Molecular evolution of Andes virus lineages leading to recent human outbreaks

Andes virus (ANDV) is exceptional among hantaviruses in its capacity for person-to-person transmission, but whether outbreaks reflect recent viral adaptation or emergence of pre-existing reservoir lineages remains unclear. We generated paired blood- and nasal-derived genomes from the MV Hondius outbreak and integrated them with a segment-linked collection of human- and rodent-derived ANDV sequences, including incomplete genomes. We developed a linkage-informed missing-segment framework that preserves isolate identity, sampling time, and cross-segment placement without imputing nucleotide state

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