Exact(2)
The most relevant clinical result of this study is that a large fraction of ambiguous nucleotides provides evidence against a recent infection event.
However, it is important to note that although it is unlikely that the HIV sequence from a recent HIV infection has a large fraction of ambiguous nucleotides, this may occur if the HIV population is founded by >1 virus, in which case diversity is large from the beginning on.
Similar(58)
In particular, intravenous drug users exhibit a larger fraction of ambiguous nucleotides than do both heterosexuals and men who have sex with men, which may suggest broader transmission bottlenecks for blood-transmitted than for sexually transmitted HIV.
Figure 1D shows that the fraction of ambiguous nucleotides provides useful information mainly on the lower bound of the age of infection: whereas sequences with f <.68% (ie, the first two quintiles) (Table 2) may stem from the early phase of an infection, this is unlikely for sequences with a larger fraction of ambiguous nucleotides.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com