Rotavirus Genotypes Show Surprising Diversity in Addis Ababa Children

Rotavirus remains one of the most formidable viral pathogens of early childhood, and a new hospital-based study from Addis Ababa, Ethiopia, offers a detailed molecular portrait of the strains now circulating in a city where the virus continues to sicken children despite more than a decade of vaccination. The research, published in BMC Infectious Diseases, detected rotavirus in nearly one in five stool samples collected from children under five years of age with acute diarrheal illness, and its genotypic characterization revealed a striking diversity of circulating strains, including three genotypes never before documented in Ethiopia.

The study was conducted as a cross-sectional investigation across selected health facilities in Addis Ababa, running from September 2023 to August 2025. Researchers collected a total of 400 stool samples from children under five presenting with acute diarrheal illness. Each sample was tested for the presence of rotavirus alphagastroenteritidis, the formally designated species name for the classic human rotavirus, and positive specimens were then subjected to genotypic analysis using the TaqMan Array Card, a real-time PCR platform that allows simultaneous detection and typing of multiple viral gene targets in a single reaction.

The results showed that rotavirus was detected in 79 of the 400 samples, corresponding to a prevalence of 19.8 percent. Of these positive specimens, 76 could be genotyped based on the viral VP7 and/or VP4 genes, the two outer capsid proteins that define the G and P genotype systems respectively. The VP7 glycoprotein determines the G genotype, while the VP4 protease-sensitive protein determines the P genotype, and the combination of the two, written as G-P, constitutes the standard nomenclature used by the global rotavirus surveillance community.

What the genotyping revealed was remarkable. Fifteen distinct G-P genotype combinations were identified among the 76 genotyped samples, a level of diversity that underscores the complex molecular ecology of rotavirus in the region. The predominant circulating genotypes were G3P[8] at 11.8 percent (9 of 76 samples), G1P[4] at 10.6 percent (8 of 76), G12P[6] at 7.9 percent (6 of 76), and G2P[4] at 7.9 percent (6 of 76). No single genotype dominated overwhelmingly, suggesting that multiple viral lineages are co-circulating simultaneously within the pediatric population of Addis Ababa.

Perhaps the most significant finding of the study was the detection of three genotypes, G8P[4], G10P[8], and G4P[8], for the first time in Ethiopia. These genotypes had not been previously reported in the country, and their identification raises important questions about viral evolution, zoonotic reservoirs, and the possible introduction of novel strains from neighboring regions. G8 and G10 genotypes are often associated with bovine rotaviruses, and their detection in human clinical specimens can indicate reassortment events between animal and human viral strains, a phenomenon that has been increasingly documented across Africa.

Ethiopia introduced the Rotarix rotavirus vaccine in 2013, adding the monovalent G1P[8] vaccine to its routine immunization schedule. Rotarix contains a single attenuated human strain, and its widespread use has been associated in many settings with a reduction in severe rotavirus disease. However, the continued detection of rotavirus in nearly 20 percent of children with acute diarrhea in Addis Ababa, more than a decade after vaccine introduction, highlights the ongoing burden of disease and the importance of understanding which strains are circulating in the post-vaccine era.

The molecular epidemiology of rotavirus is shaped by the segmented nature of its double-stranded RNA genome, which consists of eleven segments encoding six viral proteins and six nonstructural proteins. This segmented architecture allows reassortment, a process by which co-infecting viral strains can exchange gene segments and generate novel genotype combinations. Reassortment is a key driver of rotavirus diversity and is thought to contribute to the emergence of strains that may partially escape vaccine-induced immunity, making continued strain surveillance an essential component of public health planning.

The study’s findings carry particular relevance for Sub-Saharan Africa, which bears the greatest burden of rotavirus disease globally. The wide diversity of genotypes identified in Addis Ababa, including unusual genotypes not previously reported in Ethiopia, underlines the importance of continued molecular surveillance to monitor the emergence of new strains and to inform vaccine policy decisions. Understanding the local genotype distribution is critical for assessing whether current vaccines provide adequate coverage against the circulating strains and for detecting shifts in genotype prevalence that may occur over time.

The research was funded by the National Institute for Health and Care Research using UK aid from the UK Government to support global health research, with additional support from Addis Ababa University. The laboratory work was facilitated by the Malawi-Liverpool Wellcome Programme, and the study involved collaboration between Ethiopian, Malawian, and British institutions, including Addis Ababa University, Kamuzu University of Health Sciences in Blantyre, and the University of Liverpool.

As rotavirus continues to evolve in the post-vaccine era, studies of this kind provide the molecular evidence base needed to track viral change and to protect the most vulnerable populations. The detection of G8P[4], G10P[8], and G4P[8] in Ethiopia for the first time serves as a reminder that the viral landscape is dynamic, and that sustained genotypic characterization remains indispensable for understanding and ultimately reducing the burden of rotavirus disease among children in Africa and beyond.

Subject of Research: Molecular epidemiology and genotypic characterization of rotavirus among children under five years of age with acute diarrheal illness in Addis Ababa, Ethiopia: cross-sectional hospital-based study

Article Title: Molecular epidemiology and genotypic characterization of rotavirus among children under five years of age with acute diarrheal illness in Addis Ababa, Ethiopia: cross-sectional hospital-based study

Article References: Natei, G. D., Asrat, D., Kalayu, A. A., Msefula, C., Cunliffe, N. A., & Mekasha, A. (2026). Molecular epidemiology and genotypic characterization of rotavirus among children under five years of age with acute diarrheal illness in Addis Ababa, Ethiopia: cross-sectional hospital-based study. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14468-z

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14468-z

Keywords: Molecular, epidemiology, genotypic, characterization, rotavirus, children, under, five, years, acute, diarrheal, illness