Speaker
Description
HIV-1 has nine main subtypes that persist in infected populations; however, the overall diversity of HIV-1 is much larger due to recombination amongst these original subtypes. Recombination has led to many unique recombinant forms and over 100 circulating recombinant forms (CRFs), which may become more prevalent than the two parent strains in a given region. We analysed sequences taken from the Los Alamos National Laboratory HIV database and found different trends in the relative number of parents vs. recombinants for different subtype pairs depending on the country of origin. However, this does not tell us whether these differences are driven by within-host or between-host dynamics. To investigate, we developed a mathematical model of HIV-1 viral recombination that incorporates within-host dynamics (viral competition and recombination) and between-host dynamics (transmission rates and emergence time in the population) to understand which part of the dynamics influences the observed trends more. We apply this method to three scenarios of recombinant emergence in Brazil and China, showing that our model can capture the three scenarios. Given the model assumptions, we also show that within-host dynamics are an early driver in the emergence of recombinants. However, between-host events will determine the level at which a recombinant may be expressed in the population.
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