Impact of rotavirus vaccination on rotavirus hospitalisation rates among a resource-limited rural population in Mbita, Western Kenya

Genetic Profile of Rotavirus Type A in Children under 5 Years Old in Africa: A Systematic Review of Prevalence

Human type A rotavirus (RV-A) is world-recognized as the major pathogen causing viral gastroenteritis in children under 5 years of age. The literature indicates a substantial increase in the diversity of rotavirus strains across continents, especially in Africa, which can pose significant challenges including an increase of disease burden and a reduction of vaccines' effectiveness. However, few studies have mapped the variety of circulating virus strains in different regions, which may hamper decisions on epidemiological surveillance and preventive public health measures. Thus, our aim was to compile the most updated available evidence on the genetic profile of RV-A among children in Africa and determine the prevalence of different genotypes according to the geographical regions by means of a broad systematic review. Systematic searches were performed in PubMed, Scopus, Web of Science, and Scielo without language, time limits, or geographical restrictions within the African continent. We selected full-text peer-reviewed articles assessing the genetic profile (i.e., genotyping) of RV-A in children up to 5 years old in Africa. Overall, 682 records were retrieved, resulting in 75 studies included for evidence synthesis. These studies were published between 1999 and 2022, were conducted in 28 countries from the five African regions, and 48% of the studies were carried out for 24 months or more. Most studies (n = 55; 73.3%) evaluated RV-A cases before the introduction of the vaccines, while around 20% of studies (n = 13) presented data after the vaccine approval in each country. Only seven (9.3%) studies compared evidence from both periods (pre- and post-vaccine introduction). Genotyping methods to assess RV-A varied between RT-PCR, nested or multiplex RT-PCR, testing only the most common P and G-types. We observed G1 and P[8] to be the most prevalent strains in Africa, with values around 31% and 43%, respectively. Yet if all the genotypes with the following highest prevalence were added ((G1 + G2, G3, G9) and (P[8] + P[6], P[4])), these figures would represent 80% and 99% of the total prevalence. The combination G1P[8] was the most reported in the studies (around 22%). This review study demonstrated an increased strain diversity in the past two decades, which could represent a challenge to the efficacy of the current vaccine.

Deployment of Rotavirus Vaccine in Western Kenya Coincides with a Reduction in All-Cause Child Mortality: A Retrospective Cohort Study

Rotavirus is an important cause of fatal pediatric diarrhea worldwide. Many national immunization programs began adding rotavirus vaccine following a 2009 World Health Organization recommendation. Kenya added rotavirus vaccine to their immunization program at the end of 2014. From a cohort of 38,463 children in the Kisumu health and demographic surveillance site in western Kenya, we assessed how the implementation of the rotavirus vaccine affected mortality in children under 3 years of age. Following its introduction in late 2014, the span of rotavirus vaccine coverage for children increased to 75% by 2017. Receiving the rotavirus vaccine was associated with a 44% reduction in all-cause child mortality (95% confidence interval = 28-68%, p < 0.0001), but not diarrhea-specific mortality (p = 0.401). All-cause child mortality declined 2% per month following the implementation of the rotavirus vaccine (p = 0.002) among both vaccinated and unvaccinated children, but diarrhea-specific mortality was not associated with the implementation of the rotavirus vaccine independent of individual vaccine status (p = 0.125). The incidence of acute diarrhea decreased over the study period, and the introduction of the rotavirus vaccine was not associated with population-wide trends (p = 0.452). The receipt of the rotavirus vaccine was associated with a 34% reduction in the incidence of diarrhea (95% confidence interval = 24-43% reduction). These results suggest that rotavirus vaccine may have had an impact on all-cause child mortality. The analyses of diarrhea-specific mortality were limited by relatively few deaths (n = 57), as others have found a strong reduction in diarrhea-specific mortality. Selection bias may have played a part in these results-children receiving rotavirus vaccine were more likely to be fully immunized than children not receiving the rotavirus vaccine.

Community-level interventions for mitigating the risk of waterborne diarrheal diseases: a systematic review

BACKGROUND

Waterborne diarrhea diseases are among the leading causes of morbidity and mortality globally. These diseases can be mitigated by implementing various interventions. We reviewed the literature to identify available interventions to mitigate the risk of waterborne diarrheal diseases.

METHODS

We conducted a systematic database review of CINAHL (Cumulative Index to Nursing and Allied Health Literature), PubMed, Web of Science Core Collection, Cochrane library, Scopus, African Index Medicus (AIM), and LILACS (Latin American and Caribbean Health Sciences Literature). Our search was limited to articles published between 2009 and 2020. We conducted the review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement checklist. The identified studies were qualitatively synthesized.

RESULTS

Our initial search returned 28 773 articles of which 56 studies met the inclusion criteria. The included studies reported interventions, including vaccines for rotavirus disease (monovalent, pentavalent, and Lanzhou lamb vaccine); enhanced water filtration for preventing cryptosporidiosis, Vi polysaccharide for typhoid; cholera 2-dose vaccines, water supply, water treatment and safe storage, household disinfection, and hygiene promotion for controlling cholera outbreaks.

CONCLUSION

We retrieved few studies on interventions against waterborne diarrheal diseases in low-income countries. Interventions must be specific to each type of waterborne diarrheal disease to be effective. Stakeholders must ensure collaboration in providing and implementing multiple interventions for the best outcomes.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42020190411 .

Genomic characterization of an African G4P[6] human rotavirus strain identified in a diarrheic child in Kenya: Evidence for porcine-to-human interspecies transmission and reassortment

Human rotavirus strains having the unconventional G4P[6] genotype have been sporadically identified in diarrheic patients in different parts of the world. However, the whole genome of only one human G4P[6] strain from Africa (central Africa) has been sequenced and analyzed, and thus the exact origin and evolutionary pattern of African G4P[6] strains remain to be elucidated. In this study, we characterized the full genome of an African G4P[6] strain (RVA/Human-wt/KEN/KCH148/2019/G4P[6]) identified in a stool specimen from a diarrheic child in Kenya. Full genome analysis of strain KCH148 revealed a unique Wa-like genogroup constellation: G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1. NSP3 genotype T7 is commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis showed that 10 of the 11 genes of strain KCH148 (VP7, VP4, VP6, VP1-VP3, NSP1, and NSP3-NSP5) appeared to be of porcine origin, the remaining NSP2 gene appearing to be of human origin. Therefore, strain KCH148 was found to have a porcine rotavirus backbone and thus is likely to be of porcine origin. Furthermore, strain KCH148 is assumed to have been derived through interspecies transmission and reassortment events involving porcine and human rotavirus strains. To our knowledge, this is the first report on full genome-based characterization of a human G4P[6] strain from east Africa. Our observations demonstrated the diversity of human G4P[6] strains in Africa, and provide important insights into the origin and evolutionary pattern of zoonotic G4P[6] strains on the African continent.

Estimating population-based coverage of reproductive, maternal, newborn, and child health (RMNCH) interventions from health management information systems: a comprehensive review

Background

Routinely collected health facility data usually captured and stored in Health Management Information Systems (HMIS) are potential sources of data for frequent and local disaggregated estimation of the coverage of reproductive, maternal, newborn, and child health interventions (RMNCH), but have been under-utilized due to concerns over data quality. We reviewed methods for estimation of national or subnational coverage of RMNCH interventions using HMIS data exclusively or in conjunction with survey data from low- and middle-income countries (LMICs).

Methods

We conducted a comprehensive review of studies indexed in PubMed and Scopus to identify potential papers based on predefined search terms. Two reviewers screened the papers using defined inclusion and exclusion criteria. Following sequences of title, abstract and full paper reviews, we retained 18 relevant papers.

Results

12 papers used only HMIS data and 6 used both HMIS and survey data. There is enormous lack of standards in the existing methods for estimating RMNCH intervention coverage; all appearing to be highly author dependent. The denominators for coverage measures were estimated using census, non-census and combined projection-based methods. No satisfactory methods were found for treatment-based coverage indicators for which the estimation of target population requires the population prevalence of underlying conditions. The estimates of numerators for the coverage measures were obtained from the count of users or visits and in some cases correction for completeness of reporting in the HMIS following an assessment of data quality.

Conclusions

Standard methods for correcting numerators from HMIS data for accurate estimation of coverage of RMNCH interventions are needed to expand the use of these data. More research and investments are required to improve denominators for health facility-derived statistics. Improvement in routine data quality and analytical methods would allow for timely estimation of RMNCH intervention coverage at the national and subnational levels.

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.

Effectiveness of Monovalent Rotavirus Vaccine Against Hospitalization With Acute Rotavirus Gastroenteritis in Kenyan Children

BACKGROUND

Rotavirus remains a leading cause of pediatric diarrheal illness and death worldwide. Data on rotavirus vaccine effectiveness in sub-Saharan Africa are limited. Kenya introduced monovalent rotavirus vaccine (RV1) in July 2014. We assessed RV1 effectiveness against rotavirus-associated hospitalization in Kenyan children.

METHODS

Between July 2014 and December 2017, we conducted surveillance for acute gastroenteritis (AGE) in 3 Kenyan hospitals. From children age-eligible for ≥1 RV1 dose, with stool tested for rotavirus and confirmed vaccination history we compared RV1 coverage among rotavirus positive (cases) vs rotavirus negative (controls) using multivariable logistic regression and calculated effectiveness based on adjusted odds ratio.

RESULTS

Among 677 eligible children, 110 (16%) were rotavirus positive. Vaccination data were available for 91 (83%) cases; 51 (56%) had 2 RV1 doses and 33 (36%) 0 doses. Among 567 controls, 418 (74%) had vaccination data; 308 (74%) had 2 doses and 69 (16%) 0 doses. Overall 2-dose effectiveness was 64% (95% confidence interval [CI], 35%-80%); effectiveness was 67% (95% CI, 30%-84%) for children aged <12 months and 72% (95% CI, 10%-91%) for children aged ≥12 months. Significant effectiveness was seen in children with normal weight for age, length/height for age and weight for length/height; however, no protection was found among underweight, stunted, or wasted children.

CONCLUSIONS

RV1 in the Kenyan immunization program provides significant protection against rotavirus-associated hospitalization which persisted beyond infancy. Malnutrition appears to diminish vaccine effectiveness. Efforts to improve rotavirus uptake and nutritional status are important to maximize vaccine benefit.

Rotavirus prevalence and seasonal distribution post vaccine introduction in Nairobi county Kenya

Rotaviruses are one of the leading etiological agents of gastroenteritis in young children, for which a monovalent G1P(8) vaccine has been provided for free in Kenyan since July 2014. The main objective was to estimate the post vaccine prevalence and seasonal distribution of rotavirus diarrhea in children less than 5 years in Nairobi County, Kenya. Rotavirus positive samples were collected from children below 5 years of age in two hospitals within Nairobi County where vaccination status was card-confirmed. The children were examined and the demographic and clinical profiles of the children were recorded. Fecal specimens were analyzed for rotavirus antigen using an ELISA kit, followed by characterization by PAGE. Out of the total 323 samples, 49 had detectable rotavirus infection, representing 15.2% prevalence. Age distribution of rotavirus prevalence was as follows: ≤ 6 months-8.5%, 7-12 months-27.4%, 13-24 months - 41.4%, 25-36 months - 16.4% while 36-65 months had 6.3%. Rotavirus diarrhea was more common in wet and cold months of the year, the highest prevalence being observed in August (24.5%), 12.3% in both July and March, while April scored a prevalence of 10.2%. Out of the 49 rotavirus positive children, 48 had vomiting and abdominal cramps while all had fever and watery stool. The prevalence of Rotaviral diarrhea in children less than 5 years in Nairobi County Kenya has greatly reduced following the vaccine introduction and is more common during the wet and cold seasons of the year.

Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014.  Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013.

Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool.

Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%).  Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period.  

Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks.  These data will be useful in interpreting genotype patterns observed in the region during the vaccine era.

Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014.  Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%).  Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period.   Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks.  These data will be useful in interpreting genotype patterns observed in the region during the vaccine era.