Burden and epidemiology of rotavirus diarrhea in selected African countries: preliminary results from the African Rotavirus Surveillance Network

Prevalence and predictors of diarrhea among children under five in Ghana

BACKGROUND

Globally, childhood diarrhea is a major public health concern. Despite numerous interventions that have been put in place to reduce its incidence over the years, childhood diarrhea remains a problem and is the fourth leading cause of child mortality in Ghana. This study examined the predictors of diarrhea among children under the age of five in Ghana.

METHODS

Data from the 2014 Ghana Demographic and Health survey, a cross-sectional survey, was used for the purpose of this study. A total of 2,547 children under the age of five were included in this study. Logistic regression analysis was performed to establish the factors associated with childhood diarrhea and ascertain explanatory variables.

RESULTS

The prevalence of diarrhea was 11.7%. Male children (13.4%) and those living in rural areas (12%), particularly in the Brong Ahafo region (17%) recorded the highest prevalence of diarrhea. Children aged 6 to 35 months of age, maternal age and education, sex of children and region of residence were the predictors of diarrhea among children under the age of five years in this study.

CONCLUSION

To lessen the prevalence of diarrhea among children under five in Ghana, existing interventions must be evaluated in the context of the predictors identified. Based on observations deduced from this study, the Ministry of Health, Ghana Health Service and other health regulatory agencies should intensify monitoring and awareness in the various regions, particularly in the transition and savannah zones on the causes, risk factors, and methods of preventing diarrhea in children under five. Various stakeholders including government and non-governmental organizations should take into account the predictors of diarrhea identified in the design of interventions to effectively reduce morbidity and mortality associated with childhood diarrhea.

Phase III randomized clinical studies to evaluate the immunogenicity, lot-to-lot consistency, and safety of ROTAVAC® liquid formulations (ROTAVAC 5C & 5D) and non-inferiority comparisons with licensed ROTAVAC® (frozen formulation) in healthy infants

The WHO pre-qualified rotavirus vaccine, ROTAVAC®, is derived naturally from the neonatal 116E rotavirus strain, and stored at -20°C. As refrigerator storage is preferable, immunogenicity and safety of liquid formulations kept at 2-8°C, having excipients to stabilize the rotavirus, with or without buffers, were compared with ROTAVAC® in different clinical studies. Study-1, the pivotal trial for this entire product development work, was a randomized, single-blind trial with two operationally seamless phases: (i) an exploratory phase involving 675 infants in which two formulations, ROTAVAC 5C (LnHRV-1.5 mL and LnHRV-2.0 mL) containing buffer and excipients to stabilize the virus against gastric acidity and temperature, were compared with ROTAVAC®. As the immune response of ROTAVAC 5C (LnHRV-2.0 mL) was non-inferior to ROTAVAC®, it was selected for (ii) confirmatory phase, involving 1,302 infants randomized 1:1:1:1 to receive three lots of LnHRV-2.0 mL, or ROTAVAC®. Primary objectives were the evaluation of non-inferiority and lot-to-lot consistency. The secondary objectives were to assess the safety and interference with the concomitant pentavalent vaccine. As it was separately established that buffers are not required for ROTAVAC®, in Study-2, the safety and immunogenicity of ROTAVAC 5D® (with excipients) were compared with ROTAVAC® and lot-to-lot consistency was assessed in another study. All lots elicited consistent immune responses, did not interfere with UIP vaccines, and had reactogenicity similar to ROTAVAC®. ROTAVAC 5C and ROTAVAC 5D® were immunogenic and well tolerated as ROTAVAC®. ROTAVAC 5D® had comparable immunogenicity and safety profiles with ROTAVAC® and can be stored at 2-8°C, leading to WHO pre-qualification.Clinical Trials Registration: Clinical Trials Registry of India (CTRI): CTRI/2015/02/005577CTRI/2016/11/007481 and CTRI/2019/03/017934.

Genomic Analysis of Rwandan G9P[8] Rotavirus Strains Pre- and Post-RotaTeq® Vaccine Reveals Significant Distinct Sub-Clustering in a Post-Vaccination Cohort

Although the introduction of rotavirus vaccines has substantially contributed to the reduction in rotavirus morbidity and mortality, concerns persist about the re-emergence of variant strains that might alter vaccine effectiveness in the long term. The G9 strains re-emerged in Africa during the mid-1990s and have more recently become predominant in some countries, such as Ghana and Zambia. In Rwanda, during the 2011 to 2015 routine surveillance period, G9P[8] persisted during both the pre- and post-vaccine periods. The pre-vaccination cohort was based on the surveillance period of 2011 to 2012, and the post-vaccination cohort was based on the period of 2013 to 2015, excluding 2014. The RotaTeq® vaccine that was first introduced in Rwanda in 2012 is genotypically heterologous to Viral Protein 7 (VP7) G9. This study elucidated the whole genome of Rwandan G9P[8] rotavirus strains pre- and post-RotaTeq® vaccine introduction. Fecal samples from Rwandan children under the age of five years (pre-vaccine n = 23; post-vaccine n = 7), conventionally genotyped and identified as G9P[8], were included. Whole-genome sequencing was then performed using the Illumina® MiSeq platform. Phylogenetic analysis and pair-wise sequence analysis were performed using MEGA6 software. Distinct clustering of three post-vaccination study strains was observed in all 11 gene segments, compared to the other Rwandan G9P[8] study strains. Specific amino acid differences were identified across the gene segments of these three 2015 post-vaccine strains. Important amino acid differences were identified at position N242S in the VP7 genome segment of the three post-vaccine G9 strains compared to the other G9 strains. This substitution occurs at a neutralization epitope site and may slightly affect protein interaction at that position. These findings indicate that the Rwandan G9P[8] strains revealed a distinct sub-clustering pattern among post-vaccination study strains circulating in Rwanda, with changes at neutralization epitopes, which may play a role in neutralization escape from vaccine candidates. This emphasizes the need for continuous whole-genome surveillance to better understand the evolution and epidemiology of the G9P[8] strains post-vaccination.

The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites

Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in Africa is the G8P[4]. This study aimed to elucidate the entire genome and evolution of Rwandan G8P[4] strains. Illumina sequencing was performed for twenty-one Rwandan G8P[4] rotavirus strains. Twenty of the Rwandan G8P[4] strains had a pure DS-1-like genotype constellation, and one strain had a reassortant genotype constellation. Notable radical amino acid differences were observed at the neutralization sites when compared with cognate regions in vaccine strains potentially playing a role in neutralization escape. Phylogenetic analysis revealed that the closest relationship was with East African human group A rotavirus (RVA) strains for five of the genome segments. Two genome sequences of the NSP4 genome segment were closely related to bovine members of the DS-1-like family. Fourteen VP1 and eleven VP3 sequences had the closest relationships with the RotaTeq™ vaccine WC3 bovine genes. These findings suggest that the evolution of VP1 and VP3 might have resulted from reassortment events with RotaTeq™ vaccine WC3 bovine genes. The close phylogenetic relationship with East African G8P[4] strains from Kenya and Uganda suggests co-circulation in these countries. These findings highlight the need for continued whole-genomic surveillance to elucidate the evolution of G8P[4] strains, especially after the introduction of rotavirus vaccination.

Genetic diversity and Genomic analysis of G3P[6] and equine-like G3P[8] in Children Under-five from Southern Highlands and Eastern Tanzania

Rotavirus group A genomic characterization is critical for understanding the mechanisms of rotavirus diversity, such as reassortment events and possible interspecies transmission. However, little is known about the genetic diversity and genomic relationship of the rotavirus group A strains circulating in Tanzania. The genetic and genomic relationship of RVA genotypes was investigated in children under the age of five. A total of 169 faecal samples were collected from under-five with diarrhea in Mbeya, Iringa and Morogoro regions of Tanzania. The RVA were screened in children under five with diarrhea using reverse transcription PCR for VP7 and VP4, and the G and P genotypes were determined using Sanger dideoxynucleotide cycle sequencing. Whole-genome sequencing was performed on selected genotypes. The overall RVA rate was 4.7% (8/169). The G genotypes were G3 (7/8) and G6 (1/8) among the 8 RVA positives, while the P genotypes were P[6] (4/8) and P[8] (2), and the other two were untypeable. G3P[6] and G3P[8] were the identified genotype combinations. The genomic analysis reveals that the circulating G3P[8] and G3P[6] isolates from children under the age of five with diarrhea had a DS-1-like genome configuration (I2-R2-C2-M2-Ax-N2-T2-E2-H2). The phylogenic analysis revealed that all 11 segments of G3P[6] were closely related to human G3P[6] identified in neighboring countries such as Uganda, Kenya, and other African countries, implying that G3P[6] strains descended from a common ancestor. Whereas, G3P[8] were closely related to previously identified equine-like G3P[P8] from Kenya, Japan, Thailand, Brazil, and Taiwan, implying that this strain was introduced rather than reassortment events. We discovered amino acid differences at antigenic epitopes and N-linked glycosylation sites between the wild type G3 and P[8] compared to vaccine strains, implying that further research into the impact of these differences on vaccine effectiveness is warranted. The phylogenic analysis of VP7 also identified a bovine-like G6. For the first time in Tanzania, we report the emergence of novel equine-like G3 and bovine-like G6 RVA strains, highlighting the importance of rotavirus genotype monitoring and genomic analysis of representative genotypes.

Co-Surveillance of Rotaviruses in Humans and Domestic Animals in Central Uganda Reveals Circulation of Wide Genotype Diversity in the Animals

Rotavirus genotypes are species specific. However, interspecies transmission is reported to result in the emergence of new genotypes. A cross-sectional study of 242 households with 281 cattle, 418 goats, 438 pigs, and 258 humans in Uganda was undertaken between 2013 and 2014. The study aimed to determine the prevalence and genotypes of rotaviruses across co-habiting host species, as well as potential cross-species transmission. Rotavirus infection in humans and animals was determined using NSP3 targeted RT-PCR and ProSpecT Rotavirus ELISA tests, respectively. Genotyping of rotavirus-positive samples was by G- and P-genotype specific primers in nested RT-PCR assays while genotyping of VP4 and VP7 proteins for the non-typeable human positive sample was done by Sanger sequencing. Mixed effect logistic regression was used to determine the factors associated with rotavirus infection in animals. The prevalence of rotavirus was 4.1% (95% CI: 3.0–5.5%) among the domestic animals and 0.8% (95% CI: 0.4–1.5%) in humans. The genotypes in human samples were G9P[8] and P[4]. In animals, six G-genotypes, G3(2.5%), G8(10%), G9(10%), G11(26.8%), G10(35%), and G12(42.5%), and nine P-genotypes, P[1](2.4%), P[4](4.9%), P[5](7.3%), P[6](14.6%), P[7](7.3%), P[8](9.8%), P[9](9.8%), P[10](12.2%), and P[11](17.1%), were identified. Animals aged 2 to 18 months were less likely to have rotavirus infection in comparison with animals below 2 months of age. No inter-host species transmission was identified.

Epidemiology and pre-vaccine burden of rotavirus diarrhea in Democratic Republic of Congo (DRC): Results of sentinel surveillance, 2009-2019

INTRODUCTION

Since August 2009, the Democratic Republic of Congo (DRC) has implemented sentinel site surveillance for rotavirus gastroenteritis. Limited hospital studies have been carried out, in DRC, describing the epidemiology of rotavirus diarrhea before rotavirus vaccine introduction in October 2019. This analysis describes the epidemiology of rotavirus gastroenteritis and characteristics of circulating viral strains from 2009 to 2019.

MATERIALS AND METHODS

We analyzed demographic and clinic data collected from children < 5 years old enrolled at three rotavirus sentinel surveillance sites in DRC during 2009-2019, prior to rotavirus vaccine introduction in 2019. Data have been described and presented as mean ± standard deviation for quantitative variables with normal distribution, or as median with an interquartile range [Q1-Q3] for quantitative variables with non-normal distribution, or as absolute value with percentage for qualitative variables.

RESULTS

Between August 2009 and December 2019, 4,928 children < 5 years old were admitted to sentinel surveillance sites for gastroenteritis in the DRC; the rotavirus positivity rate was 60 %. There was a slight male gender predominance (56 %), and the majority of children (79 %) were 0-11 months of age. Every year, the incidence was highest between May and September corresponding to the dry and cool season. Genotyping was performed for 50 % of confirmed rotavirus cases. The most common G genotypes were G1 (39 %) and G2 (24 %) and most common P genotypes were P[6] (49 %) and P[8] (37 %). The most common G-P genotype combinations were G1P[8] (22 %), G2P[6] (16 %) and G1P[6] (14 %). Genotype distribution varied by site, age group, and year.

CONCLUSION

From 2009 to 2019, rotavirus-associated gastroenteritis represented a significant burden among DRC children under 5 who were admitted to sentinel sites. G1P[8] was the most commonly identified genotype. Continued monitoring after the introduction of rotavirus vaccine will be essential to monitor any changes in epidemiology.

Prevalence of rotavirus infection among children under five years at a tertiary institution in Nigeria

Background and objectives: Rotavirus is a significant cause of nonbacterial diarrhea, especially in infants and young children worldwide. This study evaluated the pattern of rotavirus infection in children under five years presenting with acute diarrhea in Abuja Teaching Hospital, Gwagwalada, Nigeria. Methodology: It was a cross-sectional descriptive study to describe the prevalence of rotavirus infection among children. The study enrolled children 1 to 59 months old with acute diarrhea attending General Paediatric Outpatient clinic and hospitalized in the Emergency Paediatric Unit of University of Abuja Teaching Hospital (UATH), Gwagwalada, Nigeria. Rotavirus antigen was detected in the stool by qualitative enzyme-linked immunosorbent assay (ELISA). Data were analyzed using IBM-SPSS version 25.0. Results: The study comprised of 414 diarrhoeal children aged 1–59 months, of which 226 (54.6%) were male and the mean age was 12.1 months. The overall rate of rotavirus infection was 43.0% (178/ 414). The rotavirus infection was slightly higher among females than in males (46.8% vs 39.8%; p=0.153). Children from upper and middle social classes were at 1.95 [CI=1.17–3.26] and 3.08[CI=1.77–5.34] times higher risks of rotavirus induced diarrhea than the children from the lower social class (p<0.005). Children whose mothers had post-secondary education were three times more at risk of rotavirus diarrhea [OR=3.70; CI=1.46–9.36] than those with primary or no formal education (p<0.05). Children who had never been vaccinated against rotavirus were four times more likely to suffer rotavirus infection than those who had been vaccinated [OR=3.96; 95%CI=1.13–13.89, p=0.032]. Conclusion: This study found that rotavirus was an important causative agent of diarrhea in children in Gwagwalada, Abuja. Due to low rotavirus vaccination status in children, rotavirus screening tests are necessary for children with acute diarrheal disease. J Med Sci. 2022; 16(2): 010. DOI: https://doi.org/10.55010/imcjms.16.020 *Correspondence: Felix Olaniyi Sanni, Department of Public Health, Fescosof Data Solutions, Ogun, Nigeria. Email: fescosofanalysis@gmail.com

Detection of Escherichia coli, rotavirus, and Cryptosporidium spp. from drinking water, kitchenware, and flies in a periurban community of Lusaka, Zambia

Fecal contamination with a poor water, sanitation and hygiene environment in urban informal settlements poses diarrhea risks. Little information is available on the contamination of environmental media with enteric pathogens in such settlements. We investigated the contamination of Escherichia coli, rotavirus, and Cryptosporidium spp. in water, on kitchenware, and on flies in urban informal settlements of Chawama and Kanyama, Lusaka, Zambia. These environmental media were examined by XM-G agar cultivation for E. coli and specific real-time RT-PCR assays to detect rotavirus and Cryptosporidium spp. E. coli; rotavirus, and Cryptosporidium spp. were detected in samples of household stored drinking water (6 of 10 samples, 3 of 10 samples, and 2 of 10 samples, respectively), cups (10 of 20 samples, 2 of 13 samples, 1 of 13 samples, respectively), and flies (35 of 55 samples, 5 of 17 samples, 1 of 17 samples, respectively). The ranges of rotavirus concentrations in household stored drinking water, on cups, and flies were 2.9 × 10²-2.2 × 10⁵ copies/L, 1.2 × 10²-4.3 × 10² copies/cup, and 5.0 × 10¹-2.0 × 10² copies/fly, respectively. These results indicate the contribution of drinking water and kitchenware to enteric pathogen exposure and potential role of flies in microbial transmission.

Understanding Rotavirus Vaccine Efficacy and Effectiveness in Countries with High Child Mortality

Rotavirus claims thousands of lives of children globally every year with a disproportionately high burden in low- and lower-middle income countries where access to health care is limited. Oral, live-attenuated rotavirus vaccines have been evaluated in multiple settings in both low- and high-income populations and have been shown to be safe and efficacious. However, the vaccine efficacy observed in low-income settings with high rotavirus and diarrheal mortality was significantly lower than that seen in high-income populations where rotavirus mortality is less common. Rotavirus vaccines have been introduced and rolled out in more than 112 countries, providing the opportunity to assess effectiveness of the vaccines in these different settings. We provide an overview of the efficacy, effectiveness, and impact of rotavirus vaccines, focusing on high-mortality settings and identify the knowledge gaps for future research. Despite lower efficacy, rotavirus vaccines substantially reduce diarrheal disease and mortality and are cost-effective in countries with high burden. Continued evaluation of the effectiveness, impact, and cost–benefit of rotavirus vaccines, especially the new candidates that have been recently approved for global use, is a key factor for new vaccine introductions in countries, or for a switch of vaccine product in countries with limited resources.

Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020

Background: Sapovirus has emerged as a viral cause of acute gastroenteritis. However, there is limited data on sapovirus in Egypt. . The present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis <5 years in Mansoura, Egypt from January 2019 to February 2020 by reverse transcriptase-polymerase chain reaction (RT-PCR).

Methods: The cross-sectional study enrolled a 100 children <5 years who presented with acute gastroenteritis at an outpatient clinic in Mansoura, Egypt between January 2019 and February 2020. Clinical data, demographic data and a stool sample was collected from each child. Stools were screened by microscopy for parasites and culture methods for bacteria and excluded from the study if positive for either. Specimens were also screened for rotavirus by enzyme immune assays (EIA) and sapovirus by reverse transcription PCR.

Results: The most frequently detected virus was rotavirus by ELISA 25% (25/100). RT-PCR detected sapovirus in 7% (7/100) of the stool samples. The children with sapovirus were all from rural regions and presented mainly during the winter season in Egypt 42.9% (3/7). The main presenting symptoms were fever 71.4% (5/7) and vomiting 57.1% (4/7). None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in  five samples (5/7) , 71.4%, P=0.01.

Conclusion: The present study highlights the emergence of sapovirus as a frequent pathogen associated with acute gastroenteritis in children. There is a need for a national survey program for the study of sapovirus among other pathogens associated with acute gastroenteritis for better management of such infection.

Molecular surveillance and genetic divergence of rotavirus A antigenic epitopes in Gabonese children with acute gastroenteritis

Background

Rotavirus A (RVA) causes acute gastroenteritis in children <5 years of age in sub-Saharan Africa. In this study, we described the epidemiology and genetic diversity of RVA infecting Gabonese children and examined the antigenic variability of circulating strains in relation to available vaccine strains to maximize the public health benefits of introducing rotavirus vaccine through the Expanded Programme on Immunization (EPI) in Gabon.

Methods

Stool samples were collected consecutively between April 2018 and November 2019 from all hospitalized children <5 years with gastroenteritis and community controls without gastroenteritis. Children were tested for rotavirus A by quantitative RT-PCR and subsequently sequenced to identify circulating rotavirus A genotypes in the most vulnerable population. The VP7 and VP4 (VP8*) antigenic epitopes were mapped to homologs of vaccine strains to assess structural variability and potential impact on antigenicity.

Findings

Infections were mostly acquired during the dry season. Rotavirus A was detected in 98/177 (55%) hospitalized children with gastroenteritis and 14/67 (21%) of the control children. The most common RVA genotypes were G1 (18%), G3 (12%), G8 (18%), G9 (2%), G12 (25%), with G8 and G9 reported for the first time in Gabon. All were associated either with P[6] (31%) or P[8] (38%) genotypes. Several non-synonymous substitutions were observed in the antigenic epitopes of VP7 (positions 94 and 147) and VP8* (positions 89, 116, 146 and 150), which may modulate the elicited immune responses.

Interpretation

This study contributes to the epidemiological surveillance of rotavirus A required before the introduction of rotavirus vaccination in the EPI for Gabonese children.

Modelling rotavirus concentrations in rivers: Assessing Uganda's present and future microbial water quality

Faecal pathogens can be introduced into surface water through open defecation, illegal disposal and inadequate treatment of faecal sludge and wastewater. Despite sanitation improvements, poor countries are progressing slowly towards the United Nation's Sustainable Development Goal 6 by 2030. Sanitation-associated pathogenic contamination of surface waters impacted by future population growth, urbanization and climate change receive limited attention. Therefore, a model simulating human rotavirus river inputs and concentrations was developed combining population density, sanitation coverage, rotavirus incidence, wastewater treatment and environmental survival data, and applied to Uganda. Complementary surface runoff and river discharge data were used to produce spatially explicit rotavirus outputs for the year 2015 and for two scenarios in 2050. Urban open defecation contributed 87%, sewers 9% and illegal faecal sludge disposal 3% to the annual 15.6 log₁₀ rotavirus river inputs in 2015. Monthly concentrations fell between -3.7 (Q5) and 2.6 (Q95) log₁₀ particles per litre, with 1.0 and 2.0 median and mean log₁₀ particles per litre, respectively. Spatially explicit outputs on 0.0833 × 0.0833° grids revealed hotspots as densely populated urban areas. Future population growth, urbanization and poor sanitation were stronger drivers of rotavirus concentrations in rivers than climate change. The model and scenario analysis can be applied to other locations.

Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens

Group A rotaviruses cause severe gastroenteritis in infants and young children worldwide, with P[II] genogroup rotaviruses (RVs) responsible for >90% of global cases. RVs have diverse host ranges in different human and animal populations determined by host histo-blood group antigen (HBGA) receptor polymorphism, but details governing diversity, host ranges, and species barriers remain elusive. In this study, crystal structures of complexes of the major P[II] genogroup P[4] and P[8] genotype RV VP8* receptor-binding domains together with Lewis epitope-containing LNDFH I glycans in combination with VP8* receptor-glycan ligand affinity measurements based on NMR titration experiments revealed the structural basis for RV genotype-specific switching between ββ and βα HBGA receptor-binding sites that determine RV host ranges. The data support the hypothesis that P[II] RV evolution progressed from animals to humans under the selection of type 1 HBGAs guided by stepwise host synthesis of type 1 ABH and Lewis HBGAs. The results help explain disease burden, species barriers, epidemiology, and limited efficacy of current RV vaccines in developing countries. The structural data has the potential to impact the design of future vaccine strategies against RV gastroenteritis.

Environmental determinants of E. coli, link with the diarrheal diseases, and indication of vulnerability criteria in tropical West Africa (Kapore, Burkina Faso)

In 2017, diarrheal diseases were responsible for 606 024 deaths in Sub-Saharan Africa. This situation is due to domestic and recreational use of polluted surface waters, deficits in hygiene, access to healthcare and drinking water, and to weak environmental and health monitoring infrastructures. Escherichia coli (E. coli) is an indicator for the enteric pathogens that cause many diarrheal diseases. The links between E. coli, diarrheal diseases and environmental parameters have not received much attention in West Africa, and few studies have assessed health risks by taking into account hazards and socio-health vulnerabilities. This case study, carried out in Burkina Faso (Bagre Reservoir), aims at filling this knowledge gap by analyzing the environmental variables that play a role in the dynamics of E. coli, cases of diarrhea, and by identifying initial vulnerability criteria. A particular focus is given to satellite-derived parameters to assess whether remote sensing can provide a useful tool to assess the health hazard. Samples of surface water were routinely collected to measure E. coli, enterococci and suspended particulate matter (SPM) at a monitoring point (Kapore) during one year. In addition, satellite data were used to estimate precipitation, water level, Normalized Difference Vegetation Index (NDVI) and SPM. Monthly epidemiological data for cases of diarrhea from three health centers were also collected and compared with microbiological and environmental data. Finally, semi-structured interviews were carried out to document the use of water resources, contact with elements of the hydrographic network, health behavior and condition, and water and health policy and prevention, in order to identify the initial vulnerability criteria. A positive correlation between E. coli and enterococci in surface waters was found indicating that E. coli is an acceptable indicator of fecal contamination in this region. E. coli and diarrheal diseases were strongly correlated with monsoonal precipitation, in situ SPM, and Near Infra-Red (NIR) band between March and November. Partial least squares regression showed that E. coli concentration was strongly associated with precipitation, Sentinel-2 reflectance in the NIR and SPM, and that the cases of diarrhea were strongly associated with precipitation, NIR, E. coli, SPM, and to a lesser extent with NDVI. Moreover, E. coli dynamics were reproduced using satellite data alone, particularly from February to mid-December (R2 = 0.60) as were cases of diarrhea throughout the year (R2 = 0.76). This implies that satellite data could provide an important contribution to water quality monitoring. Finally, the vulnerability of the population was found to increase during the rainy season due to reduced accessibility to healthcare and drinking water sources and increased use of water of poor quality. During this period, surface water is used because it is close to habitations, easy to use and free from monetary or political constraints. This vulnerability is aggravated by marginality and particularly affects the Fulani, whose concessions are often close to surface water (river, lake) and far from health centers.

Rotavirus breakthrough infections responsible for gastroenteritis in vaccinated infants who presented with acute diarrhoea at University Teaching Hospitals, Children's Hospital in 2016, in Lusaka Zambia

Background

In Zambia, before rotavirus vaccine introduction, the virus accounted for about 10 million episodes of diarrhoea, 63 000 hospitalisations and 15 000 deaths in 2015, making diarrhoea the third leading cause of death after pneumonia and malaria. In Zambia, despite the introduction of the vaccine acute diarrhoea due to rotaviruses has continued to affect children aged five years and below. This study aimed to characterise the rotavirus genotypes which were responsible for diarrhoeal infections in vaccinated infants aged 2 to 12 months and to determine the relationship between rotavirus strains and the severity of diarrhoea in 2016.

Methods

Stool samples from infants aged 2 to 12 months who presented to the hospital with acute diarrhoea of three or more episodes in 24 hours were tested for group A rotavirus. All positive specimens that had enough sample were genotyped using reverse transcriptase Polymerase Chain Reaction (RT-PCR). A 20-point Vesikari clinical score between 1–5 was considered as mild, 6–10 as moderate and greater or equal to 11 as severe.

Results

A total of 424 stool specimens were tested of which 153 (36%, 95% CI 31.5% to 40.9%) were positive for VP6 rotavirus antigen. The age-specific rotavirus infections decreased significantly (p = 0.041) from 2–4 months, 32.0% (49/118) followed by a 38.8% (70/181) infection rate in the 5–8 months’ category and subsequently dropped in the infants aged 9–12 months with a positivity rate of 27.2%. 38.5% of infants who received a single dose, 34.5% of those who received a complete dose and 45.2% (19/42) of the unvaccinated tested positive for rotavirus. The predominant rotavirus genotypes included G2P[6] 36%, G1P[8] 32%, mixed infections 19%, G2P[4] 6%, G1P[6] 4% and G9P[6] 3%.

Discussion and conclusion

Results suggest breakthrough infection of heterotypic strains (G2P[6] (36%), homotypic, G1P[8] (32%) and mixed infections (19%) raises concerns about the effects of the vaccination on the rotavirus diversity, considering the selective pressure that rotavirus vaccines could exert on viral populations. This data indicates that the rotavirus vaccine has generally reduced the severity of diarrhoea despite the detection of the virus strains.

Trends and determinants of diarrhea among under-five children in Ethiopia: cross-sectional study: multivariate decomposition and multilevel analysis based on Bayesian approach evidenced by EDHS 2000-2016 data

Background

Despite significant progress in the reduction of under-five child deaths over the last decades in Ethiopia, still diarrhea remains the second cause of morbidity and mortality among under five children next to pneumonia.

Objective

To show trends and determinants of diarrhea among under five children in Ethiopia based on the four Ethiopian Demographic and health surveys data (2000–2016).

Methods

A total of 10,753 in 2000, 10,039 in 2005, 10,946 in 2011 and 10,337 in 2016 under five age children were involved in this study. Multivariate decomposition and multilevel analysis based on Bayesian approach was performed.

Results

Ninety seven percent of the change in diarrhea prevalence over time was attributable to difference in behavior. Being twin (AOR = 1.3; 95% CrI 1.1–1.5), big weight (AOR = 1.63; 95% CrI 1.62–2.02), not vaccinated for rotavirus (AOR = 1.44; 95% CrI 1.12–1.9) and for measles (AOR = 1.2; 95% CrI 1.1–1.33), poor wealth status (AOR 2.6; 95% CrI 1.7–4.06), having more than three under-five children (AOR 1.3; 95% CrI 1.1–1.61), member of health insurance (AOR 2.2; 95% CrI 1.3–3.8) and long distance from the health facility (AOR 2.7; 95% CrI 2.2–3.5) were more likely to experience diarrhea.

Conclusion

The prevalence of diarrhea was significantly declined over the last sixteen years and the decline was due to difference in behavior between the surveys. Being twin, weight of child at birth, vaccinated for measles and rotavirus, number of under-five children, wealth status, distance to health facility, health insurance and child waste disposal method were significantly associated with diarrhea among under five children in Ethiopia. Therefore Ethiopian government should focus on the strengthening and scaling up of behavioral change packages of the community regarding to keeping hygiene and sanitation of the community and their environment, vaccinating their children, accessing health care services to prevent diarrheal disease.

Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014

BACKGROUND

G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.

METHODS

The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.

RESULTS

The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 × 10^- 3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.

CONCLUSIONS

At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

Whole-Genome Analyses Identifies Multiple Reassortant Rotavirus Strains in Rwanda Post-Vaccine Introduction

Children in low-and middle-income countries, including Rwanda, experience a greater burden of rotavirus disease relative to developed countries. Evolutionary mechanisms leading to multiple reassortant rotavirus strains have been documented over time which influence the diversity and evolutionary dynamics of novel rotaviruses. Comprehensive rotavirus whole-genome analysis was conducted on 158 rotavirus group A (RVA) samples collected pre- and post-vaccine introduction in children less than five years in Rwanda. Of these RVA positive samples, five strains with the genotype constellations G4P[4]-I1-R2-C2-M2-A2-N2-T1-E1-H2 (n = 1), G9P[4]-I1-R2-C2-M2-A1-N1-T1-E1-H1 (n = 1), G12P[8]-I1-R2-C2-M1-A1-N2-T1-E2-H3 (n = 2) and G12P[8]-I1-R1-C1-M1-A2-N2-T2-E1-H1 (n = 1), with double and triple gene reassortant rotavirus strains were identified. Phylogenetic analysis revealed a close relationship between the Rwandan strains and cognate human RVA strains as well as the RotaTeq^® vaccine strains in the VP1, VP2, NSP2, NSP4 and NSP5 gene segments. Pairwise analyses revealed multiple differences in amino acid residues of the VP7 and VP4 antigenic regions of the RotaTeq^® vaccine strain and representative Rwandan study strains. Although the impact of such amino acid changes on the effectiveness of rotavirus vaccines has not been fully explored, this analysis underlines the potential of rotavirus whole-genome analysis by enhancing knowledge and understanding of intergenogroup reassortant strains circulating in Rwanda post vaccine introduction.

Whole Genome Analysis of African G12P[6] and G12P[8] Rotaviruses Provides Evidence of Porcine-Human Reassortment at NSP2, NSP3, and NSP4

Group A rotaviruses (RVA) represent the most common cause of pediatric gastroenteritis in children <5 years, worldwide. There has been an increase in global detection and reported cases of acute gastroenteritis caused by RVA genotype G12 strains, particularly in Africa. This study sought to characterize the genomic relationship between African G12 strains and determine the possible origin of these strains. Whole genome sequencing of 34 RVA G12P[6] and G12P[8] strains detected from the continent including southern (South Africa, Zambia, Zimbabwe), eastern (Ethiopia, Uganda), central (Cameroon), and western (Togo) African regions, were sequenced using the Ion Torrent PGM method. The majority of the strains possessed a Wa-like backbone with consensus genotype constellation of G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while a single strain from Ethiopia displayed a DS-1-like genetic constellation of G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. In addition, three Ethiopian and one South African strains exhibited a genotype 2 reassortment of the NSP3 gene, with genetic constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T2-E1-H1. Overall, 10 gene segments (VP1–VP4, VP6, and NSP1–NSP5) of African G12 strains were determined to be genetically related to cognate gene sequences from globally circulating human Wa-like G12, G9, and G1 strains with nucleotide (amino acid) identities in the range of 94.1–99.9% (96.5–100%), 88.5–98.5% (93–99.1%), and 89.8–99.0% (88.7–100%), respectively. Phylogenetic analysis showed that the Ethiopian G12P[6] possessing a DS-1-like backbone consistently clustered with G2P[4] strains from Senegal and G3P[6] from Ethiopia with the VP1, VP2, VP6, and NSP1–NSP4 genes. Notably, the NSP2, NSP3, and NSP4 of most of the study strains exhibited the closest relationship with porcine strains suggesting the occurrence of reassortment between human and porcine strains. Our results add to the understanding of potential roles that interspecies transmission play in generating human rotavirus diversity through reassortment events and provide insights into the evolutionary dynamics of G12 strains spreading across selected sub-Saharan Africa regions.

Rotavirus Genotypes in Hospitalized Children with Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997 - 2019

Background

Rotavirus vaccine (Rotarix [RV1]) has reduced diarrhea-associated hospitalizations and deaths in Malawi. We examined the trends in circulating rotavirus genotypes in Malawi over a 22-year period to assess the impact of RV1 introduction on strain distribution.

Methods

Data on rotavirus-positive stool specimens among children aged <5 years hospitalized with diarrhea in Blantyre, Malawi before (July 1997–October 2012, n = 1765) and after (November 2012–October 2019, n = 934) RV1 introduction were analyzed. Rotavirus G and P genotypes were assigned using reverse-transcription polymerase chain reaction.

Results

A rich rotavirus strain diversity circulated throughout the 22-year period; Shannon (H′) and Simpson diversity (D′) indices did not differ between the pre- and postvaccine periods (H′ P < .149; D′ P < .287). Overall, G1 (n = 268/924 [28.7%]), G2 (n = 308/924 [33.0%]), G3 (n = 72/924 [7.7%]), and G12 (n = 109/924 [11.8%]) were the most prevalent genotypes identified following RV1 introduction. The prevalence of G1P[8] and G2P[4] genotypes declined each successive year following RV1 introduction, and were not detected after 2018. Genotype G3 reemerged and became the predominant genotype from 2017 onward. No evidence of genotype selection was observed 7 years post–RV1 introduction.

Conclusions

Rotavirus strain diversity and genotype variation in Malawi are likely driven by natural mechanisms rather than vaccine pressure.

FUT2 Secretor Status Influences Susceptibility to VP4 Strain-Specific Rotavirus Infections in South African Children

Gastroenteritis is a preventable cause of morbidity and mortality worldwide. Rotavirus vaccination has significantly reduced the disease burden, but the sub-optimal vaccine efficacy observed in low-income regions needs improvement. Rotavirus VP4 'spike' proteins interact with FUT2-defined, human histo-blood group antigens on mucosal surfaces, potentially influencing strain circulation and the efficacy of P[8]-based rotavirus vaccines. Secretor status was investigated in 500 children <5 years-old hospitalised with diarrhoea, including 250 previously genotyped rotavirus-positive cases (P[8] = 124, P[4] = 86, and P[6] = 40), and 250 rotavirus-negative controls. Secretor status genotyping detected the globally prevalent G428A single nucleotide polymorphism (SNP) and was confirmed by Sanger sequencing in 10% of participants. The proportions of secretors in rotavirus-positive cases (74%) were significantly higher than in the rotavirus-negative controls (58%; p < 0.001). The rotavirus genotypes P[8] and P[4] were observed at significantly higher proportions in secretors (78%) than in non-secretors (22%), contrasting with P[6] genotypes with similar proportions amongst secretors (53%) and non-secretors (47%; p = 0.001). This suggests that rotavirus interacts with secretors and non-secretors in a VP4 strain-specific manner; thus, secretor status may partially influence rotavirus VP4 wild-type circulation and P[8] rotavirus vaccine efficacy. The study detected a mutation (rs1800025) ~50 bp downstream of the G428A SNP that would overestimate non-secretors in African populations when using the TaqMan® SNP Genotyping Assay.

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

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

Prevalence and associated factors to rotavirus infection in children less than 5 years in Enugu State, Nigeria

Rotavirus is an important cause of morbidity and mortality in children 5 years and below. An epidemiological study was carried out to determine the prevalence of rotavirus in Enugu state and factors that contribute to the incidence in the state. Stool samples were collected from 179 children from different parts of the state. Rotavirus antigen was detected using enzyme immunoassay kit. A standardized structured questionnaire was used to obtain additional information from the parents/guardian of the children. Chi square was used to analyze the results and significance was determined at 0.05. The results showed 31.5% prevalence of rotavirus among children with acute gastroenteritis (AGE) and 25.7% prevalence in the general population. The prevalence was highest (60.9%) among children 0–12 months and decreased as the age increased. Rotavirus infection was significantly higher in bottle-fed children than in those feed exclusively breast milk. More viruses were detected in O (48.8%) and A (47.6%) blood group children than in children of other blood groups. More rotavirus caused AGE occurred in dry season compared to wet season, with highest incidence of both AGE and rotavirus infection occurring in January. Rotavirus diarrhoea was significantly associated with fever, vomiting and dehydration. The results of this study show that rotavirus continues to be an important cause of diarrhoea in children in this part of Nigeria and emphasize the need to factor in rotavirus and other viral agents in the diagnosis and treatment of diarrhoea in children 5 years and below.

Investigation of two suspected diarrhoeal-illness outbreaks in Northern Cape and KwaZulu-Natal provinces, South Africa, April-July 2013: The role of rotavirus

BACKGROUND

Suspected diarrhoeal-illness outbreaks affecting mostly children < 5 years were investigated between May and July 2013 in Northern Cape province (NCP) and KwaZulu-Natal (KZN) province. This study describes the epidemiological, environmental and clinical characteristics and diarrhoeal-illnesses causative agent(s).

METHODS

A descriptive cross-sectional study was conducted. Cases were patients presenting at healthcare facilities with diarrhoeal-illness between 09 April and 09 July 2013 in NCP and 01 May and 31 July 2013 in KZN. Laboratory investigations were performed on stools and water samples using microscopy, culture and sensitivity screening and molecular assays.

RESULTS

A total of 953 cases including six deaths (case fatality rate [CFR]: 0.6%) were recorded in the Northern Cape province outbreak. Children < 5 years accounted for 58% of cases. Enteric viruses were detected in 51% of stools, with rotavirus detected in 43%. The predominant rotavirus strains were G3P[8] (45%) and G9P[8] (42%). Other enteric viruses were detected, with rotavirus co-infections (63%). No enteric pathogens detected in water specimens. KwaZulu-Natal outbreak: A total of 1749 cases including 26 deaths (CFR: 1.5%) were recorded. Children < 5 years accounted for 95% of cases. Rotavirus was detected in 55% of stools; other enteric viruses were detected, mostly as rotavirus co-infections. The predominant rotavirus strains were G2P[4] (54%) and G9P[8] (38%).

CONCLUSION

Although source(s) of the outbreaks were not identified, the diarrhoeal-illnesses were community-acquired. It is difficult to attribute the outbreaks to one causative agent(s) because of rotavirus co-infections with other enteric pathogens. While rotavirus was predominant, the outbreaks coincided with the annual rotavirus season.

Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018

BACKGROUND

Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010-June 2014) and post- (July 2014-December 2018) RVA vaccine introduction.

METHODS

Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes.

RESULTS

We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters.

CONCLUSION

Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.

Report of the 1st African Enteric Viruses Genome Initiative (AEVGI) Data and Bioinformatics Workshop on whole-genome analysis of some African rotavirus strains held in Bloemfontein, South Africa

The University of the Free State - Next Generation Sequencing (NGS) Unit, Bloemfontein, South Africa, hosted a data and bioinformatics workshop from 19 to 22 June 2018. The workshop was coordinated by the African Enteric Viruses Genome Initiative (AEVGI) with support from the Bill & Melinda Gates Foundation. The event introduced technologies in NGS and data analysis with focus on the rotavirus (RV) genome. The workshop fostered interactions and networking between professionals, scientific experts, technicians and students. The courses provided an overview of RV diarrhoea and its burden in Africa, while highlighting the key resources and methodologies in NGS and advanced bioinformatics in deciphering vaccine impact. It was concluded that, despite the reported significant decline in RV associated-diarrhoea mortality and morbidity in Africa due to RV vaccine impact, the need for continuous surveillance and genomic characterization to better understand the ever-changing dynamics of RV strains is imperative.

Modeling of rotavirus transmission dynamics and impact of vaccination in Ghana

Background:

Rotavirus incidence remains relatively high in low-income countries (LICs) compared to high-income countries (HICs) after vaccine introduction. Ghana introduced monovalent rotavirus vaccine in April 2012 and despite the high coverage, vaccine performance has been modest compared to developed countries. The predictors of low vaccine effectiveness in LICs are poorly understood, and the drivers of subnational heterogeneity in rotavirus vaccine impact are unknown.

Methods:

We used mathematical models to investigate variations in rotavirus incidence in children <5 years old in Ghana. We fit models to surveillance and case-control data from three different hospitals: Korle-Bu Teaching Hospital in Accra, Komfo Anokye Teaching Hospital in Kumasi, and War Memorial Hospital in Navrongo. The models were fitted to both pre- and post-vaccine data to estimate parameters describing the transmission rate, waning of maternal immunity, and vaccine response rate.

Results:

The seasonal pattern and age distribution of rotavirus cases varied among the three study sites in Ghana. Our model was able to capture the spatio-temporal variations in rotavirus incidence across the three sites and showed good agreement with the age distribution of observed cases. The rotavirus transmission rate was highest in Accra and lowest in Navrongo, while the estimated duration of maternal immunity was longer (∼5 months) in Accra and Kumasi and shorter (∼3 months) in Navrongo. The proportion of infants who responded to the vaccine was estimated to be high in Accra and Kumasi and low in Navrongo.

Conclusions:

Rotavirus vaccine impact varies within Ghana. A low vaccine response rate was estimated for Navrongo, where rotavirus is highly seasonal and incidence limited to a few months of the year. Our findings highlight the need to further explore the relationship between rotavirus seasonality, maternal immunity, and vaccine response rate to determine how they influence vaccine effectiveness and to develop strategies to improve vaccine impact.

Prevalence of rotavirus A infection and the detection of type G3P[11] strain in ruminants in Yobe state, Nigeria

Rotaviruses have a worldwide distribution and the infection is associated with diarrhea in young of ruminants as well as children. However, limited data exist on its prevalence and types in Yobe state, Nigeria. Detection of rotavirus A and types in ruminant population in Yobe state was the aim of the study. A total of 470 diarrheic fecal samples were collected and tested for rotavirus and types using serology and molecular techniques respectively. A prevalence rate of 2.98% (14/470) was found in the three species with specific rates of 2.9% (6/202), 3.8% (6/158), and 1.8% (2/110) in goat, sheep, and cattle respectively. The prevalence rates of 3.6% (12/331), 1.2% (1/84), and 1.8% (1/55) were for those aged < 1-3, 4-6, and 7-9 months old, respectively, while 4.9% (9/185) and 1.7% (5/285) were in males and females respectively. Rotavirus genes VP7 and VP4 were detected in 2 (14.3%) out of the 14 ELISA-positive samples while deduced amino acid sequences of the major variable regions revealed the genes to belong to types G3P[11] strain. Significant association was found between the infection and sex (P < 0.05) unlike in the species and age groups of the ruminants. The circulation of rotavirus virus in ruminants and type G3P[11] in cattle has been confirmed in the study. Hence, there is a need for continuous surveillance, awareness campaign, and assessment of the economic losses and public health implications of rotavirus infection in Nigeria.

Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa

Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6–99.9% (99.1–100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1–VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains.

Intragenic recombination influences rotavirus diversity and evolution

Because of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least eleven of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the glycoprotein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur nonrandomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segments 7 (NSP3) and 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.

Prevalence and Genetic Diversity of Rotaviruses among under-Five Children in Ethiopia: A Systematic Review and Meta-Analysis

Rotavirus infection is the major cause of acute gastroenteritis among children globally. Sub-Saharan Africa including Ethiopia is disproportionally affected by the disease. The aims of this review were to determine the pooled prevalence of rotavirus infection among children under-five and to identify the dominant rotavirus genotypes in Ethiopia. Twelve studies were included to estimate the pooled prevalence of rotavirus acute gastroenteritis and five studies were used to determine predominantly circulating genotypes of rotavirus. The pooled prevalence of rotavirus infection was 23% (95% CI = 22%-24%). G3 (27.1%) and P[8] (49%) were the dominant G and P types, respectively. The G8 G-type uncommon in humans but highly prevalent in cattle was also reported accounting for 1% of all cases. The major G/P combinations were G12P[8] (15.4%), G3P[6] (14.2%), G1P[8] (13.6%) and G3P[8] (12.9%) collectively accounting for 56.1% of rotavirus strains. Similar to other parts of the world, the dominance of G1, G3, P[6] and P[8] genotypes was noted in Ethiopia. The increased prevalence of G12P[8] strains observed in Ethiopia was similar to observations in other geographic regions in the post-vaccine introduction period. Thus, further studies are required on the vaccine effectiveness, genotype distribution and inter-species transmission potential of rotaviruses in Ethiopia.

Etiologies of diarrhea and drug susceptibility patterns of bacterial isolates among under-five year children in refugee camps in Gambella Region, Ethiopia: a case control study

Background

Despite substantial global effort and updated clinical management guidelines, diarrhea continues to be among leading worldwide causes of morbidity and mortality in children. Infectious diarrhea, the most common form of diarrhea causes substantial morbidity and mortality among children in developing countries, and the muddled use of antibiotics needs caution due to potential problems of drug-resistance. The aim of this study is to identify etiologies of diarrhea and drug susceptibility patterns of bacterial isolates in under-five children in refugee camps in Gambella Region, Ethiopia.

Methods

An institution- based matched case control study was conducted using a questionnaire-based interview from June to December 2017 in Pugnido and Teirkidi refugee camps. Stool samples were collected and parasites causing diarrhea were identified by wet mount microscopy. Conventional culture supplemented with API 20E identification kit was used to identify Salmonella and Shigella species. Antibiotic susceptibility of bacterial isolates was investigated by using the disk diffusion method. The association between etiologies and diarrhea was analyzed using McNemar test or Fisher exact test with 95% confidence interval at a level of significance of P < 0.05.

Results

The overall prevalence of enteric pathogens were 55 (41.0%) in diarrhea cases and 18 (13.4%) in healthy controls. The detected etiologies include Giardia lambia (28), Shigella spp. (16), E. hystolyotica/dispar (13), Ascaris lumbricoides (10), Salmonella spp. (6), Cryptosporidium parvum (6), Hymenolepis nana (4) and Isospora belli (3). All isolates were sensitive to kanamycine and ceftazidime. The high resistance rate was observed against ampicillin (100%), amoxicillin (100%), erythromycin (52%), chloramphenicol (47.5%), tetracycline (40.5%), cotrimoxazole (34.8%) and amoxicillin-clavulanic acid (33%). The majorities of the isolates had a low rate of resistance to ciprofloxacin (8.7%), naldxic acid (8.7%) and amikacin (13%).

Conclusions

Giardia lamblia, E. Hystolytica/dispar, and Shigella spp are the common etiologies of diarrhea in children in the studied refugee camps. The study also showed that significant numbers of bacterial isolates were resistant to the commonly used antimicrobial drugs. Therefore, improving clinical laboratory services and promoting evidence-based drug prescription may reinforce proper use of antibiotics and reduce the emergence of microbial resistance.

Rotavirus Burden, Genetic Diversity and Impact of Vaccine in Children under Five in Tanzania

In Tanzania, rotavirus infections are responsible for 72% of diarrhea deaths in children under five. The Rotarix vaccine was introduced in early 2013 to mitigate rotavirus infections. Understanding the disease burden and virus genotype trends over time is important for assessing the impact of rotavirus vaccine in Tanzania. When assessing the data for this review, we found that deaths of children under five declined after vaccine introduction, from 8171/11,391 (72% of diarrhea deaths) in 2008 to 2552/7087 (36% of diarrhea deaths) in 2013. Prior to vaccination, the prevalence of rotavirus infections in children under five was 18.1–43.4%, 9.8–51%, and 29–41% in Dar es Salaam, Mwanza and Tanga, respectively, and after the introduction of vaccines, these percentages declined to 17.4–23.5%, 16–19%, and 10–29%, respectively. Rotaviruses in Tanzania are highly diverse, and include genotypes of animal origin in children under five. Of the genotypes, 10%, 28%, and 7% of the strains are untypable in Dar es Salaam, Tanga, and Zanzibar, respectively. Mixed rotavirus genotype infection accounts for 31%, 29%, and 12% of genotypes in Mwanza, Tanga and Zanzibar, respectively. The vaccine effectiveness ranges between 53% and 75% in Mwanza, Manyara and Zanzibar. Rotavirus vaccination has successfully reduced the rotavirus burden in Tanzania; however, further studies are needed to better understand the relationship between the wildtype strain and the vaccine strain as well as the zoonotic potential of rotavirus in the post-vaccine era.

Evaluation of the performance of a multiplex reverse transcription polymerase chain reaction kit as a potential diagnostic and surveillance kit for rotavirus in Kenya

Background

Diarrhea is a serious concern worldwide, especially in developing countries. Rotavirus is implicated in approximately 400,000 infant deaths annually. It is highly contagious elevating the risk of outbreaks especially in enclosed settings such as daycare centers, hospitals, and boarding schools. Reliable testing methods are critical for early detection of infections, better clinical management, pathogen surveillance and evaluation of interventions such as vaccines. Enzyme immunoassays have proved to be reliable and practical in most settings; however, newer multiplex reverse transcription polymerase assays have been introduced in the Kenya market but have not been evaluated locally.

Methods

Stool samples collected from an ongoing Surveillance of Enteric Pathogens Causing diarrheal illness in Kenya (EPS) study were used to compare an established enzyme immunoassay, Premier™ Rotaclone® (Meridian Bioscience, Cincinnati, Ohio, U.S.A.), that can only detect group A rotavirus against a novel multiplex reverse transcription polymerase chain reaction kit, Seeplex® Diarrhea-V ACE Detection (Seegene, Seoul, Republic of Korea), that can detect rotavirus, astrovirus, adenovirus, and norovirus genogroups I and II. Detection frequency, sensitivity, specificity, turnaround time, and cost were compared to determine the suitability of each assay for clinical work in austere settings versus public health work in well-funded institutes in Kenya.

Results

The Premier™ Rotaclone® kit had a detection frequency of 11.2%, sensitivity of 77.8%, specificity of 100%, turnaround time of 93 min and an average cost per sample of 13.33 United States dollars (USD). The Seeplex® Diarrhea-V ACE Detection kit had a detection frequency of 16.0%, sensitivity of 100%, specificity of 98.1%, turnaround time of 359 min and an average cost per samples 32.74 United States dollars respectively. The detection frequency sensitivity and specificity of the Seeplex® Diarrhea-V ACE Detection kit mentioned above are for rotavirus only.

Conclusions

The higher sensitivity and multiplex nature of the Seeplex® Diarrhea-V ACE Detection kit make it suitable for surveillance of enteric viruses circulating in Kenya. However, its higher cost, longer turnaround time and complexity favor well-resourced clinical labs and research applications. The Premier™ Rotaclone®, on the other hand, had a higher specificity, shorter turnaround time, and lower cost making it more attractive for clinical work in low complexity labs in austere regions of the country. It is important to continuously evaluate assay platforms' performance, operational cost, turnaround time, and usability in different settings so as to ensure quality results that are useful to the patients and public health practitioners.

Acute gastroenteritis associated with Rotavirus A among children less than 5 years of age in Nepal

Background

Rotavirus gastroenteritis is a major public health problem in Nepal. This study was conducted to obtain information associated with Rotavirus gastroenteritis and to perform genotyping of Rotavirus A.

Methods

Hospital based cross sectional study was conducted from January to December 2017 among children less than 5 years of age attending Kanti Children’s Hospital and Tribhuvan University Teaching Hospital. Rotavirus A antigen detection was performed by Enzyme Linked Immunosorbent Assay (ELISA) using ProSpecT Rotavirus Microplate Assay. Rotavirus A positive strains were further confirmed by genotyping using Reverse-Transcription Polymerase Chain Reaction (RT-PCR).

Results

A total of 1074 stool samples were collected, of them 770 were hospitalized, and 304 were non-hospitalized cases. Rotavirus A infection was found in 28% of children with infection rate higher in hospitalized (34%) than in non-hospitalized (14%) children. Rotavirus A detection was higher in male (31%) than in female (24%), but this was statistically not significant (p > 0.05). Rotavirus A positivity was higher in children of age group 0–23 months, this result was statistically not significant (p > 0.05) with higher frequency found in the months of November, December, January, February and March (p < 0.05). On the basis of molecular analysis of Rotavirus A genotyping, G12P[6] (46.39%) was found to be the predominant followed by G1P[8] (35.05%), G3P[8] (7.21%) and G1P[6] (5.15%) while 4.12% was mixed infection and 1.03% was partially typed (p < 0.05).

Conclusion

Rotavirus A infection occurred throughout the year, but the infection was significantly higher during the month of March. The higher frequency of rotavirus infection was observed among children of age group 0–23 months; however this was not found to be statistically significant. In this study, G12P[6] is predominant genotype observed. The results of genotyping are essential for the introduction of Rotavirus vaccine in Nepal.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4092-2) contains supplementary material, which is available to authorized users.

Observations on the epidemiology of rotavirus infection among hospitalized children younger than 5 years in 2 Ukrainian hospitals, 2007-2015

BACKGROUND

Acute gastroenteritis remains a burden among children under 5 years of age. Ukraine joined the World Health Organization's Global Rotavirus Surveillance Network in 2006, with a goal of providing accurate rotavirus burden data to aid policy makers in planning for rotavirus vaccine introduction. This analysis describes rotavirus epidemiology among Ukrainian children enrolled in Kyiv and Odesa, two large Ukrainian cities.

METHODS

Children 0-59 months of age hospitalized for acute gastroenteritis at 2 sentinel sites in Kyiv and Odesa were enrolled into the active, prospective surveillance program. In Odesa, the surveillance period was during 2007-2015 and in Kyiv, it was during 2011-2015. Acute gastroenteritis was defined as 3 or more episodes of diarrhea per day during a 24 h period, with symptom duration before hospitalization not exceeding 7 days. Guardians of enrolled children completed a questionnaire including demographic, clinical and treatment information. Each child provided a stool specimen within 2 days of hospitalization. Stools were tested for rotavirus using ProSpecT™ Rotavirus Kit (Oxoid Ltd., Great Britain), and positive specimens were genotyped. Descriptive data are reported, as well as comparison of demographic, clinical and treatment data among rotavirus positive and negative children.

RESULTS

During July 2007-June 2015, 12,350 children were enrolled in the surveillance programs and had stool specimens collected and tested for rotavirus. Overall, rotavirus infection was diagnosed in 5412/12350 (44%) of children, 929/1734 (54%) of those in Kyiv and 4483/10616 (42%) in Odesa. Rotavirus infections peaked during the winter months. Children with rotavirus acute gastroenteritis displayed more severe clinical symptoms than those without rotavirus. Predominant genotypes identified included G1P[8], G2P[4], G3 P[8], G4 P[8] and G9 P[8].

CONCLUSION

Active surveillance of acute gastroenteritis in hospitalized children younger 5 years in two large Ukrainian cities reveals a significant burden of rotavirus infection. These data provide scientific justification for incorporating rotavirus vaccines into the Ukrainian national immunization schedule.

Prevalence of rotavirus infection among children with acute diarrhoea after rotavirus vaccine introduction in Kenya, a hospital cross-sectional study

BACKGROUND

Rotavirus infection is the most common cause of acute gastroenteritis globally in children under 5 years of age and is responsible for approximately 5% of all child deaths yearly. Rotavirus vaccination is considered an effective public health strategy to prevent infection and reduce the severity of disease. Multi-centre country trials on rotavirus vaccines demonstrated efficacy rates of more than 85% in developed countries but only about 65% in developing nations. Rotavirus vaccination was introduced into the Kenya Expanded Programme on Immunization (KEPI) in 2014. The objective of our study was to determine the prevalence of rotavirus infection, severity of acute diarrhoea and to determine the rotavirus vaccination status among children aged 3-24 months presenting with acute diarrhoea at Kenyatta National Hospital after introduction of rotavirus vaccine in Kenya.

METHODS

A total of 365 children aged 3-24 months presenting with acute diarrhoea at KNH were recruited from August 2016 to April 2017. Data on rotavirus vaccination status, nutritional status, feeding practices and sociodemographic characteristics were obtained and a full clinical evaluation of the patients was done. Severity of the gastroenteritis was assessed using the 20 point Vesikari Clinical Severity Scoring System. The children who were admitted were followed up for 7 days using hospital ward registers. Comorbid conditions were established from patient's clinical records and physical examination. Stool specimens from study participants were tested for rotavirus using a commercially available enzyme linked immunosorbent immunoassay kit- ProSpecT Rotavirus Microplate Assay.

RESULTS

Majority of the children (96.7%) had received rotavirus vaccinations. The overall rotavirus prevalence was 14.5% and was higher among 17-24 months at 19.5%. The prevalence somewhat differed by gender, nutritional status, exclusive breastfeeding status, age and education level of mother/caregiver. Overall, a half of the children had severe acute diarrhoea and there were some differences in severity by child/mother characteristics.

CONCLUSION

There is still burden of rotavirus diarrhoea after introduction of rotavirus vaccine and the prevalence varies by child characteristics.

Trends for Diarrhea Morbidity in the Jasikan District of Ghana: Estimates from District Level Diarrhea Surveillance Data, 2012-2016

About 22% of childhood deaths in developing countries are attributable to diarrhea. In poor resource settings, diarrhea morbidities are correlated with poverty and socio-contextual factors. Diarrhea rates in Ghana are reported to be high, with cases estimated at 113,786 among children under-five years in 2011. This study analyzed the trends of diarrhea morbidity outcomes in the Jasikan District of Ghana. A retrospective analysis of records on diarrhea data for a five years' period (January 2012 to December 2016) was undertaken. There was a total of 17740 diarrhea case reports extracted from District Health Information Management System (DHIMS) II database in an Excel format which was then exported to Stata version 14 for data cleaning, verification, and analysis. Excel version 2016 was used to plot the actual observed cases by years to assess trends and seasonality. There was a period incidence rate of 272.02 per 1000 persons with a decreasing annual growth rate of 1.85%. Declines for diarrhea generally occurred from November to December and increased from January upwards, evidence that most cases of diarrhea in this study were reported in the harmattan season. High incidence of diarrhea was found to be common among under-five children and among females. Decreasing trend of diarrhea incidence which was identified in this research within the five years' period understudied shows that, by the year 2020, there will be a sharp decline in the incidence rate of diarrhea reported cases in Jasikan District, given improvements in the external environmental conditions in the district, all things being equal.

Impact of rotavirus vaccine introduction and genotypic characteristics of rotavirus strains in children less than 5 years of age with gastroenteritis in Ethiopia: 2011-2016

INTRODUCTION

A monovalent rotavirus vaccine was introduced in the Ethiopian Expanded Program on Immunization from November 2013. We compared impact of rotavirus vaccine introduction on rotavirus associated acute diarrhea hospitalizations and genotypic characteristics of rotavirus strains pre-and post-vaccine introduction.

METHODS

Sentinel surveillance for diarrhea among children <5 years of age was conducted at 3 hospitals in Addis Ababa, Ethiopia from 2011 to 2017. Stool specimens were collected from enrolled children and tested using an antigen capture enzyme immunoassay. Rotavirus positive samples (156 from pre- and 141 from post-vaccination periods) were further characterized by rotavirus genotyping methods to identify the predominant G and P types circulating during the surveillance era.

RESULTS

A total of 788 children were enrolled during the pre- (July 2011-June 2013) and 815 children during the post-vaccination (July 2014-June 2017) periods. The proportion of diarrhea hospitalizations due to rotavirus among children <5 years of age declined by 17% from 24% (188/788) in the pre-vaccine period and to 20% (161/185) in post-vaccine introduction era. Similarly, a reduction of 18% in proportion of diarrhea hospitalizations due to rotavirus in children <12 months of age in the post (27%) vs pre-vaccine (33%) periods was observed. Seasonal peaks of rotavirus declined following rotavirus vaccine introduction. The most prevalent circulating strains were G12P[8] in 2011 (36%) and in 2012 (27%), G2P[4] (35%) in 2013, G9P[8] (19%) in 2014, G3P[6] and G2P[4] (19% each) in 2015, and G3P[8] (29%) in 2016.

DISCUSSION

Following rotavirus vaccine introduction in Ethiopia, a reduction in rotavirus associated hospitalizations was seen in all age groups with the greatest burden in children <12 months of age. A wide variety of rotavirus strains circulated in the pre- and post-vaccine introduction periods.

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

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

Present and Future Human Emissions of Rotavirus and Escherichia coli to Uganda's Surface Waters

Rotavirus (RV) and diarrheagenic are waterborne pathogens commonly causing diarrhea in children below five years old worldwide. Our study is a first step toward a loads-concentrations-risk modeling and scenario analysis framework. We analyzed current and future human RV and indicator (EC) emissions from sanitation facilities to surface waters in Uganda using two process-based models. Emissions were estimated for the baseline year 2015 and for three scenarios in 2030 using population, excretion rates, sanitation types, and wastewater treatment. The first model is a downscaled GloWPa-Rota H1 version, producing emissions at a 1-km resolution. The second model is newly developed for Kampala and adds emissions from pit latrines and septic tanks excluded in the first model. The scenarios Business as Usual, Industrious, and Low Emissions reflect government prospects in sanitation coverage and wastewater treatment. For the first model, 6.14 × 10 RV particles d and 1.31 × 10 EC colony-forming units (CFU) d are emitted to surface waters in 2015. The RV emissions are expected to increase in 2030 by 75% for Business as Usual and 212% for Industrious and decrease by 58% in Low Emissions. Emissions from the second model are higher for Kampala than in the first model, at 3.74 × 10 vs. 5.95 × 10 RV particles d and 8.18 × 10 vs. 1.75 × 10 EC CFU d in 2015, most of which come from the onsite-not-contained category. Simulated emissions for Kampala show the importance of including onsite sanitation in our modeling. Our study is replicable in other locations and helps identify key emission sources, their hotspots, and the importance of wastewater treatment. The scenarios can guide future sanitation safety planning.

Molecular epidemiology of rotaviruses in Northwest Ethiopia after national vaccine introduction

BACKGROUND

Rotaviruses mortality among infants and young children is high in Sub-Saharan Africa. Recently, Ethiopia introduced the monovalent rotavirus vaccine in its national immunization program to decrease the burden of rotavirus disease and mortality. Rotavirus surveillance in Ethiopia is based largely on data provided by sentinel hospitals in its capital Addis Ababa.

OBJECTIVE

To assess rotavirus abundancy and diversity in outpatient infants and children outside of Addis Ababa in the early post-introduction period.

METHOD

Fecal samples were obtained from children aged less than five years presenting with diarrhea at outpatient health institutions in two cities in Northwest Ethiopia, Gondar and Bahir Dar, from November 2015 to April 2016. Basic demographic data were assessed. Real-time RT-PCR was used to detect rotavirus A RNA. Based on sequences of VP4 and VP7 gene segments phylogenetic analysis was performed.

RESULTS

Rotavirus wildtype positivity was 25% (113/450). Rotavirus infection was less common in infants below 6 months than in children of all other age-groups. Rotavirus genotype distributions were distinct between Bahir Dar and Gondar. In total, wildtype G3P[8], G2P[4], G9P[8], G12P[8], and G3P[6] rotaviruses were detected in 68 (60.2%), 21 (18.6%), 13 (11.5%), 9 (8.0%), and 2 (1.8%) of the positive samples, respectively. Wildtype G1P[8] strains were absent. The phylogenetic analysis revealed close relatedness of current rotaviruses with Ethiopian strains of the pre-vaccination period.

CONCLUSION

In the early period after the introduction of vaccination, rotaviruses in Northwestern Ethiopia were frequent in children of 6-59 months and diverse. High phylogenetic relatedness with strains of the pre-vaccine era, indicate absence of early vaccine-induced strain replacement. Future surveillance studies should be carried out throughout the country to gain comprehensive data on rotavirus strain diversity and to monitor the effect of the ongoing vaccine program on the disease burden and eventual rotavirus strain replacement.

l-Isoleucine Administration Alleviates Rotavirus Infection and Immune Response in the Weaned Piglet Model

Rotavirus (RV) infection is one of the main pathogenic causes of severe gastroenteritis and diarrhea in infants and young animals. This study aimed to determine how dietary l-isoleucine supplementation improves the growth performance and immune response in weaned piglets with RV infection. In cell culture experiment, after IPEC-J2 and 3D4/31 cells were treated by 8 mM l-isoleucine for 24 h, the gene expressions of β-defensins and pattern recognition receptors (PRR) signaling pathway were significantly increased. Then, in the in vivo experiment, 28 crossbred weaned pigs were randomly divided into two groups fed with basal diet with or without l-isoleucine for 18 days. On the 15th day, the oral RV gavage was executed in the half of piglets. Average daily feed intake and gain of piglets were impaired by RV infection (P < 0.05). RV infection also induced severe diarrhea and the increasing serum urea nitrogen concentration (P < 0.05), and decreased CD4+ lymphocyte and CD4+/CD8+ ratio of peripheral blood (P < 0.05). However, dietary l-isoleucine supplementation attenuated diarrhea and decreasing growth performance (P < 0.05), decreased the NSP4 concentration in ileal mucosa, and enhanced the productions and/or expressions of immunoglobulins, RV antibody, cytokines, and β-defensins in serum, ileum, and/or mesenteric lymph nodes of weaned piglets (P < 0.05), which could be relative with activation of PRR signaling pathway and the related signaling pathway (P < 0.05) in the weaned pigs orally infused by RV. These results indicate that dietary l-isoleucine could improve the growth performance and immune function, which could be derived from l-isoleucine treatment improving the innate and adaptive immune responses via activation of PRR signaling pathway in RV-infected piglets. It is possible that l-isoleucine can be used in the therapy of RV infection in infants and young animals.

A Phase 4, multicentre, randomized, single-blind clinical trial to evaluate the immunogenicity of the live, attenuated, oral rotavirus vaccine (116E), ROTAVAC®, administered simultaneously with or without the buffering agent in healthy infants in India

BACKGROUND

The World Health Organization recommends that rotavirus vaccines should be included in all national immunization programs. Some currently licensed oral rotavirus vaccines contain a buffering agent (either as part of a ready-to-use liquid formulation or added during reconstitution) to reduce possible degradation of the vaccine virus in the infant gut, which poses several programmatic challenges (the large dose volume or the reconstitution requirement) during vaccine administration. Because ROTAVAC®, a WHO prequalified vaccine, was derived from the 116E neonatal strain, we evaluated the immunogenicity and safety of ROTAVAC® without buffer and ROTAVAC® with buffer in a phase 4, multicentre, single-blind, randomized clinical trial in healthy infants in India.

METHODS

900 infants, approximately 6, 10 and 14 weeks of age, were assigned to 3 groups to receive ROTAVAC® (0.5 mL dose) orally: (i) 2.5 mL of citrate-bicarbonate buffer 5 minutes prior to administration of ROTAVAC® (Group I), (ii) ROTAVAC®, alone, without any buffer (Group II), or (iii) ROTAVAC®, mixed with buffer immediately before administration (Group III). Non-inferiority was compared among the groups for differences in serological responses (detected by serum anti-rotavirus IgA) and safety.

RESULTS

Geometric mean titers post vaccination at day 84 (28 days after dose 3) were 19.6 (95%CI: 17.0, 22.7), 20.7 (95%CI: 17.9, 24) and 19.2 (95%CI: 16.8, 22.1) for groups I, II and III respectively. Further, seroconversion rates and distribution of adverse events were similar among groups.

CONCLUSIONS

Administration of ROTAVAC® at a 0.5 mL dose volume without buffering agent was shown to be well tolerated and immunogenic. Given the homologous nature of the strain, it is plausible that ROTAVAC® replicates well and confers immunity even without buffer administration.

Rotavirus diarrhoea hospitalizations among children under 5 years of age in Nigeria, 2011-2016

BACKGROUND

The high burden of rotavirus acute gastroenteritis (AGE) is well documented among children under 5 years of age, with the majority of mortality occurring in developing countries. Nigeria ranked second worldwide in the number of rotavirus deaths in 2013. As Nigeria plans to introduce rotavirus vaccine soon, a pre-vaccine documentation of rotavirus disease burden is necessary to determine vaccine impact.

METHODS

Routine rotavirus surveillance was conducted during 2011-2016 in 3 sentinel sites in Nigeria using the standard WHO protocol. Children under 5 years of age hospitalized for acute gastroenteritis were enrolled and demographic, clinical and outcome data were collected. A stool sample was subsequently obtained and tested for human rotavirus antigen using the Enzyme-linked immunosorbent assay (ELISA).

RESULTS

2694 children with acute gastroenteritis were enrolled during January 2011 to December 2016; of these, 1242 (46%) tested positive for rotavirus. Among the rotavirus positive cases, 66% and 94% were younger than 12 months and 24 months respectively. Marked peaks in rotavirus positivity were seen in January of each year. Vomiting, and use of oral and intravenous fluids occurred more often in rotavirus positive cases as compared to rotavirus negative cases.

CONCLUSION

The high prevalence of rotavirus disease highlights the need for urgent introduction of rotavirus vaccine in Nigeria. Additionally, this study provides pre-vaccine introduction disease-burden data that will serve as a baseline for rotavirus vaccine impact-assessment once vaccine has been introduced in the national immunization program.

Sustained impact of rotavirus vaccine on rotavirus hospitalisations in Lusaka, Zambia, 2009-2016

BACKGROUND

Monovalent rotavirus vaccine (RV1) was introduced in Lusaka in February 2012 and rolled out countrywide in November 2013 in the routine Expanded Programme on Immunisation and administered at 6 and 10 weeks with no catch up dose. Reported here is the monitoring of rotavirus acute gastroenteritis hospitalisations at the University Teaching Hospital, Lusaka, Zambia as part of efforts to document the impact of rotavirus vaccine.

METHODS

Children <5 years hospitalised for acute gastroenteritis (AGE) from January 2009 to December 2016 were recruited into the rotavirus disease burden active surveillance and had their stools tested for rotavirus by enzyme immunoassay. We compared rotavirus-associated AGE hospitalisations of the pre-vaccine era (2009-2011) with the post-rotavirus vaccine introduction period (2013-2016).

RESULTS

With the increase in RV1 coverage in Lusaka, rotavirus AGE declined significantly from 40% of diarrhoea hospitalisation in the pre-vaccine era to 29% of diarrhoea hospitalisation in the post-vaccine era (p < 0.001) in children <5 years. After a decreasing trend in rotavirus positivity from 2013 to 2015, positivity increased to 37% in 2016. However, the post-vaccine years (2012-2016) saw substantial decline in the number tested (median decline: 34% (range: 20-43%)) and the number of positive results (median decline: 52% (range: 30-65%).

CONCLUSION

A sustained and significant decline in rotavirus AGE hospitalisations was observed in children <5 years since the introduction of RV1 in Lusaka, Zambia. Despite an increase in rotavirus positivity in 2016, the total number of children enrolled and the number of rotavirus positive children remained below baseline. The reason for the increase in rotavirus positivity in 2016 is unknown but could be due to an accumulation of susceptible children and the shifting of disease to children of older age groups. This finding underscores the need for continued monitoring of rotavirus vaccine impact.

Detection of rotavirus before and after monovalent rotavirus vaccine introduction and vaccine effectiveness among children in mainland Tanzania

BACKGROUND

Monovalent rotavirus vaccine (RV1) was introduced in Tanzania in January 2013 under the Reach Every Child initiative, to be given at ages 6 and 10 weeks. We used the sentinel hospital rotavirus surveillance system to examine the rotavirus detection rate before and after vaccine introduction and estimate vaccine effectiveness.

METHODS

Before vaccine introduction, rotavirus surveillance was established at two mainland hospitals; children admitted for acute diarrhea were eligible for enrollment and stools were tested for rotavirus antigen. We compared the rotavirus positivity rate in the pre-vaccine period (Tanga Hospital, 2009 and 2011; Bugando Medical Centre, 2012) to that from post-introduction years, 2014-2015. In 2013, surveillance was established at 9 additional hospitals. We examined rotavirus positivity among infants at these sites for 2014-2015. We obtained vaccine records and calculated vaccine effectiveness at 3 sites using case-test-negative control design.

RESULTS

At Tanga Hospital, the rotavirus positivity rate among infants was 41% (102/251) pre-vaccine and 14% (28/197) in post-vaccine years (rate ratio: 0.35 [95% CI 0.22-0.54]). At Bugando, the positivity rate was 58% (83/143) pre-vaccine, and 18% (49/277) post-introduction (rate ratio 0.30 [95% CI 0.210.44]). Results were similar among children <5 years. At the new sites, the median site rotavirus positivity rate among infants was 26% in 2014 (range 19-44%) and 18% in 2015 (range 16-33%). The effectiveness of ≥1 RV1 dose against rotavirus hospitalization among children 5-23 months was 53% (95% CI: -14, 81), and 66% (95% CI: 9-87) against hospitalization with intravenous rehydration. Following introduction, peak rotavirus activity occurred later in the year and appeared more concentrated in time.

CONCLUSION

Rotavirus surveillance data from Tanzania indicate that the rotavirus positivity rate among children hospitalized with diarrhea that were enrolled was substantially reduced after vaccine introduction. Low positivity rates among infants were detected at hospitals across the country. Overall, the data support that rotavirus vaccine has been successfully introduced and is effective in Tanzanian children.

Impact of rotavirus vaccines in low and middle-income countries

PURPOSE OF REVIEW

Rotavirus vaccines are playing a pivotal role in improving lives of infants and young children in low and middle-income countries (LMICs). Many of these countries have adopted the vaccine into their routine immunization, whereas others are considering introduction. This article provides an update on the impact of rotavirus vaccines in LMICs on morbidity and mortality in children aged less than 5 years, and their cost-effectiveness.

RECENT FINDINGS

The WHO, in 2013, updated its recommendation to prioritize introduction of rotavirus vaccines in the routine immunization schedule, without age restrictions. Despite the decreased efficacy of the vaccines in LMICs, data from Sub-Saharan Africa have demonstrated a decrease in rotavirus-related morbidity, with some sites reporting an indirect protective effect on children age ineligible to receive the vaccine. Even with improvements in sanitation, nutritional status in children, and other health-related indices in LMICs, the use of rotavirus vaccines will play an important role in preventing rotavirus-related gastroenteritis. Economic models predict a reduction in economic burden because of rotavirus-related health costs, making vaccine introduction cost-effective in resource-constrained settings.

SUMMARY

Increasing evidence from impact studies shows the significant impact of rotavirus vaccination on hospitalizations and economic burden because of rotavirus gastroenteritis in LMICs. Universal rotavirus vaccination is recommended, and introductions should be monitored by robust surveillance systems to measure effectiveness and impact.

Emergence of G12 and G9 rotavirus genotypes in the Central African Republic, January 2014 to February 2016

Objectives

Rotavirus gastroenteritis is a major cause of death among children under 5 years globally. A rotavirus gastroenteritis surveillance program started in October 2011 in the Central African Republic (CAR) with the Surveillance Epidémiologique en Afrique Centrale (SURVAC) project. We present here genotyping results showing the emergence of G9 and G12 genotypes in Central African Republic.

Results

Among 222 children hospitalized with acute gastroenteritis who had a stool sample collected at the sentinel site, Complexe Pédiatrique de Bangui (CPB), Bangui, Central African Republic, 100 (45%) were positive for rotavirus between January 2014 and February 2016. During this period the most common rotavirus strains were G1P[8] (37%), G12P[6] (27%) and G9P[8] (18%).