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Efrem Lim
Assistant Professor
Faculty
TEMPE Campus
Mailcode
6101
Biography
Efrem Lim is a virologist who uses the tools of virus discovery to study host-virus interactions in human health and disease. The Lim lab studies interactions and evolution of the human virome in development and immunity.
The Lim lab integrates molecular virology and bioinformatic approaches to understand 1) how the virome shapes the trajectory of infant development, 2) how mother-infant relationships impact the virome and microbiome in HIV disease settings, 3) how metagenomic changes induced by immunosuppression affect transplant outcome, and 4) how viruses temper the homeostasis of the urinary tract in urinary disease.
Their research is being used in precision medicine that personalizes the prevention and treatment of diseases to individuals.
https://viromelab.org/
Education
PhD, University of Washington
Publications
- Amatya R, Deem SL, Porton IJ, Wang D, Lim ES. Complete Genome Sequence of Torque teno indri virus 1, a Novel Anellovirus in Blood from a Free-Living Lemur. Genome Announcements. 2017 Jul 27;5(30). PMID: 28751399
- Baldauf HM, Stegmann L, Schwarz SM, Ambiel I, Trotard M, Martin M, Burggraf M, Lenzi GM, Lejk H, Pan X, Fregoso OI, Lim ES, Abraham L, Nguyen LA, Rutsch F, König R, Kim B, Emerman M, Fackler OT, Keppler OT. Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells. Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):2729-2734. PMID: 28228523
- Janowski AB, Krishnamurthy SR, Lim ES, Zhao G, Brenchley JM, Barouch DH, Thakwalakwa C, Manary MJ, Holtz LR, Wang D. Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals. Virology. 2017 Apr;504:36-44. PMID: 28152382
- Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D. VirusSeeker, a computational pipeline for virus discovery and virome composition analysis. Virology. 2017 Mar;503:21-30. PMID: 28110145
- Lim ES, Brennan DC. A Snapshot of Antibody-Mediated Rejection Goes Viral. Transplantation. 2017 Feb;101(2):227. PMID: 27779575.
- Lim ES, Wang D, Holtz LR. The Bacterial Microbiome and Virome Milestones of Infant Development. Trends in Microbiology. 2016 Jun 25. PMID: 2735364
- Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge MT, Wilen CB, Flagg M, Norman JM, Keller BC, Luévano JM, Wang D, Boum Y, Martin JN, Hunt PW, Bangsberg DR, Siedner MJ, Kwon DS, Virgin HW. Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host and Microbe. 2016 Mar 9;19(3):311-322. doi: 10.1016/j.chom.2016.02.011. PMID: 26962942
- Lim ES, Zhou YJ, Zhao GY, Bauer I, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nature Medicine. 2015. Sep 14. doi: 10.1038/nm.3950. PMID: 26366711
*Highlighted in Nature Reviews Gastroenterology & Hepatology. Gut microbiota: The gut virome and bacterial microbiome-the early years. 2015 Sep 29. doi: 10.1038/nrgastro.2015.169.
*Evaluated on TWiV #355: Baby’s first virome. - Lim ES, Deem SL, Porton IJ, Cao S, Wang D. Species-specific transmission of novel picornaviruses in lemurs. Journal of Virology. 2015 Apr;89(7):4002-10. PMID: 25631076
- Lim ES, Meinerz NM, Primi B, Wang D, Garcea RL. Common exposure to STL polyomavirus during childhood. Emerging Infectious Diseases. 2014 Sep;20(9):1559-61. PMID: 25148144
- Lim ES, Cao S, Holtz LR, Antonio M, Stine OC, Wang D. Discovery of rosavirus 2, a novel variant of a rodent-associated picornavirus, in children from The Gambia. Virology. 2014 Apr;454-455:25-33. PMID: 24725928
- Lim ES, Reyes A, Antonio M, Saha D, Ikumapayi UN, Adeyemi M, Stine OC, Skelton R, Brennan DC, Mkakosya RS, Manary MJ, Gordon JI, Wang D. Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing. Virology. 2013 Feb 20;436(2):295-303. PMID: 23276405
- Siebrasse EA, Reyes A, Lim ES, Zhao G, Mkakosya RS, Manary MJ, Gordon JI, Wang D. Identification of MW polyomavirus, a novel polyomavirus in human stool. Journal of Virology. 2012 Oct;86(19):10321-6. PMID: 22740408
- Lim ES, Wu LI, Malik HS, Emerman M. The function and evolution of the restriction factor Viperin in primates was not driven by lentiviruses. Retrovirology. 2012 Jun 26;9:55. PMID: 22734835
- Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, Emerman M. The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host and Microbe. 2012 Feb 16;11(2):194-204. PMID: 22284954
*Previewed by Planelles V. SAMHD1 Joins the red Queen's court. Cell Host and Microbe. 2012 Feb 16;11(2):103-5.
*Evaluated on Faculty of 1000. - Lim ES, Emerman M. HIV: Going for the watchman. Nature. 2011 Jun 29;474(7353):587-8. PMID: 21720361.
- Lim ES, Malik HS, Emerman M. Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. Journal of Virology. 2010 Jul;84(14):7124-34. PMID: 20444900
- Spindler KR, Welton AR, Lim ES, Duvvuru S, Althaus IW, Imperiale JE, Daoud AI, Chesler EJ. The major locus for mouse adenovirus susceptibility maps to genes of the hematopoietic cell surface-expressed LY6 family. Journal of Immunology. 2010 Mar 15;184(6):3055-62. PMID: 20164425
- Lim ES, Emerman M. Simian immunodeficiency virus SIVagm from African green monkeys does not antagonize endogenous levels of African green monkey tetherin/BST-2. Journal of Virology. 2009 Nov;83(22):11673-81. PMID: 19726508
Research Activity
4 R00 DK107923 (Lim) 09/16/2017 – 08/31/2020
NIH/NIDDK The Virome and Microbiome in Health and BK Disease of Kidney Transplant Patients
1 R01 HD092311 (Lehman/Lim) 09/06/2017 – 06/30/2022
NIH/NICHD Maternal-infant virome transmission: the role of HIV and antiretroviral therapy
Teaching Website
Courses
| Spring 2021 | |
|---|---|
| Course Number | Course Title |
| MIC 492 | Honors Directed Study |
| BIO 493 | Honors Thesis |
| MIC 494 | Special Topics |
| BIO 494 | Special Topics |
| MIC 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| Fall 2020 | |
|---|---|
| Course Number | Course Title |
| MIC 220 | Biology of Microorganisms |
| BIO 493 | Honors Thesis |
| MIC 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| Summer 2020 | |
|---|---|
| Course Number | Course Title |
| MIC 495 | Undergraduate Research |
| Spring 2020 | |
|---|---|
| Course Number | Course Title |
| MIC 492 | Honors Directed Study |
| BIO 495 | Undergraduate Research |
| Fall 2019 | |
|---|---|
| Course Number | Course Title |
| MIC 220 | Biology of Microorganisms |
| BIO 495 | Undergraduate Research |
| Summer 2019 | |
|---|---|
| Course Number | Course Title |
| MIC 495 | Undergraduate Research |
| Spring 2019 | |
|---|---|
| Course Number | Course Title |
| MIC 494 | Special Topics |
| BIO 494 | Special Topics |
| Fall 2018 | |
|---|---|
| Course Number | Course Title |
| MIC 220 | Biology of Microorganisms |
| Spring 2018 | |
|---|---|
| Course Number | Course Title |
| MIC 494 | Special Topics |
| BIO 494 | Special Topics |
Presentations
MIC 494/BIO 494 - Human Pathogenic Viruses and Infectious Diseases (3.0 credits)
Class is offered in Spring 2018.
Tues, Thur. 3:00 pm - 4:15 pm.
Location to be determined (Tempe campus).
Course description: Students will learn basic and advanced concepts in medical virology. The major emphasis will be on significant human diseases caused by viral pathogens including HIV, ebola, influenza, SARS, measles and others.
Course schedule and other information:
https://viromelab.org/courses/
Honors/Awards
2016 NIH Pathway to Independence Award (K99/R00), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
2013 - 2016 The Eli & Edythe Broad Fellowship, Life Sciences Research Foundation
2011 - 2012 Helen Riaboff Whiteley Graduate Fellowship Award, University of Washington, Dept. of Microbiology
2009 - 2011 Fred Hutchinson Cancer Research Center Interdisciplinary Training Fellowship
2010 Young Investigator Award. 17th Conference on Retroviruses and Opportunistic Infections (CROI)
2009 Neal B. Groman Teaching Award, University of Washington Dept. of Microbiology, Seattle, WA
Editorships
Academic Editor, PLOS ONE
Young Investigator Editorial Board, AIDS Research and Human Retroviruses