HIV-2 evades restriction by ZAP through adaptations in the U3 LTR region despite increased CpG levels

Simian immunodeficiency viruses infecting sooty mangabeys (SIVsmm) gave rise to nine groups of human immunodeficiency virus type 2 (HIV-2). Two of these (A and B) spread substantially with an estimated 1–2 million individuals affected. The evolutionary adaptations that facilitated HIV-2’s spread in humans are still poorly understood. Here, we report that diverse SIVsmm strains efficiently infect primary human T cells. However, they are more sensitive to interferon than HIV-2, indicating that interferon-stimulated genes (ISGs) pose a barrier to the successful spread of SIVsmm in humans. One of the best-known antiviral ISGs is the zinc finger antiviral protein (ZAP), which targets CpG dinucleotides in RNA. To evade ZAP-mediated restriction, many viruses, including HIV-1, suppress their CpG content. Unexpectedly, we found that HIV-2 is more resistant to ZAP restriction than HIV-1 and SIVsmm despite having 33% more CpGs. Identification of ZAP-binding sites using RNA enhanced crosslinking immunoprecipitation and analyses of chimeric HIV-2/SIVsmm viruses revealed that the determinants of ZAP resistance map to the nef/U3 region and promote HIV-2 replication in primary human T cells. Our results indicate that HIV-2 evolved a CpG-independent ZAP resistance mechanism which might have been facilitated by relaxed functional constraints acting on Nef in the human host.