Complex Recombination Landscape and Lineage Turnover in Classical Human Astroviruses

Human astroviruses are small, non-enveloped RNA viruses belonging to the family Astroviridae. Among the four species known to infect humans, the species Mamastrovirus hominis (the classical human astroviruses, formerly MAstV1) is associated with gastrointestinal illness worldwide, while three more recently identified species have been linked to lethal central nervous system infections. High substitution rates and recombination drive their rapid evolution, yet recombination patterns in classical human astroviruses remain poorly characterized. This study systematically analyzes patterns and temporal dynamics of natural recombination in classical human astroviruses. Publicly available genomes of classical human astroviruses were analyzed to identify recombination hotspots. Recombinant forms were defined as stable phylogenetic lineages unaffected by recombination, and their half-lives were estimated based on time-scaled phylogenies (BEAST2v2.7.7). Recombination in classical human astroviruses occurred most frequently at the ORF1b/ORF2 junction, but also within ORF1a, at the ORF1a/ORF1b junction, and within ORF2. Only the 3'-part of ORF1a and a fragment of ORF1b exhibited robust temporal signal, yielding substitution rates of 2.35 × 10^-3 and 2.14 × 10^-3 s/s/y, respectively. The half-lives of recombinant forms varied considerably by genomic region: longest for exchanges between the parts of ORF1a (21 years), intermediate for ORF1a/ORF1b recombinants (7-9 years), and shortest for ORF1ab/ORF2 recombinants (2.5-3.6 years). The estimated half-lives for recombinants align with those reported for human enteroviruses and noroviruses. These findings highlight the dynamics of the generation of astrovirus diversity and may inform advanced surveillance of emerging strains.