High genetic diversity of porcine rotavirus A, B, and C in Hungary with putative novel VP4 genotypes

BACKGROUND: Rotaviruses (RVs) are important enteric pathogens of swine, contributing significantly to neonatal and post-weaning diarrhea worldwide. Although rotavirus A (RVA) is the best characterized species, much less is known about the epidemiology and genetic diversity of RVB and RVC, especially in Central Europe. This study aimed to investigate the presence and genetic diversity of RVA, RVB, and RVC in diarrheic piglets in Hungary using Nanopore third-generation sequencing. RESULTS: A total of 77 fecal swab samples collected from diarrheic piglets across 19 swine farms were analyzed. All three RV species were detected, RVA and RVC were each identified in 54.5% of samples, while 40.3% was RVB positive. Coinfections involving multiple RV species were frequent, highlighting the complex etiology of piglet diarrhea. Altogether, 8 RVA, 3 RVB, and 4 RVC full-genome sequences, comprising all 11 segments, were identified. Genotyping of RVA strains revealed multiple G/P genotype combinations, with G9P[23] being the most prevalent. Whole-genome analysis demonstrated a Wa-like genomic backbone of porcine origin. In RVB, three complete VP4 sequences were obtained that could not be assigned to any known P genotype, suggesting the presence of a novel lineage. Hungarian RVC strains showed high genetic diversity, including five distinct G genotypes and one potential novel P genotype, underlining evolutionary diversity of porcine RVs. CONCLUSIONS: This study provides a comprehensive molecular characterization of RVA, RVB, and RVC circulating in Hungarian pig populations. The high prevalence of coinfections and the detection of genetically diverse and potentially novel strains emphasize the complexity of RV epidemiology in swine. These findings highlight the need for continued surveillance to better understand their role in pig health and zoonotic risk.