Mary F. Kearney, Ph.D.

HIV Dynamics and Replication Program
HIV virion image
HIV Dynamics and Replication Program
HIV DRP staff photo September 2019
HIV Dynamics and Replication Program
Melissa Fernandez work-in-progress seminar August 2018
HIV Dynamics and Replication Program
DRP Conference, October 13, 2021
HIV Dynamics and Replication Program
HIV DRP Think Tank Meeting 2017
HIV Dynamics and Replication Program
Sean Patro's poster presentation at CROI 2019
HIV Dynamics and Replication Program
John Coffin and Stephen Hughes participating in This Week in Virology podcast at 2018 Cold Spring Harbor Retroviruses Meeting
HIV Dynamics and Replication Program
Students and postbac fellows in the HIV Dynamics and Replication Program July 2019

Mary F. 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 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 other RNA viruses and to design new approaches toward targeting and killing infected cells. Currently, she also serves as a member of the NIH Women Scientists Advisors (WSA) Executive Committee and as Chair of the CCR WSA Committee; these groups promote career development and address issues affecting women scientists.

Areas of Expertise

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

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 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 Frank Maldarelli in the Clinical Retrovirology Section, in consultation with John Coffin of Tufts University and 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 individuals 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 donors to characterize the genetics of viremia in individuals on and off ART.

Determining the frequency of rare, drug-resistant variants in untreated individuals 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 before and after exposure to ART to investigate the impacts of HIV-1 diversity, low-frequency drug-resistant variants, and effective population size on the response to treatment.

NIH Scientific Focus Areas:
Clinical Research, Immunology, Microbiology and Infectious Diseases, Virology
  1. Bale MJ, Katusiime MG, Wells D, Wu X, Spindler J, Halvas EK, Cyktor JC, Wiegand A, Shao W, Cotton MF, Hughes SH, Mellors JW, Coffin JM, Van Zyl GU, Kearney MF
    mBio. 12: e00568-21, 2021. [ Journal Article ]
  2. Patro SC, Brandt LD, Bale MJ, Halvas EK, Joseph KW, Shao W, Wu X, Guo S, Murrell B, Wiegand A, Spindler J, Raley C, Hautman C, Sobolewski M, Fennessey CM, Hu WS, Luke B, Hasson JM, Niyongabo A, Capoferri AA, Keele BF, Milush J, Hoh R, Deeks SG, Maldarelli F, Hughes SH, Coffin JM, Rausch JW, Mellors JW, Kearney MF.
    Proc. Natl. Acad. Sci. USA. 116: 25891-25899, 2019. [ Journal Article ]
  3. 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 ]
  4. 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 ]
  5. 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 ]

Dr. Kearney received her Ph.D. in Biology at Catholic University in 2007 under the direction of 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 viral genetics and expression in vivo, the sources of persistent HIV 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 drug-resistance mutations in HIV and other RNA viruses.  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 elected to the NIH Women Scientist Advisors (WSA) in 2018.  She currently serves as Chair of the CCR WSA Committee, Chair of the NIH WSA Scholars Symposium, a member of the NIH WSA Executive Committee, an Organizer of the CCR Grand Rounds WSA-Sponsored Seminars, an advisor to the Biomedical Science and Bioinformatics Program at Hood College, and Guest Editor of the Viruses Special Issue on “Mechanisms of Viral Persistence.”  Dr. Kearney is the recipient of four Bench-to-Bedside Awards, three NIH Intramural AIDS Targeted Antiviral Program Awards, a U.S.–South Africa Initiative U01 Grant, an Office of AIDS Research Congressional Award, and an NCI Flex Technology Award.  In 2019 she was promoted to Senior Scientist.

Name Position
Valerie Boltz M.S. Research Biologist
Adam 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)
Jason W. Rausch, Ph.D. Staff Scientist
Wei Shao Ph.D. Programmer / Analyst (Contr)
Rachel Sklutuis Postbaccalaureate Fellow (CRTA)
Jonathan Spindler Research Biologist
Ann Wiegand M.S. Research Biologist
Elizabeth Anderson, Ph.D. Predoctoral Fellow 2011-2013

Current or Last Known Position:
Postdoctoral Fellow, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA

Michael Bale, M.S. Postbaccalaureate Fellow 2018-2020

Current or Last Known Position:
Ph.D. Student, Cornell University, New York, NY

Neeru Bhardwaj, Ph.D. Special Volunteer 2014

Current or Last Known Position:
Senior Manager, Alliance Management at Foundation Medicine, Cambridge, MA

Cailyn Barthlow Summer Student 2019

Current or Last Known Position:
Undergraduate Student, Hood College, Frederick, MD

Cristina Ceriani, Ph.D. Special Volunteer 2018

Current or Last Known Position:
Postdoctoral Research Associate, University of North Carolina HIV Cure Center, Chapel Hill, NC

Charles Coomer, M.Sc. Summer Student 2012-2014

Current or Last Known Position:
Predoctoral Fellow, NIH-Oxford-Cambridge Scholars Program, Oxford, UK, and Compton Lab (Antiviral Immunity and Resistance Section), HIV Dynamics and Replication Program

Monica Gouzoulis, B.S. Summer Student 2013-2014

Current or Last Known Position:
Molecular Biology Technician, National Institute of Allergy and Infectious Diseases, Bethesda, MD

Nicholas Johnson Summer Student 2014-2015

Current or Last Known Position:
Undergraduate Student, Bates College, Lewiston, ME

Lina Josefsson, Ph.D. Special Volunteer 2009-2010

Current or Last Known Position:
Investigator, Swedish Institute for Infectious Disease Control, Solna, Sweden

William McManus, M.S. Postbaccalaureate Fellow 2016-2018

Current or Last Known Position:
Ph.D. Student, University of Notre Dame, Notre Dame, IN

Helene Mens, M.D., Ph.D. Guest Researcher 2007-2011

Current or Last Known Position:
Physician, Copenhagen University, Copenhagen, Denmark

Victoria Musick, B.S. Summer Student 2017

Current or Last Known Position:
Graduate Student, Biomedical Science Master's Program, Hood College, Frederick, MD, and Research Associate I, Meso Scale Diagnostics, Gaithersburg, MD

Aurelie Niyongabo, M.S. Postbaccalaureate Fellow 2018-2020

Current or Last Known Position:
Ph.D. Student, University of Maryland, College Park, MD

Alex Scheltema Summer Student 2010
Tyler Snoots, B.S. Summer Student 2010-2011

Current or Last Known Position:
Production Planner, Northrop Grumman, Herndon, VA

Anuradha Sreedhara Summer Student 2017
Sloane Yu, M.D., M.B.A. Postbaccalaureate Fellow 2008-2009

Current or Last Known Position:
Cofounder and Chief Executive Officer, HubHaus LLC, San Francisco, CA; Physician, Allied Pain and Spine Institute, San Jose, CA

New Investigator Scholarships, Conference on Retroviruses and Opportunistic Infections

Jennifer Groebner and Adam Capoferri were awarded New Investigator Scholarships to present their research findings at the 2021 Conference on Retroviruses and Opportunistic Infections (CROI). Previous CROI scholarship awardees include Sean Patro and Jenna Hasson in 2020, 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 Scientists 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.

2018 Leidos Outstanding Achievement Award

Wei Shao received a Leidos Outstanding Achievement Award in 2018 for developing the Retroviral Integration Site Database ( and the Proviral Sequence Database (

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 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).

    Photo of IRP XMRV Working Group

      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.