Developments in the classification and nomenclature of arthropod-infecting large DNA viruses that contain pif genes

Abstract

Viruses of four families of arthropod-specific, large dsDNA viruses (the nuclear arthropod large DNA viruses, or NALDVs) possess homologs of genes encoding conserved components involved in the baculovirus primary infection mechanism. The presence of such homologs encoding per os infectivity factors (pif genes), along with their absence from other viruses and the occurrence of other shared characteristics, suggests a common origin for the viruses of these families. Therefore, the class Naldaviricetes was recently established, accommodating these four families. In addition, within this class, the ICTV approved the creation of the order Lefavirales for three of these families, whose members carry homologs of the baculovirus genes that code for components of the viral RNA polymerase, which is responsible for late gene expression. We further established a system for the binomial naming of all virus species in the order Lefavirales, in accordance with a decision by the ICTV in 2019 to move towards a standardized nomenclature for all virus species. The binomial species names for members of the order Lefavirales consist of the name of the genus to which the species belongs (e.g., Alphabaculovirus), followed by a single epithet that refers to the host species from which the virus was originally isolated. The common names of viruses and the abbreviations thereof will not change, as the format of virus names lies outside the remit of the ICTV.

Fig. 1

Phylogenetic analysis of members of the class Naldaviricetes. Concatenated alignments of five PIF amino acid sequences (pif-0/p74, pif-1, pif-2, pif-3, and pif-5/odv-e56), DNA polymerase (dnapol), and sulfhydryl oxidase (p33) were used to infer relationships by maximum likelihood as implemented in RAxML version 8.2.9 with substitution models and parameters selected for each alignment. Family-level classification is indicated for different clades in the midpoint-rooted tree. Abbreviations of virus names are as follows: AcMNPV, Autographa californica multiple nucleopolyhedrovirus; LdMNPV, Lymantria dispar MNPV; CpGV, Cydia pomonella granulovirus; CuniNPV, Culex nigripalpus nucleopolyhedrovirus; NeleNPV, Neodiprion lecontei NPV; OrNV, Oryctes rhinoceros nudivirus; GbNV, Gryllus bimaculatus NV; HzNV-2, Heliothis zea NV-2; PmNV, Penaeus monodon NV; ToNV, Tipula oleracea NV; GpSGHV, Glossina pallidipes salivary gland hypertrophy virus; MdSGHV, Musca domestica SGHV; AmFV, Apis mellifera filamentous virus; LbFV, Leptopilina boulardi FV; WSSV, white spot syndrome virus; CoBV, Chionoecetes opilio bacilliform virus. Endogenized nimaviruses from Marsupenaeus japonicus, Peneaus monodon, and Metapeneaus ensis were also included. This figure was reproduced and slightly modified from Kawato et al., 2019, J Virol 93:e01144-18, 10.1128/JVI.01144-18, with permission from the authors and the American Society for Microbiology.

Fig. 2

Taxonomic hierarchy of families of nuclear arthropod large DNA viruses. A new class, Naldaviricetes, was established for classification of the viruses in the four currently established families Baculoviridae, Nudiviridae, Hytrosaviridae, and Nimaviridae. A new order, Lefavirales, was introduced to include three of these families. The two viruses indicated at the top of the figure (Apis mellifera filamentous virus [3, 10] and Leptopilina boulardi filamentous virus [15]) are currently unclassified, but based on their genome content, they bear the hallmarks of members of the taxa Naldaviricetes and Lefavirales, respectively.