A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution

Abstract

Lentiviruses chronically infect a broad range of mammalian species and have been transmitted from primates to humans, giving rise to multiple outbreaks of HIV infection over the past century. Although the circumstances surrounding these recent zoonoses are becoming clearer, the nature and timescale of interaction between lentiviruses and primates remains unknown. Here, we report the discovery of an endogenous lentivirus in the genome of the gray mouse lemur (Microcebus murinus), a strepsirrhine primate from Madagascar, demonstrating that lentiviruses are capable of invading the primate germ line. Phylogenetic analysis places gray mouse lemur prosimian immunodeficiency virus (pSIVgml) basal to all known primate lentiviruses and, consistent with this, its genomic organization is intermediate between the nonprimate lentiviruses and their more derived primate counterparts. Thus, pSIVgml represents the first unambiguous example of a viral transitional form, revealing the acquisition and loss of genomic features during lentiviral evolution. Furthermore, because terrestrial mammal populations in Madagascar and Africa are likely to have been isolated from one another for at least 14 million years, the presence of pSIVgml in the gray mouse lemur genome indicates that lentiviruses must have been infecting primates for at least this period of time, or have been transmitted between Malagasy and African primate populations by a vector species capable of traversing the Mozambique channel. The discovery of pSIVgml illustrates the utility of endogenous sequences for the study of contemporary retroviruses and indicates that primate lentiviruses may be considerably older and more broadly distributed than previously thought.

Fig. 1.

Consensus pSIVgml genome. Horizontal lines above the scale-bar indicate the relative coordinates of the contigs derived from whole genome shotgun (WGS) sequences and PCR amplicons that were used to construct the consensus genome. WGS contig 2 contained a region of indeterminate sequence, indicated by a dashed line. Distinct 5 base pair target site duplication (TSD) sequences located at the 5′ and 3′ flanks of proviral insertions are shown, demonstrating the presence of at least two distinct proviruses. The schematic below the scale shows the locations of ORFs and genomic features within the consensus proviral genome sequence. Circles with inset question marks indicate the possible presence of short, spliced Rev and Tat domains toward the 5′ and 3′ ends of the env gene, respectively; the general lack of sequence similarity of these regions within lentiviruses meant that it was not possible to determine whether or not pSIVgml encodes such domains. LTR, long-terminal repeat; TAR, transactivation responsive element; PBS, primer binding site; MA, matrix; CA, capsid; NC, nucleocapsid; PR, protease; RT, reverse transcriptase; RH, RNaseH; dUTP, dUTPase; IN, integrase; SU, surface glycoprotein; TM, transmembrane; RRE, Rev responsive element.

Fig. 2.

Phylogenetic relationships among lentiviruses. The inferred timing of accessory gene acquisition and loss events, based on the principle of parsimony, and assuming no recombination between groups, is indicated. Gene acquisition/loss events that are uncertain with regard to timing or directionality are indicated by question marks. Bootstrap scores and Bayesian posterior probabilities are indicated to the left and right of the forward slash respectively, while nodes with only 100 indicated showed maximal support under both measures. See Methods for taxa definitions and sequence accession numbers. *Subsequent to its origin in the SIVsyk/SIVmon/SIVgsn lineage, the vpu gene was acquired in the HIV-1/SIVcpz lineage via recombination (33). Some primate lentiviruses have an additional gene, vpx (data not shown).

Fig. 3.

Models of viral origin. (A) Map showing geographic location of Madagascar relative to Africa. (B) Evolutionary timeline. Mammalian invasions of Madagascar are believed to have involved only five orders of terrestrial mammals—primates, rodents, carnivores, afrosoricida, and artiodactyls. Molecular and fossil data suggest the most recent colonization occurred 14 million years ago (23). The oldest known lentiviral sequences have been dated to between 7 and 11 million years old (14). (C) Proposed models of primate lentivirus evolution. Three evolutionary scenarios can be proposed to account for the presence of lentiviruses in both streprsirrhine (S) and haplorrhine (H) primates; (1) ancestral codivergence of primate lentiviruses into haplorrhine and strepsirrhine lineages in broad concert with their hosts; (2) transfer of lentiviruses between Malagasy strepsirrhines and African haplorrhines subsequent to their divergence, mediated either by a nonprimate vector or via temporary contact between Malagasy and African primate populations during intermittent periods of land-bridge or dry way-point access between the two regions (23); (3) transfer mediated by an aerial vector species.