We report the nucleotide sequence and the predicted polyprotein of a novel swine picornavirus identified in stool samples from healthy piglets by an HTS method. A recent study has shown that RNA viruses, and more precisely Picornaviridae
, represent the majority of the fecal virome in piglets (51
). The genome of this novel virus, called SPaV1, presents the typical genome organization of a member of the family Picornaviridae
, mixing characteristics of the two Parechovirus
subclades: the HPeV and LV species. Interpreted in light of the phylogeny of each protein, these characteristics may reflect the common origin of parechoviruses and SPaV1. Considering the P1, P2, and the P3 proteins, SPaV1 shares less than 40% identity with LV, the closest taxon described to date. The ICTV recommends less than 40% amino acid identity in the P1 and P2 proteins and less than 50% in the P3 protein for genus demarcation in Picornaviridae
). This new taxon fulfills these criteria and can therefore be considered a new genus in Picornaviridae
The recent discovery of a high-ranking taxonomic level represented by SPaV1 shows that our picture of the diversity of this family is still partial. Major viral genera of the Picornaviridae
are represented in several avian or mammalian species, and this host diversity may contribute to viral diversity, in addition to other factors, such as a typical error-prone RNA replication system (9
). Overall, the diversity of both the virus family (12 genera) and hosts (fish, reptiles, mammals, and birds) depicts the dynamism of the evolution of the Picornaviridae
. For the most studied groups, such as Enterovirus
, recombinations were shown to play a master role in shaping the genome, and this was not restricted to the intraspecies level (50
). Moreover, the structural and nonstructural parts of the genomes of enteroviruses were shown to evolve independently, with P1 so far being less subjected to recombination (38
). Although recombination between taxa and even genera might have occurred throughout the genome during the evolution of SPaV1, it seems unlikely that traces of such ancient events would remain detectable. SPaV1 and therefore the more highly ranked genus Pasivirus originated from one of the earliest differentiated and major clades of the Picornaviridae
(, , And ; see Fig. S2 to S4 in the supplemental material). Given the host diversity pattern observed for several of the most studied clades, in which several viral genera sometimes clustered, it is probable that other pasiviruses may infect birds, rodents, primates, or other animals (, , And ; see Fig. S2 to S4 in the supplemental material).
The clear phylogenetic relationship between SPaV1 and the parechoviruses is consistent with numerous similarities of these taxa. Despite representing a potential new genus of Picornaviridae
, SPaV1 exhibits features that have been considered to be characteristic of Parechovirus
and more specifically of LV. The low G+C percent is consistent with those of parechoviruses and related clades and contrasts with those of other Picornaviridae
. SPaV1 contains only three capsid proteins (VP0, VP3, and VP1) exhibiting remarkable features resembling those of parechoviruses and seems to be lacking a leader protein. VP3 contains the conserved KXKXXRXK motif, considered a characteristic signature of parechoviruses (). This motif belongs to a basic amino acid-rich region described as immunogenic in HPeVs (26
). Moreover, VP3 of SPaV1 shares more than 40% identity with that of LV (), and the characteristics of other capsid proteins reinforce the closeness of SPaV1 and LV. Among the resemblances, the N-terminal extremity of VP0 is shorter than those of HPeVs and lacks the myristoylation site (). Therefore, this site, described as mandatory for efficient viral infectivity of poliovirus (31
), is not required for LV and SPaV1. Another capsid protein, VP1, exhibits two insertions of unknown function at the N-terminal extremity, one (11 aa) previously described in LV (25
) and a second motif of 4 aa identified by multialignment of SPaV1, LVs, and HPeVs (). The C-terminal extremity of VP1 contains a unique 41-aa extension (43 aa for VP1 of LV) and no RGD motif but a long C-terminal extremity (). To date, RGD is the unique motif associated with viral entry mediated by integrin within parechoviruses. Among parechoviruses lacking an RGD motif, the well-studied HPeV3 has been associated with neuropathology (19
). Nevertheless, no strict association between the presence/absence of RGD and the neurovirulence of parechoviruses has been demonstrated. The absence of the RGD motif implies the existence of an alternative cell receptor. In contrast with HPeVs, LV shares with SPaV1 a cleaved 2A protein, resulting in the 2A1 and the 2A2 proteins. The 2A1 protein of SPaV1 exhibits strong homology with that of LV. Due to the absence of the GXCG region, 2A lacks proteolytic activity, and SPaV1 therefore possesses a single 3C protease, as described for LV. One of the main differences between the 2A2 proteins of SPaV1 and parechoviruses is the absence of both the H-box/NC motifs and the putative transmembrane domain.
No pathogenicity was noted in infected piglets, which is reminiscent of the high frequency of asymptomatic infections for related parechoviruses infecting humans or animals. Nevertheless, HPeVs are pathogens frequently associated with various enteric, nervous, or respiratory syndromes in young children (49
). Another parechovirus, LV, was identified in bank voles (Myodes glareolus
) in Europe and the United states (20
). Interestingly, LV has been proposed as a potential environmental trigger for human type 1 diabetes on the basis of the presence of LV antibodies, while LV RNA detection remained negative, suggesting that the etiologic agent of the disease could be a cross-reactive virus (41
). The spillover likelihood of such a virus could be greater from domestic animals than from wild animals, as seen for hepatitis E virus genotype 3, which is very prevalent but clinically silent in pigs and which frequently infects humans (43
). Therefore, SPaV1 or another pasivirus could be a more relevant trigger than LV.
Major neutralizing antigenic sites have been located within exposed BC and EF loops of the capsid proteins and are therefore suspected to shape the immunogenic specificity of picornaviruses (46
). These BC and EF loops of SPaV1 ( to ) exhibit notable differences from LV and other parechoviruses, suggesting that cross-reactions are unlikely. Therefore, without experimental data, it is difficult to state that cross-reaction between LV and SPaV1 or another yet unknown member(s) of this new genus is impossible.
SPaV1 was identified in apparently healthy piglets, suggesting that the virus presents a silent circulation at the investigated farm. Furthermore, the detection on the same farm of several strains (0.7% to 9.3% divergent from SPaV1) suggested that swine are the natural hosts of this novel and predicted diversified genus of Picornaviridae. At the individual level, sequencing revealed several polymorphisms within 3D, indicating consistent variability. A better picture of SPaV1 biology would be achieved through the study of the prevalence, tropism, geographic distribution, and genetic variation of this new virus. If the zoonotic potential of SPaV1 is attested, and despite the absence of any pathogenicity in piglets, the threat to human health should be evaluated, considering its circulation in the vicinity of human populations.