Vinay K. Pathak, 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
HIV Dynamics and Replication Program
HIV DRP Think Tank Meeting 2017
HIV Dynamics and Replication Program
Announcement of 2020 David Derse Memorial Lecture and Award
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

Vinay K. Pathak, Ph.D.

Vinay K. Pathak, Ph.D.
Senior Investigator
Head, Viral Mutation Section

Dr. Pathak has significantly advanced the field of lentiviral molecular virology with his studies of HIV-1 replication in infected cells.  Under his direction, the Viral Mutation Section has developed innovative live-cell microscopy methods to show that, in contrast to most HIV-1 replication models, intact viral cores are transported into the nucleus, complete reverse transcription in the nucleus, and disassemble (uncoat) near their integration sites just before integration.  Dr. Pathak’s group has significantly contributed to our understanding of how HIV-1 replicates in the presence of potent host restriction APOBEC3 proteins and antiviral drugs.  Additionally, Dr. Pathak’s group played a key role in discovering the origin of a newly identified retrovirus, XMRV, and in quelling a potential public health crisis by refuting the controversial claims associating this virus with chronic fatigue syndrome and prostate cancer.

Areas of Expertise

1) HIV replication, 2) host restriction factors, 3) nuclear import, 4) development of novel therapeutics, 5) high-resolution microscopy, 6) molecular virology

HIV-1 Replication, Host Restriction Factors, Antiviral Drug Resistance, and Development of Novel Therapeutics

Project 1. Elucidate HIV-1 replication in infected cells by high-resolution live-cell microscopy.  Many aspects of HIV-1 replication in infected cells, including nuclear import and capsid dissembly, which are essential for HIV-1 replication, remain poorly understood.  To gain insights into these essential steps during HIV-1 replication in infected cells, we developed a new method to label viral complexes by fluorescently tagging APOBEC3F, which is incorporated into virions.  Using this method, we showed that reverse transcription is not required for nuclear import of viral complexes, and that HIV-1 capsid interactions with host proteins are essential for nuclear import of HIV-1 capsids (Burdick et al., PNAS 2013).  The dynamics and regulation of HIV-1 nuclear import and its intranuclear movements after import had not been previously studied.  We carried out high-resolution live-cell microscopy studies of APOBEC3F-labeled viral complexes to determine the dynamics of HIV-1 nuclear envelope docking, nuclear import, and intranuclear movements by live-cell microscopy (Burdick et al., PLoS Pathog. 2017).  For several decades, retroviral core uncoating has been thought to occur in the cytoplasm in coordination with reverse transcription or at the nuclear envelope during nuclear import, but no studies have concluded that uncoating occurs in the nucleus.  We developed methods to study HIV-1 uncoating by direct labeling and quantification of viral capsid protein associated with infectious capsids.  Our results show that intact (or nearly intact) viral cores enter the nucleus through a mechanism involving interactions with host protein cleavage and polyadenylation specificity factor 6 (CPSF6), complete reverse transcription in the nucleus before uncoating, and uncoat less than 1.5 hours before integration near their genomic integration sites.  These results fundamentally change our current understanding of HIV-1 post-entry replication events including mechanisms of nuclear import, uncoating, reverse transcription, integration, and evasion of innate immunity (Burdick et al., PNAS 2020). 

Project 2. Elucidate the structure and function of APOBEC3 proteins and develop new strategies to treat and functionally cure HIV-1 infection.  Our goal is to understand the structure and function of human restriction factor APOBEC3 proteins, which are an important innate immune defense mechanism that protects against invading pathogens.  APOBEC3 proteins potently inhibit HIV-1 replication in the absence of the virally encoded Vif protein by incorporating into virions in the virus producing cells and inducing lethal G-to-A hypermutation of the viral DNA in infected target cells.  Vif overcomes these host defenses by targeting the APOBEC3 proteins for proteasomal degradation.  We have significantly contributed to elucidating the APOBEC3 and Vif determinants that interact with each other (Xu et al., PNAS 2004; Russell & Pathak, J. Virol. 2007; Smith & Pathak, J. Virol. 2010).  We have shown that A3G and A3F both inhibit viral DNA integration, but through distinctly different mechanisms (Mbisa et al., J. Virol. 2007; Mbisa et al., J. Virol. 2010).  We also developed a bimolecular fluorescence complementation assay to visualize A3G and A3F molecular interactions in living cells and observed that A3G and A3F multimerization, A3G-Gag interactions, and A3G virion incorporation require RNA binding (Friew et al., Retrovirology 2009).  We compared the antiviral activity of A3G and A3F in primary CD4+ T cells and macrophages, the natural target cells of infection, and found that while both can inhibit HIV-1 replication A3G is a more potent inhibitor of HIV-1 than A3F (Chaipan et al., J. Virol. 2013). 

Recently, in collaboration with Dr. Yong Xiong (Yale University), we determined the structure of a Vif-APOBEC3F-CTD-CBFb complex (Hu et al., Nat. Struct. Mol. Biol. 2020).  We demonstrated that APOBEC3 proteins potently induce lethal hypermutation and contribute minimally to viral genetic variation (Delviks-Frankenberry et al., PLoS Pathog 2016).  We are developing lentiviral vectors that can efficiently deliver the Vif1-resistant APOBEC3G to hematopoietic stem cells, with the goal of providing a proof of concept that delivering Vif-resistant APOBEC3G to infected patients can provide an approach for a functional cure for HIV-1 infection (Delviks-Frankenberry et al., Mol. Ther. Nucleic Acids 2019). 

Project 3.  Define mechanisms that confer resistance to nucleoside and nonnucleoside reverse transcriptase (RT) inhibitors.  Based on our previous observations on RT template switching and recombination, we proposed that the relative polymerase and RNase H activities of RT can affect the balance between RNA degradation and nucleotide excision, and that mutations that reduce RNase H activities can enhance resistance to nucleoside as well as nonnucleoside RT inhibitors.  We observed that several mutations that reduce RNase H activity affect the balance between RNA degradation and nucleotide excision and enhance nucleoside RT inhibitor resistance (Nikolenko et al., PNAS., 2005; Nikolenko et al., PNAS., 2007; Delviks-Frankenberry et al., PNAS., 2008).  Our studies have demonstrated that mutations in the connection and RNase H domains also increase resistance to nonnucleoside RT inhibitors, and suggest a parallel mechanism by which resistance to both classes of RT inhibitors can be increased (Nikolenko et al., J. Virol.., 2010).  These hypotheses were validated by characterization of RT mutations observed in patients and subsequently confirmed by other labs. 

Project 4.  Demonstrate that xenotropic murine leukemia virus-related virus (XMRV) is a laboratory recombinant and not a human pathogen.  XMRV, a gammaretrovirus, was reportedly found in prostate cancer and chronic fatigue syndrome (CFS) patients at high frequencies and thought to be a human pathogen.  However, we found that XMRV replication is severely restricted by human APOBEC3 proteins (Paprotka et al., J. Virol.., 2010), and its replication is severely restricted in human peripheral blood mononuclear cells, raising doubts about its pathogenicity in humans (Chaipan et al., J. Virol.., 2011).  To gain insights into the origin of XMRV, we analyzed prostate cancer xenografts that were passaged in nude mice and used to develop a XMRV-positive human cancer cell line.  The results showed that XMRV is most likely a recombinant between two murine endogenous proviruses that we named PreXMRV-1 and PreXMRV-2 (Paprotka et al., Science., 2011).  We concluded that the association between XMRV and human disease is due to contamination of human samples with a laboratory recombinant virus.

NIH Scientific Focus Areas:
Cell Biology, Genetics and Genomics, Microbiology and Infectious Diseases, Molecular Biology and Biochemistry, Virology
  1. Burdick RC, Li C, Munshi M, Rawson JMO, Nagashima K, Hu W-S, Pathak VK
    Proc Natl Acad Sci U S A. 117: 5486-5493, 2020. [ Journal Article ]
  2. Burdick RC, Delviks-Frankenberry KA, Chen J, Janaka SK, Sastri J, Hu W-S, Pathak VK
    PLoS Pathog. 13(8): e1006570, 2017. [ Journal Article ]
  3. Delviks-Frankenberry KA, Nikolaitchik OA, Burdick RC, Gorelick RJ, Keele BF, Hu W-S, Pathak VK
    PLoS Pathog. 12(5): e1005646, 2016. [ Journal Article ]
  4. Burdick RC, Hu W-S, Pathak VK
    Proc Natl Acad Sci U S A Plus. 110: E4780-E4789, 2013. [ Journal Article ]
  5. Paprotka T, Delviks-Frankenberry KA, Cingoz O, Martinez A, Kung H-J, Tepper CG, Hu W-H, Fivash MJ Jr, Coffin JM, Pathak VK
    Science. 333: 97-101, 2011. [ Journal Article ]

Dr. Vinay K. Pathak received his B.A. in Biology from the University of California, Los Angeles, in 1979.  He obtained his M.S. in Comparative Pathology in 1983 from the University of California, Davis, for characterization of mouse mammary tumor virus proviral integration sites near the int1 and int2 loci in mammary tumors and hyperplastic tissues in Dr. Robert Cardiff's laboratory.  He received his Ph.D. for work on characterization of the eukaryotic protein synthesis initiation factors eIF-2α and eIF-2β in Dr. John W.B. Hershey's laboratory at the University of California, Davis, in 1988.  He was a postdoctoral fellow under the guidance of Dr. Howard Temin from 1988 to 1991, where he determined the in vivo forward mutation rate of spleen necrosis virus and characterized the nature of mutations that arise during retroviral replication.  These studies were the first to report G-to-A hypermutation in a retrovirus, now known to be the result of cytidine deamination by host restriction APOBEC3 proteins.  In 1991, Dr. Pathak became an Assistant Professor in the Department of Biochemistry and the Mary Babb Randolph Cancer Center at West Virginia University.  He was promoted to Associate Professor with tenure in 1998.  He joined the National Cancer Institute in 1999 as Senior Investigator and Head of the Viral Mutation Section in the HIV Dynamics and Replication Program (renamed the HIV Dynamics and Replication Program in 2015).  Dr. Pathak was appointed as Guest Editor for the "HIV Drug Resistance" special issue of Viruses, published in 2010.  He received the NIH Asian and Pacific Islander American Organization Award for outstanding accomplishments in biomedical research and an NIH Group Merit Award in 2012 and a Special Act of Service Award in 2020.  He has received numerous research awards, including a U.S.-Russian Joint Working Group on Biomedical Research Cooperation Award, six NIH Intramural AIDS Targeted Antiviral Program (IATAP) Research Awards, eight IATAP Equipment Awards, two NIH Office of AIDS Research Innovation Awards, and two NIH Bench-to-Bedside Awards.  He served as Co-Chair (2013-2014) and Chair (2015) of the Annual Norman P. Salzman Memorial Symposium in Virology, NIH.  In 2017, he served as Co-Organizer of the Cold Spring Harbor Laboratory Retroviruses Meeting.  He is one of six Associate Chairs and the sole NCI member of the NIH-wide COVID-19 Scientific Interest Group Leadership Committee and was Co-Organizer of the widely attended NIH/FDA COVID-19 Research Symposium/Workshop in 2020.  He currently serves as a member of the NCI RNA Biology Initiative. 

Name Position
Ryan Burdick M.S. Research Biologist
Krista A. Frankenberry, Ph.D. Staff Scientist
Sushila Kumari Ph.D. Postdoctoral Fellow (Visiting)
Chenglei Li Ph.D. Postdoctoral Fellow (Visiting)
Mohamed Husen Munshi Ph.D. Postdoctoral Fellow (Visiting)
Rokeya Siddiqui Ph.D. Postdoctoral Fellow (Visiting)
Daniel Ackerman Postbaccalaureate Fellow 2014-2015

Assistant Scientist, MRI Global, Frederick, MD

Michal Bonar, Ph.D. Postdoctoral Fellow 2018

Field Applications Scientist, NanoCellect Biomedical, Inc., Washington, DC

Timothy Borbet, Ph.D. Predoctoral Fellow 2010-2011

Postdoctoral Researcher, New York University, New York, NY

Wei Bu, Ph.D. Postdoctoral Fellow 2007-2010

Research Fellow, National Institute of Allergy and Infectious Diseases, Bethesda, MD

Chawaree Chaipan, Ph.D. Postdoctoral Fellow 2009-2012

Investigator II, Novartis, Basel, Switzerland

Mollie Charon, M.D. Predoctoral Fellow 2002-2003

Resident, University of California, Davis, CA

John Chen, M.S. Postbaccalaureate Fellow 2017-2019

Graduate Student, University of Texas Medical Branch, Galveston, TX

Belete Desimmie, M.D., Ph.D. Postdoctoral Fellow 2013-2020

Resident, Internal Medicine, Marshall University, Huntington, WV

Hibiki Doi Special Volunteer 2013

Medical Student, Kyoto University, Kyoto, Japan

Yeshitila Friew, Ph.D. Postdoctoral Fellow 2004-2010

Founder and CEO, IntBiotechnologies, LLC, Brooklyn, MD

Colleen Furey Summer Student 2014

Graduate Student, Northwestern University, Chicago, IL

Ariel Hagedorn Summer Student 2012

Undergraduate Student, University of Missouri, Columbia, MO

Maria Hamscher Summer Student 2012-2013

Premed Student, University of Pittsburgh, Johnstown, PA

Carey Hwang, M.D., Ph.D. Predoctoral Fellow, M.D./Ph.D. Student 1999-2001

Executive Director and Product Development Lead, Global Clinical Development – Infectious Diseases, Merck Research Laboratories, Gwynedd, PA

Taisuke Izumi, Ph.D. Postdoctoral Fellow 2011-2014

Scientist, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD

Sanath Kumar Janaka, Ph.D Postdoctoral Fellow 2013-2016

Assistant Scientist, University of Wisconsin, Madison, WI

Abhay Jere, Ph.D. Postdoctoral Fellow 2006-2008

University of Massachusetts Medical School, Worcester, MA

Adam Ketchum Summer Student 2016

Medical Student, University of Maryland, College Park, MD

Jean Lutamyo Mbisa, Ph.D. Postdoctoral Fellow 2002-2008

Acting Head, Antiviral Unit, Public Health England, London, UK

Michael Nekorchuk, Ph.D. Postdoctoral Fellow 2014-2017

Postdoctoral Fellow, Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR

Theodore Nikolaitchik Summer Student 2014

Undergraduate Student, University of Maryland, College Park, MD

Galina Nikolenko, Ph.D. Research Fellow 2006-2009

Scientist, Meso Scale Diagnostics, Rockville, MD

Tobias Paprotka, Ph.D. Postdoctoral Fellow 2009-2011

Director of Research and Development, Eurofins Genomics, Konstanz, Germany

Dongfei Qi, Ph.D. Postdoctoral Fellow 2012-2017

Biomedical Scientist, Paragon Bioservices, Inc., Gaithersburg, MD

Sara Rasmussen, M.D., Ph.D. Predoctoral Fellow, M.D./Ph.D. Student 1999-2000

Associate Professor, University of Washington School of Medicine, and Surgical Director of Liver Transplant, Seattle Children’s Hospital, Seattle, WA

Rebecca Russell, Ph.D. Postdoctoral Fellow 2005-2008

Research Scientist and Laboratory Manager, University of Oxford, Oxford, UK

Jayalaxtri Sastri, Ph.D. Postdoctoral Fellow 2013-2016

Senior Scientist, VLP Therapeutics, Gaithersburg, MD

Shrey Shah Summer Student 2015

Undergraduate Student, University of Maryland, College Park, MD

Shruti Shah Summer Student 2019

Undergraduate Student, University of Maryland, College Park, MD

Mayu Shigemi Special Volunteer 2012

Student, Kyoto University, Kyoto, Japan

Jessica Smith, Ph.D. Postdoctoral Fellow 2008-2013

Senior Fellow, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD

Evguenia Svarovskaia, Ph.D. Research Fellow 2000-2004

Senior Director, Clinical Virology, Gilead Sciences, Foster City, CA

David Thomas, Ph.D. Scientist 2002-2005

Patent Examiner, U.S. Patent and Trademark Office, Alexandria, VA

Narasimhan Venkatachari, Ph.D. Research Fellow 2009-2013

Senior Virologist, University of Pittsburgh, Pittsburgh, PA

Yegor Voronin, Ph.D. Predoctoral Fellow 1999-2003

Chief Operating Officer, Worcester HIV Vaccine, Worcester, MA

Hongzhan Xu, M.D., Ph.D. Research Fellow 2001-2006

Director and Epidemiologist, Shanghai Pharmaceutical Group, Shanghai, China

Avanish Yendluri Summer Student 2017

Undergraduate Student, University of Maryland, College Park, MD

Wen-Hui Zhang, Ph.D. Predoctoral Fellow 1999-2002

Owner and Founder, Dr. Wen Wellness Institute, Austin, Texas

New Investigator Scholarships, Conference on Retroviruses and Opportunistic Infections

Chenglei Li and Mohamed Husen Munshi were awarded New Investigator Scholarships to present their research findings in the 2020 Conference on Retroviruses and Opportunistic Infections (CROI). CROI scholarship awardees in previous years include Mohamed Husen Munshi (2019), Belete Desimmie (2017), and Taisuke Izumi (2013).

NIH Fellows Awards for Research Excellence

Mohamed Husen Munshi received a 2020 NIH Fellows Award for Research Excellence (FARE) for travel to attend and present his work at a scientific meeting in the U.S.  This award, which acknowledges outstanding scientific research performed by intramural postdoctoral fellows, is sponsored by the NIH Fellows Committee, Scientific Directors, and Office of Intramural Training and Education and is funded by the Scientific Directors.  FARE awards are based on scientific merit, originality, experimental design, and overall quality and presentation of the abstracts.

Members of the Pathak lab who were FARE awardees in previous years include Sanath Kumar Janaka (2017), Tobias Paprotka (2012), Narasimhan Jayanth Venkatachari (2012), Wei Bu (2010), Jessica Smith (2010), Rebecca Russell (2009), Krista Delviks-Frankenberry (2008), Yeshitila Friew (2007), Patricia Henry (2007), and Galina Nikolenko (2007).

    Travel Award, CCR and DCEG Staff Scientist and Staff Clinician Retreat

    Krista Delviks-Frankenberry received a $1,500 travel award for the best oral presentation at the 14th Annual CCR and DCEG Staff Scientist and Staff Clinician Retreat in April 2018.

      Norman P. Salzman Memorial Poster Award in Virology

      Photo of Belete DesimmieBelete Desimmie won a 2016 Norman P. Salzman Memorial Poster Award in Virology for his work on APOBEC3 inhibition of HIV-1 replication.  This annual NIH-wide award is given to three postdoctoral fellows per year to recognize outstanding research in the field of virology under the mentorship of an NIH, CBER, or Leidos scientist.  Postdoctoral fellows from all NIH campuses, including Bethesda and Frederick, can apply for the award.  Dr. Desimmie presented his poster at the 18th Annual Norman P. Salzman Virology Symposium in November 2016 and received a cash award for his achievement.

       

       

      Intramural AIDS Research Fellowships

      The following Postdoctoral Fellows in the Pathak lab received Intramural AIDS Research Fellowship (IARF) awards from the Office of AIDS Research, Office of Intramural Research, and Office of Intramural Research & Training in the National Institutes of Health to support their proposed research projects:

      Belete Desimmie:  "Identification of Novel Class of HIV Replication Inhibitors Targeting the HIV-1 Vif-A3G Interactions" (2014)

      Narasimhan Jayanth Venkatachari:  "Identification of Small Molecule Inhibitors of Vif-A3G and Vif-A3F Interactions as Novel Antiviral Agents for the Treatment of HIV-1 Infection" (2010, 2011)

      IARF awards include full stipend support to successful candidates who demonstrate outstanding scientific potential through both an imaginative and thoughtful research plan and a well thought out career development plan.

        Poster Awards, Spring Research Festival at NCI-Frederick

        Taisuke Izumi won a poster award for his presentation at the 2013 NCI-Frederick Spring Research Festival. Members of the Pathak lab who won poster awards at the Spring Research Festival in previous years include Tobias Paprotka (2011), Krista Delviks-Frankenberry (2007), Rebecca Russell (2007), Patricia Henry (2006), Galina Nikolenko (2006), and Hongzhan Xu (2006).

          2013 Awards from Frederick County Science & Engineering Fair

          In 2013, Catoctin High School senior Maria Hamscher presented the research she has been conducting in the lab of Dr. Vinay K. Pathak at the 32nd Annual Frederick County Science & Engineering Fair in Frederick, Maryland.  Maria won the 2nd Place Award in Cellular & Molecular Biology, High School Division and also a Distinguishing Achievement 2nd Place Award, given by the Commissioned Officers Association of the U.S. Public Health Service, for her research entitled "Testing the P2A Cleavage System for Gene Therapy Vectors."  Since July 2012, she has been working as a Werner H. Kirsten Student Intern in the Pathak lab under the mentorship of Dr. Krista Delviks-Frankenberry. 

            NIH Asian and Pacific Islander American Organization Award

            Vinay Pathak was the recipient of the 2012 NIH Asian and Pacific Islander American Organization (APAO) Award for outstanding accomplishments in biomedical research.  Each year, the APAO honors two outstanding individuals in the NIH Asian and Pacific American community: one for Scientific Achievement, recognizing scientists who have made significant accomplishments in biomedical research; and the second for Leadership Excellence, recognizing non-scientists who exemplify leadership excellence by example, mentorship, and empowerment of Asian and Pacific Americans to promote diversity and support the overall mission of NIH.  Dr. Pathak received his Scientific Achievement award at the NIH APAO annual awards ceremony in December 2012.

                              Pathak APAO award 2012 photo

                         NIH APAO Award for Scientific Achievement — December 10, 2012

             

            Award from U.S.-Russia Joint Working Group on Biomedical Research Cooperation

            In 2012, Vinay Pathak was the recipient of one of the five grants that the U.S.-Russia Joint Working Group on Biomedical Research Cooperation awarded to National Cancer Institute intramural investigators for their highly meritorious research applications.  Dr. Pathak is the Principal Investigator on a project focused on characterizing broadly neutralizing antibodies by phage display peptide libraries.

              Norman P. Salzman Memorial Award in Virology

              Photo of Tobias PaprotkaTobias Paprotka won the 2011 Norman P. Salzman Memorial Award in Virology for his work on XMRV.  This annual NIH-wide award is given to only one postdoctoral fellow per year to recognize outstanding research in the field of virology under the mentorship of an NIH, Center for Biologics Evaluation and Research, or SAIC scientist.  Postdoctoral fellows from all NIH campuses, including Bethesda and Frederick, can apply for the award.  Dr. Paprotka presented his research at the Thirteenth Annual Norman P. Salzman Memorial Symposium in Virology on November 10, 2011 and received a plaque and a cash award for his achievement.  As Dr. Paprotka's mentor, Vinay Pathak also received a plaque at the Symposium.

               



                Postdoctoral Fellowship, Japan Society for the Promotion of Science

                Taisuke Izumi was awarded a Postdoctoral Fellowship from 2011 to 2013 by the Japan Society for the Promotion of Science. The fellowship program sponsored by this society supports meritorious biomedical research projects undertaken in NIH laboratories by Japanese postdoctoral researchers. Fellowships are awarded after a competitive review of research proposals.

                  Scholarship Award, Keystone Symposia on HIV Pathogenesis

                  Rebecca Russell was awarded a travel scholarship to present her research findings at the 2008 Keystone Symposia on HIV Pathogenesis.

                    2006 Travel Fellowship, HIV & Cancer Virology Faculty, Center for Cancer Research

                    In 2006, Jean L. Mbisa won one of the three available travel fellowships awarded by the HIV & Cancer Virology Faculty, Center for Cancer Research, National Cancer Institute.