Detection and genetic characterization of enteroviruses circulating among wild populations of chimpanzees in Cameroon: relationship with human and simian enteroviruses

Abstract

Enteroviruses (EVs), members of the family Picornaviridae, are a genetically and antigenically diverse range of viruses causing acute infections in humans and several Old World monkey (OWM) species. Despite their known wide distribution in primates, nothing is currently known about the occurrence, frequency, and genetic diversity of enteroviruses infecting apes. To investigate this, 27 chimpanzee and 27 gorilla fecal samples collected from undisturbed jungle areas with minimal human contact in Cameroon were screened for EVs. Four chimpanzee samples were positive, but none of the gorilla samples were positive. Genetic characterization of the VP1, VP4, and partial VP2 genes, the 5' untranslated region, and partial 3Dpol sequences enabled chimpanzee-derived EVs to be identified as (i) the species A type, EV76, (ii) a new species D type assigned as EV111, along with a human isolate from the Democratic Republic of Congo previously described by the International Committee on the Taxonomy of Viruses, and (iii) a new species B type (assigned as EV110) most closely related to, although a distinct type from, the SA5 isolate recovered from a vervet monkey. The identification of EVs infecting chimpanzees related to those circulating in human and OWM populations provides evidence for cross-species transmission of EVs between primates. However, the direction of transfer and the existence of primate sources of zoonotic enterovirus infections in humans require further investigation of population exposure and more extensive characterization of EVs circulating in wild ape populations.

Fig. 1.

Chimpanzee and gorilla sample locations showing the combined number from each collection site (sites with 18 samples had 9 chimpanzee and 9 gorilla samples; sites with 4 samples had 2 chimpanzee and 2 gorilla samples). The positive chimpanzee samples are indicated.

Fig. 2.

Phylogenetic comparisons of 5′UTR (positions 177 to 672, excluding the unalignable hypervariable region) (A), VP4 and partial VP2 (positions 744 to 1147) (B), and VP1 (positions 2457 to 3377) (C) from study samples and a representative sequence from each currently classified human enterovirus (sero)type and the currently available 11 (near)-complete genome sequences of enteroviruses isolated from nonhuman primates. Trees were constructed by neighbor joining using J-C corrected nucleotide pairwise distances (5′UTR) or translated amino acid pairwise distances (VP4/VP2, VP1 regions), with 100-bootstrap resampling to demonstrate robustness of groupings; values of ≥70% are shown.

Fig. 3.

(A) Phylogenetic analysis of the VP1 region LM1677 and all available (>90% complete in VP1 gene) sequences of EV76 and a representative EV91 sequence as an outgroup. (B) KK2640 and all available species D sequences. Trees were constructed by neighbor joining using maximum composite likelihood nucleotide pairwise distances with 100-bootstrap resampling to demonstrate robustness of groupings; values of ≥70% are shown.

Fig. 4.

Phylogenetic analysis of partial 3Dpol gene sequences of chimpanzee-derived enteroviruses and related viruses from species A, B, and D and those from OWMs. (A) LM1861, SA5, and species B types between positions 5873 and 6419. (B) LM1677, OWM-derived viruses and species A types between positions 6957 and 7175. (C) KK2640 and species D between positions 6252 and 7157. Trees were constructed by neighbor joining using J-C corrected nucleotide pairwise distances with 100-bootstrap resampling to demonstrate robustness of groupings; values of ≥70% are shown.