Deep-sequencing of viral genomes from treatment-naive HIV-infected persons shows positive association between intrahost genetic diversity and viral load

Background: Infection with human immunodeficiency virus type 1 (HIV)
typically results from transmission of a small and genetically uniform
viral population. Following transmission, the virus population becomes
more diverse because of recombination and acquired mutations through
genetic drift and selection. Viral intrahost genetic diversity remains a
major obstacle to the cure of HIV; however, there is a disagreement
whether intrahost viral genetic diversification associates positively or
negatively with disease progression and progression markers. Viral load is
a key progression marker and understanding its relationship to viral
intrahost genetic diversity could help design future strategies for HIV
monitoring and treatment. Methods: We analyzed deep-sequenced viral
genomes from 2,650 treatment-naive HIV-infected persons to measure the
intrahost genetic diversity of 2,447 genomic codon positions as calculated
by Shannon entropy. We tested for associations between viral load (VL) and
amino acid (AA) entropy accounting for sex, age, race, duration of
infection, and HIV population structure. Results: We confirmed that the
intrahost genetic diversity is highest in the env gene. Furthermore, we
showed that mean Shannon entropy is significantly associated with VL,
especially in infections of >24 months duration. We identified 16
significant associations between VL (p-value<2.0x10-5) and Shannon
entropy at AA positions which in our association analysis explained 13% of
the variance in VL. Conclusions: Our results elucidate that viral
intrahost genetic diversity is associated with VL and could be used as a
better disease progression marker than HIV consensus sequence variants,
especially in infections of longer duration. We emphasize that viral
intrahost diversity should be considered when studying viral genomes and
infection outcomes.