Problems of classification in the family Paramyxoviridae

Abstract

A number of unassigned viruses in the family Paramyxoviridae need to be classified either as a new genus or placed into one of the seven genera currently recognized in this family. Furthermore, numerous new paramyxoviruses continue to be discovered. However, attempts at classification have highlighted the difficulties that arise by applying historic criteria or criteria based on sequence alone to the classification of the viruses in this family. While the recent taxonomic change that elevated the previous subfamily Pneumovirinae into a separate family Pneumoviridae is readily justified on the basis of RNA dependent -RNA polymerase (RdRp or L protein) sequence motifs, using RdRp sequence comparisons for assignment to lower level taxa raises problems that would require an overhaul of the current criteria for assignment into genera in the family Paramyxoviridae. Arbitrary cut off points to delineate genera and species would have to be set if classification was based on the amino acid sequence of the RdRp alone or on pairwise analysis of sequence complementarity (PASC) of all open reading frames (ORFs). While these cut-offs cannot be made consistent with the current classification in this family, resorting to genus-level demarcation criteria with additional input from the biological context may afford a way forward. Such criteria would reflect the increasingly dynamic nature of virus taxonomy even if it would require a complete revision of the current classification.

Fig. 1

The order of the transcription units in the Paramyxoviridae. The boxes and intergenic, leader and trailer sequences are not to scale but only the order is indicated. Abbreviations N: nucleocapsid protein; P phosphoprotein, V V protein; C C protein; M membrane or matrix protein, F fusion protein; SH small hydrophobic protein, tM transmembrane protein; H haemagglutinin protein; HN haemagglutinin-neuraminidase protein; G attachment protein and L large protein (RdRp)

Fig. 2

Molecular Phylogenetic analysis by Maximum Likelihood method of 65 members of the Paramyxoviridae based on the amino acids sequences of the L or RdRp protein. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [4]. The tree with the highest log like-lihood (−173347.50) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All positions containing gaps and missing data were eliminated. There were a total of 1995 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [6]. Printed in red are those viruses which are still formally to be classified (color figure online)