Pleomorphic archaeal viruses: the family Pleolipoviridae is expanding by seven new species

Established in 2016, the familyPleolipoviridaecomprises globally distributed archaeal viruses that produce pleomorphic particles. Pseudo-spherical enveloped virions of pleolipoviruses are membrane vesicles carrying a nucleic acid cargo. The cargo can be either a single-stranded or double-stranded DNA molecule, making this group the first family introduced in the 10(th)Report on Virus Taxonomy including both single-stranded and double-stranded DNA viruses. The length of the genomes is approximately 7-17 kilobase pairs, or kilonucleotides in the case of single-stranded molecules. The genomes are circular single-stranded DNA, circular double-stranded DNA, or linear double-stranded DNA molecules. Currently, eight virus species and seven proposed species are classified in three genera:Alphapleolipovirus(five species), Betapleolipovirus(nine species), andGammapleolipovirus(one species). Here, we summarize the updated taxonomy of the familyPleolipoviridaeto reflect recent advances in this field, with the focus on seven newly proposed species in the genusBetapleolipovirus:Betapleolipovirus HHPV3, HHPV4, HRPV9, HRPV10, HRPV11, HRPV12, andSNJ2.Peer reviewe

Molecular characterization of new archaeal viruses from high salinity environments

Viruses are significant biological, ecological, and evolutionary players, which are present virtually in all types of environments where cellular life is found. It has been suggested that one way to systematize the enormous virus diversity is to group viruses based on their virion architectural principles. Indeed, in spite of the overwhelming genetic diversity, all the known viruses display a limited number of morphotypes, and thus may be grouped into a limited number of structure-based lineages. To test how far virus structural conservation extends, new virus-host systems are needed to be isolated and characterized. Hypersaline environments, where halophilic archaea often dominate, are a rich source of new viruses. Currently, viruses that infect archaea are very little studied, as only ~100 archaeal viruses have been isolated. The aim of this thesis work was to isolate new archaeal viruses from hypersaline environments. In total, 36 new viruses were isolated from salt samples collected from the Samut Sakhon saltern (Thailand¬). These isolates displayed four previously known morphotypes: myovirus-like (27 isolates), siphovirus-like (4), tailless icosahedral (1), and pleomorphic (4). Among the obtained viruses, myoviruses had the widest host ranges (up to 14 hosts), infecting archaeal strains isolated from the same location or other hypersaline environments. Two of the isolated viruses, Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica pleomorphic virus 3 (HHPV3), were characterized in molecular detail. The characterization included studies on virus infectivity under various conditions, virus life cycle, virion structural components (proteins, lipids, and nucleic acids), and virus genome sequencing and annotation. HCIV-1 is closely related to the other tailless icosahedral viruses SH1, PH1, and HHIV-2 that infect halophilic archaea. The core virion components are highly conserved in these viruses and determine their place in the PRD1-adenovirus structural lineage. This lineage comprises viruses which are distributed world-wide and infect hosts from all three domains of cellular life. HHPV3 belongs to the group of archaeal pleomorphic viruses, which share virion organization and gene synteny, but may have different genome types (circular single-stranded DNA or circular/linear double-stranded DNA) and low similarity at sequence level. Pleolipoviruses also originate from distant geographical locations. This thesis work significantly increased the number of known archaeal viruses, from ~100 to ~140, and provided insights into molecular details of the two new halophilic archaeal viruses. The limited number of observed virus morphotypes and the conserved architectural principles revealed in HCIV-1 and HHPV3 highlight that similar virus architectures are found from all over the planet, supporting the idea of viral structural lineages. Future sampling of various environments and more detailed studies on the currently available virus isolates will help to portray the true viral diversity.Virukset ovat planeettamme runsaslukuisin eliöryhmä. Ne ovat levittäytyneet käytännössä kaikkiin eri ympäristöihin, jopa kaikkein äärimmäisiin. Suolajärvet ja suolan haihduttamot ovat ympäristöjä, joissa vallitsee korkea suolapitoisuus. Niissä elää eliöitä, jotka voidaan luokitella kaikkiin kolmeen elämän domeeniin: eukaryootteihin, bakteereihin ja arkeoneihin. Halofiiliset (suolaa rakastavat) arkeonit ovat bakteereja ja eukaryootteja yleisempiä korkean suolan ympäristöissä, joissa suolapitoisuus saattaa olla jopa kylläinen. Näissä ympäristöissä on myös runsaasti viruksia, joista arkeonien virukset muodostavat suurimman joukon. Tällä hetkellä arkeoneja infektoivia viruksia on tutkittu hyvin vähän, vaikka monien tämän virusryhmän edustajista on osoitettu olevan ominaisuuksiltaan ainutlaatuisia ja mielenkiintoisia. Uusia arkeoniviruksia tarvittaisiin syventämään tietämystämme näiden virusten monimuotoisuudesta ja toiminnasta. Tämä tieto lisäisi myös ymmärrystämme virusten monimuotoisuudesta yleensä sekä auttaisi meitä hahmottamaan paremmin eri virusryhmien välisiä evolutiivisia sukulaissuhteista. Tämän väitöskirjatyön tarkoitus oli löytää uusia arkeoniviruksia Thaimaan Samut Sakhonin suolahaihduttamosta kerätyistä korkean suolan ympäristönäytteistä. Uusia arkeoniviruksia löydettiin yhteensä 36 kappaletta, jolloin tunnettujen arkeonivirusten lukumäärä nousi tämän työn myötä noin 140 virukseen. Tutkimuksessani löydetyt uudet virukset voidaan jakaa neljään erilaiseen rakennetyyppiin. Ikosahedraaliset virukset, joilla on supistumiskykyinen häntä, olivat kaikkein runsaslukuisin rakennetyyppi ja näillä viruksilla oli usein poikkeuksellisen laaja isäntäkirjo. Toisin sanoen, nämä virukset kykenivät infektoimaan useita erilaisia isäntäsoluja, jotka olivat peräisin joko samasta suolahaihduttamosta tai toisista korkean suolan ympäristöistä. Tässä työssä tutkittiin yksityiskohtaisemmin kahta uutta rasvakalvon sisältävää arkeonivirusta. Viruspartikkelin rakennekomponenttien eli proteiinien, lipidien ja nukleiinihapon analyysien perusteella paljastui, että ikosahedraalinen virus HCIV-1 on läheistä sukua halofiilisiä arkeoneja infektoiville hännättömille ikosahedraalisille viruksille (Sphaerolipoviridae-heimo), kun taas HHPV3-virus on monimuotoinen virus, jonka virioni muistuttaa rakenteeltaan kalvorakkulaa (Pleolipoviridae-heimo). Tämä tutkimus tukee aiempaa havaintoa siitä, että rakenteellisesti toisilleen sukua olevia viruksia löytyy eri puolilta planeettaamme. Virusgenomien nukleiinihapposekvensseissä esiintyy valtavasti vaihtelua, mutta virusrakenteet ovat säilyneet samankaltaisina evoluution kuluessa, koska virusten kuoriproteiinit voivat laskostua vain rajoitetulla määrällä vaihtoehtoja. Planeettamme valtavasta virusmäärästä huolimatta kaikki nykyisin tunnetut virukset kuuluvat rajattuun määrään viruslinjoja, joiden ryhmittelykriteeri perustuu rakenteeseen. Virusrakenteiden evolutiiviseen säilymiseen perustuen viruksia voidaan helposti luokitella eri rakennelinjoihin, ja se mahdollistaa myös eri virusryhmien välisten hyvin vanhojen evolutiivisten sukulaisuussuhteiden tarkastelun. Tulevaisuuden uudet viruslöydöt sekä jo tunnettujen virusten yksityiskohtaisempi tutkimus voi aikanaan paljastaa kuinka monta viruslinjaa on olemassa

The unexplored diversity of pleolipoviruses: the surprising case of two viruses with identical major structural modules

Extremely halophilic Archaea are the only known hosts for pleolipoviruses which are pleomorphic non-lytic viruses resembling cellular membrane vesicles. Recently, pleolipoviruses have been acknowledged by the International Committee on Taxonomy of Viruses (ICTV) as the first virus family that contains related viruses with different DNA genomes. Genomic diversity of pleolipoviruses includes single-stranded and double-stranded DNA molecules and their combinations as linear or circular molecules. To date, only eight viruses belong to the family Pleolipoviridae. In order to obtain more information about the diversity of pleolipoviruses, further isolates are needed. Here we describe the characterization of a new halophilic virus isolate, Haloarcula hispanica pleomorphic virus 4 (HHPV4). All pleolipoviruses and related proviruses contain a conserved core of approximately five genes designating this virus family, but the sequence similarity among different isolates is low. We demonstrate that over half of HHPV4 genome is identical to the genome of pleomorphic virus HHPV3. The genomic regions encoding known virion components are identical between the two viruses, but HHPV4 includes unique genetic elements, e.g., a putative integrase gene. The co-evolution of these two viruses demonstrates the presence of high recombination frequency in halophilic microbiota and can provide new insights considering links between viruses, membrane vesicles, and plasmids.Peer reviewe

Extremely halophilic pleomorphic archaeal virus HRPV9 extends the diversity of pleolipoviruses with integrases

Certain pleomorphic archaeal viruses are highly infectious even at saturated salt. These viruses belong to the genus Betapleolipovirus of the recently described archaeal virus family Pleolipoviridae. Pleolipoviruses comprise single-stranded or double-stranded, circular or linear DNA genomes that share countless homologues among various archaeal genetic elements. Here we describe a new extremely halophilic betapleolipovirus, Halorubrum pleomorphic virus 9 (HRPV9), which has an integrase gene. We also identified new genes encoding minor pleolipoviral structural proteins. The studies on HRPV9 enhance our knowledge on pleolipoviruses, especially their reciprocal relatedness and relation to certain archaeal plasmids, proviruses and membrane vesicles. (C) 2018 The Authors. Published by Elsevier Masson SAS on behalf of Institut Pasteur.Peer reviewe

HCIV-1 and other tailless icosahedral internal membrane-containing viruses of the family Sphaerolipoviridae

Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha-and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.Peer reviewe

Biodegradable Microparticles for Regenerative Medicine: A State of the Art and Trends to Clinical Application

peer reviewedTissue engineering and cell therapy are very attractive in terms of potential applications but remain quite challenging regarding the clinical aspects. Amongst the different strategies proposed to facilitate their implementation in clinical practices, biodegradable microparticles have shown promising outcomes with several advantages and potentialities. This critical review aims to establish a survey of the most relevant materials and processing techniques to prepare these micro vehicles. Special attention will be paid to their main potential applications, considering the regulatory constraints and the relative easiness to implement their production at an industrial level to better evaluate their application in clinical practices

Changes in loading distribution in patients with Charcot foot during long-term follow-up

Background. The inactive stage of the diabetic Charcot arthropathy foot (CA) is characterised by fixed foot deformities and an absence of inflammation. However, it remains unclear if the shape of the foot and its biomechanics change during long-term follow-up. Aim. To evaluate changes in loading distribution of the affected foot, in patients with inactive CA, during long-term follow-up. Materials and methods. Twenty seven patients with unilateral inactive CA (19 females, 8 males) were studied. Computer pedography (emed AT, novel gmbh) was performed and baseline and the last studies were analysed. Maximal peak pressures (PP) were obtained for the first and the last studies and the percentage of the PP change was calculated for the total follow-up period and for periods: 24 months, 2448 months, 48 months. Results. PP increased: under the hallux 50%; 1st metatarsal30.7%; 2nd toe20%; 2nd toe6%; midfoot9%. PP decreased under 35 toes up to 67%. Significant changes at the first period were found under 35 toes only (62%). The increase in loading under the other parts of the foot appeared at 24 months; however, these changes became significant between 24 and 48 months and peaked after 48 months of follow-up. The maximal increase of PP was noticed under the hallux, the 2nd toe, metatarsals 13 and the midfoot. Conclusions. We revealed the gradual redistribution of PP, under the different parts of the foot, in patients with inactive CA. This redistribution reflects changes in the shape of the affected foot. The loading increased under the hallux, the 2nd toe and the corresponding metatarsals, 3rd metatarsal and midfoot, and decreased under the 35 toes. These changes increased during the follow-up, becoming more pronounced after 4 or more years. Our data may be useful for constructing custom-made footwear for patients with CA