{"id":"https://openalex.org/W4413384635","doi":"https://doi.org/10.1101/2025.08.19.670320","title":"Comment on \u201cInverted repeats in the monkeypox virus genome are hot spots for mutation\u201d","display_name":"Comment on \u201cInverted repeats in the monkeypox virus genome are hot spots for mutation\u201d","publication_year":2025,"publication_date":"2025-08-20","ids":{"openalex":"https://openalex.org/W4413384635","doi":"https://doi.org/10.1101/2025.08.19.670320"},"language":"en","primary_location":{"id":"doi:10.1101/2025.08.19.670320","doi":"https://doi.org/10.1101/2025.08.19.670320","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.08.19.670320","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/08/20/2025.08.19.670320.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2025/08/20/2025.08.19.670320.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119047681","display_name":"Alexandra V Madorskaya","orcid":"https://orcid.org/0009-0008-0946-6890","observed_orcids":["https://orcid.org/0009-0008-0946-6890"]},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexandra V. Madorskaya","raw_affiliation_strings":["National Research University Higher School of Economics, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0009-0008-0946-6890","affiliations":[{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia;","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093322370","display_name":"Fedor M. Kazanov","orcid":"https://orcid.org/0009-0001-0682-8146","observed_orcids":["https://orcid.org/0009-0001-0682-8146"]},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Fedor M. Kazanov","raw_affiliation_strings":["National Research University Higher School of Economics, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0009-0001-0682-8146","affiliations":[{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia;","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067581700","display_name":"Gennady V. Ponomarev","orcid":"https://orcid.org/0000-0003-1271-9007","observed_orcids":["https://orcid.org/0000-0003-1271-9007"]},"institutions":[{"id":"https://openalex.org/I4210148309","display_name":"Vavilov Institute of General Genetics","ror":"https://ror.org/05ermrg42","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210148309"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Gennady V. Ponomarev","raw_affiliation_strings":["Vavilov Institute of General Genetics, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0000-0003-1271-9007","affiliations":[{"raw_affiliation_string":"Vavilov Institute of General Genetics, Moscow, Russia;","institution_ids":["https://openalex.org/I4210148309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090115170","display_name":"A. V. Smol'nikova","orcid":"https://orcid.org/0009-0003-6748-9103","observed_orcids":["https://orcid.org/0009-0003-6748-9103"]},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Anna Smolnikova","raw_affiliation_strings":["Lomonosov Moscow State University, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0009-0003-6748-9103","affiliations":[{"raw_affiliation_string":"Lomonosov Moscow State University, Moscow, Russia;","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119372564","display_name":"Daria V. Garshina","orcid":"https://orcid.org/0009-0000-9296-6926","observed_orcids":["https://orcid.org/0009-0000-9296-6926"]},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Daria Garshina","raw_affiliation_strings":["Lomonosov Moscow State University, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0009-0000-9296-6926","affiliations":[{"raw_affiliation_string":"Lomonosov Moscow State University, Moscow, Russia;","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Evgenii V. Matveev","orcid":"https://orcid.org/0009-0008-2103-4978","observed_orcids":["https://orcid.org/0009-0008-2103-4978"]},"institutions":[{"id":"https://openalex.org/I4210127411","display_name":"Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology","ror":"https://ror.org/02h8dsx08","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210127411"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Evgenii V. Matveev","raw_affiliation_strings":["Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0009-0008-2103-4978","affiliations":[{"raw_affiliation_string":"Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia;","institution_ids":["https://openalex.org/I4210127411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069712389","display_name":"Ruslan Kh. Abasov","orcid":"https://orcid.org/0000-0001-9179-8430","observed_orcids":["https://orcid.org/0000-0001-9179-8430"]},"institutions":[{"id":"https://openalex.org/I4210127411","display_name":"Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology","ror":"https://ror.org/02h8dsx08","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210127411"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ruslan Kh. Abasov","raw_affiliation_strings":["Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0000-0001-9179-8430","affiliations":[{"raw_affiliation_string":"Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia;","institution_ids":["https://openalex.org/I4210127411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028642432","display_name":"Dmitry N. Ivankov","orcid":"https://orcid.org/0000-0002-8224-4118","observed_orcids":["https://orcid.org/0000-0002-8224-4118"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dmitry N. Ivankov","raw_affiliation_strings":["Center for Molecular and Cellular Biology, Moscow, Russia;"],"raw_orcid":"https://orcid.org/0000-0002-8224-4118","affiliations":[{"raw_affiliation_string":"Center for Molecular and Cellular Biology, Moscow, Russia;","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016957787","display_name":"Mikhail Sergeevich Gelfand","orcid":"https://orcid.org/0000-0003-4181-0846","observed_orcids":["https://orcid.org/0000-0003-4181-0846"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mikhail S. Gelfand","raw_affiliation_strings":["Center for Molecular and Cellular Biology, Moscow, Russia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular and Cellular Biology, Moscow, Russia;","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070956718","display_name":"Marat D. Kazanov","orcid":"https://orcid.org/0000-0002-2314-5507","observed_orcids":["https://orcid.org/0000-0002-2314-5507"]},"institutions":[{"id":"https://openalex.org/I134235054","display_name":"Sabanc\u0131 \u00dcniversitesi","ror":"https://ror.org/049asqa32","country_code":"TR","type":"education","lineage":["https://openalex.org/I134235054"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Marat D. Kazanov","raw_affiliation_strings":["Sabanci University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sabanci University","institution_ids":["https://openalex.org/I134235054"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5070956718"],"corresponding_institution_ids":["https://openalex.org/I134235054"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.9077000021934509,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.9077000021934509,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.02539999969303608,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.011599999852478504,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/monkeypox-virus","display_name":"monkeypox virus","score":0.9990000128746033},{"id":"https://openalex.org/keywords/inverted-repeats","display_name":"inverted repeats","score":0.9890000224113464},{"id":"https://openalex.org/keywords/cruciform-structure","display_name":"cruciform structure","score":0.8349999785423279},{"id":"https://openalex.org/keywords/rna-secondary-structure","display_name":"RNA secondary structure","score":0.7559999823570251},{"id":"https://openalex.org/keywords/stem-loop-structure","display_name":"stem-loop structure","score":0.6959999799728394},{"id":"https://openalex.org/keywords/mutation-hotspots","display_name":"mutational hotspots","score":0.6499999761581421},{"id":"https://openalex.org/keywords/reanalysis","display_name":"reanalysis","score":0.5329999923706055}],"concepts":[{"id":"https://openalex.org/C2778011067","wikidata":"https://www.wikidata.org/wiki/Q382370","display_name":"Monkeypox","level":5,"score":0.7459733486175537},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.5717320442199707},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.48129549622535706},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4806438982486725},{"id":"https://openalex.org/C2781255879","wikidata":"https://www.wikidata.org/wiki/Q7580087","display_name":"Spots","level":2,"score":0.4477595388889313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44639480113983154},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3254815936088562},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0526946485042572},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C2781356689","wikidata":"https://www.wikidata.org/wiki/Q1986297","display_name":"Vaccinia","level":4,"score":0.0},{"id":"https://openalex.org/C40767141","wikidata":"https://www.wikidata.org/wiki/Q285697","display_name":"Recombinant DNA","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2025.08.19.670320","doi":"https://doi.org/10.1101/2025.08.19.670320","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.08.19.670320","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/08/20/2025.08.19.670320.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2025.08.19.670320","doi":"https://doi.org/10.1101/2025.08.19.670320","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.08.19.670320","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/08/20/2025.08.19.670320.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G425487729","display_name":null,"funder_award_id":"22-14-00132","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413384635.pdf","grobid_xml":"https://content.openalex.org/works/W4413384635.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2135995702","https://openalex.org/W2509685232","https://openalex.org/W2956135855","https://openalex.org/W3133827704","https://openalex.org/W4281858182","https://openalex.org/W4309410684"],"related_works":["https://openalex.org/W7117301567","https://openalex.org/W7220675914","https://openalex.org/W4309410684","https://openalex.org/W4385491294","https://openalex.org/W7125826359","https://openalex.org/W4309502646","https://openalex.org/W4378173522","https://openalex.org/W4324304910","https://openalex.org/W4385682151","https://openalex.org/W4313681503"],"abstract_inverted_index":{"Abstract":[0],"Recent":[1],"work":[2],"proposed":[3],"that":[4],"APOBEC-signature":[5],"mutations":[6,41],"in":[7,13,42],"monkeypox":[8],"virus":[9],"(MPXV)":[10],"are":[11,74],"enriched":[12],"cruci-form":[14],"structures":[15,73],"formed":[16],"by":[17],"inverted":[18],"repeats.":[19],"We":[20],"independently":[21],"reanalyzed":[22],"the":[23,27],"same":[24],"dataset":[25],"with":[26],"published":[28],"settings":[29],"and":[30,34,68],"several":[31],"complementary":[32],"approaches":[33],"found":[35],"no":[36],"statistically":[37],"supported":[38],"enrichment":[39],"of":[40,55,71],"these":[43],"structures.":[44],"While":[45],"a":[46],"modest":[47],"trend":[48],"at":[49,52],"TC":[50],"motif":[51],"3\u2019":[53],"end":[54],"hairpin":[56],"loop":[57],"contexts":[58],"cannot":[59],"be":[60],"excluded,":[61],"current":[62],"evidence":[63],"is":[64],"insufficient.":[65],"Additional":[66],"data":[67],"careful":[69],"handling":[70],"overlapping":[72],"needed":[75],"to":[76],"clarify":[77],"any":[78],"association.":[79]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2025-10-10T00:00:00"}