The Lysogenic Cycle and Latency
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In the lysogenic cycle, a temperate virus's genome integrates into the host as a prophage, replicating with it until a stressor triggers the lytic cycle.
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Lambda phage integrates into E. coli's chromosome as a prophage; herpesviruses persist latently in nerve tissue for years.
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A prophage is not cleared — it can excise and re-enter the lytic cycle long after the original infection.