Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus

Main Article Content

Emma L. Keeler
Milica Vukmirovic
Xiting Yan
Kristin Gulino
Elodie Ghedin
Naftali Kaminski
Kathleen E. Sullivan
Frederic D. Bushman
Ronald G. Collman
Misha Rosenbach


Virome, Transcriptome, Sarcoidosis, Rubella, Granuloma


Background:  Sarcoidosis is a multisystem granulomatous inflammatory disease of unclear etiology that involves the lung, skin and other organs, with an unknown antigenic trigger. Recently, evidence has been found in both immune deficient and immune competent patients for rubella virus in cutaneous granulomas. These granulomatous lesions share overlapping features with cutaneous sarcoidosis, raising the question of rubella virus in sarcoidosis.

Objective: To investigate the presence of rubella virus in sarcoidosis lung samples.

Methods: We employed metagenomic sequencing to interrogate extracellular virome preparations and cellular transcriptomes from bronchoalveolar lavage (BAL) of 209 sarcoidosis patients for rubella virus sequences.

Results: We found no evidence for rubella virus genomes in acellular fluid or rubella virus gene expression in BAL cells of sarcoidosis patients.

Conclusions: These findings argue against rubella virus infection or persistence within the lung at time of sampling as a sarcoidosis trigger.

Abstract 462 | PDF Downloads 405


1. Chen ES, Moller DR. Etiologic role of infectious agents. Semin Respir Crit Care Med. 2014;35(3):285-95. Epub 2014/07/10. doi: 10.1055/s-0034-1376859. PubMed PMID: 25007081.
2. Beijer E, Veltkamp M, Meek B, Moller DR. Etiology and Immunopathogenesis of Sarcoidosis: Novel Insights. Semin Respir Crit Care Med. 2017;38(4):404-16. Epub 2017/07/28. doi: 10.1055/s-0037-1603087. PubMed PMID: 28750457.
3. Clarke EL, Lauder AP, Hofstaedter CE, et al. Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples. Am J Respir Crit Care Med. 2018;197(2):225-34. Epub 2017/08/29. doi: 10.1164/rccm.201705-0891OC. PubMed PMID: 28846439; PubMed Central PMCID: PMC5768903.
4. Perelygina L, Faisthalab R, Abernathy E, et al. Rubella Virus Infected Macrophages and Neutrophils Define Patterns of Granulomatous Inflammation in Inborn and Acquired Errors of Immunity. Frontiers in immunology. 2021;12:796065. Epub 2022/01/11. doi: 10.3389/fimmu.2021.796065. PubMed PMID: 35003119; PubMed Central PMCID: PMC8728873.
5. Shields BE, Perelygina L, Samimi S, et al. Granulomatous Dermatitis Associated With Rubella Virus Infection in an Adult With Immunodeficiency. JAMA dermatology. 2021;157(7):842-7. Epub 2021/05/27. doi: 10.1001/jamadermatol.2021.1577. PubMed PMID: 34037685; PubMed Central PMCID: PMC8156178 Karger Inc and serving as a paid member of the advisory board for Kyowa Kirin. Dr Rosenbach reported receiving personal fees from Merck Consulting: Drug Reactions, grants from Processa Research; consulting fees from necrobiosis lipoidica trial planning, Janssen Pharmaceuticals, and Eli Lilly outside the submitted work. No other disclosures were reported.
6. Perelygina L, Icenogle J, Sullivan KE. Rubella virus-associated chronic inflammation in primary immunodeficiency diseases. Current opinion in allergy and clinical immunology. 2020;20(6):574-81. Epub 2020/10/13. doi: 10.1097/aci.0000000000000694. PubMed PMID: 33044342; PubMed Central PMCID: PMC7730704.
7. Dhossche J, Johnson L, White K, et al. Cutaneous Granulomatous Disease With Presence of Rubella Virus in Lesions. JAMA dermatology. 2019;155(7):859-61. Epub 2019/06/06. doi: 10.1001/jamadermatol.2019.0814. PubMed PMID: 31166586.
8. Leclerc-Mercier S, Moshous D, Neven B, et al. Cutaneous granulomas with primary immunodeficiency in children: a report of 17 new patients and a review of the literature. Journal of the European Academy of Dermatology and Venereology : JEADV. 2019;33(7):1412-20. Epub 2019/03/15. doi: 10.1111/jdv.15568. PubMed PMID: 30869812.
9. Buchbinder D, Hauck F, Albert MH, et al. Rubella Virus-Associated Cutaneous Granulomatous Disease: a Unique Complication in Immune-Deficient Patients, Not Limited to DNA Repair Disorders. J Clin Immunol. 2019;39(1):81-9. Epub 2019/01/05. doi: 10.1007/s10875-018-0581-0. PubMed PMID: 30607663; PubMed Central PMCID: PMC7739844.
10. Bodemer C, Sauvage V, Mahlaoui N, et al. Live rubella virus vaccine long-term persistence as an antigenic trigger of cutaneous granulomas in patients with primary immunodeficiency. Clin Microbiol Infect. 2014;20(10):O656-63. Epub 2014/01/31. doi: 10.1111/1469-0691.12573. PubMed PMID: 24476349.
11. Perelygina L, Plotkin S, Russo P, et al. Rubella persistence in epidermal keratinocytes and granuloma M2 macrophages in patients with primary immunodeficiencies. J Allergy Clin Immunol. 2016;138(5):1436-9.e11. Epub 2016/09/11. doi: 10.1016/j.jaci.2016.06.030. PubMed PMID: 27613149; PubMed Central PMCID: PMC5392721.
12. Perelygina L, Chen MH, Suppiah S, et al. Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies. PLoS Pathog. 2019;15(10):e1008080. Epub 2019/10/29. doi: 10.1371/journal.ppat.1008080. PubMed PMID: 31658304; PubMed Central PMCID: PMC6837625 Andrey Zharkikh is an employee of Myriad Genetics. This company works in cancer genetics and diagnostics without any relation to pathogen studies and treatments. This does not alter our adherence to all PLOS Pathogens policies on sharing data and materials.
13. Wanat KA, Perelygina L, Chen MH, et al. Association of Persistent Rubella Virus With Idiopathic Skin Granulomas in Clinically Immunocompetent Adults. JAMA dermatology. 2022;158(6):626-33. Epub 2022/03/27. doi: 10.1001/jamadermatol.2022.0828. PubMed PMID: 35338705; PubMed Central PMCID: PMC8957700 outside the submitted work. Dr Sullivan reported consulting fees from the Immune Deficiency Foundation and Enzyvant and being an editor for Elsevier. Dr Rosenbach reported personal fees from Merck, Novartis, Eli Lilly, AbbVie, and Processa outside the submitted work. No other disclosures were reported.
14. Moller DR, Koth LL, Maier LA, et al. Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol. Annals of the American Thoracic Society. 2015;12(10):1561-71. Epub 2015/07/21. doi: 10.1513/AnnalsATS.201503-172OT. PubMed PMID: 26193069; PubMed Central PMCID: PMC4627423.
15. Vukmirovic M, Yan X, Gibson KF, et al. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. Eur Respir J. 2021;58(6). Epub 2021/06/05. doi: 10.1183/13993003.02950-2020. PubMed PMID: 34083402.
16. Abbas AA, Taylor LJ, Dothard MI, et al. Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness. Cell Host Microbe. 2019;25(5):719-29.e4. Epub 2019/05/10. doi: 10.1016/j.chom.2019.04.001. PubMed PMID: 31071295; PubMed Central PMCID: PMC6510254.
17. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9. Epub 2012/03/06. doi: 10.1038/nmeth.1923. PubMed PMID: 22388286; PubMed Central PMCID: PMC3322381.
18. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9. Epub 2009/06/10. doi: 10.1093/bioinformatics/btp352. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
19. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-2. Epub 2010/01/30. doi: 10.1093/bioinformatics/btq033. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
20. Flygare S, Simmon K, Miller C, et al. Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol. 2016;17(1):111. Epub 2016/05/27. doi: 10.1186/s13059-016-0969-1. PubMed PMID: 27224977; PubMed Central PMCID: PMC4880956.
21. Oker-Blom C, Ulmanen I, Kääriäinen L, Pettersson RF. Rubella virus 40S genome RNA specifies a 24S subgenomic mRNA that codes for a precursor to structural proteins. J Virol. 1984;49(2):403-8. Epub 1984/02/01. doi: 10.1128/jvi.49.2.403-408.1984. PubMed PMID: 6694262; PubMed Central PMCID: PMC255479.
22. Mooney D, Edgar D, Einarsson G, Downey D, Elborn S, Tunney M. Chronic lung disease in common variable immune deficiency (CVID): A pathophysiological role for microbial and non-B cell immune factors. Critical reviews in microbiology. 2017;43(4):508-19. Epub 2017/01/11. doi: 10.1080/1040841x.2016.1268568. PubMed PMID: 28068853.
23. Wikén M, Ostadkarampour M, Eklund A, et al. Antigen-specific multifunctional T-cells in sarcoidosis patients with Lofgren's syndrome. Eur Respir J. 2012;40(1):110-21. Epub 2011/12/21. doi: 10.1183/09031936.00166110. PubMed PMID: 22183480.
24. Richmond BW, Ploetze K, Isom J, et al. Sarcoidosis Th17 cells are ESAT-6 antigen specific but demonstrate reduced IFN-γ expression. J Clin Immunol. 2013;33(2):446-55. Epub 2012/10/18. doi: 10.1007/s10875-012-9817-6. PubMed PMID: 23073617; PubMed Central PMCID: PMC3850764.

Most read articles by the same author(s)