Yes, PEP inhibits HIV replication and therefore can delay recognition of HIV by the immune system. So the rule of thumb is to count the window period after the last dose of PEP.
US testing guidelines after PEP are that the person should test up to 6 months, becouse PEP can delay seroconversion reducing the viral load at infection but not completly erasing it, and the it would take longer to have a high viral load and then longer to produce antibodies for hiv, that are the ones looked for in the tests. Thats is the logic behind the 3 and 6 months testing guideline after PEP.
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