Pandoravirus

Pandoraviruses were discovered in 2013 ^[5] in a systematic study of water samples and bottom sediments in search of new viruses of the family that infect amoeba . Like mimiviruses , they were isolated from samples that showed strong lytic activity when co-grown with Acanthamoeba . The first species of the new genus, Pandoravirus salinus , was isolated from a sample of shallow bottom sediments from the coast of central Chile , and the second species, Pandoravirus dulcis , was isolated from mud collected from the bottom of a freshwater pond near Melbourne ( Australia ). The genomes of both viruses were sequenced when they were isolated. Another virus with the morphology of Pandoravirus , Pandoravirus inopinatum , was isolated in 2008 from a patient suffering from keratitis caused by Acanthamoeba . Only six years later, due to its large size, it was possible to establish its viral nature. In 2015, its genome was sequenced ^[6] . In 2018, three more species were described: Pandoravirus macleodensis was found in freshwater samples near Melbourne , just 700 meters from where P. dulcis was found; Pandoravirus neocaledonia is isolated in brackish water of mangroves near the airport of Noumea ( New Caledonia ) and Pandoravirus quercus , found in the ground of Marseille ( France ). Then it was decided to separate the genus into a separate family. The result of a phylogenetic study of the genus carried out in the description of these three species can be illustrated by the following cladogram ^[3] :

Pandoravirus can be examined under a light microscope . Virions are ovoid particles 0.8-1.2 microns in length and 0.5 microns in diameter. Electron microscopy revealed a unique structure of these virions, which is not found in any of the described viruses. The mature virion is an empty looking compartment surrounded by a membrane , under which a shell about 70 nm thick is located. Three layers are distinguished in it: the inner electron-dense layer about 20 nm thick, the middle dark layer about 25 nm thick, similar to a dense network of parallel oriented fibrils, and the outer layer of the average electron density about 25 nm thick. At one end of the viral particle, there is an apical pore, through which the uncharacterized contents of the virion are poured into the cytoplasm of the host amoeba, passing through the channel formed by the fusion of the virus membrane and the membrane of the . Unlike mimivirus , pandoraviruses do not have an electronically dense central region that corresponds to a compacted genome ^[6] .

The genome of pandoraviruses is represented by linear double-stranded DNA with a length of 2.77 million base pairs in P. salinus , 1.93 million base pairs in P. dulcis and 2.24 million base pairs in P. inopinatum ^[6] . The GC composition of the pandoraviral genomes was high: 61.7, 63.7 and 60.7% in P. salinus , P. dulcis and P. inopinatum, respectively (the largest known GC composition in the virus is characteristic of herpes viruses : more than 70%). In P. inopinatum , 89% of the common sequences with P. dulcis and 85% with P. salinus were found . The size of the capsid and the DNA molecule, as well as its packing density, indicate that the genomic DNA of P. salinus fits easily into their capsid . In the genome of P. salinus , 2556 putative protein-coding genes were found , in P. dulcis - 1502, in P. inopinatum - 1339. The composition of the genes in P. salinus and P. dulcis is approximately the same, differences in the size of the genome are due to four segments unique to P. salinus . It has been shown that the genome of P. salinus has many transposons ^[7] . The putative proteins encoded by the P. salinus genome have a size of 26 to 2367 amino acid residues (a.a.), the average length is 258 a. about. ^{[5] [8]} In the three species described in 2018 - P. neocaledonia , P. macleodensis, and P. quercus - the genome is also represented by a linear double-stranded DNA molecule, comprising from 1.84 to 2 million base pairs. In addition, as in the previously known species of the genus Pandoravirus , their genomes also have a very high GC composition — about 60% ^[3] .

The life cycle of pandoraviruses in the amoeba Acanthamoeba castellanii lasts from 10 to 15 hours and begins with the ingestion of the virion inside the digestive vacuole formed during the phagocytosis of the viral particle. Next, pandoravirus pours its contents into the cell through the apical pore. Viral DNA and proteins enter the amoeba’s cytoplasm through the channel formed during the fusion of the virus membranes and the digestive vacuole. After this, the contents of the virus in the cytoplasm becomes invisible. After 4 hours, the amoeba core begins to strongly reorganize and loses its spherical shape. The electron-dense nucleolus gradually disappears, and a lot of impressions are formed on the nuclear membrane , forming numerous vesicles . At the periphery of the dissolving core, a peroxisome-like crystalline structure appears, disappearing as the viral particle ripens. 8-10 hours after the onset of infection, the cells are rounded and detached from the substrate, and on the periphery, where once there was a nucleus, virus particles appear. Unlike other DNA-containing viruses of eukaryotes and phages , in which a capsid is first formed, and then it is filled with the necessary contents, in pandoraviruses both processes proceed simultaneously. It is curious that the formation of the capsid begins with the tip that carries the apical pore. The replication cycle ends when the amoeba cell lyses and releases hundreds of viral particles outward ^[5] .