Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club

• Published in: Frontiers in Microbiology
• Main Authors: Sharma, Vikas, Colson, Philippe, Chabrol, Olivier, Pontarotti, Pierre, Raoult, Didier
• Other Authors: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques - CNRS Biologie (INSB-CNRS)-Institut des sciences biologiques - CNRS Biologie (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2015
• Subjects: Megavirales; Pithovirus sibericum; Domains of life; Giant virus; Informational genes; Phylogeny; Nucleocytoplasmic large DNA viruses; TRUC; [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology; permafrost
• Online Access: https://hal.science/hal-01304145; https://hal.science/hal-01304145/document; https://hal.science/hal-01304145/file/fmicb-06-00722.pdf; https://doi.org/10.3389/fmicb.2015.00722

International audience Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, include giant viruses of Acanthamoeba that were discovered over the last 12 years and are bona fide microbes. Phylogenies based on a few genes conserved amongst these megaviruses and shared by microbes classified as Eukarya, Bacteria, and Archaea, allowed for delineation of a fourth monophylogenetic group or "TRUC" (Things Resisting Uncompleted Classification) composed of the Megavirales representatives. A new Megavirales member named Pithovirus sibericum was isolated from a >30,000-year-old dated Siberian permafrost sample. This virion is as large as recently described pandoraviruses but has a genome that is approximately three to four times shorter. Our objective was to update the classification of P. sibericum as a new member of the "Fourth TRUC" club. Phylogenetic trees were constructed based on four conserved ancient genes and a phyletic analysis was concurrently conducted based on the presence/absence patterns of a set of informational genes from members of Megavirales, Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on the four conserved genes revealed that P. sibericum is part of the fourth TRUC composed of Megavirales members, and is closely related to the families Marseilleviridae and Ascoviridae/Iridoviridae. Additionally, hierarchical clustering delineated four branches, and showed that P. sibericum is part of this fourth TRUC. Overall, phylogenetic and phyletic analyses using informational genes clearly indicate that P. sibericum is a new bona fide member of the "Fourth TRUC" club composed of representatives of Megavirales, alongside Bacteria, Archaea, and Eukarya.