Viral promoters modulate transcription and hence viral replication. The HIV-1 promoter is polymorph in its transcription factors binding sites. The impact of this polymorphism on viral replication in vivo has never been addressed. On the background of a SIVmac239 genome, we have engineered three chimeras bearing the minimal promoters of HIV-1 clade B, C and E. By co-infection of four rhesus macaques, a discrepancy between the genotypes of rPBMCs-associated chimeras and of virions in the serum has been highlighted. A shift in viral genotype profiles was observed between the acute and the asymptomatic phase. These results show that subtype-specific HIV-1 promoter polymorphism is a major determinant influencing viral replication and dissemination. Notably, primary infection viremia is mainly due to HIV-1 replication in the gut.
