (250/400) of the total studied cases of diarrhea. Positive cases were analyzed by heminested multiplex RT-PCR for P and G genotypes identification. Sixty percent of them were typed as P[5]G6, 4.4% P[11]G10, 4.4% P[11]G6 and 2.4% P[5]G10. Additionally, 9.2% of the cases were initially typed as G8 combined with P[5] or P[11], but sequence analysis revealed they belonged to genotype G6, lineage Hun4-like. Partial typing was assessed in 12.0% of the cases. One of the partially typed samples was closely related to genotype G15. BRV was detected in 71% and 58% of the outbreaks registered in beef and dairy farms, respectively. A clear differential distribution of G/P types was found according to the herd type. P[5]G6 was the prevalent strain in beef herds, while P[11] was the prevalent P-type in dairy herds (71%), associated in similar proportions with G6 and G10, These findings indicate that BRV genotypes included in the current commercially available rotavirus vaccines (G6, G10, P[5] and P[11]) should protect calves from most Argentinean field strains. Nevertheless, continuous surveillance is necessary to detect the emergence of new variants.