{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T02:43:45Z","timestamp":1768272225827,"version":"3.49.0"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T00:00:00Z","timestamp":1763510400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>Efforts to improve honey bee colony health continue due to persistent high loss rates. A major focus in this area is Deformed wing virus (DWV), a key driver of colony loss. The application of modern molecular techniques has characterized the DWV genome and its high mutational rate that enables the formation of diverse quasi-species populations capable of evading host immune responses, while other work has led to the development of DWV clones suitable for sequence-specific tracking of viral dynamics. In this work we combine knowledge of these efforts to track the mutational progression in a DWV clone surrounding an area of low nucleotide diversity and compare it to its wild-type source. We achieve this through amplicon sequencing of the structural viral protein, VP2, after incubation across three generations and multiple host genetic sources. Inocula were injected into pupae, allowed to replicate, then extracted for a further two generations of injections. For the final injection generation, recipient pupae were injected with preparations from either the same genetic source or cross-fostered from other colonies. Overall, we compared the mean number and type of mutations, their proportional abundance in the read pool, and specific locations across strains. Sequencing results indicate a limited number of mutational hotspots, which were driven by silent mutations in the final injection generation of the wild-type strains. No significant differences were found among other mutation types, cross-fostering status, or interactions with host genetics. This work is an initial attempt at examining viral dynamics in a cloned system across multiple generations and treatment groups. The results provide valuable insights, which may further enhance our understanding of viral dynamics and potentially improve future honey bee therapeutics.<\/jats:p>","DOI":"10.1371\/journal.pone.0337191","type":"journal-article","created":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T18:34:01Z","timestamp":1763577241000},"page":"e0337191","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Generational mutation patterns in a honey bee Deformed wing virus via infectious clones"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6498-3275","authenticated-orcid":true,"given":"Anthony","family":"Nearman","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-3280-3823","authenticated-orcid":true,"given":"Alriana","family":"Buller-Jarrett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dawn","family":"Boncristiani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4265-9714","authenticated-orcid":true,"given":"Eugene","family":"Ryabov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5224-1100","authenticated-orcid":true,"given":"Yanping","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jay D.","family":"Evans","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,11,19]]},"reference":[{"issue":"1","key":"pone.0337191.ref001","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/00218839.2023.2264601","article-title":"A national survey of managed honey bee colony losses in the USA: results from the bee informed partnership for 2020\u201321 and 2021\u201322","volume":"63","author":"D Aurell","year":"2023","journal-title":"J Apicultural Res"},{"key":"pone.0337191.ref002","unstructured":"Steinhauer N, Wilson M, Aurell D, Bruckner S, Williams G. United States honey bee colony losses 2022\u20132023: preliminary results from the Bee Informed Partnership. 2023."},{"issue":"1","key":"pone.0337191.ref003","doi-asserted-by":"crossref","first-page":"10156","DOI":"10.1038\/s41598-019-46453-9","article-title":"Impact of nutritional stress on the honeybee colony health","volume":"9","author":"B Branchiccela","year":"2019","journal-title":"Sci Rep"},{"issue":"1","key":"pone.0337191.ref004","doi-asserted-by":"crossref","first-page":"20787","DOI":"10.1038\/s41598-022-24946-4","article-title":"Honey bee colony loss linked to parasites, pesticides and extreme weather across the United States","volume":"12","author":"L Insolia","year":"2022","journal-title":"Sci Rep"},{"issue":"9","key":"pone.0337191.ref005","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2024.e29886","article-title":"Effects of common co-occurring pesticides (a neonicotinoid and fungicide) on honey bee colony health in a semi-field study","volume":"10","author":"S Shepherd","year":"2024","journal-title":"Heliyon"},{"key":"pone.0337191.ref006","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.cois.2018.02.004","article-title":"Drivers of colony losses","volume":"26","author":"N Steinhauer","year":"2018","journal-title":"Curr Opin Insect Sci"},{"issue":"22","key":"pone.0337191.ref007","doi-asserted-by":"crossref","first-page":"7212","DOI":"10.1128\/AEM.02227-09","article-title":"Deformed wing virus implicated in overwintering honeybee colony losses","volume":"75","author":"AC Highfield","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"pone.0337191.ref008","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1046\/j.1365-2664.2001.00662.x","article-title":"The role of Varroa and viral pathogens in the collapse of honeybee colonies: a modelling approach","volume":"38","author":"SJ Martin","year":"2001","journal-title":"J Appl Ecol"},{"key":"pone.0337191.ref009","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.cois.2015.01.015","article-title":"Honey bee colony losses and associated viruses","volume":"8","author":"AJ McMenamin","year":"2015","journal-title":"Curr Opin Insect Sci"},{"issue":"4","key":"pone.0337191.ref010","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1128\/AEM.06537-11","article-title":"Dead or alive: deformed wing virus and Varroa destructor reduce the life span of winter honeybees","volume":"78","author":"B Dainat","year":"2012","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"pone.0337191.ref011","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0057540","article-title":"Varroa-virus interaction in collapsing honey bee colonies","volume":"8","author":"RM Francis","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"pone.0337191.ref012","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s40168-022-01446-1","article-title":"Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China","volume":"11","author":"N Li","year":"2023","journal-title":"Microbiome"},{"issue":"6","key":"pone.0337191.ref013","doi-asserted-by":"crossref","first-page":"969","DOI":"10.3390\/v13060969","article-title":"Ten years of deformed wing virus (DWV) in hawaiian honey bees (Apis mellifera), the dominant DWV-A variant is potentially being replaced by variants with a DWV-B coding sequence","volume":"13","author":"I Grindrod","year":"2021","journal-title":"Viruses"},{"issue":"6273","key":"pone.0337191.ref014","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1126\/science.aac9976","article-title":"Deformed wing virus is a recent global epidemic in honeybees driven by Varroa mites","volume":"351","author":"L Wilfert","year":"2016","journal-title":"Science"},{"issue":"1","key":"pone.0337191.ref015","doi-asserted-by":"crossref","first-page":"231529","DOI":"10.1098\/rsos.231529","article-title":"Shift in virus composition in honeybees (Apis mellifera) following worldwide invasion by the parasitic mite and virus vector Varroa destructor","volume":"11","author":"V Doublet","year":"2024","journal-title":"R Soc Open Sci"},{"issue":"10","key":"pone.0337191.ref016","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3000502","article-title":"Dynamic evolution in the key honey bee pathogen deformed wing virus: Novel insights into virulence and competition using reverse genetics","volume":"17","author":"EV Ryabov","year":"2019","journal-title":"PLoS Biol"},{"issue":"4","key":"pone.0337191.ref017","doi-asserted-by":"crossref","first-page":"374","DOI":"10.3390\/v12040374","article-title":"Development of a honey bee RNA virus vector based on the genome of a deformed wing virus","volume":"12","author":"EV Ryabov","year":"2020","journal-title":"Viruses"},{"issue":"3","key":"pone.0337191.ref018","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1111\/1755-0998.13526","article-title":"Beeporter: Tools for high-throughput analyses of pollinator-virus infections","volume":"22","author":"JD Evans","year":"2022","journal-title":"Mol Ecol Resour"},{"issue":"10","key":"pone.0337191.ref019","doi-asserted-by":"crossref","first-page":"2270","DOI":"10.1111\/j.0014-3820.2005.tb00935.x","article-title":"Colony-level impacts of immune responsiveness in honey bees, Apis mellifera","volume":"59","author":"JD Evans","year":"2005","journal-title":"Evolution"},{"issue":"2","key":"pone.0337191.ref020","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.jip.2004.02.004","article-title":"Transcriptional immune responses by honey bee larvae during invasion by the bacterial pathogen, Paenibacillus larvae","volume":"85","author":"JD Evans","year":"2004","journal-title":"J Invertebr Pathol"},{"issue":"1","key":"pone.0337191.ref021","doi-asserted-by":"crossref","first-page":"6448","DOI":"10.1038\/s41598-017-06623-z","article-title":"Virus and dsRNA-triggered transcriptional responses reveal key components of honey bee antiviral defense","volume":"7","author":"LM Brutscher","year":"2017","journal-title":"Sci Rep"},{"key":"pone.0337191.ref022","doi-asserted-by":"crossref","first-page":"105534","DOI":"10.1016\/j.meegid.2023.105534","article-title":"Quantitative trait loci mapping for survival of virus infection and virus levels in honey bees","volume":"116","author":"RX Lu","year":"2023","journal-title":"Infect Genet Evol"},{"issue":"3","key":"pone.0337191.ref023","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004713","article-title":"Parallel epigenomic and transcriptomic responses to viral infection in honey bees (Apis mellifera)","volume":"11","author":"DA Galbraith","year":"2015","journal-title":"PLoS Pathog"},{"issue":"11","key":"pone.0337191.ref024","first-page":"001687","article-title":"Simulated vector transmission differentially influences dynamics of two viral variants of deformed wing virus in honey bees (Apis mellifera)","volume":"102","author":"AM Ray","year":"2021","journal-title":"J Gen Virol"},{"issue":"11","key":"pone.0337191.ref025","doi-asserted-by":"crossref","first-page":"2259","DOI":"10.3390\/v15112259","article-title":"Effects of deformed wing virus-targeting dsRNA on viral loads in bees parasitised and non-parasitised by varroa destructor","volume":"15","author":"ZE Smeele","year":"2023","journal-title":"Viruses"},{"issue":"4","key":"pone.0337191.ref026","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1111\/j.1365-2583.2012.01150.x","article-title":"Reduction in deformed wing virus infection in larval and adult honey bees (Apis mellifera L.) by double-stranded RNA ingestion","volume":"21","author":"SD Desai","year":"2012","journal-title":"Insect Mol Biol"},{"issue":"5","key":"pone.0337191.ref027","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.3390\/v15051217","article-title":"Viral Co-Infections and Antiviral Immunity in Honey Bees","volume":"15","author":"AM Durand","year":"2023","journal-title":"Viruses"},{"issue":"1","key":"pone.0337191.ref028","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veaa002","article-title":"Erratum: On the stability of sequences inserted into viral genomes","volume":"6","author":"A Willemsen","year":"2020","journal-title":"Virus Evol"},{"issue":"2","key":"pone.0337191.ref029","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vez045","article-title":"On the stability of sequences inserted into viral genomes","volume":"5","author":"A Willemsen","year":"2019","journal-title":"Virus Evol"},{"issue":"3","key":"pone.0337191.ref030","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/1049-9644(92)90055-I","article-title":"Virulence and multigeneration passage of a nuclear polyhedrosis virus selected for an increased rate of vertical transmission","volume":"2","author":"JR Fuxa","year":"1992","journal-title":"Biological Control"},{"issue":"46","key":"pone.0337191.ref031","doi-asserted-by":"crossref","first-page":"18466","DOI":"10.1073\/pnas.1314923110","article-title":"Neonicotinoid clothianidin adversely affects insect immunity and promotes replication of a viral pathogen in honey bees","volume":"110","author":"G Di Prisco","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"pone.0337191.ref032","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.3390\/v3122425","article-title":"Dynamics of persistent and acute deformed wing virus infections in honey bees, Apis mellifera","volume":"3","author":"GD Prisco","year":"2011","journal-title":"Viruses"},{"issue":"22","key":"pone.0337191.ref033","doi-asserted-by":"crossref","first-page":"10732","DOI":"10.3390\/app112210732","article-title":"Impacts of Diverse Natural Products on Honey Bee Viral loads and health","volume":"11","author":"DL Boncristiani","year":"2021","journal-title":"Appl Sci"},{"key":"pone.0337191.ref034","doi-asserted-by":"crossref","first-page":"931352","DOI":"10.3389\/finsc.2022.931352","article-title":"The vectoring competence of the mite Varroa destructor for deformed wing virus of honey bees is dynamic and affects survival of the mite","volume":"2","author":"EV Ryabov","year":"2022","journal-title":"Front Insect Sci"},{"issue":"4","key":"pone.0337191.ref035","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"pone.0337191.ref036","volume-title":"R: A language and environment for statistical computing","author":"RC Team","year":"2025"},{"key":"pone.0337191.ref037","unstructured":"De Vries A, Ripley BD. ggdendro: Create dendrograms and tree diagrams using \u2018ggplot2\u2019. R package version 01-20. 2016."},{"key":"pone.0337191.ref038","unstructured":"Kassambara A, Kosinski M, Biecek P, Fabian S. survminer: Drawing Survival Curves using \u2018ggplot2\u2019. R package version 0.4.9. 2021. https:\/\/CRAN.R-project.org\/package=survminer"},{"issue":"7","key":"pone.0337191.ref039","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"BJ Callahan","year":"2016","journal-title":"Nat Methods"},{"issue":"4","key":"pone.0337191.ref040","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"21","key":"pone.0337191.ref041","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","article-title":"RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference","volume":"35","author":"AM Kozlov","year":"2019","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0337191.ref042","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"G Yu","year":"2016","journal-title":"Methods Ecol Evol"},{"issue":"9","key":"pone.0337191.ref043","doi-asserted-by":"crossref","first-page":"4039","DOI":"10.1093\/molbev\/msab166","article-title":"ggtreeExtra: compact visualization of richly annotated phylogenetic data","volume":"38","author":"S Xu","year":"2021","journal-title":"Mol Biol Evol"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0337191","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T18:34:13Z","timestamp":1763577253000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0337191"}},"subtitle":[],"editor":[{"given":"Olav","family":"Rueppell","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,11,19]]},"references-count":43,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,11,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0337191","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,19]]}}}