HIV-2 evolved ZAP resistance despite increased CpG levels

Simian immunodeficiency viruses infecting sooty mangabeys (SIVsmm) have been transmitted to humans on multiple occasions, giving rise to human immunodeficiency virus type 2 (HIV-2) groups A to I. However, only groups A and B spread significantly in humans causing an epidemic in West Africa. The reasons for this are poorly understood. Here, we show that genetically diverse SIVsmm strains efficiently infect primary human T cells. However, they are highly sensitive to type I IFN, indicating that interferon-stimulated genes (ISGs) pose a barrier to the successful spread of SIVsmm in humans. One well-known ISG is the zinc finger antiviral protein (ZAP), which specifically targets CpG dinucleotides in viral RNAs. To evade ZAP restriction, many viruses, including HIV-1, suppress their CpG content. Unexpectedly, we found that HIV-2 is less sensitive to restriction by ZAP than HIV-1 and SIVsmm despite significantly higher CpG content. Analyses of chimeric HIV-2/SIVsmm constructs, together with binding site mapping using eCLIP, revealed that the determinants of ZAP resistance map to the U3 region of the 3' LTR that overlaps with the nef gene. Our results indicate that ZAP poses a barrier to the efficient spread of SIVsmm in humans and that epidemic HIV-2 evolved a unique mechanism to evade it. Overall design: Characterization of protein-RNA interaction sites of the host protein ZAP in HIV-2 and SIVsmm infected HEK293T ZAP KO cells by using enhanced crosslinking and immunoprecipitation (eCLIP) in combination with RNA-sequencing.