Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam

Abstract

Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus (husavirus) are viruses in the order Picornavirales recently described in porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs) also includes fish stool-associated RNA virus (fisavirus) as well as members detected in insects (Drosophila subobscura and Anopheles sinensis) and parasites (Ascaris suum). As part of an agnostic deep sequencing survey of animal and human viruses in Vietnam, we detected three husaviruses in human fecal samples, two of which share 97-98% amino acid identity to Dutch husavirus strains and one highly divergent husavirus with only 25% amino acid identity to known husaviruses. In addition, the current study found forty-seven complete posavirus genomes from pigs, ten novel rat stool-associated RNA virus genomes (tentatively named rasavirus), and sixteen novel bat stool-associated RNA virus genomes (tentatively named basavirus). The five expected Picornavirales protein domains (helicase, 3C-protease, RNA-dependent RNA polymerase, and two Picornavirus capsid domain) were found to be encoded by all PPLV genomes. In addition, a nucleotide composition analysis revealed that the PPLVs shared compositional properties with arthropod viruses and predicted non-mammalian hosts for all PPLV lineages. The study adds seventy-six genomes to the twenty-nine PPLV genomes currently available and greatly extends our sequence knowledge of this group of viruses within the Picornavirales order.

Keywords: Picornavirales; basavirus; husavirus; next generation sequencing; posavirus; rasavirus; virus discovery.

Figure 1.

Maximum-likelihood phylogenetic tree of the predicted RdRP protein domain. The maximum-likelihood phylogenetic tree was constructed in IQtree under the LG + G+I amino acid substitution model as the best-fitted model with 500 pseudo-replicates. The tree was visualized in FigTree1.4.2. Branches were colored according to the enteric samples from the hosts in which viruses were identified (blue: human, red: pig feces, dark green: rat feces, light green: fish intestinal content, brown: bat feces, and purple: insects and parasites). Significant bootstrap values (>80) are indicated with an *.

Figure 2.

Average percentage of amino acid identity across PPLVs lineages. The amino acid sequences of the complete polyprotein of different lineages were individually aligned against each other using the ClustalW in Geneious. The numbers on the x- and y-axes represent the different lineages (for more detail see Supplementary Table S1).

Figure 3.

Genomic organization of different identified PPLVs lineages. The putative conserved protein domains, as determined by a conserved domain search (see ‘Methods’), and their relative position in the viral genome are illustrated. The number next to the lineage name indicates the length of each genome, the Asv1 genome (marked with an *) was only partially (<5,000 nt) sequenced. Peach blocks indicate the presence and position of an RNA helicase domain (superfamily cl21455), red blocks indicate the 3C cysteine protease domain (superfamily cl02893), light blue blocks indicate an RNA-dependent RNA polymerase (RdRP) domain (superfamily cl02808) and dark blue blocks indicate picornavirus capsid domain (superfamily cl13999). All identified conserved domains are drawn in scale related to their genome size.

Figure 4.

Discriminant analysis of the dinucleotide bias in PPLVs compared to members of the Picornaviridae for which the infectious host is known. Viruses infecting arthropods are indicated with blue circles, viruses infecting plants in green circles and viruses infecting vertebrates in red circles. The lines indicate the 95% interval. Posaviruses are plotted in white diagonals, husavirus in light yellow, basavirus in yellow, rasavirus in dark yellow, fisavirus in orange and insect/nematode infecting viruses in dark orange.