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Metatranscriptomics analysis reveals the cotton virome in the southern United States
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  • Published: 23 February 2026

Metatranscriptomics analysis reveals the cotton virome in the southern United States

  • Cesar Escalante2 nAff1,
  • Anyi M. Reyes2,
  • Chaoyang Zhao3,
  • Kipling S. Balkcom3,
  • Alana L. Jacobson2,
  • Amanda Strayer-Scherer2,
  • Kathleen M. Martin2,
  • Jenny Koebernick4,
  • Anders Huseth5,6,
  • Edmund Kozieł7,
  • Ian Small8,
  • Jeremy K. Greene9,
  • Katarzyna Otulak-Kozieł7,
  • Michael J. Mulvaney10,
  • Paul P. Price11,
  • Ricardo I. Alcalá Briseño12,
  • Sudeep Bag13 &
  • …
  • Kassie Conner14 

Scientific Reports , Article number:  (2026) Cite this article

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Biotechnology
  • Genetics
  • Microbiology
  • Molecular biology
  • Plant sciences

Abstract

High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.

Data availability

The datasets generated during and/or analyzed during the current study are available at the SRA BioProject accession number PRJNA1015735 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1015735). The complete putative viral sequences in FASTA format and the Sanger sequences from PCR products are publicly available in the GitHub repository (https://github.com/ceesgua91/Cotton_virome.git).

References

  1. USDA-FAS. Production - Cotton. (2024). https://fas.usda.gov/data/production/commodity/2631000

  2. ICAC. International Cotton Advisory Committee (ICAC). (2024). https://icac.shinyapps.io/ICAC_Open_Data_Dashboaard/#

  3. Avelar, S., Schrimsher, D. W., Lawrence, K. & Brown, J. K. First report of cotton leafroll dwarf virus associated with cotton blue disease symptoms in. Alabama Plant. Dis. 103 (3), 592–592. https://doi.org/10.1094/PDIS-09-18-1550-PDN (2019).

    Google Scholar 

  4. Aboughanem-Sabanadzovic, N. et al. First report of cotton leafroll dwarf virus in upland cotton (Gossypium hirsutum) in Mississippi. Plant. Dis. 103, 1798. https://doi.org/10.1094/PDIS-01-19-0017-PDN (2019).

    Google Scholar 

  5. Alabi, O. J. et al. First report of cotton leafroll dwarf virus infecting upland cotton (Gossypium hirsutum) in Texas. Plant. Dis. 104, 998. https://doi.org/10.1094/PDIS-09-19-2008-PDN (2020).

    Google Scholar 

  6. Ali, A. & Mokhtari, S. First report of cotton leafroll dwarf virus infecting cotton (Gossypium hirsutum) in Kansas. Plant. Dis. 104, 1880. https://doi.org/10.1094/PDIS-12-19-2589-PDN (2020).

    Google Scholar 

  7. Ali, A., Mokhtari, S. & Ferguson, C. First report of cotton leafroll dwarf virus from cotton (Gossypium hirsutum) in Oklahoma. Plant. Dis. 104, 2531. https://doi.org/10.1094/PDIS-03-20-0479-PDN (2020).

    Google Scholar 

  8. Faske, T. R., Stainton, D., Aboughanem-Sabanadzovic, N. & Allen, T. W. First report of cotton leafroll dwarf virus from upland cotton (Gossypium hirsutum) in Arkansas. Plant. Dis. 104, 2742. https://doi.org/10.1094/PDIS-12-19-2610-PDN (2020).

    Google Scholar 

  9. Iriarte, F. B. et al. First report of cotton leafroll dwarf virus in Florida. Plant. Dis. 104, 2744. https://doi.org/10.1094/PDIS-10-19-2150-PDN (2020).

    Google Scholar 

  10. Price, T. et al. First report of cotton leafroll dwarf virus in Louisiana. Plant. Health Prog. 21, 142–143. https://doi.org/10.1094/PHP-03-20-0019-BR (2020).

    Google Scholar 

  11. Tabassum, A. et al. First report of cotton leafroll dwarf virus infecting cotton in Georgia, U.S.A. Plant. Dis. 103, 1803. https://doi.org/10.1094/PDIS-12-18-2197-PDN (2019).

    Google Scholar 

  12. Thiessen, L. D. et al. First report of cotton leafroll dwarf virus in cotton plants affected by cotton leafroll dwarf disease in North Carolina. Plant. Dis. 104, 3275. https://doi.org/10.1094/PDIS-02-20-0335-PDN (2020).

    Google Scholar 

  13. Wang, H., Greene, J., Mueller, J., Conner, K. & Jacobson, A. First report of cotton leafroll dwarf virus in cotton fields of South Carolina. Plant. Dis. 104, 2532. https://doi.org/10.1094/PDIS-03-20-0635-PDN (2020).

    Google Scholar 

  14. Koebernick, J. C., Hagan, A. K., Zaccaron, M. & Escalante, C. Monitoring the distribution, incidence, and symptom expression associated with cotton leafroll dwarf virus in the southern United States using a sentinel plot system. PhytoFrontiers 4, 671–681. https://doi.org/10.1094/PHYTOFR-02-24-0008-R (2024).

    Google Scholar 

  15. Olmedo-Velarde, A., Shakhzadyan, H., Norton, R. & Heck, M. L. First report of cotton leafroll dwarf virus infecting upland cotton plants in Arizona. Plant. Dis. 237 https://doi.org/10.1094/PDIS-04-24-0928-PDN (2024).

  16. Olmedo-Velarde, A. et al. Data mining redefines the timeline and geographic spread of cotton leafroll dwarf virus. Plant. Dis. 109, 992–997. https://doi.org/10.1094/PDIS-06-24-1265-SC (2024).

    Google Scholar 

  17. Silva, T. et al. Widespread distribution and a new recombinant species of Brazilian virus associated with cotton blue disease. Virol. J. 5, 123. https://doi.org/10.1186/1743-422X-5-123 (2008).

    Google Scholar 

  18. Cauquil, J. Etudes sur une maladie d’origine virale du cotonnier, la maladie bleue. Coton et Fibres Tropicales. 32, 259–278 (1977). https://agritrop.cirad.fr/455540/

    Google Scholar 

  19. Escalante, C., Zaccaron, M. L., Jacobson, A. L. & Bowen, K. L. Molecular epidemiology of cotton leafroll dwarf virus in southeastern United States. Phytopathology 112 https://doi.org/10.1094/PHYTO-112-11-S3.1 (2022). S3.1-S3.199.

  20. Tsai, W. A., Brosnan, C. A., Mitter, N. & Dietzgen, R. G. Perspectives on plant virus diseases in a climate change scenario of elevated temperatures. Stress Biology. 2, 37. https://doi.org/10.1007/s44154-022-00058-x (2022).

    Google Scholar 

  21. Chávez-Calvillo, G. et al. Antagonism or synergism between papaya ringspot virus and papaya mosaic virus in Carica papaya is determined by their order of infection. Virology 489, 179–191 (2016).

    Google Scholar 

  22. Grupa, A., Otulak-Kozieł, K. & Syller, J. Serological, molecular and immunofluorescent evidence for interference competition between isolates of Potato virus Y. Plant. Pathol. 67, 1997–2012. https://doi.org/10.1111/ppa.12892 (2018).

    Google Scholar 

  23. Adams, I. P. et al. Next-generation sequencing and metagenomic analysis: A universal diagnostic tool in plant virology. Mol. Plant. Pathol. 10, 537–545. https://doi.org/10.1111/j.1364-3703.2009.00545.x (2009).

    Google Scholar 

  24. Roossinck, M. J., Martin, D. P. & Roumagnac, P. Plant virus metagenomics: advances in virus discovery. Phytopathology 105, 716–727. https://doi.org/10.1094/PHYTO-12-14-0356-RVW (2015).

    Google Scholar 

  25. Akinyemi, I. A., Wang, F., Zhou, B., Qi, S. & Wu, Q. Ecogenomic survey of plant viruses infecting tobacco by next generation sequencing. Virol. J. 13, 1–12. https://doi.org/10.1186/s12985-016-0639-7 (2016).

    Google Scholar 

  26. Redila, C. D., Prakash, V. & Nouri, S. Metagenomics analysis of the wheat virome identifies novel plant and fungal-associated viral sequences. Viruses 13, 2457. https://doi.org/10.3390/v13122457 (2021).

    Google Scholar 

  27. Fetters, A. M. et al. The pollen virome of wild plants and its association with variation in floral traits and land use. Nat. Commun. 13, 523. https://doi.org/10.1038/s41467-022-28143-9 (2022).

    Google Scholar 

  28. Garrett, K. A. et al. Network analysis: a systems framework to address grand challenges in plant pathology. Annu. Rev. Phytopathol. 56, 559–580. https://doi.org/10.1146/annurev-phyto-080516-035326 (2018).

    Google Scholar 

  29. Alcalá Briseño, R. I. et al. Translating virome analyses to support biosecurity, on-farm management, and crop breeding. Front. Plant. Sci. 14, 1056603. https://doi.org/10.3389/fpls.2023.1056603 (2023).

    Google Scholar 

  30. Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50, W345–W351. https://doi.org/10.1093/nar/gkac247 (2022).

    Google Scholar 

  31. Andrews, S. FastQC: A quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  32. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).

    Google Scholar 

  33. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. https://doi.org/10.1186/gb-2009-10-3-r25 (2009).

    Google Scholar 

  34. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9, 357–359. https://doi.org/10.1038/nmeth.1923 (2012).

    Google Scholar 

  35. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinform. 25, 2078–; (2079). https://doi.org/10.1093/bioinformatics/btp352 (2009).

  36. Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46. https://doi.org/10.1186/gb-2014-15-3-r46 (2014).

    Google Scholar 

  37. Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834. https://doi.org/10.1101/gr.213959.116 (2017).

    Google Scholar 

  38. Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421. https://doi.org/10.1186/1471-2105-10-421 (2009).

    Google Scholar 

  39. Cock, P. J. A., Chilton, J. M., Grüning, B. & Johnson, J. E. Soranzo, N. NCBI BLAST+ integrated into Galaxy. Gigascience 4, 39. https://doi.org/10.1186/s13742-015-0080-7 (2015).

    Google Scholar 

  40. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2 (1990).

    Google Scholar 

  41. Schoch, C. L. et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database 2020, 1–21. https://doi.org/10.1093/database/baaa062 (2020).

    Google Scholar 

  42. Hatcher, E. L. et al. Virus variation resource – improved response to emergent viral outbreaks. Nucleic Acids Res. 45, D482–D490. https://doi.org/10.1093/nar/gkw1065 (2017).

    Google Scholar 

  43. Ye, J. et al. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinform. 13, 134. https://doi.org/10.1186/1471-2105-13-134 (2012).

    Google Scholar 

  44. Sharman, M. et al. First report of cotton leafroll dwarf virus in Thailand using a species-specific PCR validated with isolates from Brazil. Australas Plant. Dis. Notes. 10, 24. https://doi.org/10.1007/s13314-015-0174-1 (2015).

    Google Scholar 

  45. Jacquat, A. G., Theumer, M. G. & Dambolena, J. S. Putative mitoviruses without in-frame UGA(W) codons: evolutionary implications. Viruses 15, 340. https://doi.org/10.3390/v15020340 (2023).

    Google Scholar 

  46. Katoh, K. & Standley, D. M. MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780. https://doi.org/10.1093/molbev/mst010 (2013).

    Google Scholar 

  47. Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973. https://doi.org/10.1093/bioinformatics/btp348 (2009).

    Google Scholar 

  48. Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38, 3022–3027. https://doi.org/10.1093/molbev/msab120 (2021).

    Google Scholar 

  49. Ayllón, M. A. et al. ICTV virus taxonomy profile: Botourmiaviridae. J. Gen. Virol. 101, 454–455. https://doi.org/10.1099/jgv.0.001409 (2020).

    Google Scholar 

  50. LISA, V. et al. Ourmia melon virus, a virus from Iran with novel properties. Ann. Appl. Biol. 112, 291–302. https://doi.org/10.1111/j.1744-7348.1988.tb02065.x (1988).

    Google Scholar 

  51. Moreno, A. B. & López-Moya, J. J. When viruses play team sports: mixed infections in plants. Phytopathology 110, 29–48. https://doi.org/10.1094/PHYTO-07-19-0250-FI (2020).

    Google Scholar 

  52. Chiba, S. et al. ICTV virus taxonomy profile: Hypoviridae 2023. J. Gen. Virol. 104, 5. https://doi.org/10.1099/jgv.0.001848 (2023).

    Google Scholar 

  53. Hillman, B. I. & Suzuki, N. Viruses of the chestnut blight fungus, Cryphonectria parasitica. Adv. Virus Res. 63, 423–472. https://doi.org/10.1016/S0065-3527(04)63007-7 (2004).

    Google Scholar 

  54. Grente, J. Les formes hypovirulentes d’Endothia parasitica et les espoirs de lutte contre le chancre du châtaignier. C. R. Hebd. Séances Acad. Agr France. 51, 1033–1037 (1965).

    Google Scholar 

  55. Anagnostakis, S. L. Chestnut blight: the classical problem of an introduced pathogen. Mycologia 79, 23–37 (1987).

    Google Scholar 

  56. ICTV & Family Mitoviridae (2023 Release). (2019). https://ictv.global/taxonomy/taxondetails?taxnode_id=202307204&taxon_name=Mitoviridae

  57. Shahi, S., Eusebio-Cope, A., Kondo, H., Hillman, B. I. & Suzuki, N. Investigation of host range of and host defense against a mitochondrially replicating mitovirus. J. Virol. 5, 93. https://doi.org/10.1128/JVI.01503-18 (2019).

    Google Scholar 

  58. García-Pedrajas, M. D., Cañizares, M. C., Sarmiento-Villamil, J. L., Jacquat, A. G. & Dambolena, J. S. Mycoviruses in biological control: from basic research to field implementation. Phytopathology 109, 1828–1839. https://doi.org/10.1094/PHYTO-05-19-0166-RVW (2019).

    Google Scholar 

  59. Hillman, B. I. & Cai, G. The family Narnaviridae: simplest of RNA viruses. Adv. Virus Res. 86, 149–176. https://doi.org/10.1016/B978-0-12-394315-6.00006-4 (2013).

    Google Scholar 

  60. Hillman, B. I. & Esteban, R. ICTV 9th report (2011): Narnaviridae. (2011). https://ictv.global/report_9th/RNApos/Narnaviridae

  61. Vainio, E. J. et al. ICTV virus taxonomy profile: Partitiviridae. J. Gen. Virol. 99, 17–18. https://doi.org/10.1099/jgv.0.000985 (2018).

    Google Scholar 

  62. Szegő, A. et al. The genome of beet cryptic virus 1 shows high homology to certain cryptoviruses present in phylogenetically distant hosts. Virus Genes. 40, 267–276. https://doi.org/10.1007/s11262-009-0432-4 (2010).

    Google Scholar 

  63. Sabanadzovic, S. & Valverde, R. A. Properties and detection of two cryptoviruses from pepper (Capsicum annuum). Virus Genes. 43, 307–312. https://doi.org/10.1007/s11262-011-0634-4 (2011).

    Google Scholar 

  64. Lesker, T., Rabenstein, F. & Maiss, E. Molecular characterization of five betacryptoviruses infecting four clover species and dill. Arch. Virol. 158, 1943–1952. https://doi.org/10.1007/s00705-013-1691-x (2013).

    Google Scholar 

  65. J Roossinck, M. Lifestyles of plant viruses. Philos. Trans. Royal Soc. 365, 1899–1905. https://doi.org/10.1098/rstb.2010.0057 (2010).

    Google Scholar 

  66. Xiao, X. et al. A novel partitivirus that confers hypovirulence on plant pathogenic fungi. J. Virol. 88, 10120–10133. https://doi.org/10.3389/fmicb.2021.653809 (2014).

    Google Scholar 

  67. Sõmera, M., Fargette, D., Hébrard, E. & Sarmiento, C. ICTV virus taxonomy profile: Solemoviridae 2021. J. Gen. Virol. 102, 001707. https://doi.org/10.1099/jgv.0.001707 (2021).

    Google Scholar 

  68. Wickner, R. B., Ghabrial, S. A., Nibert, M. L., Patterson, J. L. & Wang, C. C. Family: Totiviridae: ICTV ninth report; 2009 taxonomy release. (2009). https://ictv.global/report_9th/dsRNA/Totiviridae

  69. Ghabrial, S. A. & Nibert, M. L. Victorivirus, a new genus of fungal viruses in the family Totiviridae. Arch. Virol. 154, 373–379. https://doi.org/10.1007/s00705-008-0272-x (2009).

    Google Scholar 

  70. Zhang, P., Liu, W., Cao, M., Massart, S. & Wang, X. Two novel totiviruses in the white-backed planthopper, Sogatella furcifera. J. Gen. Virol. 99, 710–716. https://doi.org/10.1099/jgv.0.001052 (2018).

    Google Scholar 

  71. Leal, É. et al. Aedes aegypti totivirus identified in mosquitoes in the Brazilian Amazon region. Virus Genes. 59, 167–172. https://doi.org/10.1007/s11262-022-01955-z (2023).

    Google Scholar 

  72. Sabanadzovic, S., Valverde, R. A., Brown, J. K., Martin, R. R. & Tzanetakis, I. E. Southern tomato virus: The link between the families Totiviridae and Partitiviridae. Virus Res. 140, 130–137. https://doi.org/10.1016/j.virusres.2008.11.018 (2009).

    Google Scholar 

  73. Mikalsen, A. B., Haugland, Ø. & Evensen, Ø. Totiviruses of fish. Aquaculture Virol. 251–258. https://doi.org/10.1016/B978-0-12-801573-5.00016-4 (2016).

  74. Yang, X., Zhang, Y., Ge, X., Yuan, J. & Shi, Z. A novel totivirus-like virus isolated from bat guano. Arch. Virol. 157, 1093–1099. https://doi.org/10.1007/s00705-012-1278-y (2012).

    Google Scholar 

  75. Rastgou, M. et al. Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin. J. Gen. Virol. 90, 2525–2535. https://doi.org/10.1099/vir.0.013086-0 (2009).

    Google Scholar 

  76. Avelar, S. et al. Characterization of the complete genome and P0 protein for a previously unreported genotype of cotton leafroll dwarf virus, an introduced polerovirus in the United States. Plant. Dis. 104, 780–786. https://doi.org/10.1094/PDIS-06-19-1316-RE (2020).

    Google Scholar 

  77. Ramos-Sobrinho, R. et al. Cotton leafroll dwarf virus US genomes comprise divergent subpopulations and harbor extensive variability. Viruses 13, 2230. https://doi.org/10.3390/v13112230 (2021).

    Google Scholar 

  78. Tabassum, A. et al. Genome analysis of cotton leafroll dwarf virus reveals variability in the silencing suppressor protein, genotypes and genomic recombinants in the USA. PLoS One. 16, e0252523. https://doi.org/10.1371/journal.pone.0252523 (2021).

    Google Scholar 

  79. Ferguson, C. & Ali, A. Complete genome sequence of cotton leafroll dwarf virus infecting cotton in Oklahoma, USA. Microbiol. Resour. Announc. 11, e0014722 (2022). 10.1128/mra.00147 – 22.

    Google Scholar 

  80. Adegbola, R. O., Ponvert, N. D. & Brown, J. K. Genetic variability among U.S.-sentinel cotton plot cotton leafroll dwarf virus and globally available reference isolates based on ORF0 diversity. Plant. Dis. 108, 1799–1811. https://doi.org/10.1094/PDIS-02-23-0243-RE (2024).

    Google Scholar 

  81. Ferguson, C. & Ali, A. Cotton blue disease from Africa and its de facto relationship with cotton leafroll dwarf virus: a misleading etiological discrepancy. Front. Virol. 3, 1253174. https://doi.org/10.3389/fviro.2023.1253174 (2023).

    Google Scholar 

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Acknowledgements

The authors would like to thank all the cooperators across universities for establishing the cotton plots and collecting samples. We also thank the staff at the Auburn University Plant Diagnostics Lab for their assistance in sample sorting and processing.

Funding

This project was financially supported by the USDA-ARS, under agreement No. 58-6010-0-011. Partial support was provided by the USDA-NIFA Hatch funding.

Author information

Author notes

  1. Cesar Escalante

    Present address: Department of Botany and Plant Pathology, Purdue University, West Lafayette, 47907, IN, USA

Authors and Affiliations

  1. Department of Entomology and Plant Pathology, Auburn University, Auburn, 36849, AL, USA

    Cesar Escalante, Anyi M. Reyes, Alana L. Jacobson, Amanda Strayer-Scherer & Kathleen M. Martin

  2. National Soil Dynamics Laboratory, USDA-ARS, Auburn, 36849, AL, USA

    Chaoyang Zhao & Kipling S. Balkcom

  3. Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, 36849, AL, USA

    Jenny Koebernick

  4. Department of Entomology, Michigan State University, East Lansing, 48824, MI, USA

    Anders Huseth

  5. Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA

    Anders Huseth

  6. Institute of Biology, Department of Botany and Plant Physiology, Warsaw University of Life Sciences-SGGW, 159 Nowoursynowska Street, Warsaw, 02-776, Poland

    Edmund Kozieł & Katarzyna Otulak-Kozieł

  7. Department of Plant Pathology, University of Florida, Quincy, 32351, FL, USA

    Ian Small

  8. Department of Plant and Environmental Sciences, Edisto Research and Education Center, Clemson University, Blackville, 29817, SC, USA

    Jeremy K. Greene

  9. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, 39762, MS, USA

    Michael J. Mulvaney

  10. Department of Plant Pathology and Crop Physiology, Macon Ridge Research Station, LSU AgCenter, Winnsboro, 71295, LA, USA

    Paul P. Price

  11. Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, 16802, PA, USA

    Ricardo I. Alcalá Briseño

  12. Department of Plant Pathology, University of Georgia, Tifton, 31794, GA, USA

    Sudeep Bag

  13. Alabama Cooperative Extension System, Auburn University, Auburn, 36849, AL, USA

    Kassie Conner

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  1. Cesar Escalante
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Contributions

C.E. conceived the idea, carried out and supervised the experiments, and wrote the original draft; A.M.R performed the sequence validation by RT-PCR; C.Z. conducted the phylogenetic analysis and revised the original draft; K.S.B, A.L.J., and K.C. supervised the experiments, secured funding for the research, and edited the manuscript; K.M.M., E.K., K.O.-K., and R.I.A.B. contributed to the bioinformatics analysis; A.S.-S., J.K., A.H., I.S., J.K.G., M.J.M., P.P.P., and S.B. collected plant samples and edited the manuscript. All authors read and approved the final manuscript.

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Correspondence to Cesar Escalante.

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Escalante, C., Reyes, A.M., Zhao, C. et al. Metatranscriptomics analysis reveals the cotton virome in the southern United States. Sci Rep (2026). https://doi.org/10.1038/s41598-026-40828-5

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  • Received: 16 September 2025

  • Accepted: 16 February 2026

  • Published: 23 February 2026

  • DOI: https://doi.org/10.1038/s41598-026-40828-5

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Plant viruses in agriculture

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