Proposed revision to the taxonomy of the genus Pestivirus, family Flaviviridae

Abstract

We propose the creation of seven new species in the genus Pestivirus (family Flaviviridae) in addition to the four existing species, and naming species in a host-independent manner using the format Pestivirus X. Only the virus species names would change; virus isolates would still be referred to by their original names. The original species would be re-designated as Pestivirus A (original designation Bovine viral diarrhea virus 1), Pestivirus B (Bovine viral diarrhea virus 2), Pestivirus C (Classical swine fever virus) and Pestivirus D (Border disease virus). The seven new species (and example isolates) would be Pestivirus E (pronghorn pestivirus), Pestivirus F (Bungowannah virus), Pestivirus G (giraffe pestivirus), Pestivirus H (Hobi-like pestivirus), Pestivirus I (Aydin-like pestivirus), Pestivirus J (rat pestivirus) and Pestivirus K (atypical porcine pestivirus). A bat-derived virus and pestiviruses identified from sheep and goat (Tunisian sheep pestiviruses), which lack complete coding region sequences, may represent two additional species.

Fig. 1.

Amino acid sequence diversity across pestivirus genomes. Mean amino acid p-distances were computed for a sliding window of 50 amino acids shifted by 10 residues across the complete coding region for comparisons between single representatives of each accepted and proposed Pestivirus species. Positions are numbered relative to the polyprotein of BVDV-1 SD-1 (M96751). Intervals on the x-axis are not regular because of un-numbered alignment gaps. Four regions where mean distances are consistently <0.5 are indicated by grey bars. A schema of the proteins encoded by the virus genome is provided below.

Fig. 2.

Phylogenetic analysis of pestivirus polyprotein fragments. Phylogenetic trees were constructed using mega 6 [36] and based upon distances between amino acid sequences for amino acid positions 3312–3899 by maximum likelihood using a JTT+G model. Up to 15 sequences were used for each species, choosing the most divergent sequences and eliminating sequences <1 % divergent, and comprised: BVDV1 (M96751, JQ799141, KP313732, KP941591, JN400273, KF896608, KC757383, KC853441, AB078950, AF526381, LC089876, KX577637, KX987157, LT631725), BVDV2 (AF002227, LC006970, KT875169, KT832818, KJ000672, HQ258810, JF714967, AB567658, FJ527854, GQ888686, KX096718), CSFV (X87939, J04358, FJ529205, AY646427, KF669877, KP233070, KM362426, KJ619377, KC851953, GQ923951, AF407339, KU504339), BDV (AF037405, AB897785, KJ463422, KF925348, KF918753, KC963426, GU270877, U70263, AF144618), Hobi-like (FJ040215, KC788748, KC297709, JX985409, JX469119, JQ612704, HQ231763, AB871953), giraffe (AF144617, KJ660072), Aydin-like (KM408491, JX428945), pronghorn (AY781152), rat (KJ950914), Bungowannah (EF100713), APPV (KU041639, KR011347, KU194229, LT594521, KX77872, KX929062). Branches supported by >70 % of bootstrap replicates are indicated.