Mary Kearney, Ph.D.

Mary  Kearney, Ph.D.
Senior Scientist
Head, Translational Research Section

Dr. Kearney conducts research on the emergence of HIV drug resistance, the persistence of HIV during antiretroviral treatment (ART), and the sources of rebound viremia after stopping ART. Her studies, in collaboration with the Clinical Retrovirology Section led by Dr. Frank Maldarelli, have demonstrated that a diverse population of HIV-infected cells persist during ART, that some infected cells proliferate despite ART, and that residual viremia during ART can result from viral expression from these cells. Dr. Kearney heads the Translational Research Section, which aims to understand the genetics, evolution, and persistence of HIV and to design new approaches towards targeting and killing HIV-infected cells.

Link to additional information about Dr. Kearney

Areas of Expertise

1) HIV drug resistance, 2) HIV persistence, 3) HIV residual viremia, 4) HIV cure,
5) HIV evolution, 6) HIV genetics

Contact Info

Mary Kearney, Ph.D.
Center for Cancer Research
National Cancer Institute
Building 535, Room 108D
Frederick, MD 21702-1201
Ph: 301-846-6796

Studies of Clinical Resistance

The Translational Research Section (TRS) is primarily responsible for advancing the clinical and translational research efforts of the Host-Virus Interaction Branch by developing and applying new technologies to characterize and identify the sources of persistent HIV-1 viremia despite antiretroviral therapy (ART) and to evaluate the effect of HIV-1 genetic diversity, expression, and low-frequency drug resistance mutations on the response to ART. Working closely with Dr. Frank Maldarelli in the Clinical Retrovirology Section, in consultation with Dr. John Coffin of Tufts University and Dr. John Mellors of the University of Pittsburgh, the TRS collaborates with research groups worldwide to perform studies of HIV-host interactions, viral persistence during therapy, sources of rebound viremia, and the evolution of resistance.

HIV-1 persists in patients on ART despite suppression to very low levels and usually rebounds to pretherapy levels if ART is stopped.  The mechanisms that allow viremia to persist during therapy are not well understood.  Their elucidation is imperative if HIV-1 infection is ever to be cured.  Cellular reservoirs that harbor HIV-1 genomes and express viral RNA during ART are likely long-lived, proliferating cells that were infected prior to initiating therapy.  By investigating the genetics of HIV-1 plasma RNA and cellular HIV-1 DNA and RNA, the TRS aims to reveal sources of persistent virus production on ART and the sources of rebound viremia after stopping ART.  The TRS developed the gold-standard assays that allow for sequencing of HIV RNA and DNA in single virions and in single infected cells.  These assays are applied to blood and tissues from HIV-1-infected donors to characterize the genetics of viremia in patients on and off ART.

Determining the frequency of rare, drug-resistant variants in untreated patients can provide important insights into the emergence of drug resistance and into the effective population size of HIV-1.  The TRS previously developed an allele-specific PCR (ASP) assay capable of detecting specific drug resistance mutations present in 0.1-0.001% of the total virus population.  More recently, the TRS developed an ultrasensitive single-genome sequencing (uSGS) assay that provides sequence information from thousands of HIV variants present in donors’ plasma, providing templates to investigate the linkage of drug resistance mutations and to perform studies on HIV-1 evolution.  Ongoing studies include applying these and other ultrasensitive methods under development to samples collected from women before and after exposure to single-dose nevirapine (NVP) and in patients initiating standard-of-care ART to investigate the impacts of HIV-1 diversity, low-frequency drug-resistant variants, and effective population size on the response to ART.

NIH Scientific Focus Areas:
Clinical Research, Microbiology and Infectious Diseases, Virology
View Dr. Kearney's PubMed Summary.

Selected Key Publications

  1. Musick A, Spindler J, Boritz E, Pérez L, Crespo-Vélez D, Patro SC, Sobolewski MD, Bale MJ, Reid C, Keele BF, Capoferri A, Shao W, Wiegand A, Simonetti FR, Mellors JW, Hughes SH, Coffin JM, Maldarelli F, Kearney MF
    Front Microbiol. 10: 2204, 2019. [ Journal Article ]
  2. McManus WR, Bale MJ, Spindler J, Wiegand A, Musick A, Patro SC, Sobolewski MD, Musick VK, Anderson EM, Cyktor JC, Halvas EK, Shao W, Wells D, Wu X, Keele BF, Milush JM, Hoh R, Mellors JW, Hughes SH, Deeks SG, Coffin JM, Kearney MF
    J. Clin. Invest. 130: 126714, 2019. [ Journal Article ]
  3. Van Zyl GU, Katusiime MG, Wiegand A, McManus WR, Bale MJ, Halvas EK, Luke B, Boltz VF, Spindler J, Laughton B, Engelbrecht S, Coffin JM, Cotton MF, Shao W, Mellors JW, Kearney MF
    J. Clin. Invest. 127: 3827-3834, 2017. [ Journal Article ]
  4. Wiegand A, Spindler J, Hong FF, Shao W, Cyktor JC, Cillo AR, Halvas EK, Coffin JM, Mellors JW, Kearney MF
    Proc. Natl. Acad. Sci. USA. 114: E3659-E3668, 2017. [ Journal Article ]
  5. Kearney MF, Spindler J, Shao W, Yu S, Anderson EM, O'Shea A, Rehm C, Poethke C, Kovacs N, Mellors JW, Coffin JM, Maldarelli F.
    PLoS Pathog. 10: e1004010, 2014. [ Journal Article ]

Dr. Mary Kearney received her Ph.D. in Biology at Catholic University in 2007 under the direction of Drs. John Coffin, Sarah Palmer, and Venigalla Rao.  She received The Benedict T. DeCicco Award for Excellence in Graduate Research in 2008.  In 2001 she joined the HIV Drug Resistance Program (renamed the HIV Dynamics and Replication Program in 2015) as a Biologist in the Virology Core.  In 2008 she was promoted to Head of the Translational Research Unit (renamed the Translational Research Section in 2020), where she oversees a team that investigates HIV genetics and expression in vivo, the sources of persistent viremia during antiretroviral therapy (ART), the sources of rebound viremia after stopping ART, the mechanisms for maintaining the HIV reservoir, and the mechanisms for the emergence of HIV drug resistance mutations.  Dr. Kearney was awarded the NIH Director’s Award and NCI Group Award in 2012, the NCI Director's Award in 2015, the CCR Group Award in 2016, and the NIH Director’s Award in 2019.  She was a consultant to the World Health Organization from 2010 to 2016, was the keynote speaker for the launch of the Bioinformatics Program at Hood College in 2015 and for the Center for AIDS Research Symposium at the University of Pennsylvania in 2019, and was appointed to the NIH Women Scientist Advisors (WSA) in 2018.  She currently serves as Chair of the WSA Executive Committee and as an advisor to the Bioinformatics Program and Biology Department at Hood College.  Dr. Kearney is the recipient of three Bench-to-Beside Awards, three NIH Intramural AIDS Targeted Antiviral Program Awards, and a U.S.–South Africa Initiative U01 Grant. In 2019 she was promoted to Senior Scientist.


Name Position
Michael Bale M.Sc. Postbaccalaureate Fellow (CRTA)
Valerie Boltz M.S. Research Biologist
Adam Amadio Capoferri Predoctoral Fellow (Graduate Student)
Jennifer Groebner Ph.D. Postdoctoral Fellow (CRTA)
Jenna Hasson Postbaccalaureate Fellow (CRTA)
Mary Grace Katusiime Ph.D. Postdoctoral Fellow (Visiting)
Andrew Musick M.S. Research Associate II (Contr.)
Sean Patro Ph.D. Postdoctoral Fellow (CRTA)
Wei Shao Ph.D. Programmer / Analyst (Contr)
Rachel Sklutuis Postbaccalaureate Fellow (CRTA)
Jonathan Spindler Research Biologist
Ann Wiegand M.S. Research Biologist

Young Investigator Awards, Conference on Retroviruses and Opportunistic Infections

Sean Patro and Jenna Hasson were awarded New Investigator Scholarships to present their research findings at the 2020 Conference on Retroviruses and Opportunistic Infections (CROI). Previous CROI scholarship awardees include Andrew Musick in 2017 and 2018 and Chad Coomer in 2014.

2019 NIH Director's Award

Mary Kearney received a 2019 NIH Director's Award as a member of the NIH Women Scientist Advisors (WSA) Executive Committee. Nominated by the NIH Office of the Director, the Executive Committee members received this team award for leadership of the WSA in promoting recruitment, retention, and recognition of women scientists and fair treatment with respect to salary and work environment.

2015 NCI Director's Award

Members of the NCI HIV Integration Sites Analysis (ISA) team received a group award at the NCI Director's Award ceremony in November 2015 "for discoveries on HIV survival during antiretroviral therapy, revealing the importance of integration site and clonal expansion." The ISA group award recipients included Stephen Hughes, Andrea Ferris, Shawn Hill, Mary Kearney, Frank Maldarelli, Wei Shao, and Jonathan Spindler (HIV DRP); Francesco Simonetti (University of Milan); John Coffin (Tufts University); John Mellors (University of Pittsburgh); and David Wells, Ling Su, and Xiaolin Wu (Leidos Biomedical Research, Inc.).

                  Photo of NCI Integration Sites Analysis Group in Sept 2015

    XMRV Working Group Received NIH Director's Award

    Presentations at the 2009 Cold Spring Harbor Retroviruses Meeting in May 2009 suggested that xenotropic murine leukemia virus-related virus (XMRV), a novel gammaretrovirus with a potential link to prostate cancer and chronic fatigue syndrome, might be present in ~3% of the U.S. population, raising both public health issues and concern for contamination of the nation's blood supply. In response, the Intramural Research Program (IRP) of the National Cancer Institute immediately formed a multidisciplinary XMRV Working Group and charged the group with developing, implementing, and making available diagnostic reagents for rapid, accurate, and reliable detection of XMRV nucleic acids, antigens, and infectious virus. The group developed an action plan, and within three months, the SAIC Protein Expression Laboratory reported construction of 40 recombinant clones expressing all XMRV antigens and their subsequent purification for use as immunological reagents in December 2009. Importantly, these reagents were also made available (through the NIH AIDS Reagent Program) to the extramural community to accelerate XMRV research and allow sharing of a common set of reagents. A parallel effort in the HIV Dynamics and Replication Program resulted in establishing an assay to quantify XMRV DNA (from tissue) and RNA (from plasma) in November and December 2009, respectively. Since ultrasensitive XMRV nucleic acid detection methods were not available, this required in-house development and standardization, using the existing manpower and financial resources of the HIV DRP. In response to the need for "authentic" viral antigens for the development and standardization of immunological reagents by the Viral Technology Laboratory, the large-scale virus culture facilities of the SAIC AIDS and Cancer Virus Program were recruited for XMRV production. Finally, researchers of the HIV DRP developed the DERSE indicator cell line for detection of infectious XMRV. In contrast to traditional virological methods, this novel assay reduced the time needed to detect low levels of replicating XMRV in cell culture from months to a matter of weeks.

    Subsequent studies have demonstrated that XMRV does not pose a threat to public health. Despite this, events between October 2009 and October 2010 highlighted the ability of dedicated scientists of the IRP to respond very quickly to a potential public health crisis by assembling a multidisciplinary team with a single goal of rapidly preparing, standardizing, and making available reagents for diagnostic virology. In every instance, reagents were prepared with existing manpower and resources, and without a serious interruption in the normal work flow or productivity of each group involved. Their non-XMRV work continued unimpeded. The success of this effort relied on close cooperation between all groups to establish and meet important deadlines. In addition to their individual contributions, the XMRV Working Group made reagents and technologies available to the general scientific community, and performed additional diagnostic analysis of samples supplied by federal, intramural, and extramural laboratories. In February 2012, the external XMRV Working Group (the Blood XMRV Scientific Research Working Group) received a Special Recognition Award from the Department of Health and Human Services, recognizing their exemplary team performance for "evaluating XMRV, a potential threat to the blood supply." In July 2012, members of the IRP XMRV Working Group were similarly recognized for their outstanding work by receiving the NIH Director's Award.

    The IRP XMRV Working Group included:

    Stuart Le Grice, HIV DRP
    Alan Rein, HIV DRP
    Vineet KewalRamani, HIV DRP
    Mary Kearney, HIV DRP
    James Hartley, Protein Expression Laboratory, SAIC-Frederick
    Rachel Bagni, Viral Technology Laboratory, SAIC-Frederick
    Jeffrey Lifson, AIDS and Cancer Virus Program, SAIC-Frederick

    The NIH Director's Award to the IRP XMRV Working Group was highlighted in an issue of The Poster newsletter (link to NIH Director's Award feature).


                      IRP XMRV Working Group photo

      Award for Excellence in Graduate Research, Catholic University of America

      Mary Kearney was awarded the Benedict T. DeCicco Award for Excellence in Graduate Research in 2008 by the Biology Faculty of the Catholic University of America.