Genetic diversity and cross-species transmissibility of bat-associated picornaviruses from Spain

Abstract

Background: Emerging zoonotic diseases arise from cross-species transmission events between wild or domesticated animals and humans, with bats being one of the major reservoirs of zoonotic viruses. Viral metagenomics has led to the discovery of many viruses, but efforts have mainly been focused on some areas of the world and on certain viral families.

Methods: We set out to describe full-length genomes of new picorna-like viruses by collecting feces from hundreds of bats captured in different regions of Spain. Viral sequences were obtained by high-throughput Illumina sequencing and analyzed phylogenetically to classify them in the context of known viruses. Linear discriminant analysis (LDA) was performed to infer likely hosts based on genome composition.

Results: We found five complete or nearly complete genomes belonging to the family Picornaviridae, including a new species of the subfamily Ensavirinae. LDA suggested that these were true vertebrate viruses, rather than viruses from the bat diet. Some of these viruses were related to picornaviruses previously found in other bat species from distant geographical regions. We also found a calhevirus genome that most likely belongs to a proposed new family within the order Picornavirales, and for which genome composition analysis suggested a plant host.

Conclusions: Our findings describe new picorna-like viral species and variants circulating in the Iberian Peninsula, illustrate the wide geographical distribution and interspecies transmissibility of picornaviruses, and suggest new hosts for calheviruses.

Keywords: Bat viruses; Calheviruses; Host inference; Interspecies transmission; Phylogenetics; Picornaviruses; Viral diversity; Viral metagenomics; Virus evolution.

Fig. 1

Bat captures for virome analysis. Names of the localities where sampling was carried out and the number of fecal samples collected are indicated

Fig. 2

Genome organization of viruses identified in this study belonging to Picornaviridae family. Open reading frames for each mature protein (L, VP1-4, 2A-C, 3A-D) are shown as colored regions and mapped to P1, P2, or P3 polyproteins accordingly

Fig. 3

Phylogenetic trees of the Picornaviridae family for the P1 and 3D^pol regions. The newly described viruses are placed in the context of ICTV-approved viruses. Ampivirus A1 (accession KP770140) was selected as an outgroup for both trees. Phylogenetic inference was performed with the Bayesian MCMC algorithm using a GTR + I + G4 substitution model, and 12 and 8 million generations for P1 and 3D^pol phylogenies, respectively. Posterior probabilities for each node are indicated (values of 1 are omitted)

Fig. 4

Phylogenetic analysis of the RdRp region for Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Noraviridae, Picornaviridae, and Secoviridae families, previously known calheviruses, and Castelló calhevirus. Phylogenetic inference was performed with the Bayesian MCMC algorithm using 10 million generations and a Rtrev + G4 substitution model. Posterior probabilities for each node are indicated (values of 1 are omitted)

Fig. 5

Linear discriminant analysis for the prediction of picornaviruses hosts. A. Confusion matrix obtained with the training dataset of 1065 viral genomes. B. Posterior probabilities for the classification of novel picorna-like genomes into each class (values below 0.01 are omitted). C. Biplots of linear discriminant analysis. Novel picorna-like sequences described in this study are shown with black dots