*These authors contributed equally.

2024

Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their infants.
Žuštra A, Leonard VR, Holland LA, Hu JC, Mu T, Holland SC, Wu LI, Begnel ER, Ojee E, Chohan BH, Richardson BA, Kinuthia J, Wamalwa D, Slyker J, Lehman DA, Gantt S, Lim ES.
Research Square (preprint)

Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.
Maqsood R, Holland LA, Wu LI, Begnel ER, Adhiambo J, Owiti P, Chohan BH, Gantt S Kinuthia J, Wamalwa D, Ojee E, Richardson BA, Slyker J, Lehman DA, Lim ES.
Research Square (preprint)

Longitudinal alterations in the Urinary Virome of Kidney Transplant Recipients are Influenced by BK viremia and Patient Sex.
Maqsood R, Wu LI, Brennan DC, Lim ES.
Research Square (preprint)

Longitudinal cervicovaginal microbiome and virome alterations during ART and discordant shedding in women living with HIV.
Kaelin EA, Mitchell C, Soria J, La Rosa A, Ticona E, Coombs RW, Frenkel LM, Bull ME, Lim ES.
Research Square (preprint)

Human adenovirus outbreak at a university campus monitored by wastewater and clinical surveillance.
Holland SC, Smith MF, Holland LA, Maqsood R, Hu JC, Murugan V, Driver EM, Halden RU, Lim ES.
medRxiv (preprint)

Influenza Virus Genomic Surveillance, Arizona, USA, 2023-2024.
Maqsood R, Smith MF, Holland LA, Sullins RA, Holland SC, Tan M, Hernandez Barrera GM, Thomas AW, Islas M, Kramer JL, Nordstrom L, Mulrow M, White M, Murugan V, Lim ES.
Viruses

Seasonality of Respiratory, Enteric and Urinary Viruses Revealed by Wastewater Genomic Surveillance.
Smith MF*, Maqsood R*, Sullins RA, Driver EM, Halden RU, Lim ES.
mSphere (In Press)

2023

Genomic Sequencing Surveillance to Identify Respiratory Syncytial Virus Mutations, Arizona, USA.
Holland LA*, Holland SC*, Smith MF, Leonard VR, Murugan V, Nordstrom L, Mulrow M, Salgado R, White M, Lim ES.
Emerging Infectious Diseases
      - Press release: Decoding RSV: Study explores viral mutations with implications for vaccine effectiveness
      - Feature article: Why pathogen surveillance is critical during a “tripledemic”

Viral anti-inflammatory serpin reduces immuno-coagulopathic pathology in SARS-CoV-2 mouse models of infection.
Zhang L, Li YH, Kibler K, Kraberger S, Varsani A, Turk J, Elmadbouly N, Aliskevich E, Spaccarelli L, Estifanos B, Enow J, Zanetti IR, Saldevar N, Lim E, Schlievert J, Browder K, Wilson A, Juan FA, Pinteric A, Garg A, Monder H, Saju R, Gisriel S, Jacobs B, Karr TL, Florsheim EB, Kumar V, Wallen J, Rahman M, McFadden G, Hogue BG, Lucas AR.
EMBO Molecular Medicine

Digital PCR discriminates between SARS-CoV-2 Omicron variants and immune escape mutations.
Holland SC, Holland LA, Smith MF, MB Lee, Hu JC, Lim ES.
Microbiology Spectrum
      - Press release: Unveiling COVID variants: Digital PCR testing could improve personalized treatment.

HIV and SARS-CoV-2 infection in postpartum Kenyan women and their infants.
Begnel ER, Chohan BH, Ojee E, Adhiambo J, Owiti P, Ogweno V, Holland LA, Fish CS, Richardson BA, Khan AK, Maqsood R, Lim ES, Sadarangani M, Lehman DA, Slyker J, Kinuthia J, Wamalwa D, Gantt S.
PLoS One

Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA.
Smith MF*, Holland SC*, MB Lee, Hu JC, Pham NC, Sullins RA, Holland LA, Mu T, Thomas AW, Fitch R, Driver EM, Halden RU, Villegas-Gold M, Sanders S, Krauss JL, Nordstrom L, Mulrow M, White M, Murugan V, Lim ES.
mBio
      - Press release: Comprehensive statewide study tracks rapid spread of SARS-CoV-2 variants.

Leveraging an established neighbourhood-level, open access wastewater monitoring network to address public health priorities: a population-based study.
Bowes DA, Driver EM, Kraberger S, Fontenele RS, Holland LA, Wright J, Johnston B, Savic S, Newell ME, Adhikari S, Kumar R, Goetz H, Binsfeld A, Nessi K, Watkins P, Mahant A, Zevitz J, Deitrick S, Brown P, Dalton R, Garcia C, Inchausti R, Holmes W, Tian X-J, Varsani A,  Lim ES, Scotch M, Halden RU.
The Lancet Microbe

2022

One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021.
Yaglom HD, Maurer M, Collins B, Hojnacki J, Monroy-Nieto J, Bowers JR, Packard S, Erickson DE, Barrand ZA, Simmons KM, Brock BN, Lim ES, Smith S, Hepp CM, Engelthaler DM.
PLoS One

Comparison of nucleocapsid and spike antibody ELISAs for determining SARS-CoV-2 seropositivity in Kenyan women and infants.
Fish CS, Owiti P, Begnel ER, Itell HL, Ojee E, Adhiambo J, Ogweno V, Holland LA, Richardson BA, Khan AK, Maqsood R, Gantt S, Lim ES, Slyker J, Kinuthia J, Overbaugh J, Wamalwa D, Lehman DA, Chohan BH.
Journal of Medical Virology

SARS-CoV-2 Delta variant N gene mutations reduce sensitivity to the TaqPath COVID-19 multiplex molecular diagnostic assay.
Holland SC, Bains A, Holland LA, Smith MF, Sullins RA, Mellor NJ, Thomas AW, Johnson N, Murugan V, Lim ES.
Viruses

University-Associated SARS-CoV-2 Omicron BA.2 Infections, Maricopa County, Arizona, USA, 2022.
Fowle N, Garrett B, Floyd OL, Collins J, Krasnow AD, Islas M, Holland SC, Smith MF, Lim ES, Jarrett NM, Scott SE.
Emerging Infectious Diseases

Extensive Wastewater-Based Epidemiology as a Resourceful Tool for SARS-CoV-2 Surveillance in a Low-to-Middle-Income Country through a Successful Collaborative Quest: WBE, Mobility, and Clinical Tests.
Sosa-Hernández JE, Oyervides-Muñoz MA, Melchor-Martínez EM, Driver EM, Bowes DA, Kraberger S, Lucero-Saucedo SL, Fontenele RS, Parra-Arroyo L, Holland LA, Peña-Benavides SA, Newell ME, Martínez-Ruiz M, Adhikari S, Rodas-Zuluaga LI, Kumar R, López-Pacheco IY, Castillo-Zacarias C, Iqbal HMN, Lim ES, Salas-Limón D, Varsani A, Halden RU, Parra-Saldívar R.
Water

Virus-Derived Chemokine Modulating Protein Pre-Treatment Blocks Chemokine-Glycosaminoglycan Interactions and Significantly Reduces Transplant Immune Damage.
Zanetti IR, Burgin M, Zhang L, Yeh ST, Ambadapadi S, Kilbourne J, Yaron JR, Lowe KM, Daggett-Vondras J, Fonseca D, Boyd R, Wakefield D, Clapp W, Lim E, Chen H, Lucas A.
Pathogens

Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants.
Kaelin EA, Rodriguez C, Hall-Moore C, Hoffmann JA, Linneman LA, Ndao IM, Warner BB, Tarr PI, Holtz LR, Lim ES.
Nature Microbiology
      - Press release: Viruses in the gut may warn of a deadly disease in preterm infants.

Dynamic changes in breast milk microbiome in the early postpartum period of Kenyan women living with HIV are influenced by antibiotics but not antiretrovirals.
Maqsood R, Skidmore PT, Holland LA, Au JL, Khan AK, Wu LI, Ma N, Begnel ER, Chohan BH, Adhiambo J, John-Stewart G, Kiarie J, Kinuthia J, Chung MH, Richardson BA, Slyker J, Lehman DA, Lim ES.
Microbiology Spectrum
      - Press release: Antibiotic, antiretroviral drug effects on breast milk explored for mothers living with HIV.

Cervicovaginal DNA virome alterations are associated with genital inflammation and microbiota composition.
Kaelin EA*, Skidmore PT*, Laniewski P, Holland LA, Chase DM, Herbst-Kralovetz MM, Lim ES.
mSystems
      - Press release: Viral transformations in the female genital tract can spell trouble for women’s health.

2021

Genomic Sequencing Surveillance Identifies Emergence of SARS-CoV-2 E484K variant B.1.243.1 in Arizona.
Skidmore PT, Kaelin EA, Holland LA, Maqsood R, Wu LI, Mellor NJ, Blain JM, Harris V, LaBaer J, Murugan V, Lim ES.
Emerging Infectious Diseases

Andrographolide attenuates Gut-Brain-axis associated pathology in Gulf War Illness by modulating Bacteriome-Virome associated inflammation and microglia-neuron proinflammatory crosstalk.
Saha P, Skidmore PT, Holland LA, Mondal A, Bose D, Seth R, Sullivan K, Janulewicz P, Horner R, Klimas N, Nagarkatti M, Nagarkatti P, Lim ES, Chatterjee S.
Brain Sciences

Breast milk virome and bacterial microbiome resilience in Kenyan women living with HIV.
Maqsood R, Reus JB, Wu LI, Holland LA, Nduati R, Mbori-Ngacha D, Maleche-Obimbo E, Begnel ER, Gantt S, Ojee E, Wamalwa D, John-Stewart G, Slyker J, Lehman DA, Lim ES.
mSystems

Endogenization of a prosimian retrovirus during lemur evolution.
Apakupakul K, Deem SL, Maqsood R, Sithiyopasakul P, Wang D, Lim ES.
Viruses

High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants.
Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA, Holm RH, Hoogesteijn von Reitzenstein N, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A.
Water Research

2020

An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona.
Ladner JT, Larsen BB, Bowers JR, Hepp CM, Bolyen E, Folkerts M, Sheridan K, Pfeiffer A, Yaglom H, Lemmer D, Sahl JW,
Kaelin EA, Maqsood R, Bokulich NA, Quirk G, Watt TD, Komatsu K, Waddell V, Lim ES, Caporaso JG, Engelthaler DM, Worobey M, Keim P.
mBio
      - Press release: Arizona genetic research group tracks initial spread of SARS-CoV-2.

An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020).
Holland LA*, Kaelin EA*, Maqsood R, Estifanos B, Wu LI, Varsani A, Halden RU, Hogue BG, Scotch M, Lim ES.
Journal of Virology
      - Press release: ASU scientific team finds new, unique mutation in coronavirus study.

SV40 large T antigen is not responsible for the loss of STING in 293T cells but can inhibit cGAS-STING interferon induction.
Reus JB, Trivino-Soto GS, Wu LI, Kokott K, Lim ES.
Viruses

Immune protection is dependent on the gut microbiome in a lethal mouse gammaherpesviral infection.
Yaron JR, Ambadapadi S, Zhang L, Chavan RN, Tibbetts SA, Keinan S, Varsani A, Maldonado J, Kraberger S, Tafoya AM, Bullard WL, Kilbourne J, Stern-Harbutte A, Krajmalnik-Brown R, Munk BH, Koppang EO, Lim ES, Lucas AR.
Scientific Reports

2019

2018

Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community.
Lim ES, Rodriguez C, Holtz LR.
Microbiome

Characterization of BK polyomaviruses from kidney transplant recipients suggests a role for APOBEC3 in driving in-host virus evolution.
Peretti A, Geoghegan EM, Pastrana DV, Smola S, Feld P, Sauter M, Lohse S, Ramesh M, Lim ES, Wang D, Borgogna C, FitzGerald PC, Bliskovsky V, Starrett GJ, Law EK, Harris RS, Killian JK, Zhu J, Pineda M, Meltzer PS, Boldorini R, Gariglio M, Buck CB.
Cell Host and Microbe

2017

An Intracellular Pathogen Response Pathway Promotes Proteostasis in C. elegans. 
Reddy KC, Dror T, Sowa JN, Panek J, Chen K, Lim ES, Wang D, Troemel ER.
Current Biology

Complete Genome Sequence of Torque teno indri virus 1, a Novel Anellovirus in Blood from a Free-Living Lemur.
Amatya R, Deem SL, Porton IJ, Wang D, Lim ES. 
Genome Announcements

Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells.
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.
Proc Natl Acad Sci USA

Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals.
Janowski AB, Krishnamurthy SR, Lim ES, Zhao G, Brenchley JM, Barouch DH, Thakwalakwa C, Manary MJ, Holtz LR, Wang D.
Virology

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.
Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D.
Virology

A Snapshot of Antibody-Mediated Rejection Goes Viral.
Lim ES, Brennan DC.
Transplantation

Pre-2016

The Bacterial Microbiome and Virome Milestones of Infant Development. 
Lim ES, Wang D, Holtz LR.
Trends in Microbiology (2016)

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. 
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.
Cell Host Microbe (2016)
      - Preview: The HIV-Associated Enteric Microbiome Has Gone Viral. Cell Host Microbe.

Early life dynamics of the human gut virome and bacterial microbiome in infants.
Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR.
Nature Medicine (2015)
      - Highlighted in Nature Reviews Gastroenterology & Hepatology.
      - Featured in This Week in Virology (TWiV #355): Baby's first virome.

Species-specific transmission of novel picornaviruses in lemurs.
Lim ES, Deem SL, Porton IJ, Cao S, Wang D.
Journal of Virolology (2015)

Common exposure to STL polyomavirus during childhood. 
Lim ES, Meinerz NM, Primi B, Wang D, Garcea RL.
Emerging Infectious Diseases (2014)

Discovery of rosavirus 2, a novel variant of a rodent-associated picornavirus, in children from The Gambia.
Lim ES, Cao S, Holtz LR, Antonio M, Stine OC, Wang D.
Virology (2014)

Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing.
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.
Virology (2013)

Identification of MW polyomavirus, a novel polyomavirus in human stool.
Siebrasse EA, Reyes A, Lim ES, Zhao G, Mkakosya RS, Manary MJ, Gordon JI, Wang D.
Journal of Virology (2012)

The function and evolution of the restriction factor Viperin in primates was not driven by lentiviruses. 
Lim ES, Wu LI, Malik HS, Emerman M. (2012)
Retrovirology (2012)

The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx.
Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, Emerman M.
Cell Host Microbe (2012)
      - Preview: SAMHD1 Joins the Red Queen's Court. Cell Host Microbe

HIV: Going for the watchman.
Lim ES, Emerman M.
Nature (2011)

Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. 
Lim ES, Malik HS, Emerman M.
Journal of Virology (2010)

The major locus for mouse adenovirus susceptibility maps to genes of the hematopoietic cell surface-expressed LY6 family. 
Spindler KR, Welton AR, Lim ES, Duvvuru S, Althaus IW, Imperiale JE, Daoud AI, Chesler EJ.
Journal of Immunology (2010)

Simian immunodeficiency virus SIVagm from African green monkeys does not antagonize endogenous levels of African green monkey tetherin/BST-2.
Lim ES, Emerman M.
Journal of Virology (2009)