Genetic diversity of rotavirus strains in children with diarrhea in Lagos, Nigeria

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.

Rotavirus and bacterial diarrhoea among children in Ile-Ife, Nigeria: Burden, risk factors and seasonality

BACKGROUND

Diarrhoea is a leading cause of death among under-five children globally, with sub-Saharan Africa alone accounting for 1/3 episodes yearly. Viruses, bacteria and parasites may cause diarrhoea. Rotavirus is the most common viral aetiology of diarrhoea in children less than five years globally. In Nigeria, there is scarce data on the prevalence/importance, burden, clinical/risk factors and seasonality of rotavirus and bacteria and this study aims to determine the role of rotavirus and bacteria on diarrhoea cases in children less than five years in Ile-Ife, Nigeria.

METHODS

Socio-demographic data, environmental/risk factors and diarrhoiec stool samples were collected from children less than five years presenting with acute diarrhoea. Rotavirus was identified using ELISA. Bacteria pathogens were detected using cultural technique and typed using PCR. Diarrhoeagenic E. coli (DEC) isolates were subjected to antimicrobial susceptibility testing. Pathogen positive and negative samples were compared in terms of gender, age-group, seasonal distribution, and clinical/risk factors using chi-square with two-tailed significance. SPSS version 20.0.1 for Windows was used for statistical analysis.

RESULTS

At least one pathogen was detected from 63 (60.6%) children having gastroenteritis while 28 (44.4%) had multiple infections. Rotavirus was the most detected pathogen. Prevalence of rotavirus mono-infection was 22%, multiple infection with bacteria was 45%. Mono-infection prevalence of DEC, Shigella spp., and Salmonella spp. were 5.8% (6/104), 5.8% (6/104), and 2.9% (3/104) and co-infection with RVA were 23.1% (24/104), 21.2% (22/104) and 10.6% (11/104) respectively. All rotaviral infections were observed in the dry season. The pathotypes of DEC detected were STEC and EAEC. Parent earnings and mid-upper arm circumference measurement have statistical correlation with diarrhoea (p = 0.034; 0.035 respectively).

CONCLUSION

In this study, rotavirus was more prevalent than bacteria and occurred only in the dry season. Among bacteria aetiologies, DEC was the most common detected. Differences in seasonal peaks of rotavirus and DEC could be employed in diarrhoea management in Nigeria and other tropical countries to ensure optimal limited resources usage in preventing diarrhoea transmission and reducing indiscriminate use of antibiotics.

Prevalence and relative risk of Rotavirus Gastroenteritis in children under five years in Nigeria: a systematic review and meta-analysis

Rotavirus is responsible for most cases of gastroenteritis and mortality in children below 5 years of age, especially in developing countries, including Nigeria. Nonetheless, there is limited data on the nationwide estimate for the prevalence of rotavirus. This systematic review and meta-analysis sought to determine the pooled prevalence of rotavirus infections and its relative risk among children below 5 years of age in Nigeria. Eligible published studies between 1982 and 2021 were accessed from 'PubMed', 'Science Direct', 'Google Scholar' and 'African Journal Online', 'Web of Science', 'Springer', 'Wiley' were systematically reviewed. The pooled prevalence, relative risk and regional subgroup analyses were calculated using the random effects model at 95% confidence interval (CI). A total of 62 selected studies, including 15 studies case-control studies, were processed in this review from a pooled population of 18,849 children. The nationwide pooled prevalence of rotavirus among children below 5 years of age in Nigeria was 23% (CI 95%; 19-27). Regional subgroup analysis showed that the Southern region had a prevalence of 27% (CI 95%; 21-32) while the Northern region had a 20% (CI 95%; 16-25%) prevalence, although the difference was not significant (P = 0.527). Rotavirus was implicated in most cases of acute gastroenteritis with a relative risk of 5.7 (95% CI: 2.9-11.2). The high prevalence and relative risk of rotavirus infections among children in Nigeria shows that rotavirus is an important cause of acute gastroenteritis in Nigeria. Thus, there is a need for further surveillance, especially at community levels together with the introduction of rotavirus vaccines into the national immunization program.

Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine

Objective

This cross-sectional study investigated the circulating strains of rotavirus and screened for noravirus in Ibadan, Nigeria as the country introduces the rotavirus vaccine into its national immunization program.

Methods

Sixty-five stool samples were collected from children younger than 5 years with clinically diagnosed diarrhea and screened for the presence of rotavirus and norovirus using RT-PCR. Rotavirus-positive samples were further analyzed to determine the G and P genotypes using semi-nested multiplex PCR.

Results

The rates of rotavirus and norovirus positivity were 30.8% and 10.8%, respectively, whereas the rate of rotavirus and norovirus mixed infection was 4.6%. G1 was the predominant VP7 genotype, followed by G2, G9, and G1G2G9, whereas the predominant VP4 genotype was P[4], followed by P[6], P[8], and P[9]. The mixed P types P[4]P[8] and P[4]P[6] were also detected. G1P[4] was the most common VP4 and VP7 combination, followed by G2P[4], G1[P6], G1P[8], G2P[6], G2P[9], G9P[6], G2G9P[4], G2P[4]P[6], G1P[4]P[8], G2G9P[8], G1G2G9P[8], and G1[non-typable] P[non-typable], which were detected in at least 5% of the samples. Four samples had a combination of non-typable G and P types.

Conclusions

It is essential to monitor the circulation of virus strains prior to and during the implementation of the immunization program.

Group A Rotavirus G1P[6] Associated Fatalities in Diarrheic Nigerian Infants, Possible Impact of Enterovirus Environmental Enteric Dysfunction, and Implications for Rota-Vaccinology

Group A rotavirus (RVA) diarrhea disease and mortality are yet unabated, particularly in developing countries. As global knowledge of specific strains associated with infant mortality is crucial for successful vaccination efforts, candidate RVA strains detected in mortality and fatal cases of severely diarrheic hospitalized infants in Akure, Nigeria were investigated.

Fecal samples from comatose patients were tested for RVAs, other diarrhea viruses, and enteric bacterial pathogens. Genomic dsRNA was extracted from 10% rotavirus positive stool suspension, the VP4 and VP7 genes were reverse transcribed and amplified by one-step reverse transcription polymerase chain reaction (PCR) and genotyped by seminested multiplex PCR. Amplicons were sequenced, aligned by ClustalW, and phylogenetic analyses were conducted in MEGA6. Sequences data were deposited to GenBank and DDBJ.

Medical examination and microbiological analyses upheld viral diarrhea. EIA revealed RVA and enterovirus. PCR identified virulent RVA strain GIP[6] whose VP7 nucleotide sequences shared a common cluster with Cuban isolate G1P[6], while the VP4 P[6] sequences were related to Asian strains. Reassortant RVA G1P[6] was found in fatal diarrhea cases and mortality of a Nigerian child. RVA coinfection with enterovirus and associated biomarkers of environmental enteric dysfunction in infantile diarrhea should henceforth be evaluated. Current rotavirus vaccines may fare badly against the prevailing virulent strains. The disease severity and outcome necessitates a wider epidemiological study, a review and inclusion of the P[6] genotype in future rotavirus vaccines.