Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses

Abstract

African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% GϩC content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus.IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.KEYWORDS giant viruses, pacmanvirus, Asfarviridae, Acanthamoeba castellanii, NCLDV, faustovirus, kaumoebavirus, African swine fever virus T he discovery impacts of "giant viruses," such as Acanthamoeba polyphaga mimivirus (1), pandoraviruses (2), and pithoviruses (3), and their interactions with the world of protists are very common and do not need a long introduction. A large community of previously unknown viruses is emerging among the former nucleocytoplasmic large DNA viruses (NCLDV). We are witnessing a growing number of new isolates with extraordinary properties in gene content, particle resistance, and/or morphological appearance (3-7). Genome sequencing and advances in coculture isolation strategies have led to an increase in the discovery of new viruses (8,9). Some NCLDV are well studied because of their role in infecting algae, in the case of Phycodnaviridae (10), or in swine and wild boar infections, in the case of members of the Asfarviridae (11). The

Virus–Host Coevolution with a Focus on Animal and Human DNA Viruses

“…The second host switch happened at a later evolutionary stage in the sensu lato asfarviruses. Within this group a few apparently related viruses infect protists and pigs too (Alonso et al 2018;Andreani et al 2017;Bajrai et al 2016).…”

ICTV Virus Taxonomy Profile: Asfarviridae

“…The unclassified faustoviruses, kaumoebavirus and Pacmanvirus [7], have about 30 genes related to those of African swine fever virus, but their genomes are considerably larger (about 400 kbp compared to 170-194 kbp).…”

Advantages and limits of metagenomic assembly and binning of a giant virus

“…Viral particles were quantified by flow cytometry. Data were acquired using log scales for instrument scatter parameters, side scatter (SSC), associated with DNA content detected by Fluorescein (FITC) parameter after SYBR green staining as previously described (Andreani et al, 2017) . Thresholds were adjusted on the SSC parameter and 10000 events per sample were acquired.…”