Molecular epidemiology of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm

Abstract

Retrospective molecular epidemiology was performed on samples from four sooty mangabey (SM) colonies in the United States to characterize simian immunodeficiency virus SIVsm diversity in SMs and to trace virus circulation among different primate centers (PCs) over the past 30 years. The following SIVsm sequences were collected from different monkeys: 55 SIVsm isolates from the Tulane PC sampled between 1984 and 2004, 10 SIVsm isolates from the Yerkes PC sampled in 2002, 7 SIVsm isolates from the New Iberia PC sampled between 1979 and 1986, and 8 SIVsm isolates from the California PC sampled between 1975 and 1977. PCR and sequencing were done to characterize the gag, pol, and env gp36 genes. Phylogenetic analyses were correlated with the epidemiological data. Our analysis identified nine different divergent phylogenetic lineages that cocirculated in these four SM colonies in the Unites States in the past 30 years. Lineages 1 to 5 have been identified previously. Two of the newly identified SIVsm lineages found in SMs are ancestral to SIVmac251/SIVmac239/SIVmne and SIVstm. We further identified the origin of these two macaque viruses in SMs from the California National Primate Research Center. The diversity of SIVsm isolates in PCs in the United States mirrors that of human immunodeficiency virus type 1 (HIV-1) group M subtypes and offers a model for the molecular epidemiology of HIV and a new approach to vaccine testing. The cocirculation of divergent SIVsm strains in PCs resulted in founder effects, superinfections, and recombinations. This large array of SIVsm strains showing the same magnitude of diversity as HIV-1 group M subtypes should be extremely useful for modeling the efficacy of vaccination strategies under the real-world conditions of HIV-1 diversity. The genetic variability of SIVsm strains among PCs may influence the diagnosis and monitoring of SIVsm infection and, consequently, may bias the results of pathogenesis studies.

FIG. 1.

SIVsm diversity in SM colonies from four primate centers in the United States. Lineages are clusters of SIVs that are highly related and branch together. Newly characterized strains are color coded (blue, TNPRC; red, YNPRC; green, NIRC; pink, CNPRC). Lineage 1 contains the previously reported strains SIVsmB670, SIVsmPBj, SIVsm236/660/543-3, and SIVsmPGM (http://hiv-web.lanl.gov). Reference SIVsm strains and strains from wild-caught SMs are shown in black, whereas HIV-2 strains are shown in light gray. Lineages 8 and 9 include strains isolated from different species of macaques that were experimentally or accidentally infected. The trees are based on gag (500 bp) (a), pol (592 bp) (b), and env (405 bp) (c) fragments after gap-containing sites were removed. The phylogenetic trees were estimated by the neighbor-joining method using amino acid sequences. The reliability was estimated from 1,000 bootstrap replicates; only bootstrap values relevant for lineage definition are shown. Bars, number of amino acid replacements (0.01) per site. The strain nomenclature includes the assigned lineage, the primate center of origin, the year of strain collection, and the monkey identification number.

FIG. 1.

SIVsm diversity in SM colonies from four primate centers in the United States. Lineages are clusters of SIVs that are highly related and branch together. Newly characterized strains are color coded (blue, TNPRC; red, YNPRC; green, NIRC; pink, CNPRC). Lineage 1 contains the previously reported strains SIVsmB670, SIVsmPBj, SIVsm236/660/543-3, and SIVsmPGM (http://hiv-web.lanl.gov). Reference SIVsm strains and strains from wild-caught SMs are shown in black, whereas HIV-2 strains are shown in light gray. Lineages 8 and 9 include strains isolated from different species of macaques that were experimentally or accidentally infected. The trees are based on gag (500 bp) (a), pol (592 bp) (b), and env (405 bp) (c) fragments after gap-containing sites were removed. The phylogenetic trees were estimated by the neighbor-joining method using amino acid sequences. The reliability was estimated from 1,000 bootstrap replicates; only bootstrap values relevant for lineage definition are shown. Bars, number of amino acid replacements (0.01) per site. The strain nomenclature includes the assigned lineage, the primate center of origin, the year of strain collection, and the monkey identification number.

FIG. 1.

SIVsm diversity in SM colonies from four primate centers in the United States. Lineages are clusters of SIVs that are highly related and branch together. Newly characterized strains are color coded (blue, TNPRC; red, YNPRC; green, NIRC; pink, CNPRC). Lineage 1 contains the previously reported strains SIVsmB670, SIVsmPBj, SIVsm236/660/543-3, and SIVsmPGM (http://hiv-web.lanl.gov). Reference SIVsm strains and strains from wild-caught SMs are shown in black, whereas HIV-2 strains are shown in light gray. Lineages 8 and 9 include strains isolated from different species of macaques that were experimentally or accidentally infected. The trees are based on gag (500 bp) (a), pol (592 bp) (b), and env (405 bp) (c) fragments after gap-containing sites were removed. The phylogenetic trees were estimated by the neighbor-joining method using amino acid sequences. The reliability was estimated from 1,000 bootstrap replicates; only bootstrap values relevant for lineage definition are shown. Bars, number of amino acid replacements (0.01) per site. The strain nomenclature includes the assigned lineage, the primate center of origin, the year of strain collection, and the monkey identification number.

FIG. 2.

Molecular epidemiology of SIVsm lineages in different primate centers in the United States. The lineage prevalence in each SM colony was estimated based on the present results. Not all of the animals at YNPRC and CNPRC were tested. Therefore, additional SIVsm lineages may be present and the relative prevalence of SIVsm lineages may be different from that established based on limited sampling. Due to the close relationship in gag between lineage 4 strains and SIVmac (lineage 8), it is possible that lineage 4 or its ancestors circulated at CNPRC. However, based on the current data, there is no proof of its presence at CNPRC. Therefore, the alternative hypothesis that lineage 4 was imported directly from Africa to the NIRC cannot be ruled out. Transfers of SIV-infected animals from CNPRC to other primate centers are shown.

FIG. 3.

Phylogenetic tree of the LTR-gag fragment (450 bp after gap-containing sites were removed). This tree was constructed to include the CNPRC strains. SIVsm strains representative for each lineage were included. See the legend to Fig. 1 for details concerning color codes and the details of tree construction.

FIG. 4.

Phylogenetic evidence of intragenic recombination in gag. Neighbor-joining phylogenetic trees of the 5′ (bp 1 to 500) and 3′ (bp 501 to 727) gag fragments show distinct clustering patterns for 21 “lineage 1” strains. These strains (red) cluster with lineage 1 strains in the 5′ tree and with lineage 2 strains in the 3′ tree. The clustering patterns suggest that together these 21 strains share the same recombinant ancestry and therefore define a recombinant form.