Virome Analysis of Small Mammals from the Brazilian Amazon

Abstract

The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from eleven bats, seven opossums, and eight rodents from the two locations were screened by high-throughput sequencing for virome analysis. Viral reads were assigned into twenty viral families, from which the most abundant was Retroviridae. Host order, tissue type, and season showed a significant effect on viral composition. Five viral genomes of bat ERVs with intact genes were recovered, showing the need to understand their endogenous nature. In addition, a new Buritiense virus (Hantaviridae) strain was also obtained, supporting its circulation in Santa Bárbara do Pará and expanding its genomic information. Together, these findings reinforce the need for continuous surveillance in wild animals, especially in the Amazon region, to anticipate potential threats to public health.

Keywords: Chiroptera; Didelphimorphia; Rodentia; deforestation; metagenomics.

Figure 1

Sample collection location.

Figure 2

Viral Diversity analysis in small mammals from Peixe-Boi and Santa Bárbara do Pará. Heatmap representing the relative abundance (log-transformed scale) of viral families detected in different samples, grouped hierarchically by similarity of viral composition. The columns represent the samples, with the tissue type represented by letters V, L, and B and the location by colors blue or red, and the rows correspond to the viral families (A), boxplot comparing the Shannon diversity index between the two collection sites (B), boxplot of the Shannon diversity index comparing three host orders with adjusted p-values indicated for pairwise comparisons (C), Venn diagrams showing the number of shared and exclusive viral families between the two collection sites (D), and between the host orders (E).

Figure 3

Beta diversity analysis of viral families considering location and host order (A), beta diversity analysis of viral families considering tissue and host order (B), and beta diversity analysis of viral families considering season and location (C).

Figure 4

Functional domains in the obtained bat ERV sequences. Each domain is represented and named by color.

Figure 5

Maximum likelihood phylogenetic tree based on the nucleotide alignment of the gag (A), pol (B), and env (C) genes of retroviruses. The best nucleotide substitution models were the TVM + F + I + G4 for the gag and pol genes and the TVM + F + G4 for the env gene. Branches with lilac tips represent betaretroviruses and green tips represent gammaretroviruses. The obtained bat ERV sequences are highlighted in red.

Figure 6

Functional domains in the S (A), M (B), and L (C) segments of the Buritiense virus. Each domain is represented and named by color.

Figure 7

Maximum likelihood phylogenetic tree based on the amino acid alignment of the S (A), M (B), and L (C) segments of hantaviruses. The best amino acid substitution models were the Q.insect + I + G4 for the S and M segments and the Q.insect + I + R5 for the L segment. Branches with blue tips represent orthohantaviruses, orange tips represent thottimviruses, and green tips represent mobatviruses. The obtained BURV sequences are highlighted in red.