Novel Primate Bocaparvovirus Species 3 Identified in Wild Macaca Mulatta in China

Abstract

Primate bocaparvovirus (BOV) is a possible cause of respiratory disorders and gastroenteritis in humans. However, the diversity and evolution of these viruses remain largely unknown, despite the identification of a growing number of BOVs in non-human primates (NHPs). Here, we report the identification of a novel BOV (provisionally named Macaca mulatta bocaparvovirus [MmBOV]) in the feces of wild Macaca mulatta in China by viral metagenomic analysis. Seven of 400 fecal samples from Macaca mulatta were positive for MmBOV. An almost complete genome sequence of 4,831 nucleotides was obtained, which had genomic organization and protein motifs similar to human bocaviruses (HOBVs), and shared characteristically low G/C content and weak codon usage bias. Sequence analyses of NS1, NP1, and VP1 revealed that MmBOV was most closely related to HBOV4 of Primate bocaparvovirus 2 (approximately 68.4%/70.6%, 73.3%/67.6%, and 70.4%/73.1% nucleotide/amino acid identities, respectively). Additionally, phylogenetic analysis revealed that MmBOV formed an independent peripheral branch, but clustered closely with those of the Primate bocaparvovirus species in the BOV genus (particularly HBOV4). These data strongly suggest that HBOV4 originated from NHP bocaparvoviruses around 200-300 years ago, and that NHPs may act as HBOV reservoirs. Following the International Committee of Taxonomy for Viruses guidelines, we propose MmBOV as a new species (tentatively named Primate bocaparvovirus 3) in the genus Bocaparvovirus, which is the first report of a novel species of primate BOV. Our data facilitate future research on the genetic diversity and evolution of primate bocaparvoviruses and highlight the importance of bocaparvovirus surveys in wild NHPs.

Keywords: Macaca mulatta; Novel species; Phylogenetic analysis; Primate bocaparvovirus (BOV); Sequence analysis.

Fig. 1

Genomic organization of MmBOV. (A) Genomic organization of MmBOV and known primate bocaparvoviruses. (B) Partial NS1 nucleotide sequence alignment of MmBOV and known primate bocaparvoviruses. (C) Genomic features of MmBOV and other primate bocaparvoviruses. (D) Amino acid sequence alignment of partial VP1 proteins of MmBOV and other primate bocaparvoviruses. The phospholipase A2 motif, consisting of the calcium binding region and catalytic residues, are shown. HBOV human bocaparvovirus, GBOV gorilla bocaparvovirus, CPZh2 central chimpanzee bocaparvovirus.

Fig. 2

Comparative sequence analysis of MmBOV. A Almost complete genomic sequence identity of MmBOV and other known primate bocaparvoviruses, determined by Simplot analysis. B Variable region-based sequence alignment of MmBOV and other primate bocaparvoviruses. VR-III, VR-VI-VIII, and VR-IX are indicated in pink color. The identical residues among the human bocaparvoviruses are highlighted by gray color.

Fig. 3

Phylogenetic tree of MmBOV and other bocaparvoviruses based on almost complete nucleotide sequences. The tree of complete nucleotide sequences was reconstructed using the maximum-likelihood method with 1000 bootstrap replicates. The viruses from species Primate bocaparvovirus 1, 2, 3 are shown by green, blue and pink, respectively. The position of MmBOV is marked by ■.

Fig. 4

Phylogenetic tree of MmBOV in bocaparvoviruses based on three complete coding sequences. The MmBOV trees were constructed based on the complete nucleotide sequences of NS1 (A), NP1 (B), and VP1 (C), aligned with those of other primate bocaparvoviruses using the maximum-likelihood method with datasets of 1000 replicates using MEGA 6.0 software. The viruses from species Primate bocaparvovirus 1, 2, 3 are shown by green, blue and pink, respectively. The position of MmBOV is marked by ■.