Complex Recombination Landscape and Lineage Turnover in Classical Human Astroviruses.

Area of Science:

• Virology
• Molecular Evolution

Background:

• Human astroviruses (family Astroviridae) are RNA viruses causing gastrointestinal and neurological diseases.
• Recombination is a key driver of viral evolution, but its patterns in classical human astroviruses are not well understood.

Purpose of the Study:

• To systematically analyze recombination patterns and temporal dynamics in classical human astroviruses.
• To identify recombination hotspots and estimate the half-lives of recombinant viral lineages.

Main Methods:

• Analysis of publicly available classical human astrovirus genomes.
• Identification of recombination hotspots and stable phylogenetic lineages.
• Estimation of recombinant half-lives using time-scaled phylogenies (BEAST2).

Main Results:

• Recombination frequently occurred at the ORF1b/ORF2 junction, within ORF1a, at the ORF1a/ORF1b junction, and within ORF2.
• Substitution rates were estimated for ORF1a (2.35 × 10⁻³) and ORF1b (2.14 × 10⁻³).
• Recombinant half-lives varied by genomic region, ranging from 2.5–3.6 years (ORF1ab/ORF2) to 21 years (within ORF1a).

Conclusions:

• Recombination significantly contributes to the generation of astrovirus diversity.
• Estimated recombinant half-lives are comparable to those of enteroviruses and noroviruses.
• Findings can inform surveillance strategies for emerging astrovirus strains.