This study investigates the functional roles of site-specific N6-methyladenosine (m6A) modifications in HIV-1 RNA using single-molecule epitranscriptomic analysis. The authors developed a novel method, nanopore direct RNA sequencing (DRS), to analyze full-length, single RNA molecules at the nucleotide level. They found that HIV-1 RNA contains a surprisingly simple modification landscape, with three predominant m6A modifications near the 3' end. These modifications are more densely installed in spliced viral messenger RNAs than in genomic RNAs and play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. The study also reveals that HIV-1 generates diverse RNA subspecies with distinct m6A ensembles, and maintaining multiple m6As on its RNAs provides additional stability and resilience to viral replication. The findings suggest an unexplored viral RNA-level evolutionary strategy where m6As serve as a bet-hedging mechanism to minimize the risk of losing these modifications during viral replication.This study investigates the functional roles of site-specific N6-methyladenosine (m6A) modifications in HIV-1 RNA using single-molecule epitranscriptomic analysis. The authors developed a novel method, nanopore direct RNA sequencing (DRS), to analyze full-length, single RNA molecules at the nucleotide level. They found that HIV-1 RNA contains a surprisingly simple modification landscape, with three predominant m6A modifications near the 3' end. These modifications are more densely installed in spliced viral messenger RNAs than in genomic RNAs and play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. The study also reveals that HIV-1 generates diverse RNA subspecies with distinct m6A ensembles, and maintaining multiple m6As on its RNAs provides additional stability and resilience to viral replication. The findings suggest an unexplored viral RNA-level evolutionary strategy where m6As serve as a bet-hedging mechanism to minimize the risk of losing these modifications during viral replication.