1. What next for prevention of pneumococcal
disease in light of serotype replacement?
Rick Malley, MD
Boston Children’s Hospital
Harvard Medical School
Meningitis and Septicaemia in Children and Adults
British Museum, London
November 14-15 2017
I’m fed up with this guy – let’s
become pathogenic

2. PotentialConflictofInterestDisclosure
I disclose the following financial relationships with commercial
entities that produce health care-related products or services
relevant to the content I am planning, developing, or presenting:
Company Relationship Content Area
Merck Scientific
Advisor
Vaccines
I also disclose membership on the Scientific Advisory Board of
Arsanis Biosciences, and Advanced InhalationTherapies
I am a Scientific Founder, consultant and member of the Board of
Directors of Affinivax, Inc.
Funding from: NIH, PATH, Bill and Melinda Gates Foundation,
TRP andTIDO (Boston Children’s Hospital)

3. Importance of bacterial polysaccharides
as vaccine targets
Antibodies to polysaccharides are the basis of protection of
many of our most successful bacterial vaccines

4. 4
Surface Polysaccharides are key virulence factors
of pneumococcus
• The surface Ps defines the
serotype
•90+ serotypes of
pneumococcus
• Protects organism from
killing by complement or
phagocytes
• Antibody to Ps is protective:
drives antigenic diversity
Bar = 100 nm

5. Polysaccharide vaccines induce a T cell-independent
response
Polysaccharide-
specific
antibody
*
*
B cell
v Directly stimulate B cells
v No memory, no boosting
v Do not induce protective Ab response in children <2 years
v Repeat doses in adults may induce tolerance

6. Conjugate vaccines induce a CD4+ T-cell-dependent
response
B
*
*
CD4
Protein
Polysaccharide-
Specific
Antibody
Memory B
Cells
[Ab]
Conjugate Ps
2mos 12mos

7. CD4+ Th17 responses help control mucosal colonization
by encapsulated organisms, including pneumococcus

8. CD4+ Th17 responses help control mucosal colonization
by encapsulated organisms, including pneumococcus

9. Manufacturing Process for Prevnar-7™
Large Scale Fermentation and Purification of Saccharide
QC
7-V
Conjugates Are Mixed to Formulate Vaccine
QC
Each Type of Saccharide is Separately Activated
and Conjugated to CRM197 Protein Carrier
QC
4 6B 9V 14 18C 19F 23F

10. QC Testing of pneumococcal conjugate vaccine
Vaccines are not “well-defined biologicals”
• Release testing does not fully guarantee potency and
consistency of the product
• Therefore “the Process is the Product”
• Must assure and verify that all steps in the process are
precisely controlled

11. QC Testing of pneumococcal conjugate vaccine
Carrier Protein
Bulk
Conjugate
Final Vaccine
Polysaccharide
Activated
Saccharide1. Identity
2. Polysaccharide composition
3. Moisture content
4. Protein impurity
5. Nucleic acid impurity
6. Pyrogen content
7. Molecular size
distribution
1. Extent of activation
2. Molecular size distribution
1. Identity
2. Purity
3. Toxicity
4. Extent of derivatisation (if
appropriate) NR
1. Identity
2. Residual reagents
3. Saccharide:protein ratio &
conjugation
markers
4. Capping markers
5. Saccharide content NR
6. Conjugated v. free saccharide
7. Protein content
8. Molecular size distribution
9. Sterility
10. Specific toxicity of carrier
11. Endotoxin content
1. Identity
2. Sterility
3. Saccharide content (of
each)
4. Residual moisture
5. Endotoxin content
6. Adjuvant content (if
used)
7. Preservative content (if
used)
8. General safety test
9. pH
10. Inspection
Formulation
1. Extent of activation
2. Molecular size distribution
Courtesy of Neil
Ravenscroft
~500 QC tests

12. February 17th, 2000: US FDA approves the licensure of a
seven-valent pneumococcal vaccine (PCV7,Wyeth/Pfizer)
Since then:
• PCV10 in Europe in 2009
• PCV13 in US in 2010
Impressive success of conjugate vaccines in US,
with near-total eradication of the 7, now 13,
serotypes included in the vaccine
•Remarkable impact on herd protection, most
notable in elderly
•Efficacy against pneumonia

13. Some issues with current vaccine conjugates
+ serotype 3 story
+ 19A/F story

14. But this is not the case…

15. Other issues with current vaccine conjugates:
Price
In US: price of Pneumococcal conjugate =
$160 per dose (4 doses per child)
Critical role of GAVI in reducing price and
ensuring availability of vaccine to poorest
countries (Pfizer pricing to GAVI: $3.10 per
dose, 3 doses per child)
40% of GAVI’s budget is dedicated to providing
pneumococcal conjugate vaccine to the
developing world
However, this effort is entirely dependent on
governments and NGOs, is still relatively
expensive, and does not cover non GAVI-
eligible countries
GAVI countries 2016

16. Given success and nature of conjugates, following
premises have been adopted by most:
1. A vaccine that does not confer broad protection
against invasive disease is a nonstarter
2. A vaccine that does not confer broad protection
against colonization is also a nonstarter
Assumptionforfuturepneumococcalvaccine
development

17. Option 1: Expanded (and possibly lower cost)
polysaccharide-protein conjugates
Advantages:
Technology known
Correlates of protection known
Path to licensure clear
Disadvantages:
Limitation on total number of ST that can be included
Complexity and cost of manufacture
Possible interference
Serotype replacement

18. OPTION 2: Killed whole cell pneumococcal vaccine
Courtesy of David Briles
First pneumococcal vaccine: Killed whole cells (ca. 1911)
Revisited in 1996 by Porter Anderson (+ student)
Support from MRF

19. 1. Vaccine protects against colonization and invasive disease by
multiple serotypes
Preclinical findings

20. 1. Vaccine protects against colonization and invasive disease by
multiple serotypes
2. Various routes of immunization effective
• Intranasal
• Oral
• Sublingual
• Transcutaneous
• Subcutaneous/Intramuscular (selected)
Preclinical findings

21. 1. Vaccine protects against colonization and invasive disease by
multiple serotypes
2. Various routes of immunization effective
• Intranasal
• Oral
• Sublingual
• Transcutaneous
• Subcutaneous/Intramuscular (selected)
3. Various adjuvants effective
• Cholera toxin, cholera toxin B (mucosal)
• LT and mutant derivatives (mucosal, transcutaneous)
• Aluminum hydroxide (selected)
Preclinical findings

22. 1. Vaccine protects against colonization and invasive disease by
multiple serotypes
2. Various routes of immunization effective
• Intranasal
• Oral
• Sublingual
• Transcutaneous
• Subcutaneous/Intramuscular (selected)
3. Various adjuvants effective
• Cholera toxin, cholera toxin B (mucosal)
• LT and mutant derivatives (mucosal, transcutaneous)
• Aluminum hydroxide (selected)
4. Dual mechanism of protection
• Antibody-mediated (vs. sepsis), transferable
• CD4+ IL-17A-mediated (vs. colonization), transferable
Preclinical findings

23. First WCV clinical trial initiated in February 2012
§ Phase I trial in healthy adult (18-40) volunteers sponsored by
PATH
§ Setting: CRO in Seattle, WA
§ SPWCV comprised of killed whole cell antigen adsorbed with
aluminum hydroxide
§ Three dose cohorts, each individual to receive 3 vaccinations
with same dose 28 days apart; placebo comparator (saline) in
each cohort

24. VAC-002 Trial: Summary of Results
1. Safe, well tolerated: mild pain and tenderness at site, no
hematologic or chemical signals
2. Rise in antipneumococcal antibodies (directed against
whole cell as well as against individual proteins)
3. Enhancement ofT cell responses in peripheral blood
4. Protection by passive transfer

25. WCV current status and plans
§ Phase 2 clinical trials in Kenya (M. Alderson, PATH)
• Dose-escalation in adults and toddlers almost
completed
• Preliminary look at impact on colonization in
toddlers (all ST)
§ Biofarma (Bandung, Indonesia) has taken over
manufacture of the vaccine, multiple lots evaluated for
potency and stability
§ Further clinical studies planned by PATH with K.
Mulholland’s group in Indonesia, under auspices of
BMGF

26. OPTION 2: Killed whole cell pneumococcal vaccine
(summary)
Advantages:
Simplicity of manufacture
Exposes host to numerous antigens at same time
Some historical suggestions of efficacy
Proteins not modified
Disadvantages:
Very complex antigen
Precise mechanisms of protection hard to define
Acceptability?
Licensure path unclear

27. OPTION 2: Killed whole cell pneumococcal vaccine:
Licensure issues
§ In contrast to PCVs, there are no known correlates of
protection for WCV
§ In theory, could envision one of the following
approaches:
• Demonstration of impact on carriage
• Demonstration of impact on otitis media
• Demonstration of impact on non-bacteremic pneumonia
• Demonstration of impact on bacteremia in country that
has not yet implemented PCV
• Placebo-controlled vs. PCV as control?

28. OPTION 3: Proteins alone
§ Selection of two or more genetically conserved
proteins (ie. common to the greatest majority of
clinical isolates of pneumococci)
§ Several candidates that confer protection against
invasive disease in animal models have been
identified, and several have been evaluated in
Phase I trials (e.g. PspA, StkP+PcsB, PhtD, Ply)
§ How about antigens that confer protection
against colonization?

29. Collaboration between Genocea Biosciences, Boston Children’s
Hospital and PATH: Identification of Th17 antigens
Intranasally immunized with pneumococcal
whole cell antigen
CD4+T cells
isolated from
splenocytes
Incubate and assay IL-17A
in supernatant
Peritoneally derived
macrophages pulsed with
TIGR4 expression library
Mofffit, Gierahn et al., Cell Host & Microbe, 2011

30. Genocea Biosciences clinical trials: Immunization with
Th17 antigens
1. Phase I trial of three putativeTh17 antigens (SP_2108,
SP_0148 and SP_1912) combined and adsorbed on
aluminum hydroxide, and injected intramuscularly,
successfully completed in US (GEN-004)
2. GEN-004 then underwent Phase II clinical trials in healthy
adults in Liverpool (S. Gordon’s intentional pneumococcal
exposure model)
• About 25% reduction in carriage density compared to
placebo
• Had been powered for 50% reduction
• Program de-prioritized

31. OPTION 3: Proteins alone (summary)
Advantages:
Relative simplicity of manufacture
Likely would require several proteins for coverage against
both disease and colonization, but feasible
Proteins not modified
Disadvantages:
Vaccine against what?
Licensure path unclear

32. OPTION 4: Combination PS and protein vaccine
• An attractive option would be to include these proteins
as carriers for polysaccharides, to generate
• Antibodies to PS
• Antibodies to proteins
• CD4+ Th17 responses to proteins

33. Carriers in traditional conjugate technology
Carrier protein
e.g. CRM197, Tetanus toxoid,
OMPC, protein D
Capsular polysaccharide (target)
Protein used in conventional
conjugates is generally an irrelevant
(nonprotective) protein (possible
exception of protein D, although very
controversial).
One advantage of using the protein as
a carrier is that licensure of the product
would not depend on demonstration of
efficacy of the proteins, since it is
included primarily as a carrier

34. Can we improve on the concept? The Multiple
Antigen Complex Presenting System (MAPS)
MAPS complex
Rhizavidin
fusion
Biotinylation
PS antigen
Protein
antigens
Ab response
Poor Ab response
EnhancedAb
response
Th1 response
Th17 response
T-dependent
Ab response
Zhang, Lu and Malley, PNAS 2013

35. Advantages over conventional conjugation
1. Enhanced efficiency of manufacture of MAPS complex
(>90% at laboratory scale and now scale-up, compared to
30-40% for conventional conjugates
2. Efficiency of manufacture and purification of protein
carriers, with associated reduced costs and ease of tech
transfer
3. Little to no PS epitope modification or damage due to
controlled biotinylation of the PS and attachment via
affinity-interactions with protein rather than cross-linking
4. Modular process, allowing for rapid optimization

36. Pneumococcal MAPS: 13 PS and comparison with
PCV13

37. Pneumococcal MAPS: Protection against
carriage
Protection against colonization

38. OPTION 4: Combination protein + polysaccharide
Advantages:
Same advantages as traditional conjugates
Potential added benefit of conserved pneumococcal proteins
Antibody to proteins
Th17 responses to proteins
Does not require demonstration of efficacy of proteins
Disadvantages:
New proteins
New technology
Minor: Indication for universal coverage will not be granted
based on clinical trials, would require Phase IV trials

39. Conclusions/Discussion
§ Concern that current strategy may not result in sustained
reduction in pneumococcal disease or may not be affordable
§ Recent experience with conjugate vaccines strongly supports
concept that reduction in transmission (with PS conjugate,
+/-protein or whole cell vaccines) is the key to a successful
strategy
§ Good justification for consideration of alternative/adjunctive
approaches, particularly for developing world settings
§ Several adaptations of current approaches or novel
strategies can be considered, each with theoretical
advantages and disadvantages

40. “Professor? May I be excused? My
brain is full”
Questions/Comments?