The Rotavirus SpatioTrasncriptomics (Rota-Omics) study is a multidisciplinary research project aimed at understanding why oral rotavirus vaccines perform less effectively in some low- and middle-income countries, including Zambia. Rotavirus remains one of the leading causes of severe diarrheal disease in infants and young children worldwide, despite the widespread introduction of vaccines such as Rotarix® and Rotavac®. Although these vaccines have greatly reduced childhood deaths in many countries, vaccine effectiveness is often lower in settings where the burden of disease is highest. Understanding the reasons behind this reduced protection is critical for improving child health globally.

A major focus of the study is Environmental Enteropathy (EE), also known as Environmental Enteric Dysfunction (EED), a chronic inflammatory condition of the small intestine that is common in low-resource settings. EE is associated with damage to the intestinal lining, chronic immune activation, poor nutrient absorption, and impaired gut barrier function. These changes are thought to interfere with the body's ability to respond effectively to oral vaccines, which rely on strong intestinal immune responses.

The RotaOmics study uses a systems biology approach to investigate how the immune system, gut microbiome, nutrition, and intestinal inflammation interact to influence rotavirus vaccine responses. The term "omics" refers to advanced technologies that allow researchers to study genes, proteins, microbes, and other biological processes at a large scale. By combining these approaches, the study aims to identify biological markers and immune pathways associated with strong or weak vaccine responses.

The study involves the collection of samples such as blood, stool, saliva, and breast milk from mothers and infants at different time points before and after vaccination. These samples are analysed using laboratory methods including antibody testing, molecular pathogen detection, microbiome sequencing, and immune profiling. The study also evaluates markers of gut inflammation and intestinal health.

One important goal of the project is to identify correlates of protection, which are measurable biological indicators that predict whether a vaccine is likely to protect against disease. Identifying these markers could help guide the development of improved vaccines or supportive interventions to enhance vaccine performance in vulnerable populations.

The study also contributes to a broader understanding of mucosal immunity, which refers to immune responses occurring in the gastrointestinal tract. Since many enteric infections begin in the gut, understanding intestinal immune function is important not only for rotavirus vaccines but also for other oral vaccines and diarrheal diseases.

In addition to its scientific objectives, RotaOmics includes a strong capacity-building component. The project supports training for local scientists, clinicians, and laboratory personnel in areas such as molecular biology, immunology, genomics, bioinformatics, and data analysis. By strengthening local research expertise and infrastructure, the study aims to support long-term scientific development and improve regional capacity for infectious disease research and outbreak response.

Overall, the RotaOmics study seeks to generate new insights into why oral rotavirus vaccines underperform in some settings and to identify strategies that may improve vaccine effectiveness and child health outcomes in Zambia and similar regions worldwide.

Inclusion Criteria:

• Age ≥ 18 years and ≤ 50 years.
• Able and willing to provide written informed consent.
• Reside within Lusaka district and available for scheduled follow-up.
• Willing to undergo two endoscopy procedures with serial sample collection.

Exclusion Criteria:

• Pregnant or breastfeeding.
• Active gut disease requiring treatment (e.g., active peptic ulcer disease, gastrointestinal bleeding).
• Known severe immunodeficiency (HIV with CD4 < 200 cells/mm³, current cancer chemotherapy, systemic corticosteroids equivalent to >20 mg/day prednisolone for >2 weeks).
• Severe comorbidities rendering endoscopy unsafe (e.g., severe cardiopulmonary disease, uncontrolled hypertension, oropharyngeal abnormalities).
• Use of anticoagulants where suspension is unsafe or unwillingness to withhold anticoagulation when clinically indicated.
• Receipt of any live vaccine within 30 days prior to enrolment or planned live vaccine within 30 days after Rotarix administration.
• Any condition judged by the investigator to compromise participant safety or data integrity.
• Participants who had a recent diarrhoea episode, or who have taken NSAID drugs or antibiotics, will be eligible for re-assessment after a month without this disqualifier.

Pregnancy testing and counselling: Women of reproductive potential will require a negative urine pregnancy test within 24 hours prior to endoscopy and vaccination and will be counselled to avoid pregnancy during the first 30 days post-vaccination.

Healthy adults living in Chawama, a densely populated peri-urban setting in proximity to the study recruitment site.

Due to requirements of the ethics committee, the study is not permitted to share individual participant data unless otherwise requested for and approved by the University of Zambia Biomedical Research Ethics Committee.