Quantitation of group A rotavirus by real-time reverse-transcription-polymerase chain reaction: correlation with clinical severity in children in South India

Semi-quantitative assessment of gastrointestinal viruses in stool samples with Seegene Allplex gastrointestinal panel assays: a solution to the interpretation problem of multiple pathogen detection?

PURPOSE

The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections.

METHODS

The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined.

RESULTS

After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting.

CONCLUSION

By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.

Differences in Rotavirus Shedding and Duration by Infant Oral Rotavirus Vaccination Status in Dhaka, Bangladesh 2011 - 2014

To evaluate how breakthrough rotavirus disease contributes to transmission, we examined the impact of rotavirus vaccination on fecal shedding and duration of illness. We used multivariable linear regression to analyze rotavirus quantity by RT-qPCR and duration among 184 episodes of rotavirus diarrhea positive by ELISA in the PROVIDE study. Vaccinated children had less fecal viral shedding compared to unvaccinated children (mean difference = -0.59 log copies per gram of stool, 95% CI: -0.99, -0.19). Duration of illness was on average 0.47 days (95% CI: -0.23, 1.17) shorter among vaccinated children. Rotarix vaccination reduces shedding burden among breakthrough cases of RVGE.

Differences in epidemiology of enteropathogens in children pre- and post-rotavirus vaccine introduction in Kilifi, coastal Kenya

Background

Kenya introduced Rotarix^® (GlaxoSmithKline Biologicals, Rixensart, Belgium) vaccination into its national immunization programme beginning July 2014. The impact of this vaccination program on the local epidemiology of various known enteropathogens is not fully understood.

Methods

We used a custom TaqMan Array Card (TAC) to screen for 28 different enteropathogens in 718 stools from children aged less than 13 years admitted to Kilifi County Hospital, coastal Kenya, following presentation with diarrhea in 2013 (before vaccine introduction) and in 2016–2018 (after vaccine introduction). Pathogen positivity rate differences between pre- and post-Rotarix^® vaccination introduction were examined using both univariate and multivariable logistic regression models.

Results

In 665 specimens (92.6%), one or more enteropathogen was detected, while in 323 specimens (48.6%) three or more enteropathogens were detected. The top six detected enteropathogens were: enteroaggregative Escherichia coli (EAggEC; 42.1%), enteropathogenic Escherichia coli (EPEC; 30.2%), enterovirus (26.9%), rotavirus group A (RVA; 24.8%), parechovirus (16.6%) and norovirus GI/GII (14.4%). Post-rotavirus vaccine introduction, there was a significant increase in the proportion of samples testing positive for EAggEC (35.7% vs. 45.3%, p = 0.014), cytomegalovirus (4.2% vs. 9.9%, p = 0.008), Vibrio cholerae (0.0% vs. 2.3%, p = 0.019), Strongyloides species (0.8% vs. 3.6%, p = 0.048) and Dientamoeba fragilis (2.1% vs. 7.8%, p = 0.004). Although not reaching statistical significance, the positivity rate of adenovirus 40/41 (5.8% vs. 7.3%, p = 0.444), norovirus GI/GII (11.2% vs. 15.9%, p = 0.089), Shigella species (8.7% vs. 13.0%, p = 0.092) and Cryptosporidium spp. (11.6% vs. 14.7%, p = 0.261) appeared to increase post-vaccine introduction. Conversely, the positivity rate of sapovirus decreased significantly post-vaccine introduction (7.8% vs. 4.0%, p = 0.030) while that of RVA appeared not to change (27.4% vs. 23.5%, p = 0.253). More enteropathogen coinfections were detected per child post-vaccine introduction compared to before (mean: 2.7 vs. 2.3; p = 0.0025).

Conclusions

In this rural Coastal Kenya setting, childhood enteropathogen infection burden was high both pre- and post-rotavirus vaccination introduction. Children who had diarrheal admissions post-vaccination showed an increase in coinfections and changes in specific enteropathogen positivity rates. This study highlights the utility of multipathogen detection platforms such as TAC in understanding etiology of childhood acute gastroenteritis in resource-limited regions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-022-00506-z.

Seasonal pattern in occurrence of rotavirus infection (RV) in diarrheic children, calves and piglets from Bareilly, India

Rapid and reliable diagnosis for diarrhoeal disease is critically important for the differentiation of etiological agents and subsequent suitable treatment modalities. The objective of the study is to reveal the seasonal pattern in the occurrence of rotavirus in diarrheic children, calves and piglets from Bareilly, Uttar Pradesh, India. A total of 115 diarrhoeal samples were collected, out of which 51 were collected during post-monsoon/autumn (September 2018-November 2018) and 64 during the winter season (December 2018-February 2019). The samples were collected from children <5 years (n = 50), piglets <3 months (n = 35) and calves <6 months of age (n = 30). These samples were screened by ribonucleic acid-polyacrylamide gel electrophoresis (RNA-PAGE) and reverse transcriptase-polymerase chain reaction (RT-PCR) by targeting the VP6 gene of rotavirus A (RVA) and the two were compared. In RNA-PAGE 29.4% (5/17), 6.3% (1/16) and 0% (0/18) samples collected from children, calves and piglets, respectively were rotavirus positive during the autumn season while 45.5% (15/33), 21.4% (3/14) and 17.7% (3/17) samples in the winter season. In RT-PCR, 41.2% (7/17), 12.5% (2/16) and 0% (0/18) samples were rotavirus positive in the autumn season while 51.5% (17/33), 28.6% (4/14) and 29.4% (5/17) samples in winter season collected from children, calves and piglets, respectively. On statistical analysis, no significant difference between the season and number of positives in children and calves (p > 0.05) was observed, however in piglets significantly higher number of RVA positives were detected in the winter season than autumn (p < 0.01). The diagnostic test comparison of RNA-PAGE and RT-PCR showed no statistically significant difference in detecting the RVA positives (p > 0.05). Overall the percent positivity showed a seasonal pattern with higher positivity in winter as compared to autumn season.

The Challenges and Opportunities of Next-Generation Rotavirus Vaccines: Summary of an Expert Meeting with Vaccine Developers

The 2nd Next Generation Rotavirus Vaccine Developers Meeting, sponsored by PATH and the Bill and Melinda Gates Foundation, was held in London, UK (7-8 June 2022), and attended by vaccine developers and researchers to discuss advancements in the development of next-generation rotavirus vaccines and to consider issues surrounding vaccine acceptability, introduction, and uptake. Presentations included updates on rotavirus disease burden, the impact of currently licensed oral vaccines, various platforms and approaches for next generation rotavirus vaccines, strategies for combination pediatric vaccines, and the value proposition for novel parenteral rotavirus vaccines. This report summarizes the information shared at the convening and poses various topics worthy of further exploration.

Epidemiological significance of the occurrence and persistence of rotaviruses in water and sewage: a critical review and proposal for routine microbiological monitoring

Globally, waterborne gastroenteritis attributable to rotaviruses is on the increase due to the rapid increase in population growth, poor socioeconomic conditions, and drastic changes in climatic conditions. The burden of diarrhea is quite alarming in developing nations where the majority of the populations still rely on untreated surface water that is usually polluted for their immediate water needs. Humans and animals of all ages are affected by rotaviruses. In humans, the preponderance of cases occurs in children under 5 years. Global efforts in advancing water/wastewater treatment technologies have not yet realized the objective of complete viral removal from wastewater. Most times, surface waters are impacted heavily by inadequately treated wastewater run-offs thereby exposing people or animals to preventable health risks. The relative stability of rotaviruses in aquatic matrices during wastewater treatment, poor correlation of bacteriological indicators with the presence of rotaviruses, and their infectiousness at a low dose informed the proposal for inclusion in the routine microbiological water screening panel. Environmental monitoring data have been shown to provide early warnings that can complement clinical data used to monitor the impact of current rotavirus vaccination in a community. This review was therefore undertaken to critically appraise rotavirus excretion and emission pathways, and the existence, viability and persistence in the receiving aquatic milieu. The efficiency of the current wastewater treatment modality for rotavirus removal, correlation of the current bacteriological water quality assessment strategy, public health risks and current laboratory methods for an epidemiological study were also discussed.

A shift in circulating rotaviral genotypes among hospitalized neonates

In neonates, rotavirus (RV) infection is generally nosocomial. The control of rotaviral infection within hospital settings is challenging due to prolonged shedding of the virus and contamination of the surrounding environment. There are few studies that have reported asymptomatic infection within neonates. In this study, neonates were screened for RV infection and possible clinical manifestations that may play a role in RV acquisition were analysed. Stool samples were collected from 523 hospitalized neonates admitted for > 48 h in a low-cost and higher-cost tertiary centre. RV antigen was screened using ELISA and the samples which tested positive were confirmed by semi-nested RT-PCR. RV was detected in 34% of participants and genotypes identified included G12P[11] (44.4%), G10 P[11] (42.6%), G10G12P[11] (10.1%) and G3P[8] (2.9%). ICU admissions were associated with higher viral shedding (p < 0.05). Hospitalization in the low-cost facility ICU was associated with higher RV acquisition risk (p < 0.05). RV was detected in higher rates (36.9%) among neonates with gastrointestinal manifestations. G10P[11] was the predominant genotype for several years (1988–2016) among neonates within India. The preponderance of an emerging G12P[11] genotype and heterotypic distribution was documented. RV surveillance is important to identify emerging strains and establish the road ahead in managing RV infection.

Molecular Epidemiology of Rotavirus Strains in Symptomatic and Asymptomatic Children in Manhiça District, Southern Mozambique 2008-2019

Group A rotaviruses remain the leading cause of diarrhoea in children aged <5 years. Mozambique introduced rotavirus vaccine (Rotarix^®) in September 2015. We report rotavirus genotypes circulating among symptomatic and asymptomatic children in Manhiça District, Mozambique, pre- and post-vaccine introduction. Stool was collected from enrolled children and screened for rotavirus by enzyme-immuno-sorbent assay. Positive specimens were genotyped for VP7 (G genotypes) and VP4 (P genotypes) by the conventional reverse transcriptase polymerase chain reaction. The combination G12P[8] was more frequently observed in pre-vaccine than in post-vaccine introduction, in moderate to severe diarrhoea (34%, 61/177 vs. 0, p < 0.0001) and controls (23%, 26/113 vs. 0, p = 0.0013) and mixed genotypes (36%, 24/67 vs. 7% 4/58, p = 0.0003) in less severe diarrhoea. We observed changes in post-vaccine compared to pre-vaccine introduction, where G3P[4] and G3P[8] were prevalent in moderate to severe diarrhoea (10%, 5/49 vs. 0, p = 0.0002; and 14%, 7/49 vs. 1%, 1/177, p < 0.0001; respectively), and in less severe diarrhoea (21%, 12/58 vs. 0, p = 0.003; and 24%, 14/58 vs. 0, p < 0.0001; respectively). Our surveillance demonstrated the circulation of similar genotypes contemporaneously among cases and controls, as well as switching from pre- to post-vaccine introduction. Continuous surveillance is needed to evaluate the dynamics of the changes in genotypes following vaccine introduction.

High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases

Despite the global use of rotavirus vaccines, vaccine breakthrough cases remain a pediatric health problem. In this study, we investigated suspected rotavirus vaccine breakthrough cases using next-generation sequencing (NGS)-based viral metagenomics (n = 102) and a panel of semiquantitative reverse transcription-PCR (RT-qPCR) (n = 92) targeting known enteric pathogens. Overall, we identified coinfections in 80% of the cases. Enteropathogens such as adenovirus (32%), enterovirus (15%), diarrheagenic Escherichia coli (1 to 14%), astrovirus (10%), Blastocystis spp. (10%), parechovirus (9%), norovirus (9%), Clostridioides (formerly Clostridium) difficile (9%), Dientamoeba fragilis (9%), sapovirus (8%), Campylobacter jejuni (4%), and Giardia lamblia (4%) were detected. Except for a few reassortant rotavirus strains, unusual genotypes or genotype combinations were not present. However, in addition to well-known enteric viruses, divergent variants of enteroviruses and nonclassic astroviruses were identified using NGS. We estimated that in 31.5% of the patients, rotavirus was likely not the cause of gastroenteritis, and in 14.1% of the patients, it contributed together with another pathogen(s) to disease. The remaining 54.4% of the patients likely had a true vaccine breakthrough infection. The high prevalence of alternative enteropathogens in the suspected rotavirus vaccine breakthrough cases suggests that gastroenteritis is often the result of a coinfection and that rotavirus vaccine effectiveness might be underestimated in clinical and epidemiological studies.

Systematic Review on the Correlation of Quantitative PCR Cycle Threshold Values of Gastrointestinal Pathogens With Patient Clinical Presentation and Outcomes

Background: Quantitative (q) polymerase chain reaction (PCR) cycle threshold (Ct) values represent the number of amplification cycles required for a positive PCR result and are a proxy of pathogen quantity in the tested sample. The clinical utility of Ct values remains unclear for gastrointestinal infections. Objectives: This systematic review assesses the global medical literature for associations between Ct values of gastrointestinal pathogens and patient presentation and clinical outcomes. Data Sources: MEDLINE, EMBASE, Cochrane library databases: searched January 14-17, 2020. Study Eligibility Criteria: Studies reporting on the presence or absence of an association between Ct values and clinical outcomes in adult and pediatric populations were included. Animal studies, reviews, meta-analyses, and non-English language studies were excluded. Participants: Humans infected with gastrointestinal pathogens, detected with qPCR. Interventions: Diagnostics assessing Ct values. Extracted data were reported narratively. Results: Thirty-three eligible studies were identified; the most commonly studied pathogens were Clostridioides difficile (n = 15), norovirus (n = 10), and rotavirus (n = 9). Statistically significant associations between low C. difficile Ct values and increased symptom severity or poor outcome were reported in 4/8 (50%) studies, and increased risk of death in 1/2 (50%) studies; no significant associations were found between Ct value and duration of symptoms or length of hospital stay. Among studies of norovirus, 5/7 (71%), mainly genogroup II, reported symptomatic cases with significantly lower median Ct values than controls. Significantly lower rotavirus Ct values were also observed in symptomatic cases vs. controls in 3/7 (43%) studies, and associated with more severe symptoms in 2/2 studies. Contradictory associations were identified for non-C. difficile bacterial and parasitic pathogens. Conclusions: In conclusion, some studies reported clinically useful associations between Ct values and patient or healthcare outcomes; additional, well-designed, large-scale trials are warranted based on these findings. Systematic Review Registration: [PROSPERO], identifier [CRD42020167239].

Community transmission of rotavirus infection in a vaccinated population in Blantyre, Malawi: a prospective household cohort study

BACKGROUND

Rotavirus vaccine effectiveness is reduced among children in low-income countries. Indirect (transmission-mediated) effects of rotavirus vaccine might contribute to the total population effect of vaccination. We aimed to examine risk factors for transmission of rotavirus to household contacts in Blantyre, Malawi, and estimated the effectiveness of rotavirus vaccine in preventing transmission of infection to household contacts.

METHODS

In this prospective household cohort study, we recruited children born after Sept 17, 2012, and aged at least 6 weeks (vaccine-eligible children) with acute rotavirus gastroenteritis and their household contacts, in four government health facilities in Blantyre, Malawi. Clinical data, a bulk stool sample, and 1-2 mL of serum were collected from case children at presentation. Clinical data and stool samples were also prospectively collected from household contacts over 14 days from presentation. A single stool sample was collected from control households containing asymptomatic children who were frequency age-matched to case children. Samples were tested for rotavirus using semi-quantitative real-time PCR and for anti-rotavirus IgA using a semi-quantitative sandwich ELISA. Risk factors for household transmission of rotavirus infection and clinical disease, including disease severity and faecal shedding density, were identified using mixed effects logistic regression. Vaccine effectiveness against transmission was estimated as 1 minus the ratio of secondary attack rates in vaccinated and counterfactual unvaccinated populations, using vaccine effectiveness estimates from the associated diarrhoeal surveillance platform to estimate the counterfactual secondary attack rate without vaccination.

FINDINGS

Between Feb 16, 2015, and Nov 11, 2016, we recruited 196 case households (705 members) and 55 control households (153 members). Household secondary attack rate for rotavirus infection was high (434 [65%] of 665 individuals) and secondary attack rate for clinical disease was much lower (37 [5%] of 698). Asymptomatic infection in control households was common (40 [28%] of 144). Increasing disease severity in an index child (as measured by Vesikari score) was associated with increased risk of transmission of infection (odds ratio 1·17 [95% CI 1·06-1·30) and disease (1·28 [1·08-1·52]) to household contacts. Estimated vaccine effectiveness against transmission was 39% (95% CI 16-57).

INTERPRETATION

Rotavirus vaccine has the potential to substantially reduce household rotavirus transmission. This finding should be considered in clinical and health economic assessments of vaccine effectiveness.

FUNDING

Wellcome Trust, US National Institutes of Health, and US National Institute of Allergy and Infectious Diseases.

Rotavirus in Calves and Its Zoonotic Importance

Rotavirus is a major pathogen responsible for diarrheal disease in calves, resulting in loss of productivity and economy of farmers. However, various facets of diarrheal disease caused by rotavirus in calves in the world are inadequately understood, considering that diarrheal disease caused by rotavirus is a vital health problem in calves that interrupts production benefits with reduced weight gain and increased mortality, and its potential for zoonotic spread. The pathological changes made by rotavirus are almost exclusively limited to the small intestine that leads to diarrhea. It is environmentally distributed worldwide and was extensively studied. Reassortment is one of the important mechanisms for generating genetic diversity of rotaviruses and eventually for viral evolution. So, the primary strategy is to reduce the burden of rotavirus infections by practicing early colostrum's feeding in newborn calves, using vaccine, and improving livestock management. Rotaviruses have a wide host range, infecting many animal species as well as humans. As it was found that certain animal rotavirus strains had antigenic similarities to some human strains, this may be an indication for an animal to play a role as a source of rotavirus infection in humans. Groups A to C have been shown to infect both humans and animals. The most commonly detected strains in both human and animals are G2, G3, G4, and G9, P [6]. Therefore, this review was made to get overview epidemiology status and zoonotic importance of bovine rotavirus.

Duration and Density of Fecal Rotavirus Shedding in Vaccinated Malawian Children With Rotavirus Gastroenteritis

Quantifying rotavirus shedding among vaccinated individuals will aid understanding of vaccine indirect effects. Serial stool samples were collected from 196 children who presented with rotavirus gastroenteritis to health facilities in Blantyre, Malawi, and were tested for rotavirus using a VP6 semi-quantitative, real-time polymerase chain reaction. The median duration of fecal shedding was 28 days (95% CI, 19–28). The median copy numbers for peak shedding were 1.99 × 10⁷ (interquartile range, 3.39 × 10⁶ to 6.37 × 10⁷). The fecal viral load was positively associated with disease severity and negatively associated with serum anti-rotavirus immunoglobin A. High and persistent rotavirus shedding among vaccinated children with breakthrough disease may contribute to ongoing transmission in this setting.

Clinical Profile, Risk-Factors, and Outcome of Rotaviral Diarrhea and Non-rotaviral Diarrhea Among Under-Five Children at Cuttack, Odisha, India

OBJECTIVE

To understand the prevalence of rotavirus diarrhea and its associated clinical and socio-demographic characteristics.

METHODS

The prospective hospital-based study was conducted at SVP Post Graduate Institute of Pediatrics and SCB Medical College, Odisha, India among children under-five years of age from April 2016 to July 2019. From all eligible children admitted at hospital, a case-report form containing information on clinical and socio-demographic characteristics was collected and an attempt was made to collect stool sample. A simple logistic regression method was used to assess factors associated with rotavirus diarrhea.

RESULTS

Of the 1963 children, median (IQR) age was 12 (8-19) mo with a female/male ratio was 1:2.05. The prevalence of rotavirus diarrhea was 36.4% (95% CI, 34.2%-38.6%). Children in the age group of 6-11 (OR 1.64, 95% CI, 1.24-2.18), 12-23 (OR 1.73, 95% CI, 1.31-2.29) mo had higher odds of getting rotavirus diarrhea, compared to those in that of 24-59 mo. The prevalence of wasting, stunting, underweight among children with rotavirus diarrhea was 25.2% (95% CI, 22%-28.4%), 2.1% (95% CI, 1.1%-3.1%), 9.0% (95% CI, 6.8%-11.2%), respectively.

CONCLUSION

The results of this study confirmed that diarrhea remains an important cause of hospitalization in children. Further studies are required in the community for Rotavirus and its genotyping.

High prevalence of circulating DS-1-like human rotavirus A and genotype diversity in children with acute gastroenteritis in Thailand from 2016 to 2019

Background

Human rotavirus A (RVA) infection is the primary cause of acute gastroenteritis (AGE) in infants and young children worldwide, especially in children under 5 years of age and is a major public health problem causing severe diarrhea in children in Thailand. This study aimed to investigate the prevalence, genotype diversity, and molecular characterization of rotavirus infection circulating in children under 15 years of age diagnosed with AGE in Thailand from January 2016 to December 2019.

Methods

A total of 2,001 stool samples were collected from children with gastroenteritis (neonates to children <15 years of age) and tested for RVA by real-time polymerase chain reaction (RT-PCR). Amplified products were sequenced and submitted to an online genotyping tool for analysis.

Results

Overall, 301 (15.0%) stool samples were positive for RVA. RVA occurred most frequently among children aged 0-24 months. The seasonal incidence of rotavirus infection occurred typically in Thailand during the winter months (December-March). The G3P[8] genotype was identified as the most prevalent genotype (33.2%, 100/301), followed by G8P[8] (10.6%, 32/301), G9P[8] (6.3%, 19/301), G2P[4] (6.0%, 18/301), and G1P[6] (5.3%, 16/301). Uncommon G and P combinations such as G9P[4], G2P[8], G3P[4] and G3P[9] were also detected at low frequencies. In terms of genetic backbone, the unusual DS-1-like G3P[8] was the most frequently detected (28.2%, 85/301), and the phylogenetic analysis demonstrated high nucleotide identity with unusual DS-1-like G3P[8] detected in Thailand and several countries.

Conclusions

A genetic association between RVA isolates from Thailand and other countries ought to be investigated given the local and global dissemination of rotavirus as it is crucial for controlling viral gastroenteritis, and implications for the national vaccination programs.

Prevalence and diversity of enteric pathogens among cholera treatment centre patients with acute diarrhea in Uvira, Democratic Republic of Congo

BACKGROUND

Cholera remains a major global health challenge. Uvira, in the Democratic Republic of the Congo (DRC), has had endemic cholera since the 1970's and has been implicated as a possible point of origin for national outbreaks. A previous study among this population, reported a case confirmation rate of 40% by rapid diagnostic test (RDT) among patients at the Uvira Cholera Treatment Centre (CTC). This study considers the prevalence and diversity of 15 enteric pathogens in suspected cholera cases seeking treatment at the Uvira CTC.

METHODS

We used the Luminex xTAG® multiplex PCR to test for 15 enteric pathogens, including toxigenic strains of V. cholerae in rectal swabs preserved on Whatman FTA Elute cards. Results were interpreted on MAGPIX® and analyzed on the xTAG® Data Analysis Software. Prevalence of enteric pathogens were calculated and pathogen diversity was modelled with a Poisson regression.

RESULTS

Among 269 enrolled CTC patients, PCR detected the presence of toxigenic Vibrio cholerae in 38% (103/269) of the patients, which were considered to be cholera cases. These strains were detected as the sole pathogen in 36% (37/103) of these cases. Almost half (45%) of all study participants carried multiple enteric pathogens (two or more). Enterotoxigenic Escherichia coli (36%) and Cryptosporidium (28%) were the other most common pathogens identified amongst all participants. No pathogen was detected in 16.4% of study participants. Mean number of pathogens was highest amongst boys and girls aged 1-15 years and lowest in women aged 16-81 years. Ninety-three percent of toxigenic V. cholerae strains detected by PCR were found in patients having tested positive for V. cholerae O1 by RDT.

CONCLUSIONS

Our study supports previous results from DRC and other cholera endemic areas in sub-Sahara Africa with less than half of CTC admissions positive for cholera by PCR. More research is required to determine the causes of severe acute diarrhea in these low-resource, endemic areas to optimize treatment measures.

TRIAL REGISTRATION

This study is part of the impact evaluation study entitled: "Impact Evaluation of Urban Water Supply Improvements on Cholera and Other Diarrheal Diseases in Uvira, Democratic Republic of Congo" registered on 10 October 2016 at clinicaltrials.gov Identification number: NCT02928341 .

Accuracy and Cross-Reactivity of Rapid Diagnostic Tests for Norovirus and Rotavirus in a Real Clinical Setting

Background

Rapid diagnostic test (RDT) of norovirus and rotavirus is commonly used for outbreak screening and patient management. Varying accuracy of the test and cross-reactivity has been reported and could affect the outcome of management. The primary purpose of this study is to provide the accuracy of norovirus and rotavirus rapid diagnostic tests and to analyze the cross-reactivity of both tests.

Materials and Methods

Stool samples collected from every acute diarrhea patient aged <15 years old who was admitted at Bhumibol Adulyadej Hospital, Bangkok, Thailand, from November 2014 to September 2016 underwent the following test: QuickNaviTM – Norovirus2 for norovirus, VIKIA^® Rota-Adeno for rotavirus, and aerobic bacterial culture. Real-time reverse transcription polymerase chain reaction was used as a gold standard for virus detection. False-positive results determined cross-reactivity.

Results

From 358 stool specimens, the sensitivity of RDTs for norovirus and rotavirus was 27.5% and 44.8%, respectively. The specificity of RDTs for norovirus and rotavirus was 97.7% and 91.6%, respectively. False positive results of RDT for norovirus occurred in 6 samples (1.7%) and 22 samples (6.1%) in RDT for rotavirus. Rotavirus RDT was found to have cross-reactivity with 11 norovirus infection and 3 bacterial infected stools.

Conclusion

We found that the RDTs for both rotavirus and norovirus have high specificity but low sensitivity. Cross-reactivity was observed in positive rotavirus RDT with half of it being norovirus.

Rotavirus A in Brazil: Molecular Epidemiology and Surveillance during 2018-2019

Rotavirus A (RVA) vaccines succeeded in lowering the burden of acute gastroenteritis (AGE) worldwide, especially preventing severe disease and mortality. In 2019, Brazil completed 13 years of RVA vaccine implementation (Rotarix™) within the National Immunization Program (NIP), and as reported elsewhere, the use of Rotarix™ in the country has reduced childhood mortality and morbidity due to AGE. Even though both marketed vaccines are widely distributed, the surveillance of RVA causing AGE and the monitoring of circulating genotypes are important tools to keep tracking the epidemiological scenario and vaccines impact. Thus, our study investigated RVA epidemiological features, viral load and G and P genotypes circulation in children and adults presenting AGE symptoms in eleven states from three out of five regions in Brazil. By using TaqMan^®-based one-step RT-qPCR, we investigated a total of 1536 stool samples collected from symptomatic inpatients, emergency department visits and outpatients from January 2018 to December 2019. G and P genotypes of RVA-positive samples were genetically characterized by multiplex RT-PCR or by nearly complete fragment sequencing. We detected RVA in 12% of samples, 10.5% in 2018 and 13.7% in 2019. A marked winter/spring seasonality was observed, especially in Southern Brazil. The most affected age group was children aged >24-60 months, with a positivity rate of 18.8% (p < 0.05). Evaluating shedding, we found a statistically lower RVA viral load in stool samples collected from children aged up to six months compared to the other age groups (p < 0.05). The genotype G3P[8] was the most prevalent during the two years (83.7% in 2018 and 65.5% in 2019), and nucleotide sequencing of some strains demonstrated that they belonged to the emergent equine-like G3P[8] genotype. The dominance of an emergent genotype causing AGE reinforces the need for continuous epidemiological surveillance to assess the impact of mass RVA immunization as well as to monitor the emergence of novel genotypes.

High prevalence of DS-1-like rotavirus infection in Thai adults between 2016 and 2019

Rotavirus infection is the most common cause of viral diarrhea in infants and young children but uncommon and usually asymptomatic in adults. In the winter of 2017–2018, a large-scale outbreak of rotavirus in both children and adults was reported in Thailand. The current study focused on the prevalence, genotyping, and molecular characterization of rotavirus infections in Thai adults from July 2016 to December 2019. In 2,598 stool samples collected from adult residents of Bangkok (aged #x2265; 15 years) with acute gastroenteritis, rotavirus was detected via real-time RT-PCR analysis of the VP6 gene. G, P and I genotypes were determined by direct sequencing of VP7, VP4, and VP6 genes, respectively. Our results showed 8.7% (226/2,598) of stool samples were positive for rotavirus. The incidence of rotavirus was high during the winter season of 2017–2018 (17.7%) compared to another studied periods (4.5% between July 2016- October 2017 and 2.8% between March 2018- December 2019). Nucleotide sequencing of VP7 and VP4 revealed G3P[8] as the predominant strain (33.2%,75/226), followed by G9P[8] (17.3%,39/226), and G2P[4] (15.0%,34/226). Uncommon G and P combinations were additionally detected at low frequencies. VP6 sequencing was conducted to discriminate I genotype between the Wa and DS-1 genogroup. The unusual DS-1-like G3P[8] strain was most prevalent amomg rotavirus strains detected in this study (29.6%, 67/226), and the corresponding VP7 sequences showed high nucleotide identity with unusual DS-1-like globally circulating strains. Our study demonstrates that rotavirus outbreaks in adults are attributable not only to high prevalence of RV infection but also the unusual DS-like genogroup. The collective findings reinforce the importance of investigating rotavirus diagnosis in adults suffering from acute gastroenteritis and taking appropriate preventive measures.

Etiologic features of diarrheagenic microbes in stool specimens from patients with acute diarrhea in Thailand

Many microbial species have been recognized as enteropathogens for humans. Here, we predicted the causative agents of acute diarrhea using data from multiplex quantitative PCR (qPCR) assays targeting 19 enteropathogens. For this, a case-control study was conducted at eight hospitals in Thailand. Stool samples and clinical data were collected from 370 hospitalized patients with acute diarrhea and 370 non-diarrheal controls. Multiple enteropathogens were detected in 75.7% and 13.0% of diarrheal stool samples using multiplex qPCR and bacterial culture methods, respectively. Asymptomatic carriers of enteropathogens were found among 87.8% and 45.7% of individuals by qPCR and culture methods, respectively. These results suggested the complexity of identifying causative agents of diarrhea. An analysis using the quantification cut-off values for clinical relevance drastically reduced pathogen-positive stool samples in control subjects from 87.8% to 0.5%, whereas 48.9% of the diarrheal stool samples were positive for any of the 11 pathogens. Among others, rotavirus, norovirus GII, Shigella/EIEC, and Campylobacter were strongly associated with acute diarrhea (P-value < 0.001). Characteristic clinical symptoms, epidemic periods, and age-related susceptibility to infection were observed for some enteropathogens. Investigations based on qPCR approaches covering a broad array of enteropathogens might thus improve our understanding of diarrheal disease etiology and epidemiological trends.

Surveillance data confirm multiyear predictions of rotavirus dynamics in New York City

Prediction skill is a key test of models for epidemic dynamics. However, future validation of models against out-of-sample data is rare, partly because of a lack of timely surveillance data. We address this gap by analyzing the response of rotavirus dynamics to infant vaccination. Syndromic surveillance of emergency department visits for diarrhea in New York City reveals a marked decline in diarrheal incidence among infants and young children, in line with data on rotavirus-coded hospitalizations and laboratory-confirmed cases, and a shift from annual to biennial epidemics increasingly affecting older children and adults. A published mechanistic model qualitatively predicted these patterns more than 2 years in advance. Future efforts to increase vaccination coverage may disrupt these patterns and lead to further declines in the incidence of rotavirus-attributable gastroenteritis.

Multivalent Rotavirus Vaccine and Wild-type Rotavirus Strain Shedding in Australian Infants: A Birth Cohort Study

Background

Rotavirus vaccines have reduced moderate-to-severe gastroenteritis episodes in infants and young children. Nevertheless, knowledge gaps exist concerning rotavirus vaccine shedding and vaccine impact upon mild and asymptomatic wild-type infections. Our primary objective was to investigate vaccine shedding in Australian infants where the multivalent human-bovine reassortant rotavirus vaccine, RotaTeq, was part of the routine vaccination schedule.

Methods

The Observational Research in Childhood Infectious Diseases (ORChID) birth cohort study was conducted in Brisbane, Australia, from September 2010 to October 2014. Newborn infants were enrolled progressively and followed until their second birthday. Parents recorded daily symptoms and mailed weekly stool swab samples from their infants to the laboratory where reverse-transcription polymerase chain reaction testing was performed, and rotavirus-positive samples underwent genotyping to distinguish between vaccine and wild-type strains.

Results

Rotavirus was detected in 1068 of 11139 (9.6%) stool swabs from 158 infants, and 994 (93.1%) were genotyped. RotaTeq vaccine strains accounted for 951 of 994 (95.7%) typed rotavirus-positive swabs. Proportions of infants shedding RotaTeq after the first, second, and third vaccine doses were 87.0%, 57.4%, and 47.3%, respectively, and median (interquartile range) shedding duration after vaccine doses 1-3 was 3 (1-8), 1.5 (1-3), and 1 (1-2), weeks, respectively. In contrast, the incidence rate of wild-type rotavirus episodes was 10.3 (95% confidence interval, 6.8-15.6) per 100 child-years of observation.

Conclusions

RotaTeq vaccine virus was detected in stool samples from 47%-87% of infants after each vaccine dose. Genotyping is an essential tool for differentiating between rotavirus vaccine and wild-type strains and monitoring vaccine impact in children.

Clinical Trial Registration

NCT01304914.

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.

Evaluation of different genomic regions of Rotavirus A for development of real time PCR

The nucleotide alignment of all 11 genes of human Rotavirus A (RVA) strains revealed suitability of NSP2, NSP3 and VP6 genes for the development of real time PCR (qRT-PCR). Evaluation of qRT-PCR assays using known rotavirus ELISA positive and negative fecal specimens showed non-overlapping ranges of Mean ±3SD cycle threshold (Ct) values for NSP3 and VP6 based assays. Using serial dilutions of purified RVA, high sensitivity of VP6 qRT-PCR assay (1.95 × 10^-5 pg/μL of RNA) was recorded as compared to NSP2 and NSP3 qRT-PCR assays (1.95 × 10^-4 pg/μL of RNA). Further, evaluation of the VP6 qRT-PCR assay involving 266 fecal specimens and frequency polygon analysis of the data indicated cut-off value of 35 for Ct with high sensitivity (126/131, 96%) and specificity (12/12, 100%). This VP6 qRT-PCR assay will be a useful diagnostic tool to evaluate clinical presentations in rotaviral gastroenteritis under different conditions such as breast feeding and administration of rotavirus vaccines.

Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study

BACKGROUND

Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens.

METHODS

We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples.

RESULTS

We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms.

CONCLUSIONS

Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections.

Species A rotaviruses isolated from hospitalized patients over 5 years of age in Kolkata, India, in 2012/13

In hospital-based diarrhoeal disease surveillance at Infectious Diseases & Beliaghata-General Hospital (May-2012 to April-2013), Kolkata, India, stool samples were collected from patients < 5 years (n = 830) and > 5 years of age (n = 728) hospitalized with diarrhea. Group-A rotavirus (GARV) was identified by ELISA followed by multiplex RT-PCR. In children < 5 years of age, 53.4% of the samples were positive for GARV. In patients > 5 years to 90 years old, only 6.04% (n = 44) tested positive for GARV. G2P[4] strains (n = 16 [36.36%]) were the most prevalent, followed by G9P[4] strains (n = 13 [29.54%]), while P[4]-(n = 30 [68.18%]) was most prevalent among the P genotypes. The GARV strains G2, G9 and P[4] detected in adults clustered together in the phylogenetic tree with the GARV strains identified in children (< 5 years) during the same period. Rotavirus positivity was high among female patients (75%), suggesting that caregivers (mother/grandmother/older-siblings) may get infected through young children or may act as carriers for transmission.

Real-time RT-PCR, a necessary tool to support the diagnosis and surveillance of rotavirus in Mexico

Rotavirus produces diarrhea in children under 5 years old. Most of those conventional methods such as polyacrylamide gel electrophoresis (PAGE) and reverse transcription-polymerase chain reaction (RT-PCR) have been used for rotavirus detection. However, these techniques need a multi-step process to get the results. In comparison with conventional methods, the real-time RT-PCR is a highly sensitive method, which allows getting the results in only one day. In this study a real-time RT-PCR assay was tested using a panel of 440 samples from patients with acute gastroenteritis, and characterized by PAGE and RT-PCR. The results show that the real-time RT-PCR detected rotavirus from 73% of rotavirus-negative samples analyzed by PAGE and RT-PCR; thus, the percentage of rotavirus-positive samples increased to 81%. The results indicate that this real-time RT-PCR should be part of a routine analysis, and as a support of the diagnosis of rotavirus in Mexico.

Identification of group B rotavirus as an etiological agent in the gastroenteritis outbreak in Maharashtra, India

Acute gastroenteritis outbreak occurred at Pargaon, Maharashtra, India in 1789 cases with an attack rate of 32.5% between November to December 2015. The stool specimens (n = 32) were investigated for different enteric viral agents using conventional methods. Transmission electron microscopy and RNA polyacrylamide gel electrophoresis respectively identified morphologically distinct rotavirus particles in 28% and RNA migration pattern of Group B Rotavirus (GBR) in 72% of the specimens. Reverse transcription polymerase chain reaction and nucleotide sequencing confirmed presence of GBR in 97% of the samples analyzed. The predominance of GBR infections and absence or insignificant presence of other agents confirmed GBR as an etiological agent of the gastroenteritis outbreak occurred in Maharashtra, India.

Rotavirus infection

Rotavirus infections are a leading cause of severe, dehydrating gastroenteritis in children <5 years of age. Despite the global introduction of vaccinations for rotavirus over a decade ago, rotavirus infections still result in >200,000 deaths annually, mostly in low-income countries. Rotavirus primarily infects enterocytes and induces diarrhoea through the destruction of absorptive enterocytes (leading to malabsorption), intestinal secretion stimulated by rotavirus non-structural protein 4 and activation of the enteric nervous system. In addition, rotavirus infections can lead to antigenaemia (which is associated with more severe manifestations of acute gastroenteritis) and viraemia, and rotavirus can replicate in systemic sites, although this is limited. Reinfections with rotavirus are common throughout life, although the disease severity is reduced with repeat infections. The immune correlates of protection against rotavirus reinfection and recovery from infection are poorly understood, although rotavirus-specific immunoglobulin A has a role in both aspects. The management of rotavirus infection focuses on the prevention and treatment of dehydration, although the use of antiviral and anti-emetic drugs can be indicated in some cases.

Health impact and cost-effectiveness of a domestically-produced rotavirus vaccine in India: A model based analysis

Background

Currently, Indian officials are incorporating a domestically manufactured rotavirus vaccine (based on the 116E rotavirus strain) into the country’s universal immunization program; this vaccine will cost significantly less than western rotavirus vaccines. Here, we examine the public health impact, cost, and cost-effectiveness of universal vaccination in India using the 116E vaccine. This work will allow comparison of universal 116E vaccination with other approaches to child mortality reduction, shed light on the future burden of rotavirus disease in India, and help stakeholders understand future resource needs.

Methods

Using information from published literature, we developed a dynamic simulation model of rotavirus transmission, natural history, and related utilization among Indian infants followed until age five. Infection risk depended on the degree of viral shedding in the population. Infection risk and severity were influenced by age, number of previous infections, and vaccination history. Probabilities of inpatient and outpatient health services utilization depended on symptom severity. With the model, we compared a strategy of nationwide 116E vaccination to one of no vaccination. Costs were considered from the perspective of all payers (including families) and from the societal perspective.

Results

We estimated that an established 116E vaccination program would reduce symptomatic rotavirus infection by 13.0%, while reducing population-wide rotavirus mortality by 34.6% (over 34,000 lives annually). Rotavirus outpatient visits would decline by 21.3%, and hospitalization would decline by 28.1%. The cost per disability-adjusted life year (DALY) averted was estimated at 3,429 Rupees (approximately $56). Predicted mortality reduction in children born during the first five years of vaccination implementation was nearly identical to that in children born in later years (34.4% versus 34.6%).

Conclusions

116E vaccination of Indian infants would likely substantially reduce rotavirus-related morbidity, mortality, and utilization at a cost considered highly cost-effective by standard criteria. Nearly the entire mortality reduction benefit of vaccination was attributable to direct protection of those vaccinated, as opposed to indirect “herd immunity” effects.

Group A rotaviruses circulating prior to a national immunization programme in Nigeria: Clinical manifestations, high G12P[8] frequency, intra-genotypic divergence of VP4 and VP7

Nigeria having approximately 50 000 Rotavirus A (RVA) deaths annually is yet to introduce RVA vaccine into routine national immunization; therefore surveillance of RVA strains circulating before vaccine introduction is essential in evaluating impact of the intervention. Stool samples and sociodemographic data of diarrhoeic children, <5 years were collected between August 2012 and December 2013. While a high prevalence of RVA infection (47.6%; 49/103) was observed by quantitative reverse transcription real time PCR, only 25% (26/103) had high RVA genome concentrations and were antigen positive. G and P types were obtained for 31 and 37 samples respectively. G12P[8] strains were predominant (30.6%; 16/31); Other genotypes found included G9, G3, G2 and P[4], P[6], P[8]. A G12 + G2/P[8] + P[6] mixed infection was detected. The P[8] genotype showed divergence with strains distributed in lineage III and IV. Compared to the vaccines, changes in antigenic sites of VP8* and VP7 were found. The finding of the G2P[6] genotype combination and emergence of G12 strains support observations in most of the recent RVA studies from Africa. P[6] is common in many African countries, in contrast to countries in Europe and the Americas. In conclusion, this study shows the circulation of other RVA genotypes compared to the common RVA genotypes in Nigeria. PCR results should be interpreted with caution to avoid significant bias from samples with low RVA genome concentrations. These findings provide important information on the detection and molecular epidemiology of RVA prior to vaccination and contribute as a baseline for future evaluations after possible vaccine introduction.

In vitro Antiviral Activity of Rubia cordifolia Aerial Part Extract against Rotavirus

The root of Rubia cordifolia has been used traditionally as a hemostatic agent, while the aerial part of the plant consisting of leaf and stem is known to exhibit anti-diarrheal properties and has been widely used as a remedy in many parts of China. As rotavirus is one of the most commonly associated diarrhea-causing pathogen, this study aims to investigate the anti-rotaviral effect of R. cordifolia aerial part (RCAP). The cytotoxicity of RCAP toward MA-104 cells was evaluated using the WST-8 assay. Colloidal gold method and real time polymerase chain reaction (qPCR) assay were used to confirm the findings of the antiviral assay. Then, 4',6-diamidino-2-phenylindole (DAPI) staining method was subsequently used to investigate the mode of death among the cells. And the representative components of aqueous extract were isolated and identified. It was shown that both the viability of MA-104 cells and the viral load were reduced with increasing concentration of the extract. DAPI staining showed that virus-induced apoptosis was the cause of the low cell viability and viral load, an effect which was accelerated with incubation in the aqueous herbal extract. The major compounds postulated to exhibit this activity were isolated from the aqueous herbal extract and identified to be compounds Xanthopurpurin and Vanillic Acid. This study showed that RCAP extract effectively inhibited rotavirus multiplication by promoting virus-induced apoptosis in MA-104 cells.

Cost-Effectiveness of Rotavirus Vaccination in France-Accounting for Indirect Protection

BACKGROUND

Vaccination against rotavirus has shown great potential for reducing the primary cause of severe childhood gastroenteritis. Previous economic evaluations of rotavirus vaccination in France have not modeled the potential impact of vaccines on disease burden via reduced transmission.

OBJECTIVE

To determine the cost-effectiveness of the introduction of pentavalent rotavirus vaccination into the French infant vaccination schedule.

METHODS

We developed an age-structured model of rotavirus transmission calibrated to 6 years of French gastroenteritis incidence and vaccine clinical trial data. We evaluated the cost-effectiveness of pentavalent rotavirus vaccination considering that 75% of infants would receive the three-dose vaccine course.

RESULTS

Our model predicts that rotavirus vaccination will decrease rotavirus gastroenteritis incidence and associated clinical outcomes in vaccinated and unvaccinated individuals, delay the seasonal peak of infection, and increase the age of infection. From the societal perspective, our base-case scenario predicts that vaccination coverage would be cost-effective at €115 or €135 per vaccine course at €28,500 and €39,500/quality-adjusted life-year (QALY) gained, respectively, and suggests that almost 95% of the financial benefits will be recouped within the first 5 years following vaccination implementation. From the third-party payer perspective, incremental cost-effectiveness ratios ranged from €12,500 to €20,000/QALY, respectively. Our uncertainty analysis suggests that findings were sensitive to various assumptions including the number of hospitalizations, outpatient visits, and the extent of QALY losses per rotavirus episode.

CONCLUSIONS

Introducing pentavalent rotavirus vaccination into the French infant vaccination schedule would significantly reduce the burden of rotavirus disease in children, and could be cost-effective under plausible conditions.

Fusion of the mouse IgG1 Fc domain to the VHH fragment (ARP1) enhances protection in a mouse model of rotavirus

A variable fragment of a heavy chain antibody (VHH) directed against rotavirus, also referred to as anti-rotavirus protein 1 (ARP1), was shown to confer protection against rotavirus induced diarrhea in infant mouse model of rotavirus induced diarrhea. In this study, we have fused the mouse IgG1 Fc to ARP1 to improve the protective capacity of ARP1 by inducing an Fc-mediated effector function. We have shown that the Fc-ARP1 fusion protein confers significantly increased protection against rotavirus in a neonatal mouse model of rotavirus-induced diarrhea by reducing the prevalence, duration and severity of diarrhea and the viral load in the small intestines, suggesting that the Fc part of immunoglobulins may be engaged in Fc-mediated neutralization of rotavirus. Engineered conventional-like antibodies, by fusion of the Fc part of immunoglobulins to antigen-specific heavy-chain only VHH fragments, might be applied to novel antibody-based therapeutic approaches to enhance elimination of pathogens by activation of distinct effector signaling pathways.

Measuring indirect effects of rotavirus vaccine in low income countries

Widespread introduction of rotavirus vaccines has led to major reductions in the burden of rotavirus gastroenteritis worldwide. Vaccine effectiveness is diminished, however, in low income countries, that harbour the greatest burden of rotavirus attributed morbidity and mortality. Indirect effects of rotavirus vaccine (herd immunity and herd protection) could increase population level impact and improve vaccine cost effectiveness in such settings. While rotavirus vaccine indirect effects have been demonstrated in high and middle income countries, there are very little data from low income countries where force of infection, population structures and vaccine schedules differ. Targeted efforts to evaluate indirect effects of rotavirus vaccine in low income countries are required to understand the total impact of rotavirus vaccine on the global burden of rotavirus disease.

Distinct Roles of Type I and Type III Interferons in Intestinal Immunity to Homologous and Heterologous Rotavirus Infections

Type I (IFN-α/β) and type III (IFN-λ) interferons (IFNs) exert shared antiviral activities through distinct receptors. However, their relative importance for antiviral protection of different organ systems against specific viruses remains to be fully explored. We used mouse strains deficient in type-specific IFN signaling, STAT1 and Rag2 to dissect distinct and overlapping contributions of type I and type III IFNs to protection against homologous murine (EW-RV strain) and heterologous (non-murine) simian (RRV strain) rotavirus infections in suckling mice. Experiments demonstrated that murine EW-RV is insensitive to the action of both types of IFNs, and that timely viral clearance depends upon adaptive immune responses. In contrast, both type I and type III IFNs can control replication of the heterologous simian RRV in the gastrointestinal (GI) tract, and they cooperate to limit extra-intestinal simian RRV replication. Surprisingly, intestinal epithelial cells were sensitive to both IFN types in neonatal mice, although their responsiveness to type I, but not type III IFNs, diminished in adult mice, revealing an unexpected age-dependent change in specific contribution of type I versus type III IFNs to antiviral defenses in the GI tract. Transcriptional analysis revealed that intestinal antiviral responses to RV are triggered through either type of IFN receptor, and are greatly diminished when receptors for both IFN types are lacking. These results also demonstrate a murine host-specific resistance to IFN-mediated antiviral effects by murine EW-RV, but the retention of host efficacy through the cooperative action by type I and type III IFNs in restricting heterologous simian RRV growth and systemic replication in suckling mice. Collectively, our findings revealed a well-orchestrated spatial and temporal tuning of innate antiviral responses in the intestinal tract where two types of IFNs through distinct patterns of their expression and distinct but overlapping sets of target cells coordinately regulate antiviral defenses against heterologous or homologous rotaviruses with substantially different effectiveness.

Two distinct families of interferons (IFNs), type I (IFN-α/β) and type III (IFN-λ) IFNs, are quickly produced in response to virus infection and engage distinct receptors to invoke shared rapid and broad-spectrum antiviral mechanisms against invading pathogens. However, the relative importance of type I and type III IFNs in protecting different organ systems against specific viruses or distinct strains of an individual virus remains to be fully explored. Here we demonstrated in suckling mice that neither type I nor type III IFNs are effective in blocking intestinal replication of murine rotavirus, rather, viral clearance is dependent upon adaptive immune responses. In contrast, both IFN types cooperate to control intestinal replication and extra-intestinal spread of simian rotavirus in neonatal mice. Unexpectedly, we found that although intestinal epithelial cells (IECs) respond to both types of IFNs in neonatal mice, responsiveness of IECs to type I IFNs, but not type III IFNs, is diminished in adult mice. Transcriptional analysis showed that both types of IFN receptors induced overlapping intestinal antiviral responses, which were abrogated only when both receptor types were deleted. Overall, these findings reveal a well-coordinated spatial and temporal regulation of antiviral defenses by type I and type III IFNs in the gastrointestinal tract that varies significantly depending on the viral strain examined.

One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples

Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8-100% sensitivity, 99.7-100% specificity, 85-95% efficiency and a limit of detection of 4-60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81-92% efficiency and limit of detection of 150-600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8-100% sensitivity, 100% specificity, 86-89% efficiency and a limit of detection of 12-400 copies per singleplex reactions. The VP4 qRT-PCRs exhibited 82-90% efficiency and limit of detection of 120-4000 copies in multiplex reaction. Discussion. The one-step multiplex qRT-PCR assay will facilitate high-throughput rotavirus genotype characterization for monitoring circulating rotavirus wild-type strains causing rotavirus infections, determining the frequency of Rotarix® and RotaTeq® vaccine strains and vaccine-derived reassortants associated with AGE, and help to identify novel rotavirus strains derived by reassortment between vaccine and wild-type strains.

Did Large-Scale Vaccination Drive Changes in the Circulating Rotavirus Population in Belgium?

Vaccination can place selective pressures on viral populations, leading to changes in the distribution of strains as viruses evolve to escape immunity from the vaccine. Vaccine-driven strain replacement is a major concern after nationwide rotavirus vaccine introductions. However, the distribution of the predominant rotavirus genotypes varies from year to year in the absence of vaccination, making it difficult to determine what changes can be attributed to the vaccines. To gain insight in the underlying dynamics driving changes in the rotavirus population, we fitted a hierarchy of mathematical models to national and local genotype-specific hospitalization data from Belgium, where large-scale vaccination was introduced in 2006. We estimated that natural- and vaccine-derived immunity was strongest against completely homotypic strains and weakest against fully heterotypic strains, with an intermediate immunity amongst partially heterotypic strains. The predominance of G2P[4] infections in Belgium after vaccine introduction can be explained by a combination of natural genotype fluctuations and weaker natural and vaccine-induced immunity against infection with strains heterotypic to the vaccine, in the absence of significant variation in strain-specific vaccine effectiveness against disease. However, the incidence of rotavirus gastroenteritis is predicted to remain low despite vaccine-driven changes in the distribution of genotypes.

Rapid genotyping of human rotavirus using SYBR green real-time reverse transcription-polymerase chain reaction with melting curve analysis

AIM: To develop a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay to genotype rotavirus (G and P) in Alberta from January 2012 to June 2013.

METHODS: We developed and validated a different approach to perform rotavirus G and P genotyping using a two-step SYBR green RT-PCR (rt-gPCR) by selecting genotype-specific primers of published conventional RT nested PCR (cnRT-PCR) assay and optimizing the amplification conditions. cDNA was first synthesized from total RNA with SuperScript™ II reverse transcriptase kit followed by amplication step using monoplex SYBR green real-time PCR. After the PCR reaction, melting curve analysis was used to determine specific genotype. Sixteen samples previously genotyped using cnRT-PCR were tested using the new assay and the genotyping results were compared as sensitivity analysis. Assay specificity was evaluated by testing other gastroenteritis viruses with the new assay. The amplicon size of each available genotype was determined by gel-electrophoresis and DNA sequences were obtained using Sanger-sequencing method. After validation and optimization, the new assay was used to genotype 122 pediatric clinical stool samples previously tested positive for rotavirus using electron microscopy between January 2012 and June 2013.

RESULTS: The new rt-gPCR assay was validated and optimized. The assay detected G1 to G4, G9, G12 and P[4] and P[8] that were available as positive controls in our laboratory. A single and clear peak of melting curve was generated for each of specific G and P genotypes with a T_m ranging from 80 °C to 82 °C. The sensitivity of rt-gPCR was comparable to cnRT-PCR with 100% correlation of the 16 samples with known G and P genotypes. No cross reaction was found with other gastroenteritis viruses. Using the new rt-gPCR assay, genotypes were obtained for 121 of the 122 pediatric clinical samples tested positive for rotavirus: G1P[8] (42.6%), G2P[4] (4.9%), G3P[8] (10.7%), G9P[8] (10.7%), G9P[4] (6.6%), G12P[8] (23.0%), and unknown GP[8] (0.8%). For the first time, G12 rotavirus strains were found in Alberta and G12 was the second most common genotype during the study period. Gel electrophoresis of all the genotypes showed expected amplicon size for each genotype. The sequence data of the two G12 samples along with other genotypes were blasted in NCBI BLAST or analyzed with Rota C Genotyping tool (http://rotac.regatools.be/). All genotyping results were confirmed to be correct.

CONCLUSION: rt-gPCR is a useful tool for the genotyping and characterization of rotavirus. Monitoring of rotavirus genotypes is important for the identification of emerging strains and ongoing evaluation of rotavirus vaccination programs.

Detection of Rotavirus in children with acute gastroenteritis in Zagazig University Hospitals in Egypt

Introduction:

Rotavirus is the major cause of acute gastroenteritis (AGE) in infants and young children all over the world. The objective of the study was to compare different methods for detecting rotavirus and to assess the burden of rotavirus as a causative agent for AGE in children younger than five.

Methods:

This case control study included 65 children with AGE and 35 healthy control children. They were chosen from the Pediatric Department of Zagazig University Hospitals from October 2014 to March 2015. Stool samples were obtained and assayed for rotavirus by the immunochromatography test (ICT), enzyme linked immunosorbent assay (ELISA) and quantitative real time RT-PCR (qr RT-PCR).

Results:

Fifty out of the 65 patients (76.9%) were positive for qr RT-PCR. Forty-five (69.2%) and 44 (67.7%) were positive for ICT and ELISA, respectively. There was a significant association between the severity of the disease as determined by the Vesikari score and rotavirus infection.

Conclusion:

This study demonstrated that ICT is a useful method for the rapid screening of group A rotavirus in fecal specimens, because it is rapid, inexpensive, easy to perform, and requires very little equipment. In addition, this study highlights the substantial health burden of rotavirus AGE among children less than five.

Methods of analysis of enteropathogen infection in the MAL-ED Cohort Study

Studies of diarrheal etiology in low- and middle-income countries have typically focused on children presenting with severe symptoms to health centers and thus are best equipped to describe the pathogens capable of leading to severe diarrheal disease. The Etiology, Risk Factors and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) cohort study was designed to evaluate, via intensive community surveillance, the hypothesis that repeated exposure to enteropathogens has a detrimental effect on growth, vaccine response, and cognitive development, which are the primary outcome measures for this study. In the setting of multiple outcomes of interest, a longitudinal cohort design was chosen. Because many or even the majority of enteric infections are asymptomatic, the collection of asymptomatic surveillance stools was a critical element. However, capturing diarrheal stools additionally allowed for the determination of the principle causes of diarrhea at the community level as well as for a comparison between those enteropathogens associated with diarrhea and those that are associated with poor growth, diminished vaccine response, and impaired cognitive development. Here, we discuss the analytical methods proposed for the MAL-ED study to determine the principal causes of diarrhea at the community level and describe the complex interplay between recurrent exposure to enteropathogens and these critical long-term outcomes.

Prevalence of Rotaviruses Groups A and C in Egyptian Children and Aquatic Environment

The objective of this study is to compare the prevalence of rotaviruses groups A and C in Egyptian children and aquatic environment. From 110 stool specimens of children with acute diarrhea and using RT-PCR, 35 samples (31.8 %) were positive for human rotavirus group A and 15 samples (13.6 %) were positive for human rotavirus group C. From 96 samples collected from Zenin wastewater treatment plant over a 2-year period (November 2009-October 2011) and using RT-PCR, rotavirus group A was detected in (4/24) 16.7 %, (5/24) 20.8 %, (4/24) 16.7 %, and (4/24) 16.7 %, while rotavirus group C was detected in (2/24) 8.3 %, (3/24) 12.5 %, (3/24) 12.5 %, and (0/24) 0 % in raw sewage, after primary sedimentation, after secondary sedimentation, and after final chlorination, respectively. Moreover, from 96 samples collected from El-Giza water treatment plant over a 2-year period (November 2009-October 2011), rotavirus group A was detected in (7/24) 29.2 %, (6/24) 25 %, (5/24) 20.8 %, and (3/24) 12.5 %, while rotavirus group C was detected in (3/24) 12.5 %, (1/24) 4.2 %, (1/24) 4.2 %, and (0/24) 0 % in raw Nile water, after sedimentation, after sand filtration, and after final chlorination, respectively. Using SYBR Green real-time RT-PCR, the number of human rotavirus group A genome or infectious units was higher than rotavirus group C. VP6 sequence analysis of the RT-PCR positive rotavirus group C samples revealed that four clinical specimens and three environmental samples showed similar sequences clustered with Moduganari/Human Nigerian strain AF 325806 with 98 % homology, and two clinical specimens and one environmental sample showed similar sequences clustered with Dhaka CB/Human Bangladesh strain AY 754826 with 97 % homology.