Background: Rotavirus is a double-stranded RNA virus of the Reoviridae family and the most common cause of diarrhea in children. This study determined the prevalence and genotypes of Rotavirus in humans and animals in Calabar, Nigeria.

Methods: A total of 1000 faecal samples were collected (400 from children ≤ 5 years and 600 from animals—dogs, pigs and cattle). Samples were tested for Rotavirus using ELISA and genotyping was performed using Multiplex RT-PCR. Questionnaires were used to obtain demographic data from human participants. Data was analysed using SPSS version 25 and significant variations were determined using the Chi Square test.

Results: Of the 1,000 samples analysed, 64 tested positive, yielding an overall prevalence of 6.4%. The distribution of PCR-confirmed Rotavirus infection across species included the following: pigs (20/200, 10.0%); dogs (4/200, 2.0%); cattle (0/200, 0.0%) and humans (40/400, 10.0%). The prevalence of Rotavirus varied markedly among host species with higher rates in humans and pigs (χ² = 33.12, df = 3, p < 0.0001). Eight different Rotavirus A gene (G and P) combinations were detected in humans while only two were detected in animals. Of the 64 genotypes, 24 (37.5%) were obtained from animals (pigs and dogs) and 40 (62.5%) from humans. The predominant genotype in humans was (G10,P8) (9, 22.5%), and in animals, it was (G9,P8) (13, 65%). Meanwhile, two genotypes (G9,P8) and (P8) were common in both humans and animals. Monthly analysis showed that the highest prevalence of Rotavirus was observed in January (26.3%), while the lowest was in June (0%). There was no significant difference in the distribution of rotavirus by month (χ²=0.450; P=0.994).

Conclusion: Rotavirus A is common in both humans and animals in the study area. The presence of similar genotypes highlights the potential for zoonotic transmission to humans. There is a need to improve rotavirus vaccine coverage for children in the study area.