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

Rotavirus A Infection Prevalence and Spatio-Temporal Genotype Shift among Under-Five Children in Amhara National Regional State, Ethiopia: A Multi-Center Cross-Sectional Study

Background: Globally, rotavirus (RV) A (RVA) is the most common cause of severe and sometimes fatal diarrhea in young children. It is also the major cause of acute gastroenteritis among children in Ethiopia. Currently, the WHO has prequalified four RVA vaccines for universal childhood immunization. Ethiopia introduced the monovalent Rotarix vaccine into its national immunization program in 2013. Since then, only a few studies on the burden and genotype distribution of RVA infection post-vaccine introduction have been conducted (mostly at sentinel surveillance sites). Therefore, this study aimed to assess RVA prevalence and genotype distribution among children under five years in Ethiopia (February 2021-December 2022). Methods: This multi-center hospital-based cross-sectional study involved 537 diarrheic children under-five years old. Rotavirus A detection was conducted using a one-step reverse-transcriptase polymerase chain reaction (RT-PCR). Genotyping was conducted by Sanger sequencing of the VP7 (complete) and VP4 (partial) genes. Descriptive analysis and Pearson's chi-squared test were carried out using SPSS version 29. Phylogenetic analysis with 1000 bootstrap replicates was performed using MEGA version 11 software. Statistical significance was set at p < 0.05 for all analyses. Results: The prevalence of RVA infection among diarrheic children was 17.5%. The most prevalent G-types identified were G3 (37%), the previously uncommon G12 (28%), and G1 (20%). The predominant P-types were P[8] (51%), P[6] (29%), and P[4] (14%). The three major G/P combinations observed were G3P[8] (32.8%), G12P[6] (28.4%), and G1P[8] (19.4%). Phylogenetic analysis revealed clustering of Ethiopian strains with the globally reported strains. Many strains exhibited amino acid differences in the VP4 (VP8* domain) and VP7 proteins compared to vaccine strains, potentially affecting virus neutralization. Conclusions: Despite the high RVA vaccination rate, the prevalence of RVA infection remains significant among diarrheic children in Ethiopia. There is an observable shift in circulating RVA genotypes from G1 to G3, alongside the emergence of unusual G/P genotype combinations such as G9P[4]. Many of these circulating RVA strains have shown amino acid substitutions that may allow for neutralization escape. Therefore, further studies are warranted to comprehend the emergence of these unusual RVA strains and the diverse factors influencing the vaccine's diminished effectiveness in developing countries.

Spatial distribution of rotavirus immunization coverage in Ethiopia: a geospatial analysis using the Bayesian approach

Introduction

Rotavirus causes substantial morbidity and mortality every year, particularly among under-five children. Despite Rotavirus immunization preventing severe diarrheal disease in children, the vaccination coverage remains inadequate in many African countries including Ethiopia. Measuring rotavirus immunization coverage in a lower geographic area can provide information for designing and implementing a targeted immunization campaign. This study aimed to investigate the spatial distributions of rotavirus immunization coverage in Ethiopia.

Methods

Rotavirus immunization coverage data were obtained from the recent Ethiopian Demographic and Health Survey (EDHS 2019). Covariate data were assembled from different publicly available sources. A Bayesian geostatistics model was used to estimate the national rotavirus immunization coverage at a pixel level and to identify factors associated with the spatial clustering of immunization coverages.

Result

The national rotavirus immunization coverage in Ethiopia was 52.3% (95% CI: 50.3, 54.3). The immunization coverage varied substantially at the sub-national level with spatial clustering of low immunization coverage observed in the Eastern, Southeastern, and Northeastern parts of Ethiopia. The spatial clustering of the rotavirus immunization coverage was positively associated with altitude of the area [mean regression coefficient (β): 0.38; 95% credible interval (95% CrI): 0.18, 0.58] and negatively associated with travel time to the nearest cities in minutes [mean regression coefficient (β): − 0.45; 95% credible interval (95% CrI): (− 0.73, − 0.18)] and distance to the nearest health facilities [mean regression coefficient (β): − 0.71908; 95% credible interval (95% CrI): (− 1.07, − 0.37)].

Conclusions

This study found that the rotavirus immunization coverage varied substantially at sub-national and local levels in Ethiopia. The spatial clustering of rotavirus immunization coverage was associated with geographic and healthcare access factors such as altitude, distance to health facilities, and travel time to the nearest cities. The immunization program should be strengthened in Ethiopia, especially in the Eastern, Southeastern, and Northeastern parts of the Country. Outreach immunization services should be also implemented in areas with low coverage.

Establishment of Sandwich ELISA for Quality Control in Rotavirus Vaccine Production

Non-replicating rotavirus vaccines are alternative strategies that may improve the protective efficacy of rotavirus vaccines in low- and middle-income countries. The truncated spike protein VP4 (aa26-476, VP4*)was a candidate antigen for the development of recombinant rotavirus vaccines, with higher immunogenicity and protective efficacy compared to VP8* and VP5* alone. This article describes the development of three genotype-specific sandwich ELISAs for P[4], P[6], and P[8]-VP4*, which are important for quality control in rotavirus vaccine production. Our results showed that the detection systems had good specificity for the different genotype VP4* and were not influenced by the E. coli host proteins. Moreover, the detection systems play an important role in determining whether the target protein was contaminated by VP4* proteins of other genotypes. They can also detect the adsorption rate of the adjuvant to the P[4], P[6], P[8]-VP4* protein during the process development. The three detection systems will play an important role in the quality control and process development of VP4* based rotavirus vaccines and facilitate the development of recombinant rotavirus vaccines.

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.

Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction

Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less than 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations: G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n = 37, 67.2%) and comprised three distinct G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 Lineage). Both the two G3 lineages have been recently detected in several countries. Our study is the first to document African children infected with G3 Lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage.

<p>Determinants of Acute Diarrhea Among Children Under-Five in Northeast Ethiopia: Unmatched Case–Control Study</p>

Background

Diarrheal disease is the second leading causes of death among under-five children. Most of the death due to diarrhea is reporting in developing countries. To prevent this highly prevalent problem, identifying the contributing factors across different settings is necessary. Therefore, this study aimed to identify the determinants of acute diarrhea among under-five children in the Northeast part of Ethiopia.

Methods

An institution-based unmatched case–control study was conducted among 306 under-five children from March to April 2019. A systematic random sampling technique was employed to select study participants. Data were collected by face to face interviews using a pretested structured questionnaire. Data were entered using Epi-info 7 and analyzed with SPSS version 20.0. We applied logistic regression analysis. Those variables with p-value <0.05 were significant determinants of acute diarrhea.

Results

Improper child’s stool disposal [AOR=4.12; 95% CI (1.25,13.5)], absence of home-based water treatment [AOR=2.85; 95% CI (1.27,6.42)], did not wash hand at critical times [AOR=5.47; 95% CI (1.68,17.8)], did not practice exclusive breastfeed [AOR=3.32; 95% CI (1.21,9.14], unable to get counseling from health professionals [AOR= 3.23; 95%,CI (1.15,13.5)], provide left over food to the child [AOR=2.96; 95% CI (1.19,7.32)], and maternal diarrhea [AOR=6.06; 95% CI (2.42,15.22)] were determinants of acute diarrhea among under five children.

Conclusion

Most of the determinants of acute diarrhea could be preventable. Thus, collaborative intervention by emphasizing health education about the importance of personal and environmental hygiene, safe food handling, exclusive breastfeeding practice, and home-based water treatment are essential.

Inequalities in Rotavirus Vaccine Uptake in Ethiopia: A Decomposition Analysis

A previous study in Ethiopia reported significant variation in rotavirus vaccine uptake across socioeconomic strata. This study aims to quantify socioeconomic inequality of rotavirus vaccine uptake in Ethiopia and to identify the contributing factors for the inequality. The concentration curve (CC) and the Erreygers Normalized Concentration Index (ECI) were used to assess the socioeconomic related inequality in rotavirus vaccine uptake using data from the 2016 Ethiopian Demographic and Health Survey. Decomposition analysis was conducted to identify the drivers of inequalities. The CC for rotavirus vaccine uptake lay below the line of equality and the ECI was 0.270 (p < 0.001) indicating that uptake of rotavirus vaccine in Ethiopia was significantly concentrated among children from families with better socioeconomic status. The decomposition analysis showed that underlining inequalities in maternal health care services utilization, including antenatal care use (18.4%) and institutional delivery (8.1%), exposure to media (12.8%), and maternal educational level (9.7%) were responsible for the majority of observed inequalities in the uptake of rotavirus vaccine. The findings suggested that there is significant socioeconomic inequality in rotavirus vaccine uptake in Ethiopia. Multi-sectoral actions are required to reduce the inequalities, inclusive increasing maternal health care services, and educational attainments among economically disadvantaged mothers.

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.

Full genome characterization of human G3P[6] and G3P[9] rotavirus strains in Lebanon

Rotaviruses are the most common infectious agents causing severe diarrheal diseases in young children globally. Three rare human rotavirus strains, two G3P[9] and one G3P[6], were detected in stool samples of children under 5 years of age hospitalized for gastroenteritis in Lebanon during the course of a surveillance study. Complete genomes of these strains were sequenced using VirCapSeq-VERT, a capture based high-throughput sequencing method. Genomic sequences were further characterized by using phylogenetic analyses with global RVA G3P[6]/P[9] strains, other vaccine and reference strains. Genetic analysis revealed that the G3P[6] strain emerged as a DS-1/Wa-like mono-reassortant strain with a potential Ethiopian origin. The two G3P[9] strains possessed a mixed DS-1/Wa/AU-1-like origin indicating that these may have evolved via multiple reassortment events involving feline, human and bovine rotaviruses. Furthermore, analysis of these strains revealed high antigenic variability compared to the vaccine strains. Additional studies are essential to fully understand the evolutionary dynamics of G3P[6]/P[9] strains spreading worldwide and their implications on vaccine effectiveness.

Rotavirus-associated acute diarrhea outbreak in West Shewa Zone of Oromia Regional State, Ethiopia, 2017

Introduction

Rotavirus causes severe-diarrheal diseases in infants. An estimation of 138 million rotavirus-associated diarrheal cases and 215,000 deaths occur every year globally. In December 2016, West-Shewa zone in Ethiopia reported unidentified gastrointestinal diarrhea outbreak. We investigated to identify the causative agent of the outbreak to support response operations.

Methods

Medical records were reviewed, and the daily line list was collected from health facilities. Descriptive data analysis was done by time, person and place. Stool specimens were first tested by antigen capture enzyme immunoassay (EIA) technique and further confirmed by reverse-transcription polymerase chain reaction (RT-PCR) as a gold standard. The product of RT-PCR was genotyped for each gene using G1-G4, G8-G9 and G12 primers for VP7 gene and P(4), P(6), P(8) and P(14) primers for VP4 gene.

Results

A total of 1,987 diarrheal cases (5.7 per 1000) and five deaths (case-fatality rate 0.25%) were identified and epidemiologically-linked to confirmed rotavirus from December 2016 to February 2017. Among the cases, 1,946 (98%) were < 5 children. Fourteen (74%) of the 19 tested stool specimens were positive for rotavirus by EIA and RT-PCR. Majority of strains detected were G12P(6) (25%) and G-negative P(8) (25%) followed by G9P(8) (19%), G1P(8) (13%) and G3/G2 P(8), G12P(8), and G-negative P(6) (6% each).

Conclusion

Diarrheal outbreak which occurred in West-Shewa zone of Ethiopia was associated with rotavirus and relatively more affected districts with low vaccination coverage. Routine rotavirus vaccination quality and coverage should be evaluated and the surveillance system needs to be strengthened to detect, prevent and control a similar outbreak.

Genomic characterization of uncommon human G3P[6] rotavirus strains that have emerged in Kenya after rotavirus vaccine introduction, and pre-vaccine human G8P[4] rotavirus strains

A monovalent rotavirus vaccine (RV1) was introduced to the national immunization program in Kenya in July 2014. There was increased detection of uncommon G3P[6] strains that coincided temporally with the timing of this vaccine introduction. Here, we sequenced and characterized the full genomes of two post-vaccine G3P[6] strains, RVA/Human-wt/KEN/KDH1951/2014/G3P[6] and RVA/Human-wt/KEN/KDH1968/2014/G3P[6], as representatives of these uncommon strains. On full-genomic analysis, both strains exhibited a DS-1-like genotype constellation: G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that all 11 genes of strains KDH1951 and KDH1968 were very closely related to those of human G3P[6] strains isolated in Uganda in 2012-2013, indicating the derivation of these G3P[6] strains from a common ancestor. Because the uncommon G3P[6] strains that emerged in Kenya are fully heterotypic as to the introduced vaccine strain regarding the genotype constellation, vaccine effectiveness against these G3P[6] strains needs to be closely monitored.