DHVI Annual Report 2015_Digital

Annual Report
EMERGING INFECTIONS RESEARCH TO IMPROVE GLOBAL HEALTH
2015-2016

THE DUKE HUMAN VACCINE INSTITUTE | 2016

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Contents
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05
06
08
10
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27
31
32
34
39
By the numbers
Overview
Leadership
Investigators
Gifts of Support
Scientific Breakthroughs
DHVI Centers
Good Manufacturing Practice Faciliy
Resources for Scientific Discovery
Publications
Get Involved

By the Numbers
36Investigators
65
Awards
*FY2015
NIH
Foundations
Corp.
45
15
5
163Staff
By focusing on the scientific “bottlenecks”
for the development of HIV, TB, and other
vaccines, DHVI investigators continue to
make significant contributions to overcome
global health challenges.
The Duke Human Vaccine Institute was formed to support interdisciplinary efforts across Duke to develop
vaccines and therapeutics for HIV and other emerging infections that threaten the health of our nation
and our world. Since 1990, DHVI investigators have been at the forefront in the battle against AIDS and
specifically in the quest for an HIV vaccine.
$
45M
Annual budget
B cell Development and Differentiation | B cell Immunoregulation | Mycobacteriology
B cell Immunotechnology | B cell Repertoire Analysis | Biostatistics Center
Host Defense Research | HIV Pathogenesis & Prevention | Immune Recognition
Immune Responses & Virology | Immunology Virology Quality Assessment Center
Molecular Virology | Neonatal Viral Pathogen Immunity | Plague Pathogenesis
T cell Biology & Immune Reconstitution | Vaccine Vector Immunology |
X-ray Crystallography Shared Resource
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Director’s Message
Mission
The Duke Human Vaccine Institute
will develop innovative diagnostics,
vaccines and therapeutics to
prevent and treat diseases of
global importance, work to
implement them to eliminate
health disparities, and train the
next generation of scientists.
DHVI investigators have led efforts for driving subdominant broad
neutralizing antibody lineages for vaccine strategies using the
membrane bound trimer, as well as intermediate and minimal
immunogens. Additionally, DHVI investigators are using novel
approaches to expand the induction of bnAbs.
Supporting our state of the art vaccine development efforts is the
DHVI’suniqueexperiencemanaginglarge,complexprogramssuch
as the Duke Center for HIV/AIDS Vaccine Immunology (CHAVI-ID)
where we celebrated our 10th anniversary this year, the External
Quality Assurance Program Oversight Laboratory (EQAPOL), and
the Immunology Virology Quality Assessment Center (IVQAC).
Overview
The Duke Human Vaccine Institute (DHVI) continues to lead with cutting edge vaccine research
against infectious diseases that impact global health. The investigators at DHVI conduct
basic and translational research to develop novel vaccines, therapeutics and diagnostics for
diseases such as HIV-1, tuberculousis, influenza, malaria, ebola, cytomegalovirus and now the
zika flavivirus . Several DHVI investigator led basic science discoveries are currently being
produced in Good Manufacturing Practice (CGMP) facilities for early phase vaccine trials.
Frederic M. Hanes Professor, Medicine and
Immunology and Global Health
Director, Duke Human Vaccine Institute
Director, Duke Center for HIV/AIDS Vaccine
Immunology and Immunogen Discovery
We are excited to share that we have completed construction of the DHVI’s own CGMP Facility unit to produce
our own experimental vaccines for early phase clinical trials. Making our own vaccine for human clinical trials
will speed the pace by which new vaccines are tested and allow for rapid progress. We anticipate commissioning
the facility in the first quarter of 2016.This is another way that DHVI is leading in efforts to develop new vaccines
for difficult to treat diseases.
Please enjoy this review of the programs and the accomplishments
of DHVI. I hope that you will consider supporting in our effort to
protect and improve global health.
Over the past year, the DHVI has made innovative discoveries in the field of HIV-1 vaccine development. One
challenge is that current HIV-1 vaccine candidates have been unable to induce adequate amounts of broadly
neutralizing antibodies.
Barton Haynes, MD
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Leadership
The DHVI offers a highly collaborative environment in which its resources enable research teams to focus on complex scientific questions. Core
laboratories house advanced equipment and highly skilled technical teams to support projects in a manner that helps to efficiently advance
the science. Administrative management teams at the institute bring extensive financial and grants management, project management and
compliance support to faculty, students and staff engaged in our research endeavors. These have helped to develop best practices for the
administration of large research programs.
The DHVI continues to look for new innovative approaches to advance our work and to be prepared to respond to global public health threats as
they emerge. One example of this is the recently designed and constructed CGMP facility. Becoming fully operational in 2016, this facility will
enable the DHVI to develop pilot material for early Phase I clinical trials quicker than has been previously possible. By doing so, we hope to be
able to quickly assess new vaccines in humans and determine which should move forward in an expanded clinical assessment.
We hope that you will enjoy reading this report and learning more about the institute and its programs. We also look forward to hearing from
those who have an interest in helping to support the mission of The Duke Human Vaccine Institute.
Dr.TomarasistheDirectorof
ResearchfortheDHVIand
isresponsibleforfacilitating
cutting-edge,collaborativeand
interdisciplinaryresearchconsistent
withthegoalsandmissionofthe
Institute.Sheservesastheprimary
liaisonbetweentheresearchstaffand
theadministrationandcontributes
tobothshort-termandlong-term
strategicplanning.Additionally,in
2015,Dr.Tomarastogether,with
Dr.Thielman,inDukeUniversity’s
DivisionofInfectiousDiseases,wrote
andwereawardeda2.1milliondollar
T32traininggrantfromtheNational
InstitutesofHealthforpostdoctoral
researchtraining.
Georgia Tomaras, PhD
Director of Research
Mr. Denny oversees the daily
operations of the DHVI and its
programs and helps to develop
long term strategic initiatives to
assure that the DHVI remains
scientifically competitive. He
works with the leadership team
to develop and implement
best practices for each area of
responsibility and to assure
that the DHVI maintains the
highest regulatory and financial
compliance performance.
Thomas Denny, MSc, MPhil
Chief Operating Officer
From Thomas Denny, COO
Dr. Tony Moody is the Chief
Medical Officer and Director of
the DHVI Repository. In these
roles, he provides support for
the collaborative work occurring
at the DHVI and with its many
collaborators around the
world. He is also the Principal
Investigator of the Laboratory of
B Cell Immunotechnology, which
focuses on developing techniques
to understand the development
of antibodies in infection, after
vaccination, or in other human
disease states.
Tony Moody, MD
Chief Medical Officer
Dr. Saunders is the Associate
Director of Research and leads
DHVI’s pre-production protein
research effort. Dr. Saunders
oversees the design, expression,
and purification of a variety of
human and pathogen-derived
proteins. In addition to the
protein design and production
effort, he also leads the
Institute’s antibody isolation
endeavors to characterize
adaptive immune responses in
rhesus monkeys and humans.
Kevin Saunders, PhD
Associate Director of
Research
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Dr. Richard Frothingham directs
the Regional Biocontainment
Laboratory (RBL) at Duke. The
RBL supports research to develop
treatments and vaccines against
hazardous microbes including
tuberculosis, plague, and
influenza. Under the direction
of Dr. Frothingham, during the
recent Ebola outbreak, Duke
clinicians received advanced
training in the proper use of
personal protective equipment.
Richard Frothingham, MD
Director, Regional
Biocontainment Laboratory
Cherie Lahti is primarily
responsible for the financial
management and grants
administration of all projects
awarded to the institute. Under
Cherie’s leadership, the DHVI
finance team works with Principal
Investigators in managing grant
expenditures, effort allocation,
budgets, subcontracts, grant
applications and non-competitive
renewals. In addition, the group
provides senior leadership
with financial analysis and
recommendations for short-term
and long-term planning.
Cherie Lahti, MBA
Director of Finance
Gregory Sempowski, PhD
Scientific Director, DHVI
Shared Resources
Dr. Sempowski is the scientific
Director of the DHVI Shared
Resources. Dr. Sempowski is
highly collaborative and works
closely with investigators from
Duke, UNC Chapel Hill, Wake
Forest, Boston University,
Memorial Sloan Kettering,
University of Georgia, University
of Arizona and the Radiation
Effect Research Foundation
(Hiroshima, Japan). Additionally,
Dr. Sempowski has developed an
independent research program
studying immunosenescence
associated with aging and host
response to infectious diseases.
Dr. Kelly Soderberg oversees all
efforts put forth by the DHVI
program management team.
Continuing to support the
scientific advancements at the
DHVI, the program team has been
an integral part of the success
of our large efforts in vaccine
research. Program management
is expected to grow as the DHVI
moves even further down the
translational pathway and
expands into additional infectious
disease vaccine research.
Kelly Soderberg, PhD
Director of Program
Management
Working in collaboration with
investigators worldwide, we are committed
to performing the translational research
necessary to take products
from “bench to bedside.
Barton Haynes | Director

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Investigators
Munir Alam, PhD
Garnett Kelsoe, DSc, MS, MS
Director, Laboratory of
Immune Recognition
Professor, Department of
Immunology, DUSOM
Mattia Bonsignori, MD
Richard Frothingham, MD
Nathan Nicely, PhD Sallie Permar, MD, PhD
Director, Laboratory of B cell
Repertoire Analysis
Plague Pathogenesis
Director, Regional
Biocontainment Laboratory
Director, Duke University
X-ray Crystallography
Shared Resource
Director, Laboratory
of Neonatal Pathogen
Immunity
Associate Professor of Surgery
Associate Research Professor
in Molecular Genetics and
Microbiology, DUSOM
Director, ImmunologyVirology
Quality Assessment Center
COO, DHVI
Director, Laboratory of Host
Defense Research
Director, DHVI
Guido Ferrari, MDThomas Denny, MSc, MPhil
Barton Haynes, MD, PhD
Genevieve Fouda, MD, PhD
Kwan-Ki Hwang, PhD
Samuel L. Katz, MD Sunhee Lee, PhD
Assistant Professor
Monoclonal Antibody
Facility
Chairman Emeritus of
Pediatrics, DUSOM
Mycobacteriology
Feng Gao, MD
Molecular Virology
Laura P. Hale, MD, PhD
Mary Klotman, MD Hua-Xin Liao, MD, PhD
Professor,
Department of Pathology
Chair, Department of
Medicine, Duke University
School of Medicine
Director, Laboratory of Protein
Expression
David Montefiori, PhD David Pickup, PhDTony Moody, MD
Director,LaboratoryforAIDS
VaccineResearch&Development
Professor, Department
of Molecular Genetics and
Microbiology, DUSOM
Director, Laboratory of B cell
Immunotechnology
Chief Medical Office, DHVI

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David Pisetsky, MD, PhD
Medicine, Rheumatology,
and Immunology, DUSOM
Kevin Saunders, PhD
Medical Instructor
Associate Director of
Research, DHVI
Marcella Sarzotti-Kelsoe,
PhDMD, PhD
Director, Duke Center for
AIDS Research Central
Quality Assurance Program
Greg Sempowski, PhD
Herman Staats, PhD
Director, Shared Resources,
Director, Laboratory of T
cell Biology & Immune
Reconstitution
Professor of Pathology,
Associate Professor of
Immunology, Associate
Professor of Medicine, Duke
University School of Medicine
Medical Instructor
Director, Laboratory of B
cell Immunoregulation
Division Chief, Pediatric
Allergy and Immunology,
Duke University Medical
Center
John W. Sleasman, MD
Xiaoying (Shaunna)
Shen, PhD
Laurent Verkoczy, PhD
Leonard D. Spicer, PhD
Jae-Sung Yu, PhD
Radiology, Department of
Biochemistry, DUSOM
Laboratory of Protein
Expression
Geeta K. Swamy, MD
Associate Professor,
Department of Obstetrics
and Gynecology,Division of
Maternal Fetal Medicine,
Director, Obstetrics Clinical
Research, DUSOM
Georgia Tomaras, PhD
Emmanuel (Chip) Walter
Director,LaboratoryofImmune
ResponsesandVirology
Professor,Departments
ofSurgery,Immunology,
MolecularGeneticsand
Microbiology
DirectorofResearch,DHVI
Director,DukeTranslational
MedicineInstituteClinical
VaccineUnit
AssociateDirector,PrimaryCare
ResearchConsortium,Duke
ClinicalResearchInstitute
Director, Biostatistics and
Bioinformatics Center
Nathan Vandergrift, PhD
Professor, Departments of
Immunology and Surgery,
Duke University School of
Medicine
Director, Cytometry
Innovation and
Engineering
Kent Weinhold, PhD John Whitesides, PhD

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Gifts of Support
A primary goal for the immediate future is to acquire the resources that will allow us to continue to be an
intellectual and financial resource as well as a research-training powerhouse for Duke University, while making
major breakthroughs in the prevention of infectious diseases. With additional resources, DHVI can begin to
export the DHVI model of success to other Duke groups.
Private philanthropy, from both individuals and foundations, is absolutely essential to our ability to conduct
the kind of innovative exploration that leads to new cures, more effective therapies, and improved diagnosis
against the most complex and devastating diseases of our time. Your gift to the DHVI will help us achieve our
mission of developing innovative diagnostics, vaccines and therapeutics to prevent and treat diseases of global
importance, while working to eliminate health disparities, and train the next generation of scientists.
Sarah Nicholson
Assistant Vice President
Duke School of Medicine
Development and Alumni Affairs
sarah.nicholson@duke.edu
(919) 385-3160
DHVI has an annual budget of about $45,000,000 and has maintained this level of funding for
ten years.
If you would like information on the many different
ways you can help, please contact Sarah Nicholson.
dhvi.duke.edu/about-institute/make-gift
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Scientific Breakthroughs
HIV
Influenza
Malaria
Ebola
Tuberculosis
CMV
Zika

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Diversion of an HIV Vaccine Immune Response by Antibodies
Reactive with Gut Microbiome
The finding by a Duke Medicine-led research team suggests that a successful vaccine approach would need to
somehow mask this easily induced, but ineffective antibody response, or stimulate a different antibody response
altogether.
“With this study, we wanted to know whether a vaccine induced the same diverted, ineffective antibody response
that occurs with acute HIV infection,” said Barton F. Haynes, M.D., director of the DHVI and senior author of the
study appearing online in Science Magazine on July 30.
“We know that the intestinal microbiome can influence the types of antibodies that develop after birth when
the microbiome is established,” Haynes said. “Our study raises the hypothesis that the microbiome imprinted
the immune system to make these cross-reactive antibodies. It suggested that one way to improve the antibody
response may be to block the undesired HIV sites during vaccination, or to vaccinate earlier in life to imprint the
immune system on desired HIV regions.”
A recent HIV vaccine trial testing the HIV envelope as an immunogen was unsuccessful for
protection against HIV infection. A new study has found that this vaccine selectively recruited
antibodies which react with both the HIV envelope and common intestinal microbes — a
phenomenon previously reported by the same investigators to occur in the setting of acute
HIV infection.
HIV- AIDS
HIV is a virus spread through certain body fluids that attacks the body’s immune system,
specifically the CD4 cells, often called T cells. Over time, HIV can destroy so many of these cells
that the body can’t fight off infections and disease. These special cells help the immune system
fight off infections. Untreated, HIV reduces the number of CD4 cells (T cells) in the body. This
damage to the immune system makes it harder and harder for the body to fight off infections
and some other diseases. Opportunistic infections or cancers take advantage of a very weak
immune system and signal that the person has AIDS.
Photo credit: NIAID

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Haynes said the experimental vaccine induced antibodies that targeted a region of the HIV virus called gp41,
which is part of the virus’s outer envelope. But these antibodies were non-neutralizing and were not able to stop
the virus from infecting CD4 T cells.
What’s more, the gp41 region is a molecular mimic of some intestinal microbiome bacterial and self antigens that
the body’s B cells are trained on, raising the hypothesis that the vaccine essentially stimulated a diversion that kept
the immune system busy, allowing the virus to flourish.
“It’s another way that the virus evades the immune system,” Haynes said. “It gives the virus a
leg up in escaping the early antibody response, by primarily inducing antibodies that cannot
neutralize HIV.”
“The keys to inducing a successful HIV antibody response may be to mitigate or get around the virus’s ability to
divert preexisting B cells that are cross-reactive with intestinal microbiota,” Said Dr. Wilton Williams, lead author
of the study. “We are currently exploring early vaccination strategies and exploring new designs of the HIV viral
envelope to induce the correct antibodies.”
Because the microbiome serves as a training ground to teach the immune system how to fight pathogens, HIV’s
ability to mimic common microbiota suggests that a successful HIV vaccine approach might also include early
childhood immunizations.This could provide a way to prime the immune system to better identify and attack HIV.
The study received funding from the National Institute of Allergy and Infectious Diseases, part of the National
Institutes of Health, Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (UM1 AI100645); the Duke
University Center for AIDS Research; and the Vaccine Research Center at NIAID.
The keys to inducing a successful HIV
antibody response may be to mitigate or
get around the virus’s ability to divert
preexisting B cells that are cross-reactive
with intestinal microbiota. We are currently
exploring early vaccination strategies and
exploring new designs of the HIV viral
envelope to induce the correct antibodies.
Wilton Williams, PhD | Lead author
Article credit: Duke Medicine News and Communications 2015

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Antibody Response Linked To Lower Mother-to-Child
HIV Transmission
Mother-to-child transmissions account for about 250,000 HIV infections per year worldwide, despite greatly
expanded access to antiretroviral drug regimens that can interrupt transmission into low-resource settings.
Ongoing problems with access to the drugs, late initiation of the drug regimens during pregnancy, and acute
maternal infection during pregnancy and breastfeeding all contribute to the ongoing infant transmission.
Even in the absence of antiretroviral drug regimens, however, the majority of newborns are naturally protected
against HIV, despite chronic virus exposure. The Duke research team sought to define what is different in the
babies who become infected compared to those who don’t.
HowmostbabiesareprotectedfromacquiringHIVfromtheirinfectedmothershasbeenamatter
of scientific controversy. Now researchers at Duke Medicine provide new data identifying an
effective antibody response that had long been discounted as inadequate to confer protection.
HIV- AIDS
We know that mothers
pass antibodies to
fetuses in-utero, but a
true understanding of
how maternal antibodies
were contributing to
protection had never
been established.
Sallie Permar, MD, MSH | Lead author, Principal Investigator
Permar and colleagues at the
DHVI and the Fred Hutchison
Cancer Research Center analyzed
data from a U.S. study in the
1990s that predated therapies
such as AZT. The study included
mothers and babies, yielding
information about risk factors
and transmissions in a pre-
treatment environment.
Photo credit: Duke Photography14

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By profiling the immune responses of mothers in this early study, the researchers were able to pinpoint the
differences between those who transmitted the virus to their infants, and those who did not. Among mothers
whose babies were shielded from infection, they found a strong antibody response to a particular region on the
HIV virus envelope (the HIV envelope third variable or V3 loop) that has been considered too variable and too
inaccessible to be a relevant target for a neutralizing antibody.
“That was very surprising,” Permar said, “because this type of weak neutralizing antibody response, which had
previously been thought to be inconsequential for HIV transmission, could potentially be effective in preventing
mother-to-child transmission. And there are current HIV vaccine candidates, such as recombinant HIV envelope
protein immunization, in early-stage clinical testing that can elicit this type of response.” Permar said the team’s
study raises a compelling question about why the V3 neutralizing antibody response seems to be enough to
reduce mother-to-child transmission, yet is not protective in other modes of HIV transmission.
Permar said additional research at Duke will focus on testing newer experimental HIV vaccines to raise this
potentially protective antibody response in mothers to neutralize her virus and thereby protect the baby.
“We hope this will be a major clue to making a vaccine to effectively prevent all mother-to-child HIV transmission,
since these antibodies are the type that our current experimental HIV vaccines can boost,” said
Tony Moody, MD, a co-author and DHVI chief medical officer.
Funding included grants from the National Institute of Allergy and Infectious Diseases, part of the National
Institutes of Health (5-UM1-AI100645, 5-P30-AI064518) and HIV Vaccine Trials Network.
“The difference in mother-to-infant transmission might be that the infant is only being exposed to the
mother’s virus, and the infant is born with antibodies that are transferred from the mother,” Permar said. “The
presence of antibodies that were raised against the mother’s virus prior to exposure to the same virus makes
the infant transmission setting very different from that of other modes of HIV transmission. So how well the
mother’s antibody can neutralize her own virus could be the key to whether the baby is infected.”
We may be closer than
previously thought to testing
a vaccine that protects infants
by inducing a common HIV-
specific antibody response.
Tony Moody, MD | Co-author
The study was published online June 8, 2015, in the Journal of Clinical Investigation.

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Duke Research Teams Win Large Federal Grants for HIV Vaccine Studies
Two research teams at Duke Medicine have received large, multi-year grants from the National
Institutes of Health to pursue projects on HIV vaccine development.
This grant represents an exciting
collaborative effort. It combines our
long-standing interest in developing integrase
defective lentiviral vectors as a safe approach
to persistent immunogen expression along
with expertise within the Duke Human Vaccine
Institute that is focused on innovative envelope
immunogen design and B cells.
The NIAID presented a second grant of more than $11 million over five years to a collaborative effort led by Sallie
Permar, M.D., Ph.D., associate professor in the Department of Pediatrics at Duke, and involving researchers at the
University of North Carolina and the University of California, Davis.
Klotman’s grant will support two research projects and two core facilities that together will aim to develop a
safe, effective HIV vaccine using a vector delivery strategy to drive a successful immune response.
Klotman’s collaborators include Andrea Cara, Ph.D., a Duke visiting scholar; Tony Moody, MD, associate professor
of pediatrics and director of the Laboratory of B cell Immunotechnology in the DHVI; and Sampa Santra, Ph.D.,
assistant professor of medicine at Harvard University and a member of the Center for Virology and Vaccine
Research at Beth Israel Deaconess Medical Center.
Both grants draw on the longstanding expertise in the Duke Center for HIV/AIDS Vaccine Development led by
Barton Haynes, MD. Permar’s grant funds two projects and three core facilities to develop a maternal and infant
vaccine approach to eliminate pediatric HIV-1 infections.
Mary Klotman, MD | Chair, Department of Medicine | Duke University School of Medicine
The National Institute of Allergy and Infectious Diseases (NIAID) awarded a five-year grant totaling more than $9
million to a team led by Mary Klotman, MD, chair of the Department of Medicine at the Duke University School
of Medicine.
HIV- AIDS

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Influenza
Influenza is one of the most common infections worldwide. Each year, new influenza
vaccines are needed that incorporate currently circulating strains because influenza
viruses mutate and change every year.These new strains can emerge in either epidemic
or pandemic waves. Influenza vaccination has been shown to be effective in reducing
influenza disease and this has led to recommendations for near universal vaccination
in the US.
The annual changes that occur in influenza viruses usually make the previous year’s
vaccine ineffective in providing long-lasting protection. Furthermore, it is possible that
a new influenza strain, such as those that circulate in birds, could infect the human
population resulting in a new global lethal pandemic. Finding a vaccine strategy that
results in long-lasting protection against multiple influenza strains is a goal of the
DHVI Influenza Vaccine Program.
Influenza receptor binding site antibodies
New tools for studying
influenza antibodies
Original Antigenic Sin /
Immune Memory
Protection against influenza infection is primarily due to antibodies made by the body in response to vaccination
or infection. Most of these antibodies are highly specific, reacting primarily with the influenza strains in the
vaccine or the one causing infection. In recent years, antibodies that have the ability to neutralize many strains
of influenza have been discovered, and one group of these antibodies block influenza viruses by interfering with
the ability of a virus protein called hemagglutinin to bind to its target on human cells. If a vaccine could elicit
these antibodies, called receptor binding site antibodies, the vaccine might be able to prevent infection with
many strains of influenza viruses. DHVI is actively pursuing vaccine strategies to elicit this class of antibodies
with the hope of creating a universal influenza vaccine.
The DHVI is actively working to understand
how receptor binding site antibodies, and other
broadly protective antibodies, arise in humans.
To do this, we have partnered with Stephen
Harrison at Boston Children’s Hospital to study
the structural basis for the activity of these
antibodies, to develop new tools for their study,
and to design vaccine candidates for testing. As
part of this collaboration, we recently reported
that receptor binding site antibodies in humans
could arise from multiple different starting
points, suggesting that this class of antibodies
might be easier to induce than similar
antibodies against HIV-1.
In some cases, exposure to new strains of influenza
may produce a response that is directed toward strains
seen in prior years of infection or vaccination rather
than to that being seen in the present infection or
vaccination.Thisphenomenonhasbeencalledoriginal
antigenic sin (OAS) and has been described not just
for influenza but has been observed for many kinds
of pathogens. Work at DHVI previously showed that
for influenza, OAS was more likely to occur following
infection compared with vaccination. Using that
knowledge, we are developing strategies to leverage
the OAS phenomenon with the goal of eliciting
receptor binding site antibodies that can provide long-
lasting protection against many influenza strains.

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Malaria
Malaria, which is caused by infection with parasites of the genus
Plasmodium, predominantly by P. falciparum, remains a significant
public health problem worldwide and a leading cause of morbidity
and mortality in tropical and sub-tropical regions. P. falciparum is
transmitted to humans from mosquitoes of the genus Anopheles,
the non-human carrier of the parasite, through bites. Half of world’s
population is at risk of malaria, with an estimated 198 million cases
occurred globally and more than 584,000 deaths annually, mostly in
the African region and among children under the age of 5 years (World
Health Organization. World Malaria Report 2014).
Despite extensive efforts to control and treat malaria, including public health measures and
widespread usage of anti-malaria drugs, the most cost-effective solution to prevent infection
and control the malaria endemic is to develop a vaccine.
Dr. Tomaras leads a team that is actively working
on developing methods to enable identification
of correlates of protection for malaria vaccines.
Technical and conceptual advances from DHVI’s
work on the relationship between antibody
specificity, subclass and HIV-1 protective efficacy are
being applied to the evaluation of candidate malaria
vaccines to identify potential correlates. Her work, in
collaboration with Dr. Munir Alam, focuses on the
evaluation of the biophysical interactions between
antibodies and antigenic determinants exposed
during the pre-erythrocytic stages of P. falciparum.
Dr. Bonsignori leads a team committed to isolate
and characterize malaria-specific monoclonal
antibodies from B and plasma cells of vaccine
recipients and infected individuals. By leveraging
the established platform for B cell repertoire
analysis and antibody production developed at
the DHVI, his work focuses on characterizing the
functional repertoire of vaccine-induced malaria-
specific monoclonal antibodies with diverse
specificities and evaluating clonal persistence and
evolution, as well as differences between naturally
occurring and vaccine-induced antibodies.
Detailed analysis of vaccines can reveal potential immune correlates of
protection and lead to testable hypotheses about the mechanism of
action critical to further vaccine improvement.

19
Ebola
Ebola is a rare and deadly disease
caused by infection with a strain
of Ebola virus. The 2014 Ebola
epidemic is the largest in history,
affecting multiple countries in
West Africa. The risk of an Ebola
outbreak affecting multiple people
in the U.S. is very low.The disease is
spread through direct contact with
blood and body fluids of a person
already showing symptoms of
Ebola. Ebola is not spread through
the air, water, food, or mosquitoes.
Following on what
we have been doing
with a conserved region T
cell vaccine for HIV, we are
applying the same kind of
strategy to the Ebola virus.
Bette Korber, PhD | Collaborator
In addition to immunizing non-human primates with
proteins and extracting antibodies, investigators
at The DHVI are working with investigators at Los
Alamos National Laboratory as well as The University
of Oxford to generate two different structural mosaic
Ebola envelope proteins to use as potential vaccine
antigens for vaccination against Ebola.
Because Ebola has an extremely variable envelope protein, the
idea is that the vaccine antigen would raise T-cell responses
that are cross-reactive to several common variants of the Ebola
viral envelope. The structural envelope mosaics are made from
combinations of 3 artificial proteins that a group led by Dr.
Korber, at LANL, designed using computational methods. The
artificial proteins mimic several different envelope epitopes
so that T-cells that are generated would recognize several
different Ebola virus variants.
In this particular work, the DHVI, as well as others, will test
the effectiveness of two different structural mosaics for
generating T-cell responses in mice. If mice vaccinated with
the mosaics produce T-cell responses to Ebola, then future
studies might include vaccination in non-human primates to
confirm that the immune response to the vaccines is similar
in those animals. The long-term goal is to develop vaccine
antigens for human immunization trials and effective human
vaccines against Ebola.
This work is a collaboration between Bette Korber, PhD (Los
Alamos National Laboratory), Tom Hanke, MSc, BSc, PhD
(University of Oxford), and Barton Haynes (The DHVI).

20
TB is a disease caused by a bacterium called
Mycobacterium tuberculosis. The bacteria
usually attack the lungs, but TB bacteria can
attack any part of the body such as the kidney,
spine, and brain. If not treated properly, TB
disease can be fatal. TB disease was once the
leading cause of death in the United States.
Tuberculosis Vaccine Improvement
M. tuberculosis is an extraordinarily successful pathogen that has managed to latently infect nearly one third of
humanity and is responsible for an estimated two million deaths annually. The success of this pathogen is linked
to its ability to manipulate the intracellular environment of phagocytic cells in the host. Many lines of evidence
indicate that M. tuberculosis has evolved mechanisms to evade host immunity, in some cases by inhibiting the
priming and effector functions of these T cell subsets. For example, the manipulation of cell death (apoptosis) by
virulent mycobacteria is a well-known survival and immune-modulating strategy. By blocking apoptosis of cells
early after infection, M. tuberculosis prevents or delays presentation of its antigens and thus fails to stimulate
effective T cell responses.
Tuberculosis remains a major global health problem, despite the widespread use of the
Mycobacterium bovis bacillus Calmette-Guerin (BCG) vaccine and drug therapies. Coinfection
withMycobacteriumtuberculosisandHIV,aswellasmultidrug-resistant(MDR)andextensively
drug-resistant (XDR) tuberculosis, makes TB control difficult, complex and challenging.
Tuberculosis
The Lee lab is currently studying these immune evasion
strategies of M. tuberculosis and is researching novel
approaches for improving mycobacterial vaccines
by manipulating mycobacterial proteins responsible
for evasion of host immune responses. In particular,
studies of mycobacterial modulation of apoptosis and
autophagy, as innate and adaptive immunity defense
against intracellular pathogens, are main focuses of
the lab. We have screened M. tuberculosis transposon
mutant library and isolated 23 pro-apoptotic and 12
pro-autophagic mutants that are not able to inhibit
infection-induced host innate responses.
Some of these M. tuberculosis mutant strains
demonstrated enhanced immune responses in mice
and thus could be important targets incorporated
into TB vaccine candidates. The major long-term
goal of our laboratory is to engineer safe and more
effective live TB vaccines that will contribute to the
global control of tuberculosis and also reduce the
emergence of drug resistant strains.

21
Surface Binding Human M. tuberculosis Monoclonal Antibodies
Our long-term goal is to develop an efficacious
TB vaccine that induces antibodies capable of
preventing Mtb infection. Critical to achieving this
goal is a clear understanding of the contribution of B
cells and the humoral response to the control of MTB
in infected hosts. We have identified three murine
Mtb surface binding monoclonal antibodies (mAbs)
that reduce Mtb burden in lung at early time points
after experimental Mtb aerosol infection in mice. The
mAbs block entry of the bacterium into lung cells and
also divert the bacteria from alveolar macrophages
toward other phagocytic cells.
Most humans with Mtb infection generate poor
responses to the surface of the Mtb bacterium, but
we have identified a small subset of humans (about
7%) who produce high-titer high-avidity antibodies
to the Mtb surface. We are isolating monoclonal
antibodies from these individuals in order to identify
the targets of these antibodies. These targets
may serve as the basis for a preventive vaccine to
be administered prior to Mtb infection. We also
evaluating human surface binding antibodies as
potential therapeutic agents for humans infected
with extensively drug-resistant Mtb (XDR-TB).
Cell-mediated immunity is a major component of host defense against M. tuberculosis (Mtb)
infection. The predominant Th1 CD4+ cell response reduces progression of Mtb infection, but
does not prevent establishment of infection or clear established infection. Mtb antibodies
can play a significant role in protection as demonstrated by vaccination studies and by
administration of either polyclonal or monoclonal antibodies. However, the mechanisms
underlying antibody-mediated protection from Mtb infection remain unclear.
Dr. Richard Frothingham and
coworkers have developed a
murine model of latent
M. avium infection that
mimics many aspects of
latent human infection with
environmental mycobacteria.
21

22
Tuberculosis
Buruli Ulcer Vaccine Development
Despite the progress made in early detection and treatment of BU, surgical excision of the lesions with skin
grafting remains the only treatment for advanced ulcers. Thus, a vaccine against MU is imperative to protect at-
risk populations in hyper-endemic areas. Currently, there are no specific vaccines against BU.
Similartotheresponsesofthetwobest-understoodmycobacteriaofclinicalinterest,M.tuberculosis(Mtb)andM.
leprae, Th1-type cellular immune responses are essential for control of MU. However, despite early development
ofT cell immunity in experimental mouse infections, the host response is not sufficient to inhibit the proliferation
of highly virulent MU strains. To test if vaccination triggering heightened MU specific cell mediated immunity
will elicit a more effective and prolonged protective immunity against virulent MU infection, we constructed
recombinant mycobacterial strains overexpressing the MU antigen 85A (Ag85A). This recombinant BCG showed
significantly improved antigen-specific T cell responses, correlating with the protection against virulent MU in
the mouse footpad model. This result warrants the development of an attenuated, live, BU vaccine that can
induce strong immune responses against species-specific antigens, which we are currently working on.
At the Laboratory of Mycobacteriology, we have developed safe and effective vaccines for
Buruli ulcer caused by M. ulcerans. Buruli ulcer is an emerging ulcerative skin disease caused
by infection with Mycobacterium ulcerans (MU). It is one of the 17 Neglected Tropical Diseases
(NTDs) prioritized by World Health Organization. The extensive cutaneous and subcutaneous
lesions provoked by BU often lead to grotesque deformities and permanent disability of the
human host. Often young children succumb to the infection.
Laboratory of Mycobacteriology focuses its research
on: the development of safe and effective vaccines
and immunotherapeutics for tuberculosis via novel
strategies and approaches; evaluation of alternative
methods to enhance the efficacy of current
mycobacterial vaccines; development of recombinant
mycobacterial vehicles capable of eliciting strong
immune responses to HIV and other foreign antigens;
and study of the virulence and immunogenicity of
drug-resistant strains of MTB.
Sunhee Lee, PhD | Director
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23
Tuberculosis
Stable Expression of Lentiviral Antigens by Quality-Controlled
Recombinant Mycobacterium bovis BCG Vectors
However, successful generation of recombinant BCG strains possessing consistent insert expression has
encountered challenges in stability. At the Laboratory of Plague Pathogenesis, we developed a method for the
development of large recombinant BCG accession lots which stably express the lentiviral antigens, human
immunodeficiency virus (HIV) gp120 and simian immunodeficiency virus (SIV) Gag, using selectable leucine
auxotrophiccomplementation.Successfulestablishmentofvaccinestabilitystemsfromstringentqualitycontrol
criteria which not only screen for highly stable complemented BCG ΔleuCD transformants but also thoroughly
characterize postproduction quality.
Importantly, these quality assurance procedures were indicative of overall vaccine stability, were predictive for
successful antigen expression in subsequent passaging both in vitro and in vivo, and correlated with induction
of immune responses in murine models. Production of large, well-defined recombinant BCG ΔleuCD lots can
allow confidence that vaccine materials for immunogenicity and protection studies are not negatively affected
by instability or differences between freshly grown production batches.
The well-established safety profile of the tuberculosis vaccine strain, Mycobacterium bovis bacille
Calmette-Guérin (BCG), makes it an attractive vehicle for heterologous expression of antigens from
clinically relevant pathogens.
Laboratory of Plague Pathogenesis focuses on
Yersinia pestis, the bacterial cause of bubonic and
pneumonic plague. The goals of the Frothingham
laboratory are to define specific protective
mechanisms that are a part of the host response to
plague and to use this information to develop better
drugs and vaccines against plague infection.
Richard Frothingham, MD, FACP, CBSP | Director
23

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Cytomegalovirus (CMV)complicates1%ofallpregnanciesandresultsin8,000severeinfectionsinU.S.childrenannually,
resulting in hepatitis, neutropenia, brain damage, seizures, and vision and hearing loss. It is the leading nongenetic
cause of infant hearing loss, accounting for 25% of all hearing loss, and causes more permanent disabilities in U.S.
children then spina bifida or Down syndrome. Much like the rubella vaccine eliminated congenital rubella syndrome
inthiscountry,avaccinethatinducesprotectionmaternalimmuneresponsesinneededtoprotectagainstcongenital
CMV. Thus, a team of DHVI researchers, led by Sallie Permar, MD, PhD, are working to identify the maternal immune
responses that are required to protect against placental transmission of CMV in mother-infant cohort studies.
Monkey Model Discovery Could Spur CMV Vaccine Development
Cytomegalovirus (CMV) is the leading infectious cause of birth defects worldwide, but scientists
have been frustrated in their efforts to develop a vaccine to protect against infections. Among
the most confounding problems is the lack of animal models that aptly mimic CMV passing
from mother to unborn child, as it does in humans. Aside from guinea pigs, which have limited
similarities to humans, no other mammals were known to pass the virus to their fetuses.
Or so it has seemed.
Now researchers have discovered that rhesus monkeys can, in fact, transmit the virus across the placenta to their
unborn offspring. This finding, reported online during the week of October 19 in the Proceedings of the National
Academy of Sciences, establishes the first primate model that researchers can use to study mother-to-fetus CMV
infections and spur development of potential vaccine approaches.
CMV is related to the herpes viruses that cause
chicken pox and mononucleosis, and in most
people, it results in mild to no symptoms
of disease when they acquire an infection.
However, in about a third of instances when
women who have never been exposed to CMV
contract the virus during pregnancy, they can
pass an infection to the fetus. About a quarter
of those infants will go on to have neurologic
impairment.TheCentersforDiseaseControland
Prevention reports that about 5,000 children
a year in the U.S. are born with permanent
problems resulting from CMV infections,
including deafness, blindness, seizures and
cognitive delays.
A huge impediment to CMV vaccine
development has been our lack of ability to
determine what immune responses would
be needed to protect against mother-to-
fetus transmission. This requires good
animal models, where we can manipulate
each arm of the immune system to
evaluate its role in congenital infection.
Sallie Permar, MD, PhD
“This is a situation of great concern and we need to work to prevent it,” Permar said. “After the rubella vaccine was
developed in the 1960s, schools for the deaf and blind had to close their doors because there were far fewer children who
had suffered congenital rubella infections and needed the services.That’s the kind of impact a CMV vaccine could have.”
Cytomegalovirus

25
In addition to establishing a primate model
for congenital infection, we gained new
information about the importance of the
maternal immune system in protecting the fetus.
Whereas CMV transmission among immune-
competent mothers did not result in fetal disease,
transmission in mothers with compromised T cell
immunity led to severe fetal outcome.
Kristy Bialas, PhD | Lead author
Using macaques at the New England Primate Research Center, Harvard Medical School, that were specially bred to
be free of CMV and all herpes viruses, they depleted the CD4 “helper” T cells that play an important role in antibody
responses. When infected with CMV a week later, all the animals passed the virus through the placenta, resulting in
miscarriageinthreeofthefouranimals.“Thistoldusnotonlythattheviruscouldbetransmittedthroughtheplacenta,
but that the mother’s immune system was playing an important role in the severity of the infection,” Permar said.
In a second experiment, Permar and Kaur infected CMV-negative animals with the virus, and left their immune
systems intact. Among this group, CMV was transmitted to two of three offspring in utero, but the animals were
born with no major neurological deficits – mimicking what often occurs in humans.
In a third control group of animals, the researchers studied females that had naturally been infected with CMV earlier
in their lives, and depleted their CD4 helperT cells during pregnancy.The mothers had little to no circulating virus and
the offspring appeared to be unaffected by the CD4 helperT cell depletion.
Permar said the next stage of research will be to determine whether neutralizing antibody responses would
be enough to protect against transmission of severe disease, or whether a T-cell vaccine would be the better
approach. In addition to Permar and Bialas, study authors at Duke included Eduardo Cisneros De La Rosa; Erika L
Kunz; Jennifer Kirchherr; Qihua Fan; and Allison Hall.
Permar said simple approaches to vaccine development,
suchascreatingaweakenedvirustotriggerimmunity,have
failed, because the virus has evolved alongside humans
to elude the immune system. So having a non-human
primate model – something of a higher order than guinea
pigs–becameimperative.Permarsaidfindingthemother-
to-fetus transmission in the rhesus macaques became a
hunt. She enlisted the help of co-senior author Amitinder
KaurofTulaneNationalPrimateResearchCenter,anexpert
in CMV-specific immunity in rhesus macaques.
Most macaques are infected with the rhesus version
of CMV before adulthood, yet their young are born
withoutthehearinglossorneurologicalproblemsthat
human babies can acquire in utero. In an earlier study,
coauthor Peter Barry of the University California at
Davis found that infection of a macaque fetus directly
through the abdomen resulted in a similar disease to
that in humans. Permar and Kaur wanted know if the
infection could pass through the placenta.

26
Yet, unlike these other two globally mobile arboviruses, the ZKV epidemic in the Americas stands out as
particularly alarming due to its association with poor pregnancy outcomes, including fetal demise, infant death,
and severe fetal neurologic damage.
An epidemic of this proportion will result in a generation of disabled children in areas of the world that suffer
from limited health care resources, leaving a costly societal burden in its wake.
An effective maternal vaccine is the only intervention that will protect all infants against ZKV-associated
permanent brain damage and birth defects. The success of a maternal vaccine has been demonstrated by the
elimination of congenital rubella syndrome in the Americas through the introduction of a rubella vaccine. Yet a
considerable gap exists in our understanding of the natural immune responses that develop to infection and its
impact on virus transmission and disease, impeding the way forward for development of an effective vaccine.
The recent, rapid spread of Zika Virus (ZKV) from a locally-harbored epizootic arbovirus has
been a public health wake up call. Carried and transmitted by the Aedes species of mosquitos,
this epidemic follows a now familiar pattern of spread to that of Chikengunya, and West Nile
Virus, which were both newly spread from primarily tropical zones to the western hemisphere
within the last two decades.
Zika
Researchers at the DHVI, along with researchers at Universidade
Federal do Espirito Santo (UFES) in Victoria, Brazil, hypothesize
that a prime-boost immunization strategy of the ZKV Env protein
expressed in a Yellow Fever vector and/or a TLR-adjuvanted envelope
purified protein will elicit high magnitude and specific binding and
neutralizing antibody responses against Zika virus.
The team of researchers plan to identify ZKV infection in women in
the early phases of pregnancy, perform a detailed characterization
of the ZKV binding and neutralizing antibody assays, as well as the
cross reactivity to endemic serotypes of dengue virus, and then relate
these antibody responses to fetal outcome.
The first step towards
developing an effective
vaccine is to understand
the natural immune
responses against the
virus, particularly in
pregnant women, and their
impact on fetal outcome.

27
DHVI Centers
The vaccine strategy of the Duke CHAVI-ID is based on
identifying and targeting novel HIV-1 vulnerabilities to B, T
and NK cell immune responses and using this information
to design vaccines that will induce protective immunity at
the time and location of HIV-1 transmission.
The CHAVI-ID consortium has continued to conduct “big
science” that is both qualitatively and quantitatively
different than what can be accomplished by individuals
alone. Additionally, the Duke CHAVI-ID has succeeded in
speeding up the tempo of the work, sharpening the focus,
and answering questions that have been intractable for
the field for many years.
Finally, the work in the CHAVI-ID has defined the host-HIV
interaction that has justified HIV development to date
and, on this work, charted a course for successful HIV
vaccine development.
2015 marked the 10th anniversary for the Duke Center for HIV/AIDS Vaccine
Immunology (CHAVI). The current CHAVI-ID is a consortium that was
established by the National Institute for Allergy and Infectious Diseases
(NIAID) to undertake the immunologic research that will tackle the major
scientific obstacles in the development of an effective HIV-1 vaccine.
CHAVI - ID
The laboratory program at Duke is led by Georgia Tomaras,
PhD, and is comprised of three laboratories (David Montefiori,
Guido Ferrari, Georgia Tomaras) working together to
comprehensively evaluate vaccines, including vaccine
immunogens designed by Dr. Haynes, Director of DHVI.
The Duke laboratory works in partnership with the Fred
Hutchinson Cancer Research Center, Seattle, WA.
The goal of the HIV Vaccine Trials Network
laboratory program, NIH/NIAID is to provide
cutting edge immune monitoring of HIV-1 vaccine
clinical trials.
HVTN
27

28
The goal of the EQAPOL program is to support the development, implementation and oversight of external
quality assurance (EQA) programs that monitor laboratories involved in HIV/AIDS research and vaccine trials
around the world. In addition to EQA programs, the EQAPOL program has established and continues to add to an
HIV Viral Diversity Panel that represents the current genetic and geographic diversity of HIV.
The EQAPOL program currently administers five EQA programs with over 70 participating sites worldwide
to assess proficiency in the following assays: interferon-gamma (IFN-y), Enzyme-linked Immunosorbent
Spot (ELISpot) assay, Intracellular Cytokine Staining by Flow Cytometry, Luminex bead-based assay, A3R5 HIV
neutralizing antibody assay, and HIV incidence assay (ICS) testing (newly added in late 2015).
The IQA is a resource designed to help domestic and international immunologists evaluate and enhance the
integrity and comparability of immunological laboratory determinations performed on patients enrolled in
multi-site HIV/AIDS therapeutic, vaccine and prevention investigations.
As part of the IQA program, two Proficiency Testing (PT) efforts are administered: a PT for Peripheral Blood
Monoclonal Cell (PBMC) cryopreservation and a PT program for CD4 and CD8 immunophenotyping via flow
cytometry. In addition, the IQA program assists the current and future NIAID-sponsored clinical trial networks
and collaborating study groups, including the AIDS Clinical Trials Group (ACTG), the International Maternal
Pediatric Adolescent AIDS Clinical Trials (IMPAACT), the HIV Vaccine Trials Network (HVTN), the HIV Prevention
Trials Network (HPTN), and the Microbicide Trials Network (MTN), in a variety of capacities.
In support of these programs, the Immunology and Virology
Quality Assessment Center (IVQAC) maintains a College
of American Pathologists (CAP)-accredited biorepository,
which contains well-characterized cryopreserved peripheral
blood mononuclear cells (PBMCs) for use in EQA testing
and viral culture. The IFN-y ELISpot, Flow Cytometry and
Luminex EQA programs are ISO/IEC 17043 accredited by the
American Association for Laboratory Accreditation (A2LA) as
a Proficiency Testing provider (A2LA Cert. 3614.01).
In September 2010, the DHVI became the home of the NIAID DIADS External
Quality Assurance Oversight Program Laboratory (EQAPOL) under the
leadership of Thomas Denny, MSc, MPhil.
The Immunology and Virology Quality Assessment Center (IVQAC) is the
home of the NIAID DAIDS Immunology Quality Assessment (IQA) program.
Thomas Denny, MSc, MPhil, has led the IQA program since 1999.
The goal of the EQAPOL Viral Diversity program is to establish a panel of fully characterized viruses from acute/
early and chronic HIV infections. The panel of viruses can be used for various applications, including:
• Impact of genetic diversity on assay performance
• Developing/validating new assays
• Assisting regulators to evaluate test kits
• Monitoring HIV drug resistance
• Informing vaccine development
The current EQAPOL Viral Diversity panel
includes over 220 viral isolates representing 6
subtypes (A, B, C, D, F, G), 2 sub-subtypes (F1, F2),
9 CRFs (01, 02, 04, 14, 22, 24, 47, 59, 70), 49 URFs,
HIV-2, and 3 group O viruses from 30 countries
EQAPOL
IQA

29
Through the IQA proficiency testing programs, over 200 sites worldwide are served helping to ensure quality
and consistency in data generated from these sites. The PBMC cryopreservation program currently includes
86 domestic and international sites. The domestic immunophenotyping PT program currently services 60
laboratories across the United States, Canada and Puerto Rico. The IQA domestic immunophenotpying program
is accredited by the American Association for Laboratory Accreditation (A2LA) as a Proficiency Testing provider
(A2LA Cert. 3614.01).
In addition, the IQA reviews the performance and offers remediation to the international DAIDS laboratories
participating in the UK NEQAS Immune Monitoring program. Currently, there are 63 laboratories from 18
countries participating in the UK NEQAS/IQA review and monitoring program for CD4 enumeration.
The DCVU conducts clinical investigations through funding provided by government (NIAID DMID and CDC) and
industry.Two major projects of the DCVU are the NIAID DMIDVaccine andTreatment Evaluation Unit (VTEU) and the
Clinical Immunization Safety Assessment (CISA) Project. Both projects rely on the extensive scientific and research
expertise afforded by the Duke HumanVaccine Institute (DHVI) and the Duke Clinical Research Institute (DCRI).
The Duke Clinical Vaccine Unit (DCVU), led by Emmanuel “Chip” Walter, MD,
MPH, is a consortium of investigators across multiple disciplines committed
to conducting clinical investigations related to the control and prevention of
infectious disease with an overarching goal of furthering our understanding
of vaccine immune responses and correlates of protection from infection.
DCVU
During this year, Dr. Walter was appointed to the Advisory
Committee on Immunization Practices (ACIP) The ACIP
consists of medical and public health experts that develop
recommendations on how to use vaccines to control diseases
in the United States. Dr. Swamy was appointed to the
National Vaccine Program Office’s National Vaccine Advisory
Committee (NVAC) Maternal Immunization Working Group.
The working group is charged to identify barriers to and
opportunities for developing vaccines for pregnant women and
make recommendations to the Assistant Secretary of Health to
overcome these barriers. Dr. Swamy was also appointed to the
American College of Ob/Gyn’s (ACOG) Immunization Expert
Work Group. The work group serves in an advisory capacity to
many ACOG standing committees such as the Committees on
Obstetric Practice, Gynecologic Practice, Adolescent Health,
and Health Care for Underserved Women as they develop
clinical guidelines and patient resources.
Photo credit:
Duke Medicine News and Communications

30
The VTEU funding mechanism enables VTEU sites to compete for projects including study concept generation,
protocol development, protocol implementation, and laboratory endpoint analysis.
Successful project bids:
Led by Drs. Walter and Swamy, Duke joined a network of six other sites from across the country to address
vaccine safety issues and help prevent adverse events following immunization. Since becoming a CISA site in
2012, Duke has participated in numerous vaccine safety studies:
Dukewasselectedasoneofthreesitestoassessthesafetyoflive-attenuatedintranasallyadministeredinfluenza
vaccine in asthmatic children. Additionally, Duke was awarded a study to assess the safety of simultaneous vs.
sequential administration of IIV and Tdap vaccines in pregnancy.
In September 2013, the Duke Clinical Vaccine Unit was named a NIH Vaccine
Trial Evaluation Unit (VTEU) with Dr. Chip Walter and Dr. Geeta Swamy as
the Co-Principal Investigators. The Duke VTEU joins eight other VTEU units
around the country. VTEUs play a key role in the development of new and
improved vaccines and therapies against infectious diseases.
The Duke Clinical Vaccine Unit is a member of the CDC-sponsored Clinical
Immunization Safety Assessment (CISA) Project to assist safety experts from
the CDC’s Immunization Safety Office (ISO) in providing a comprehensive
vaccine safety public health service to the nation.
VTEU
CISA
1. Conducted influenza vaccination studies in pediatric populations against variant H3N2 and geriatric
populations against H7N9 influenza strains. The later investigation included the use of MF59 adjuvant
2. Drafted a protocol and initiated implementation for a Phase I study to examine the pharmacokinetics of
a therapeutic drug for tuberculosis (PA-824) in patients with known hepatic impairment
3. Drafted a protocol and initiated implementation and endpoint laboratory analysis for a study to
examine early anti-fungal treatment of patients with community acquired pneumonia (CAP) in
Valley Fever-endemic areas and received funding to better elucidate genomic signatures associated with
coccidioides infection with an overarching goal of developing improved diagnostic tests
4. Initiated and completed enrollment in a Phase I study to examine the safety and immunogenicity of an
inactivated West Nile Virus vaccine
5. Begun work on developing and implementing a protocol to examine short versus long-course antibiotic
treatment of CAP in pediatric populations
6. Received funding to conduct a clinical trial and endpoint laboratory analyses testing a new anti-
botulism toxin monoclonal antibody cocktail
7. Became a core site to conduct immunology assays for T and B cell activation using clinical samples
collected as part of VTEU studies
1. Examining whether providing young children with antipyretics immediately following inactivated
influenza vaccine (IIV) affects the immune response and rates of fever following vaccination
2. Examining the safety of administering Tdap vaccine to pregnant women
3. Conducting a clinical trial in adolescents and young adults assessing pre-vaccination hydration as a
strategy to prevent presyncope and/or syncope following receipt of an intramuscular vaccine

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Good Manufacturing
Practice Facility
In 2015, the DHVI embarked on an ambitious mission to plan, design and build a CGMP facility that would
enable DHVI research teams to manufacture new vaccines for use in “proof of concept” experimental medicine
Phase I clinical trials.
The new facility will utilize both Quality Assurance (QA) and Quality Control (QC) protocols and audits to ensure
that that all CGMP requirements are met for the manufacture and release of immunogens. QC will be managed
by the Quality Assurance for Duke Vaccine Immunogenicity Programs (QADVIP), which currently oversees all
DHVI clinical trials materials Env production by KBI, Biopharma, and a gp41 peptide vaccine by CPC, Inc, and
Infectious Disease Research Institute (IDRI).
Construction has now been completed and we are in the process of performing the commissioning and
certification activities. We expect the CGMP facility to be fully operational in the first quarter of 2016.
Since its inception in 2012, the DHVI protein production facility (PPF) has been funded by
the Bill & Melinda Gates Foundation and has produced more than 120 proteins for the Gates
Collaboration for AIDS Vaccine Development grantees, and currently makes approximately
150mg of purified protein per month. The PPF operates using a set of standards embracing
applicable elements of Good Laboratory Practices (GLP) and Current Good Manufacturing
Practice Facility (CGMP) regulations for the production of proteins used for research.
Having a CGMP facility as part
of the DHVI makes us one of
the most globally advanced
vaccine institutes in the country.
It positions the DHVI teams
to advance our HIV vaccine
development efforts, while having
an infrastructure to respond to
emerging public health threats
Thomas Denny | Chief Operating Officer, DHVI
31

32
Resources for
Scientific Discovery
Regional Biocontainment Laboratory and Research Support Units
Clinical Support
Gregory Sempowski, PhD | Thomas Alderman | Richard Frothingham, MD
Tony Moody, MD
The Regional Biocontainment Laboratory (RBL) at Duke was built with funding from NIH to support basic research
to develop drugs, diagnostics, and vaccines for emerging and reemerging infections and biodefense.
The RBL has a comprehensive safety and operations program to provide state-of-the-art biocontainment facilities
for BSL2, BSL3, and Select Agent research. The RBL was fully-commissioned in late 2007 and is divided into three
research support units (Immunology, Virology and Bacteriology).
The RBL Immunology team has a long track record of performing single-plex high-throughput antigen-
specific antibody binding titer assessment for multiple species including mice, humans and NHPs and runs an
international proficiency testing program for multiplex luminex bead-based cytokine profining assays for NIAID
(EQAPOL). The Immunology unit also performs TCR sequencing, and immune reconstitution monitoring with
the Duke patented sjTREC assay.
The RBL Virology unit has extensive experience with a wide-range of viruses and has a particular focus on
influenza viruses and neutralization assays. The RBL has mouse, rabbit and ferret challenge models to support
DHVI/Duke investigators and their collaborators.
The DHVI Accessioning Unit (AU) provides support for procurement, processing and storage of samples derived
from human and animal studies/trials. The AU provides IRB and IACUC protocol submission and oversight
support to DHVI investigators.
Comprehensive Shared Resources or Cores are available to the DHVI and overall Duke
community and their collaborators. The DHVI has assembled a group of state-of-the-art
instruments, techniques and services to support basic and translational research initiatives
in vaccine immunology, immune reconstruction, host-pathogen interactions, emerging
infectious diseases and biodefense.
shared-resources.dhvi.duke.edu

33
Flow Cytometry and Cell Sorting
Gregory Sempowski, PhD
The DHVI Research Flow Cytometry Facility serves the polychromatic analytical and cell sorting needs of the the
DHVI and Duke Community. The Flow Facility offers state-of-the-art cytometric support to investigators in basic,
developmental, and clinical research at BSL2 and 3 on six instruments.
Sequencing X-ray Crystallography
Feng Gao Nathan Nicely
The DHVI Viral Genetic Analysis Facility (VGAF)
offers large-scale fluorescent DNA sequencing,
sequence analysis, PCR purification, and a
variety of other genetic analysis assays. The
state-of-the-art DNA sequencing technology
yields high quality sequences of up to 1000
bases per read. The VGAF is well-equipped to
handle large volumes of sequencing orders and
is committed to meet the need of researchers at
the DHVI and the Duke community.
The DHVI Macromolecular X-ray Crystallography
Facility offers services to all research laboratories
on the Duke campus in solving and publishing
macromolecular crystal structures. Facility staff
assist with crystallization trials, data collection,
phasing, refinement, and analysis. This facility
offers automated crystallization systems and high-
resolution X-ray diffraction image collection.
Surface Plasmon Resonance
S. Munir Alam
The DHVI Biomolecular Interaction Analysis (BIA) Facility provides specialized applications and support in Surface
Plasmon Resonance (SPR) based biomolecular interaction analyses to basic and clinical researchers within the
DHVI/Duke Community. The facility offers state-of-the-art SPR BIAcore and ForteBio Biolayer interferometry
(BLI) instruments for monitoring real time interactions and diverse sets of measurements that include binding
affinity, kinetics, resolution of binding mechanism.

34
Recent Publications
Bradley T, Fera D, Bhiman J, Eslamizar L, Lu X, Anasti K, Zhang R, Sutherland LL, Scearce RM, Bowman CM, Stolarchuk C, Lloyd KE,
Parks R, Eaton A, Foulger A, Nie X, Karim SS, Barnett S, Kelsoe G, Kepler TB, Alam SM,Montefiori DC, Moody MA, Liao HX, Morris L,
SantraS,HarrisonSC,HaynesBF.StructuralConstraintsofVaccine-InducedTier-2AutologousHIVNeutralizingAntibodiesTargeting
the Receptor-Binding Site. Cell Rep. 2016 Jan 5;14(1):43-54. doi: 10.1016/j.celrep.
Wilton B. Williams, Hua-Xin Liao, M. Anthony Moody, Thomas B. Kepler, S. Munir Alam, Feng Gao, Kevin Wiehe, Ashley M. Trama,
Kathryn Jones, Ruijun Zhang, Hongshuo Song, Dawn J. Marshall, John F. Whitesides, Kaitlin Sawatzki, Axin Hua, Pinghuang Liu,
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Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Robb ML, Michael NL, Kim JH, Soderberg KA, Giorgi EE, Blair L, Korber
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Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A,
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Tomescu C, Seaton KE, Smith P,Taylor M, Tomaras GD, Metzger DS, Montaner LJ. Innate Activation of MDC and NK Cells in High-risk
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