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

Post-vaccinated asymptomatic rotavirus infections: A community profile study of children in Surabaya, Indonesia

BACKGROUND

Rotavirus gastroenteritis accounts for significant childhood morbidity and mortality worldwide. Vaccination using RotarixTM (GSK) and RotaTeq^® (Merck) was introduced due to the tremendous disease burden. The possibility of asymptomatic infections following vaccinations was poorly understood. This study examined rotavirus cases in post-vaccinated children, their clinical manifestations and the genotypes of isolated strains.

METHODS

Stool samples of healthy, vaccinated children under 5 years of age in Surabaya were collected monthly for 1 year between January 2016 and February 2017. Episodes of gastroenteritis were reported, and samples were collected. Rotavirus was identified using multiplex reverse transcription Polymerase Chain Reaction (QIAGEN, Inc., Valencia, CA). Clinical manifestations were measured using the Vesikari score. The genotype was analyzed by Applied Biosystems (Foster, CA).

RESULTS

A total of 109 stool samples were collected from 30 subjects, of which 22 received Rotarix; 8 RotaTeq. Nine out of 109 samples were collected during diarrhea episodes of 8 subjects. Two asymptomatic rotavirus infections were identified by RT-PCR. The genotypes isolated were G1P[8] and G3P[8].

CONCLUSIONS

Asymptomatic rotavirus infections can occur in post-vaccinated children. Strains identified were homologous to serotypes eliciting gastroenteritis in unvaccinated children of the same community.

Distribution of Rotavirus Genotypes Ccirculating in Ahvaz, Iran in 2016

Background

Group A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and provide a strategy for the development of appropriate vaccines.

Methods

A total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016. All samples were screened by latex agglutination for the presence of rotavirus antigen. Rotavirus-positive samples were further analyzed by the semi-multiplex RT-PCR, and the sequencing was performed for G/P genotyping.

Results

Findings showed that 32% of the specimens were RVA-positive. Among the 32 VP7 genotyped strains, the predominant G genotype was G9 (37.5%), followed by G2 (21.9%), G1 (12.5%), G12 (9.4%), G4 (9.4%), G2G9 (6.3%), and G3 (3.1%). Among the 31 VP4 genotyped strains, P[8] genotype was the dominant (62.5%), followed by P[4] (31.3%) and P[4] P[8] (3.1%). The genotypes for G and P were identified for 31 rotaviruses (96.87%), but only one strain, G9, remained non-typeable for the P genotype. The most prevalent G/P combination was G9P[8] (28.5%), followed by G2P[4] (18.8%), G1P[8] (9.4%), G12P[8] (9.4%), G4P[8] (9.4%), G2G9P[4] (6.3%), G9P[4] P[8] (3.1%), G3P[8] (3.1%), G9P[4] (3.1%), G2P[8] (3.1%), and G9P[non-typeable] (3.1%).

Conclusion

A novel rotavirus strain, G12, was detected, for the first time, in patients from the southwest of Iran. Comprehensive investigations are required to evaluate the emergence of this strain.

Genotyping and Clinicoepidemiological Characterization of Rotavirus Acute Gastroenteritis in Egyptian Children

Group A rotavirus (RVA) acute gastroenteritis (AGE) is a common cause of severe childhood diarrhea. The dominant circulating RVA genotypes in a given region may vary between and within the geographic regions and from year to year. Our cross-sectional study was designed to determine the burden of RVA genotypes among children with AGE admitted to referral Children Hospital at Egypt prior to implementation of the vaccine. Stool samples with clinico-epidemiological data were collected from 92 children ≤ 3 years-old with AGE. RVA G and P typing were performed with type-specific primers. RVA was detected in 48.9% of patients. Higher rates of RVA infections, 73.3% were detected in infants < 1 year-old. Breast-fed infants were significantly fewer in RVA positive group (P = 0.0006). Non-breastfeeding was a major risk factor for RVA AGE (OR 0.3, P = 0.02). RVA diarrhea occurred mostly in autumn and winter months (55.4% and 26.6%) with a significant difference in autumn (P = 0.0005) and was associated with vomiting and dehydration (OR; 1.66, P = 0.021 & 1.4, P = 0.03). RVA genotypes G1P[8] (26.7%), G9P[8] (20%) and G3P[8] (15.6%) were accounting for 62.3% of RVA AGE. G9 was significantly associated with mucus diarrhea, than G1 or G3 which were associated with watery diarrhea (P = 0.025). Also, G9 was significantly associated with loose stool for > 5 days (P = 0.006) and 54.4% of G9 patients had severe dehydration. The diversity of RVA strains detected in Nile Delta Egypt and emergence of G9 RVA highlight the need to apply vaccines against this genotype in Egypt.

Genotyping and clinical factors in pediatric diarrhea caused by rotaviruses: one-year surveillance in Surabaya, Indonesia

BACKGROUND

Rotavirus infections are a major cause of diarrhea in children in both developed and developing countries. Rotavirus genetics, patient immunity, and environmental factors are thought to be related to the severity of acute diarrhea due to rotavirus in infants and young children. The objective of this study was to provide a correlation between rotavirus genotypes, clinical factors and degree of severity of acute diarrhea in children under 5 years old in Surabaya, Indonesia.

METHODS

A cross-sectional study was conducted in children aged 1-60 months with acute diarrhea hospitalized in Soetomo Hospital, Surabaya, Indonesia from April to December 2013. Rotavirus in stool specimens was identified by ELISA and genotyping (G-type and P-type) using multiplex reverse transcription PCR. Severity was measured using the Ruuska and Vesikari scoring system. The clinical factors were investigated included patient's age (months), hydration, antibiotic administration, nutritional state, co-bacterial infection and co-viral infection.

RESULTS

A total of 88 children met the criteria; 80.7% were aged 6-24 months, watery diarrhea was the most common type (77.3%) and 73.6% of the subjects were co-infected with bacteria, of which pathogenic Escherichia coli was the most common (42.5%). The predominant VP7 genotyping (G-type) was G2 (31.8%) and that of VP4 genotyping (P-type) was P[4] (31.8%). The predominant rotavirus genotype was G2P[4] (19.3%); G1P[4] and G9P[4] were uncommon with a prevalence of 4.5%. There were significant differences between the common genotype and uncommon genotype with respect to the total severity score of diarrhea (p <0.05). G3, G4 and G9 were significantly correlated with severe diarrhea (p = 0.009) in multivariate analyses and with frequency of diarrhea (>10 times a day) (p = 0.045) in univariate analyses, but there was no significant correlation between P typing and severity of diarrhea. For combination genotyping of G and P, G2P[4] was significantly correlated with severe diarrhea in multivariate analyses (p = 0.029).

CONCLUSIONS

There is a correlation between rotavirus genotype and severity of acute diarrhea in children. Genotype G2P[4] has the highest prevalence. G3, G4, G9 and G2P[4] combination genotype were found to be associated with severe diarrhea.

Rotavirus G2P[4] detection in fresh vegetables and oysters in Mexico City

Rotaviruses are the principal cause of dehydration caused by diarrhea in children younger than 2 years of age. Although these viral infections have mainly been associated with ingestion of fecally contaminated food and water, few studies have addressed the presence of the virus in food that is consumed raw or slightly cooked. In this work, 30 oyster samples and 33 vegetable samples were examined for the presence of rotavirus genotypes to evaluate their potential to produce gastrointestinal infections. The rotaviruses were identified by reverse transcriptase PCR amplification of the VP7 gene. G and P genotyping was also performed by reverse transcriptase PCR, with a detection sensitivity of up to 15 PFU/ml. Rotaviruses were found in 17 (26.9%) of 63 samples (10 oysters and 7 vegetables). The G2 genotype was found in 11 (64.7%) of 17 of the rotavirus strains, and 16 (94.1%) of 17 had the P[4] genotype. The combined genotypes found most frequently were G2P[4] (10 [58.82%] of 17), GNTP[4] (6 [35.29%] of 17), and G2P[NT] (1 [5.8%] of 17).

Identifying etiological agents causing diarrhea in low income Ecuadorian communities

Continued success in decreasing diarrheal disease burden requires targeted interventions. To develop such interventions, it is crucial to understand which pathogens cause diarrhea. Using a case-control design we tested stool samples, collected in both rural and urban Ecuador, for 15 pathogenic microorganisms. Pathogens were present in 51% of case and 27% of control samples from the urban community, and 62% of case and 18% of control samples collected from the rural community. Rotavirus and Shigellae were associated with diarrhea in the urban community; co-infections were more pathogenic than single infection; Campylobacter and Entamoeba histolytica were found in large numbers in cases and controls; and non-typhi Salmonella and enteropathogenic Escherichia coli were not found in any samples. Consistent with the Global Enteric Multicenter Study, focused in south Asia and sub-Saharan Africa, we found that in Ecuador a small group of pathogens accounted for a significant amount of the diarrheal disease burden.

Rotavirus Diarrhea among Children in Taiz, Yemen: Prevalence-Risk Factors and Detection of Genotypes

Diarrheal diseases are a great public health problem; they are among the most causes leading to morbidity and mortality of infants and children particularly in developing countries and even in developed countries. Rotavirus is the most common cause of severe gastroenteritis in infants and young children in both developed and developing countries. The purpose of this study was to determine the incidence rate of Rotavirus infection, its genotypes, and risk factors among children with diarrhea in Taiz, Yemen. 795 fecal samples were collected from children (less than 5 years old), suffering from diarrhea and attending the Yemeni-Swedish Hospital (YSH) in Taiz , Yemen, from November 2006 to February 2008. Rotavirus was detected by enzyme linkage immunosorbent assay (ELISA) on stool specimens of children. Genotypes of Rotavirus were characterized by reverse transcriptase-polymerase chain reaction (RT-PCR) and polyacrylamide gel electrophoresis (PAGE). The results showed that 358 (45.2%) were Rotavirus-positive and the most prevalent genotypes were G2P[4] (55%), followed by G1P[8] (15%). In addition, Rotavirus was found through the whole year; however, higher frequency during the summer season (53.4%) and lower frequency during the winter season (37.1%).

Synergistic effects between rotavirus and coinfecting pathogens on diarrheal disease: evidence from a community-based study in northwestern Ecuador

In developing countries where diarrheal disease is a leading cause of morbidity and mortality in children under 5 years of age, enteric coinfection is common. There is little understanding, however, of the biologic interaction between coinfecting pathogens. The authors investigated the potential for synergistic interaction between coinfecting pathogens on diarrhea pathogenesis using an epidemiologic framework. They conducted community-based, case-control studies in 22 communities in northwestern Ecuador between 2003 and 2008. Risk ratios of diarrhea associated with single infections and coinfections were estimated. Interaction between coinfecting pathogens was assessed through departure from risk ratio additivity and multiplicativity after adjustment for age. On the additive scale, the authors found departure from the null value of 0 for rotavirus-Giardia coinfections (interaction contrast ratio = 8.0, 95% confidence interval: 3.1, 18.9) and for rotavirus-Escherichia coli coinfections (interaction contrast ratio = 9.9, 95% confidence interval: 2.6, 28.4). On the multiplicative scale, they found departure from the value of 1 for rotavirus-Giardia coinfections (multiplicative interaction = 3.6, 95% confidence interval: 1.3, 8.7). This research provides epidemiologic evidence for synergism between rotavirus and other enteric pathogens. During coinfection, the pathogenic potential of each organism appears to be enhanced. The potential for pathogenesis to be more severe in the presence of a rotavirus coinfection amplifies the need for rotavirus vaccination.

Rethinking indicators of microbial drinking water quality for health studies in tropical developing countries: case study in northern coastal Ecuador

To address the problem of the health impacts of unsafe drinking water, methods are needed to assess microbiologic contamination in water. However, indicators of water quality have provided mixed results. We evaluate five assays (three for Escherichia coli and one each for enterococci and somatic coliphage) of microbial contamination in villages in rural Ecuador that rely mostly on untreated drinking water. Only membrane filtration for E. coli using mI agar detected a significant association with household diarrheal disease outcome (odds ratio = 1.29, 95% confidence interval = 1.02-1.65 in household containers and odds ratio = 1.18, 95% confidence interval = 1.02-1.37) in source samples. Our analysis and other published research points to the need for further consideration of study design factors, such as sample size and variability in measurements, when using indicator organisms, especially when relating water quality exposure to health outcomes. Although indicator organisms are used extensively in health studies, we argue that their use requires a full understanding of their purposes and limitations.

Burden and typing of rotavirus group A in Latin America and the Caribbean: systematic review and meta-analysis

The efficacy of licensed rotavirus vaccines has only been shown against certain rotavirus group A (RV-A) types. It is critical to understand the burden of rotavirus gastroenteritis (RVGE) and its prevalent types to assess the potential impact of these vaccines in Latin America and the Caribbean (LA&C). We performed a systematic review and meta-analyses of all the available evidence reported from 1990 to 2009 on the burden of rotavirus disease and strains circulating in LA&C. Eligible studies--185 country-level reports, 174 951 faecal samples--were selected from MEDLINE, Cochrane Library, EMBASE, LILACS, regional Ministries of Health, PAHO, regional proceedings, doctoral theses, reference lists of included studies and consulting experts. Arc-sine transformations and DerSimonian-Laird random-effects model were used for meta-analyses. The proportion of gastroenteritis cases due to rotavirus was 24.3% (95%CI 22.3-26.4) and the incidence of RVGE was 170 per 1000 children-years (95%CI 130-210). We estimated a global annual mortality for 22 countries of 88.2 (95%CI 79.3-97.1) deaths per 100 000 under 5 years (47 000 deaths).The most common G type detected was G1 (34.2%), followed by G9 (14.6%), and G2 (14.4%). The most common P types detected were P[8] (56.2%), P[4] (22.1%) and P[1] 5.4%, and the most prevalent P-G type associations were P[8]G1 17.9%, P[4]G2 9.1% and P[8]G9 8.8%. In the last 10 years, G9 circulation increased remarkably and G5 almost disappeared. More recently, G12 appeared and P[4]G2 re-emerged. To our knowledge, this is the first meta-analysis of rotavirus infection and burden of disease in LA&C.

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

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

Asymptomatic rotavirus infections in England: prevalence, characteristics, and risk factors

Rotavirus is a major cause of infectious intestinal disease in young children; a substantial prevalence of asymptomatic infection has been reported across all age groups. In this study, the authors determined characteristics of asymptomatic rotavirus infection and potential risk factors for infection. Healthy persons were recruited at random from the general population of England during the Study of Infectious Intestinal Disease in England (1993-1996). Rotavirus infection was identified using reverse-transcription polymerase chain reaction. Multivariable logistic regression was used to compare exposures reported by participants with rotavirus infection with those of participants who tested negative. Multiple imputation was used to account for missing responses in the data set. The age-adjusted prevalence of asymptomatic rotavirus infection was 11%; prevalence was highest in children under age 18 years. Attendance at day care was a risk factor for asymptomatic rotavirus infection in children under age 5 years; living in a household with a baby that was still in diapers was a risk factor in older adults. The results suggest that asymptomatic rotavirus infection is transmitted through the same route as rotavirus infectious intestinal disease: person-to-person contact. More work is needed to understand the role of asymptomatic infections in transmission leading to rotavirus disease.

Rotavirus disease and vaccination: impact on genotype diversity

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

Rapid changes in rotaviral genotypes in Ecuador

Previous studies suggest that the emerging G9P[8] genotype was the most prevalent rotavirus genotype in Ecuador during 2005. This present study provides a temporal analysis of the distribution of rotavirus genotypes in two locations within Ecuador by adding additional years (2006 - early 2008) to the originally reported 2005 data. Data were collected in a rural (northern coastal Ecuador) and urban (Quito) area. In the rural area, a community sample of cases (those presenting diarrhea) and controls (those not presenting diarrhea) were collected between August 2003 and March 2008 resulting in a total of 3,300 stool samples (876 cases and 2,424 controls). Of these samples, 260 were positive for rotavirus by an immunochromatographic test (196 cases and 64 controls). In Quito, 59 fecal samples were collected from children presenting diarrhea and diagnosed with rotavirus. An RT-PCR analysis of samples collected between 2005 and 2007 suggested that G9 was replaced by G1 and G2 in the rural and urban settings. During this period G9 decreased from 79% to 9% while G2 increased from 0% to 43% in the rural communities, and G9 decreased from 79% to 37% while G2 increased from 3% to 57% in the urban area of Quito. This rapid replacement of G9 by G1 and G2 reinforces the necessity of surveillance to inform vaccination programs.

Characterization of novel VP7, VP4, and VP6 genotypes of a previously untypeable group A rotavirus

Rotavirus is the most common cause of acute gastroenteritis among infants and young children throughout the world, but rotavirus cases in developing countries account for nearly all of the approximately 600,000 annual deaths. We studied the epidemiology of rotavirus in 22 rural communities in northern coastal Ecuador over a five-year period. From 250 rotavirus positive stool specimens, the percentage that could not be RT-PCR genotyped for VP4 and VP7 was 77% and 63%, respectively. The possibility of sample degradation was considered but discounted after an experimental examination of rotavirus stability and EM visualization of rotavirus-like particles in several untypeable samples. Finally, alternate primers were used to amplify Ecu534, a sample that was untypeable using most published VP4 and VP7 primers. Characterization of the VP7, VP4, and VP6 full gene segments revealed novel genotypes and nucleotide mismatches with most published primer sequences. When considered with other findings, our results suggest that primer mismatch may be a widespread cause of genotyping failure, and might be particularly problematic in countries with greater rotavirus diversity. The novel sequences described in this study have been given GenBank accession numbers EU805775 (VP7), EU805773 (VP4), EU805774 (VP6) and the RCWG has assigned them novel genotypes G20P[28]I13, respectively.

Enhancement of detection and quantification of rotavirus in stool using a modified real-time RT-PCR assay

A sensitive and specific real-time RT-PCR assay to detect rotavirus in stool samples was optimized and validated using a wide range of rotavirus genotypes. The target of the original TaqMan(R) assay is an 87 bp fragment of the highly conserved non-structural protein 3 (NSP3) gene. Here we modified the original assay by introducing degeneracy into the forward primer to account for sequence variation between rotavirus genotypes, added four nucleotides at the 3' end of the reverse primer to reduce its stability, and modified the probe label. Amplification and detection conditions were optimized using purified dsRNA from two cultivated strains. The limit of detection of the modified assay was calculated to be approximately 44 genome copies per reaction. To validate the reactivity of the assay, 103 archived RNAs that had been extracted from stools and genotyped during routine U.S. surveillance were tested. Samples were selected to represent both rare and common genotypes that have been detected in U.S. children. Nine genotypes known to be circulating in the United States were detected by the real-time assay demonstrating broad reactivity. In addition, other enteric viruses were not detected demonstrating that the assay is specific for rotavirus and does not cross-react with other viruses potentially present in stool samples. This real-time assay is an important addition to the arsenal of molecular tools available to quickly identify rotavirus in stool samples during routine surveillance.