Efrem Lim

Efrem.Lim@asu.edu
(480) 965-8667
Biodesign Institute, BDA 320B Tempe

School of Life Sciences

Assistant Professor

Faculty, TEMPE Campus, Mailcode 6101

Biodesign Center for Fundamental & Applied Microbiomics

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/

Curriculum Vitae

Education:

PhD, University of Washington

Research Website:

https://viromelab.org/

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:

https://viromelab.org/courses/

Courses

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

Expertise Areas:

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Efrem Lim