Additional Documentation HIV superinfection is rare and does not contribute to drug resistance in the EUResist/Virolab cohort

The detection of superinfection involves an assessment whether the sequences obtained from a patient diverged from a last common ancestor within that patient, or several lineages were introduced by independent infection events. First we tested whether sequence divergence can be used to identify viral sequences of polyphyletic origin. In principle, a conservative divergence threshold could be estimated, based on the average within-host divergence between two time points: sequences more divergent than the threshold could be used