Identification and molecular characterization of new simian T cell lymphotropic viruses in nonhuman primates bushmeat from the Democratic Republic of Congo

Abstract

Four types of human T cell lymphotropic viruses (HTLV) have been described (HTLV-1 to HTLV-4) with three of them having closely related simian virus analogues named STLV-1, -2, and -3. To assess the risk of cross-species transmissions of STLVs from nonhuman primates to humans in the Democratic Republic of Congo, a total of 330 samples, derived from primate bushmeat, were collected at remote forest sites where people rely on bushmeat for subsistence. STLV prevalences and genetic diversity were estimated by PCR and sequence analysis of tax-rex and LTR fragments. Overall, 7.9% of nonhuman primate bushmeat is infected with STLVs. We documented new STLV-1 and STLV-3 variants in six out of the seven species tested and showed for the first time STLV infection in C. mona wolfi, C. ascanius whitesidei, L. aterrimus aterrimus, C. angolensis, and P. tholloni. Our results provide increasing evidence that the diversity and geographic distribution of PTLVs are much greater than previously thought.

FIG. 1.

Nonhuman primate sampling sites in the Democratic Republic of Congo.

FIG. 2.

Primate T cell lymphotropic virus (PTLV) phylogeny inferred using 195-bp tax-rex sequences. Numbers correspond to internal branch support derived from 100 bootstrap replicates (only values above 80 are shown). Scale bar represents the number of nucleotide substitutions per site. Groves' primate taxonomy nomenclature is used. Nonhuman primates are coded using the first letter of the genus followed by the first two letters of the species name: Cwo, Cercopithecus wolfi; Cas, Cercopithecus ascanius; Cne, Cercopithecus neglectus; Can, Colobus angolensis; Pth, Piliocolobus tholloni; and Lat, Lophocebus aterrimus. New sequences from this study are highlighted in italic and bold.

FIG. 3.

Inference of PTLV-1 phylogeny using 418 bp (3′ end LTR) (a), 401bp (5′ end LTR) (b), and 750 bp (c) LTR sequences. Numbers correspond to internal branch support derived from 100 bootstrap replicates (only values above 75 are shown). Scale bar represents the number of nucleotide substitution per site. Groves' primate taxonomy nomenclature is used (Groves, 2001). Nonhuman primates are coded using the first letter of the genus followed by the first two letters of the species name: Cwo, Cercopithecus wolfi; Cas, Cercopithecus ascanius; Cne, Cercopithecus neglectus; Can, Colobus angolensis; Pth, Piliocolobus tholloni; and Lat, Lophocebus aterrimus. Sequences from this study are highlighted in italic and bold.

FIG. 3.

Inference of PTLV-1 phylogeny using 418 bp (3′ end LTR) (a), 401bp (5′ end LTR) (b), and 750 bp (c) LTR sequences. Numbers correspond to internal branch support derived from 100 bootstrap replicates (only values above 75 are shown). Scale bar represents the number of nucleotide substitution per site. Groves' primate taxonomy nomenclature is used (Groves, 2001). Nonhuman primates are coded using the first letter of the genus followed by the first two letters of the species name: Cwo, Cercopithecus wolfi; Cas, Cercopithecus ascanius; Cne, Cercopithecus neglectus; Can, Colobus angolensis; Pth, Piliocolobus tholloni; and Lat, Lophocebus aterrimus. Sequences from this study are highlighted in italic and bold.

FIG. 3.

Inference of PTLV-1 phylogeny using 418 bp (3′ end LTR) (a), 401bp (5′ end LTR) (b), and 750 bp (c) LTR sequences. Numbers correspond to internal branch support derived from 100 bootstrap replicates (only values above 75 are shown). Scale bar represents the number of nucleotide substitution per site. Groves' primate taxonomy nomenclature is used (Groves, 2001). Nonhuman primates are coded using the first letter of the genus followed by the first two letters of the species name: Cwo, Cercopithecus wolfi; Cas, Cercopithecus ascanius; Cne, Cercopithecus neglectus; Can, Colobus angolensis; Pth, Piliocolobus tholloni; and Lat, Lophocebus aterrimus. Sequences from this study are highlighted in italic and bold.

FIG. 4.

Inference of PTLV-3 phylogeny using 589 bp tax-pX-LTR sequences. Numbers correspond to internal branch support derived from 100 bootstrap replications (only values above 85 are shown). Scale bar represents the number of nucleotide substitutions per site. Primate taxonomy nomenclature is according to Groves (Groves, 2001). Nonhuman primates are coded using the first letter of the genus followed by the first two letters of the species name: Lal, Lophocebus albigena; Cag, Cercocebus agilis; Cce, Cercopithecus cephus. Sequences in italic and bold text are from the current study.