The Vif protein of human immunodeficiency virus type 1 (HIV-1) promotes viral 
replication by downregulation of the cell-encoded, antiviral APOBEC3 proteins. 
These proteins exert their suppressive effects through the inhibition of viral 
reverse transcription as well as the induction of cytidine deamination within 
nascent viral cDNA. Importantly, these two effects have not been characterized 
in detail in human CD4(+) T cells, leading to controversies over their possible 
contributions to viral inhibition in the natural cell targets of HIV-1 
replication. Here we use wild-type and Vif-deficient viruses derived from the 
CD4(+) T cells of multiple donors to examine the consequences of APOBEC3 protein 
function at natural levels of expression. We demonstrate that APOBEC3 proteins 
impart a profound deficiency to reverse transcription from the initial stages of 
cDNA synthesis, as well as excessive cytidine deamination (hypermutation) of the 
DNAs that are synthesized. Experiments using viruses from transfected cells and 
a novel method for mapping the 3' termini of cDNAs indicate that the inhibition 
of reverse transcription is not limited to a few specific sites, arguing that 
APOBEC3 proteins impede enzymatic processivity. Detailed analyses of mutation 
spectra in viral cDNA strongly imply that one particular APOBEC3 protein, 
APOBEC3G, provides the bulk of the antiviral phenotype in CD4(+) T cells, with 
the effects of APOBEC3F and APOBEC3D being less significant. Taken together, we 
conclude that the dual mechanisms of action of APOBEC3 proteins combine to 
deliver more effective restriction of HIV-1 than either function would by 
itself.