{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:46:10Z","timestamp":1792788370874,"version":"4.5.0"},"update-to":[{"DOI":"10.12688\/f1000research.179903.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:00:00Z","timestamp":1787961600000}}],"reference-count":40,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:00:00Z","timestamp":1787961600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Research Council (ERC) under the European Union\u2019s Horizon Europe research and innovation programme","award":["101117204"],"award-info":[{"award-number":["101117204"]}],"id":[{"id":"https:\/\/ror.org\/0472cxd90","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Helsinki University Library"},{"name":"Kone Foundation","id":[{"id":"https:\/\/ror.org\/05jwty529","id-type":"ROR","asserted-by":"crossref"}]},{"name":"the University of Helsinki and Research Council of Finland by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC and Horizon MSCA","award":["101120407"],"award-info":[{"award-number":["101120407"]}],"id":[{"id":"https:\/\/ror.org\/05k73zm37","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Research Council of Finland","award":["330977"],"award-info":[{"award-number":["330977"]}],"id":[{"id":"https:\/\/ror.org\/05k73zm37","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    Pleomorphic archaeal viruses are widespread and abundant in hypersaline environments and beyond. Still, a relatively low number of isolates are available for this viral group. Here, we present the complete genome sequence of Halorubrum pleomorphic viruses 8 (HRPV-8), which was previously isolated from the Samut Sakhon solar saltern, Thailand, on a\n                    <ns3:italic>Halorubrum<\/ns3:italic>\n                    species. The HRPV-8 genome was assembled into a circular 10,824-bp-long contig with a GC content of 63.2%. The genome annotation resulted in 12 open reading frames, including a VP4-like spike protein-encoding gene, which is a hallmark of pleomorphic archaeal viruses. Seven and three putative proteins in HRPV-8 were 99\u2013100% identical to their counterparts in Halorubrum pleomorphic viruses 2 and 6 (HRPV-2 and HRPV-6), respectively, members of the genus\n                    <ns3:italic>Alphapleolipovirus.<\/ns3:italic>\n                    The average nucleotide identity values within these three viral genomes were 92\u201396%. According to VIRIDIC analyses of intergenomic similarities, HRPV-8 represents its own species. Thus, based on the observed pleolipoviral genome architecture and sequence similarities to other alphapleolipoviruses, we propose to classify HRPV-8 as a new species within the\n                    <ns3:italic>Alphapleolipovirus<\/ns3:italic>\n                    genus of the\n                    <ns3:italic>Pleolipoviridae<\/ns3:italic>\n                    family.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.179903.2","type":"journal-article","created":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T11:19:08Z","timestamp":1788002348000},"page":"654","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Complete Genome Sequence of Halorubrum Pleomorphic Virus 8"],"prefix":"10.12688","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3746-5533","authenticated-orcid":false,"given":"Tatiana","family":"Demina","sequence":"first","affiliation":[{"name":"Department of Microbiology, Faculty of Agriculture and Forestry Helsinki Uusimaa University of Helsinki"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4172-3128","authenticated-orcid":false,"given":"Elina","family":"Laanto","sequence":"additional","affiliation":[{"name":"Department of Biological and Environmental Science and Nanoscience Center Jyv\u00e4skyl\u00e4 Central Finland University of Jyv\u00e4skyl\u00e4"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanna M.","family":"Oksanen","sequence":"additional","affiliation":[{"name":"Department of Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences Helsinki Uusimaa University of Helsinki"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,8,29]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e1010998","DOI":"10.1371\/journal.pgen.1010998","article-title":"Revisiting Evolutionary Trajectories and the Organization of the Pleolipoviridae Family.","volume":"19","author":"T Alarc\u00f3n-Schumacher","year":"2023","journal-title":"PLoS Genet."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e2205037119","DOI":"10.1073\/pnas.2205037119","article-title":"Isolation of a Virus Causing a Chronic Infection in the Archaeal Model Organism Haloferax Volcanii Reveals Antiviral Activities of a Provirus.","volume":"119","author":"T Alarc\u00f3n-Schumacher","year":"2022","journal-title":"Proc. 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Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.13344\/j.microbiol.china.220199","article-title":"\u6781\u7aef\u55dc\u76d0\u591a\u5f62\u6027\u53e4\u83cc\u75c5\u6bd2HRPV13\u7684\u5206\u79bb\u9274\u5b9a\u53ca\u751f\u7269\u5b66\u7279\u6027.","author":"S Shanshan","year":"2022 May 20","journal-title":"\u5fae\u751f\u7269\u5b66\u901a\u62a5."}],"updated-by":[{"DOI":"10.12688\/f1000research.179903.3","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000}}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/15-654\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-654\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-654\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T07:04:14Z","timestamp":1792047854000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/15-654\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,29]]},"references-count":40,"URL":"https:\/\/doi.org\/10.12688\/f1000research.179903.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/f1000research.179903.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.209050.r516734","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.209050.r516734","asserted-by":"object"}],"is-version-of":[{"id-type":"doi","id":"10.12688\/f1000research.179903.3","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,29]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/15-654\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.198462.r481714, Jimmy Saw, George Washington University, Washington, 01 Jun 2026, version 1, 1 approved","URL":"https:\/\/f1000research.com\/articles\/15-654\/v1#referee-response-481714","order":0,"name":"referee-response-481714","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Tatiana Demina<\/b>; \n<i>Posted: 20 Aug 2026<\/i>; We thank the reviewer for the comments, which we have addressed in the revised manuscript: a typo in the pleolipoviral genome size range has been corrected, and raw reads from HRPV-8 whole genome sequencing have been deposited in the European Nucleotide Archive (ENA).","URL":"https:\/\/f1000research.com\/articles\/15-654\/v2#referee-comment-16969","order":1,"name":"referee-comment-16969","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.209050.r516734, Ingrida Olendrait\u0117, EMBL-EBI, Cambridgeshire, 01 Oct 2026, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/15-654\/v2#referee-response-516734","order":2,"name":"referee-response-516734","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Tatiana Demina<\/b>; \n<i>Posted: 08 Oct 2026<\/i>; We thank the reviewer for valuable comments and suggestions on how the work could be improved. We have revised the article based on these points, and below are our answers (A) to reviewer\u2019s questions\/comments (Q).  Q:\n<i> low number of isolates<\/i> \n<i>Isolates can be understood as members of the same species - but you have a unique species; so maybe a low number of isolated or described species?<\/i>  A: We have changed wording to \u201ca low number of isolated and described species\u201d, as it reflects the original point indeed more accurately. --- Q: \n<i>Halorubrum pleomorphic viruses 8 (HRPV-8)<\/i> \n<i>Not viruses - should be \u201cvirus\u201d, correct?<\/i>  A: Yes, the typo has been corrected. --- Q:\n<i> Seven and three putative proteins in HRPV-8 were 99\u2013100% identical to their counterparts in Halorubrum pleomorphic viruses 2 and 6 (HRPV-2 and HRPV-6), respectively,<\/i> \n<i>seven and three &gt;...&lt; respectively - a very big gap between the HRPV-2 and -6 and the first words; reads a bit clunky<\/i>.  A: We have reduced the gap by moving \u201cin HRPV-8\u201d to the beginning of the sentence. --- Q: \n<i>Additionally - 12 ORFs doesn\u2019t mean 12 proteins (peptides); so 7 and 3 here do not really mean much (unless you are talking about ORFs), because we don\u2019t know how many are not identical. In short: ORF is not the same as protein.<\/i>  A: In this case, 12 ORFs encoded 12 proteins, and to avoid confusion with the terms, we have revised the text: \u201cThe genome was predicted to encode 12 proteins, including ...\u201d. --- Q: \n<i>The average nucleotide identity values within these three viral genomes were 92\u201396%.<\/i> \n<i>Is this for a full genome?<\/i>  A: These average nucleotide identity (ANI) values were obtained using FastANI, which calculates whole-genome ANI, \u201cdefined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes\u201d (https:\/\/github.com\/ParBliSS\/FastANI). --- Q: \n<i>Overall nucleotide similarity between the genomes of pleolipoviruses is relatively low,<\/i> \n<i>It would be interesting to see these numbers (what is relatively low?) - as for your new virus you report protein and nucleotide identity which is quite high&nbsp; (99-100 or 92-96) - this could be very useful in the introduction to provide context.<\/i>  A: We agree that additional context would be useful here. However, to support the statement quantitatively, nucleotide identity\/similarity values would need to be calculated consistently across all pleomorphic viruses. Rather than introducing additional comparative data, we removed the phrase about the low similarity, as these additional analyses would be beyond the scope of the Introduction. --- \n<i>Q: &lt;\u2026&gt; Here, we present the complete genome sequence of HRPV-8 and suggest its classification within the genus Alphapleolipovirus of the family Pleolipoviridae.<\/i> \n<i>After finishing reading the introduction it is not clear if in 2015 the HRPV-8 had genome sequence or it was just isolated and some plaque assays etc done. This is important to assess the novelty of your work (and to understand if it's a new isolate of the same species or new species, or finally a complete genome etc). Whatever was lacking - it would be good to explicitly mention in the introduction.<\/i>  A: The isolate was obtained and first reported in the study by Atanasova et al in 2015, but its genome sequence stayed unknown back then. In this study, we sequenced and annotated the genome of the that same isolate reported earlier. The isolate represents its own species (for which no other isolates are available), and its classification is currently under processing by ICTV. We have clarified the text by stating that \u201cIn this study, we sequenced and annotated the genome of this HRPV-8 isolate\u201d. --- Q: \n<i>value threshold of 1e-5<\/i> \n<i>It\u2019s usually 10e-5<\/i>  A: We have used the default BLASTn value at the IMG\/VR v.4 (https:\/\/img.jgi.doe.gov\/cgi-bin\/vr\/main.cgi?section=WorkspaceBlast&amp;page=viralform), which is 1e-5. --- Q: \n<i>Pairwise amino acid identities in HRPV-8, Halorubrum pleomorphic virus 2 (HRPV-2), and Halorubrum pleomorphic virus 6 (HRPV-6) proteins were calculated using EMBOSS Needle (Madeira et al., 2024). I<\/i>  \n<i>It would be useful to provide accessions here (not necessarily just in the results table) if you have for HRPV-2 and -6 - so it\u2019s exactly clear what was compared.<\/i>  A: Indeed, accession numbers add clarity, and they have been added to Table 2. --- Q: \n<i>Raw data included 6,754,300 read pairs, which were trimmed to 6,183,469 read pairs.<\/i> \n<i>Filtered; trimming is from the start\/end of a read - so base pairs would be trimmed and then some of the reads wouldn\u2019t pass the length threshold or be discarded due to quality. So trimming is different action.<\/i> \n<i>To improve readability you could just say&nbsp; \u201cAfter trimming and quality control, 6,183,469 reads remained and were assembled into 461 contigs ().<\/i>  A: We have changed the wording according to this suggestion. --- Q: \n<i>terminal 55-bp-long repeats, which reflected the assembly artifact from a circular template,<\/i> \n<i>Repeats might arise due to assemblers and k-mer sizes for non-circular templates as well. I\u2019d add some softening confidence word: which reflected the possible assembly artifact due to a circular template<\/i> \n<i>Do you know that this virus has a circular template for sure? Has it been shown before?&nbsp; If yes - citation could be helpful here. <\/i> \n<i>The 77-kmer is a strong support. I would love to see if there are any \u201csplit reads\u201d&nbsp; to show a read which would cover both contig ends. <\/i> \n<i>Also by mapping back the reads you could see if coverage drops around the joined sequence or it\u2019s similar coverage throughout.<\/i>  A: We have no experimental evidence of the circular nature of the HRPV-8 genome, so we have added some softening words to these lines, as suggested. We have also additionally mapped reads to the HRPV-8 sequence linearized at different positions and observed read coverage across the entire genome (no uncovered positions) and no apparent coverage drop around the original contig ends. These results have been added. --- Q: \n<i>as well as multiple hits to the sequences of halophilic archaea<\/i> \n<i>So your sequence potentially has integrated into archaeal genomes? Does this sentence mean it\u2019s matching archaeal genomes or viruses of halophilic archaea? From your table 1 it seems as only to archaeal viruses.<\/i>  A: Pleolipoviral sequences are often found as putative proviruses in archaeal genomes. We have moved mentioning the hits to archaeal genomes into a separate sentence to distinguish them from the matches to viral genomes. Table 1 contains hits only to viral genomes (as stated in its heading), since the focus of this study is on pleomorphic virus isolates rather than proviral elements in archaeal genomes. --- Q: \n<i>HRPV-8 genome annotation with Phold resulted in 12 predicted ORFs, most of which encoded gene products of unknown functions ( Table 2).<\/i> \n<i>6 had unknown functions - so it\u2019s half, not most<\/i>  A: Thanks for noticing this, it has been corrected. --- Q: \n<i>In the table, lengths of the ORFs in amino acids could be useful (easier to compute in mind than nucleotide coordinates) to understand if it\u2019s polyproteins or peptides, especially when evaluating the coverage \/ identity. It can of course be inferred from nucleotide coordinates.<\/i>  A: The putative protein lengths in amino acids were added to the table. --- \n<i>As a next step ideas: <\/i> Q:\n<i> structural comparisons of proteins with unknown functions?<\/i>  A: In this work, we used sequence-and structure-based predictions as well as comparison to other pleolipoviruses for predicting putative functions HRPV-8 proteins, but indeed, further comparative structural analyses and experimental validation will be needed to determine the functions of the remaining uncharacterized proteins. We have added this point to the Conclusions. --- Q:\n<i> It would be great to see genus + members of the family phylogenetic tree? Maybe of the hallmark gene if it\u2019s too complex computationally otherwise?<\/i>  The phylogenetic tree of current and newly proposed species within the Pleolipoviridae family is already made as part of the taxonomic proposal that has been recently submitted to ICTV. It will be available from the ICTV website once processed. --- Q:\n<i> Species significance could have been described in a bit more detail.<\/i>  A: The HRPV-8 genome expands the currently limited collection of cultivated pleomorphic archaeal viruses and provides an additional reference for studying species-level diversity within the family Pleolipoviridae as well as pleolipovirus evolution in general. We have added some text along these lines to the Conclusions.","URL":"https:\/\/f1000research.com\/articles\/15-654\/v2#referee-comment-17383","order":3,"name":"referee-comment-17383","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"The work was supported by the Research Council of Finland (TD: grant 330977) and the Kone Foundation (TD). This project has received funding from the European Research Council (ERC) under the European Union\u2019s Horizon Europe research and innovation programme to EL (grant agreement No 101117204). HMO was supported by the University of Helsinki and Research Council of Finland by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC and Horizon MSCA 101120407. Open access funded by Helsinki University Library. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}