Cell Cycle Regulation of Merkel Cell Polyomavirus Replication and Genome Inheritance in Single Cells

Abstract

Merkel cell polyomavirus (MCV) establishes a near-ubiquitous, asymptomatic infection in humans but on rare occasions drives Merkel cell carcinoma, an aggressive skin cancer. How MCV replication is coordinated with host cell-cycle progression, and how this coordination shapes infected-cell fate, has remained unresolved. Here we combine reporter virus live-cell imaging, pharmacologic cell-cycle perturbation, flow cytometry, and single-cell transcriptomics to examine MCV replication dynamics. VP1 late gene expression occurs almost exclusively during late S or G2, is associated with prolonged G2 arrest, and frequently culminates in cell death. Strikingly, cells that divide before virus replication give rise to daughter cells that synchronously initiate viral replication and VP1 expression, revealing mitotic inheritance of silent viral genomes, a pattern seen for viruses with a known latency lifecycle. Single-cell RNA sequencing further identifies a transient antiviral and inflammatory response that is subsequently suppressed in surviving, cell cycle arrested cells. These findings define the cell-cycle logic, inheritance, and host consequences of MCV replication at single-cell resolution.