Abstract
The highly diverse virus family Picornaviridae presently comprises 68 approved genera with 158 species plus many unassigned viruses. In order to better match picornavirus taxonomy to the functional and genomic groupings between genera, the establishment of five subfamilies (Caphthovirinae, Kodimesavirinae, Ensavirinae, Paavivirinae and Heptrevirinae) is proposed. The subfamilies are defined by phylogenetic analyses of 3CD (precursor of virus-encoded proteinase and polymerase) and P1 (capsid protein precursor) coding sequences and comprise between 7 and 22 currently approved virus genera. Due to the high within-subfamily and between-subfamily divergences of the picornavirus genera, p-distance estimates are unsuited for the demarcation of subfamilies. Members of the proposed subfamilies typically show some commonalities in their genome organisations, including VP1/2A cleavage mechanisms and possession of leader proteins. Other features, such as internal ribosomal entry site types, are more variable within and between members of genera. Some subfamilies are characterised by homology of proteins 1A, 2A, 2B and 3A encoded by members, which do not belong to the canon of orthologous picornavirus proteins. The proposed addition of a subfamily layer to the taxonomy of picornaviruses provides a valuable additional organisational level to the family that acknowledges the existence of higher-level evolutionary groupings of its component genera.
Highlights
Viruses of the family Picornaviridae have small (~30 nm), non-enveloped capsids with T=1/pseudo T=3 symmetry [11]
With the exception of dicipiviruses, all picornavirus genomes possess a single open reading frame (ORF) that is flanked on both sides by untranslated regions (UTRs) with signal structures for the initiation of translation and replication
ORF1 encodes the CP precursor, whereas ORF2 yields the non-structural proteins. Translation of both polyproteins is facilitated by two separate internal ribosome entry site (IRES)
Summary
Viruses of the family Picornaviridae have small (~30 nm), non-enveloped capsids with T=1/pseudo T=3 symmetry [11]. Their RNA genomes have positive-strand polarity and Handling Editor: Sead Sabanadzovic. The nonstructural proteins function in virus replication and include 2 Chel, a helicase with a typical fold of P-loop ATPases, 3BVPg, a small genome-linked oligopeptide, 3 Cpro, a chymotrypsin-like cysteine proteinase, and 3Dpol, an RNAdependent RNA polymerase (RdRP) ORF1 encodes the CP precursor, whereas ORF2 yields the non-structural proteins. Translation of both polyproteins is facilitated by two separate IRESs. The CP domains and the Hel-Pro-Pol domains of the polyprotein are known as the ’CP module’ and the ’Hel-Pro-Pol core replicative module’ or as the ’Hel-Pro-Pol
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