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Our new method to quantitatively analyze viral population dynamics enabled us to observe the relative competitiveness and adaption of different viral variants and provided a valuable tool for studying HIV subpopulation emergence, persistence, and decline during ART. After transmission, the virus is able to diversify into complex subpopulations due to its rapid replication cycle and high mutation rate.

Single genome sequences were obtained from 3 pigtail macaques infected with a recombinant simian immunodeficiency virus containing the RT coding region from HIV-1 (RT-SHIV) and treated with short-course efavirenz monotherapy 13 weeks post-infection followed by daily combination antiretroviral therapy (ART) beginning at week 17.At the same time, 6 variants containing K103N (AAC) or K103N (AAT) were detected, which formed 4 subpopulations.

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