Novel Rodent Arterivirus Detected in the Brazilian Amazon

Abstract

As part of a continuous effort to investigate the viral communities associated with wild mammals at the human-animal interface in an Amazonian metropolitan region, this study describes the detection of a novel rodent-borne arterivirus. A sample containing pooled organs of Oecomys paricola was submitted to RNA sequencing, and four sequences taxonomically assigned as related to the Arteriviridae family were recovered, corresponding to an almost complete genome of nearly 13 kb summed. In the phylogenetic analysis with the standard domains used for taxa demarcation in the family, the tentatively named Oecomys arterivirus 1 (OAV-1) was placed within the clade of rodent- and porcine-associated viruses, corresponding to the Variarterivirinae subfamily. The divergence analysis, based on the same amino acid alignment, corroborated the hypothesis that the virus may represent a new genus within the subfamily. These findings contribute to the expansion of the current knowledge about the diversity, host and geographical range of the viral family. Arterivirids are non-human pathogens and are usually species-specific, but the susceptibility of cell lines derived from different organisms should be conducted to confirm these statements for this proposed new genus in an initial attempt to assess its spillover potential.

Keywords: Arteriviridae; RNA viruses; RNA-seq; Sigmodontinae; arterivirus.

Figure A1

P-distance (inferior left) and PPD (superior right) calculated based on the five concatenated domains alignment used for the phylogenetic inference. Cells with values under the estimated threshold are highlighted for subfamilies (red/blue) and genera (yellow/gray). Outlier values are written in bold font. Genera and some subfamilies are identified by their prefixes.

Figure 1

Map of the collection area in the Expedito Ribeiro village in Santa Bárbara do Pará municipality (Pará state, Brazil) and its location in the Brazilian territory. Traps were placed in the open field surrounding the human habitations (A1–A3), the forest fragment border (B1–B3) and its most interior region (C1–C3). The IBGE (2017) [12] and Copernicus Sentinel (2017) [13] databases were consulted to prepare the maps.

Figure 2

Oecomys arterivirus 1 (OAV-1) partial genome. The sequences above are represented as contiguous for illustrative purposes, highlighting the genome organization. The non-sequenced regions are identified as blank gaps. Contigs are numbered from 1 to 4. In the zoomed sequence, domains in gray were concatenated for the phylogenetic inference. 3CLpro, 3C-like protease; NiRAN, nidovirus RdRp-associated nucleotidyltransferase; RdRp, RNA-dependent RNA polymerase; ZBD, Zn-binding domain; Helicase 1, super-family 1 helicase; E, envelope protein; GP2-GP5a, envelope glycoproteins; N: nucleocapsid protein.

Figure 3

Phylogenetic inference of the currently recognized species of Arteriviridae family based on the concatenated sequences of the 3CLpro, NiRAN, RdRP, ZBD and HEL1 domains. Genera are distinguished by color and can be identified in the species name. The sequence of this study is highlighted in red.

Figure 4

Boxplot graph showing the amino acid distance range between the Variarterivirinae and Simarterivirinae subfamilies and arterivirids outside their taxa, or intergroup distances (1), distances between them and OAV-1 (2), and distances within each subfamily, or intragroup distances (3), based on the same alignment used to generate the phylogenetic inference.