We describe a mathematical model and Monte Carlo (MC) simulation of viral evolution
during acute infection. We consider both synchronous and asynchronous processes of viral
infection of new target cells. The model enables an assessment of the expected sequence
diversity in new HIV-1 infections originating from a single transmitted viral strain, estimation
of the most recent common ancestor (MRCA) of the transmitted viral lineage, and estimation
of the time to coalesce back to the MRCA. We also calculate the probability of the MRCA …