125742 S1 M4 4.2.1 r 20 0211

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BioNTech SE  
An der Goldgrube 12  
55131 Mainz, Germany  
Phone: +49 (0)6131 9084 -0 
Telefax: +49 (0)6131 9084 -390 
R&D DATA REPORT N o. R-20-0211  
In Vitro Expression of  BNT162b2  Drug Substance 
and Drug Product  
Version 0 2 
Date: 17 SEP 2020  
Reported by  
Test item: BNT162b2  
Key words: COVID19, modRNA, ATM material, Western blot, immunofluorescence , 
FACS  
This R&D report consists of 22 pages.  
 
Confidentiality Statement: The information contained in this document is the property and copyright of  
BioNTech RNA Pharmaceuticals GmbH. Therefore, this document is provided in confidence to the recipient (e.g. 
regulatory authorities, IECs/IRBs,  investigators, auditors, inspectors). No information contained herein shall be 
published, disclosed, or reproduced without prior written approval of the proprietors.  
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TABLE OF CONTENTS  
LIST OF FIGURES  ................................ ................................ ...............  3 
LIST OF TABLES  ................................ ................................ .................  3 
LIST OF ABBREVIATION S ................................ ................................ .. 4 
RESPONSIBILITIES  ................................ ................................ .............  5 
1 SUMMARY  ................................ ................................ ...........................  6 
2 GENERAL INFORMATION  ................................ ................................ .. 7 
2.1 Sponsor and Test Facilities  ................................ ................................ .. 7 
2.2 Participating Personnel  ................................ ................................ .........  7 
2.3 Study Dates  ................................ ................................ ..........................  8 
2.4 Guidelines and Regulations  ................................ ................................ .. 8 
2.5 Changes and Deviations  ................................ ................................ ....... 8 
2.6 Documentation and Archive  ................................ ................................ .. 8 
3 MATERIALS AND METHOD S ................................ ..............................  9 
3.1 Test Item  ................................ ................................ ...............................  9 
3.2 Control Item  ................................ ................................ ..........................  9 
3.3 Test System  ................................ ................................ ..........................  9 
3.4 Materials  ................................ ................................ ...............................  9 
3.5 Methods  ................................ ................................ ..............................  11 
3.5.1  Study Design  ................................ ................................ ......................  12 
3.5.2  Transfection of RNA Constructs in HEK293T Cells  ............................  12 
3.5.3  Western Blot Analysis  ................................ ................................ .........  13 
3.5.4  FACS Analysis  ................................ ................................ ....................  13 
3.5.5  Immunofluorescence  ................................ ................................ ..........  14 
4 TABLES AND FIGURES  ................................ ................................ .... 15 
5 CONCLUSION  ................................ ................................ ....................  17 
6 DOCUMENT HISTORY  ................................ ................................ ...... 18 
7 REFERENCES  ................................ ................................ ...................  19 
8 APPENDIX  ................................ ................................ .........................  20 
Appendix  1: Certificates of Analysis  ................................ ....................  20 
BNT162b2 -RNA  ................................ ................................ ..................  20 
BNT162b2  ................................ ................................ ..........................  21 
Appendix  2: FACS gating strategy  ................................ ......................  22 
  
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LIST OF FIGURES  
Figure  1: Western blot analysis for detection of BNT162b2 antigen expression  .. 15 
Figure  2: FACS analysis of transfection frequency and cell viability  ....................  15 
Figure  3: Immunofluorescence staining of transfected cells  ................................  16 
  
LIST OF TABLES  
Table  1: Equipment  ................................ ................................ ...............................  9 
Table  2: Consumables  ................................ ................................ .........................  10 
Table  3: Reagents  ................................ ................................ ...............................  10 
Table  4: Antibodies and recombinant protein controls  ................................ .........  11 
  
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LIST OF ABBREVIATION S 
ATM  Animal trial material  
BNT162b2  Investigational vaccine in this study (DP)  
BNT162b2 -RNA  Investigational vaccine in this study (DS)  
COVID -19 Coronavirus disease emerged in 2019  
DNA  Deoxyribonucleic acid 
DP Drug product  
DS Drug substance  
ER Endoplasmic reticulum  
FACS  Fluorescence -activated cell sorting  
GFP Green fluorescent protein  
HEK Human embryonic kidney  
modRNA  modified RNA  
PAGE  Polyacrylamide gel electrophoresis  
RBD  Receptor binding domain  
RNA  Ribonucleic acid  
S protein  Spike protein  
S1 Subdomain 1 of the S  protein  
SARS -CoV-2 Severe acute respiratory syndrome -Coronavirus -2 
saRNA  self-amplifying RNA  
SDS Sodium dodecyl sulfate  
SOP  Standard operating procedure  
uRNA  unmodified RNA  
V9 Antigen variant of the generated variants of the S  protein  
 
  
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2 GENERAL INFORMATION  
2.1 Sponsor and Test Facilities  
Sponsor  
BioNTech RNA Pharmaceuticals GmbH  
An der Goldgrube 12  
55131 Mainz  
Germany  
 
Test Facilities  
BioNTech RNA Pharmaceuticals GmbH  
An der Goldgrube 12  
55131 Mainz  
Germany  
2.2 Participating Personnel  
Responsible person:  
(as defined in SOP -100-024) 
BioNTech RNA Pharmaceuticals GmbH  
An der Goldgrube 12  
55131 Mainz  
Author:  
BioNTech RNA Pharmaceuticals GmbH  
Experimenter:  
Western blot , FACS  
BioNTech RNA Pharmaceuticals GmbH  
Experimenter:  
Immunofluorescence  
 
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2.3 Study Dates  
Start of experiments:   22 JUN 2020  
Completion of experiments:  14 AUG  2020  
2.4 Guidelines and Regulations  
All experiments are executed in accordance with the existing standard operating 
procedures and described processes from BioNTech  SE. Applicable documents are 
listed below.  
 SOP -020-009 Ansetzen von Medien und Zusätzen für die Zellkultur  
 SOP -030-038 Standardisierte Kultivierung von Zellen  
 SOP -030-039 Zellzahlbestimmung mittels Neubauer Zählkammer  
 SOP -030-117 Du rchführung einer SDS Polyacrylamid Gelelektrophorese 
(SDS -PAGE)  
 LA-50-255-000 Direkte / Indirekte Immunfluoreszenzfärbung  
2.5 Changes and Deviations  
Not applicable. There is no formal R&D plan available.  
2.6 Documentation and Archive  
Study plans and reports are st ored and archived according to SOP -100-003 Archiving 
of Paper -Based Documents.  
Raw data and evaluated data are saved at  
 P:\BioNTechRNA \RN9391R00_CoV -VAC\04_Preclinic \04_in 
vitro\CorVac_IDV.invitro#050_b1_b2_b3c_DS_and_DP_IVE  
 P:\BioNTechRNA \RN9391R00_CoV -VAC\04_Preclinic \04_in 
vitro\CorVac_IDV.invitro#059_HEK_IF_microscopy_at  
 P:\BioNTechRNA \RN9391R00_CoV -VAC\04_Preclinic \04_in 
vitro\CorVac_IDV.invitro#064_mod9 -WB_IVE  
 Lab book MeGl, No. 2034  
 Lab book MeGl, No. 2035   
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3 MATERIALS AND METHOD S 
3.1 Test Item  
BNT162b2 -RNA  (ATM  RNA ): For CoA see  Appendix  1: Certificate s of Analysis . 
BNT162b2 (ATM LNP): For CoA see  Appendix  1: Certificate s of Analysis . 
 RNA batch: RNA -RF200321 -06, 97.5% integrity  
 Polymun batch RBP020.2 LNP with the lot: CoVVAC/270320  
3.2 Control Item  
 Modified  RNA GFP , p4.AGA_eGFP, RNA_RF200309_01c, 96% integrity  
3.3 Test System  
 In vitro  test system, cell culture, HEK293T cells  
3.4 Materials  
Table  1: Equipment  
Product name  Provider  
Microscope IX53  Olympus Life Science  
Microscope SP8  Leica  
HeraCell 150i incubator  Thermo Fisher Scientific  
Vortexer  Neolab  
Biological Safety Cabinet HeraSafe2020  Thermo Fisher Scientific  
Trans -Blot Turbo Transfer System  Bio-Rad 
Gel Dokumentation System ChemiDoc MP Imaging system , 
Detektor Supercooled  CCD -30 °C, Pixel  (Graustufen) 65535  Bio-Rad 
Vacuum pump BVC -vacuu -control  Vacuubrand  
Pipette Eppendorf Research, 10 -100 μL  Eppendorf  
Pipette Eppendorf Research, 100 -1,000 μL  Eppendorf  
Pipette Eppendorf Research, 20 -200 μL  Eppendorf  
Centrifuge 5810R  Eppendorf  
FACSCanto II  BD 
Leica Application Suite LAS -X Version 3.1.5.16308  Leica  
FlowJo software version 10.6.2  FlowJo LLC, BD Biosciences  
Image Lab software version 5.0.  Bio-Rad 
 
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Table  2: Consumables  
Product name  Application/specification  Article no.  Provider  
12-well plates  Tissue culture  665180  Greiner -bio-one  
96-well plates  Tissue culture  650101  Greiner -bio-one  
Safe-lock tubes  1.5 mL  0030120.086  Eppendorf  
Tubes  15 mL  188271  Greiner -bio-one  
Filter tips  20-200 μL  30077555  Eppendorf  
Filter tips  100-1,000 μL  10212393  Eppendorf  
Filter tips  0.1-10 μL  30077512  Eppendorf  
Aspirating pipets  2 mL w/o plug  710183  Greiner -bio-one  
Serological pipets  10 mL  607160  Greiner -bio-one  
 
Table  3: Reagents   
Product name  Application/specification  Article no.  Provider  
RiboJuice  Transfection reagents  TR-1013  Merck Millipore  
FBS superior  Fetal bovine serum  81D2925  Biochrom GmbH  
DPBS  No calcium, no magnesium  14190 -094  Thermo Fisher 
Scientific  
StemPro™ Accutase™  Cell Dissociation Reagent  A11105 -01  Thermo Fisher 
Scientific  
Opti-MEM GlutaMAX  Reduced serum medium  51985034  Thermo Fisher 
Scientific  
EDTA  0.5 M 03690 -
100ML  Sigma -Aldrich  
DMEM, high glucose, 
GlutaMAX™ Supplement, 
pyruvate  Cell culture  31966047  Thermo Fisher 
Scientific  
BSA Bovine serum albumin  GAUBSA01 -
64 Eurobio  
Triton X -100 Immunofluorescence  X100 -100ML  Sigma Aldrich  
Hoechst  1:5,000 H3570  Life Technologies  
PFA, 32%  Fixation  15714 -5 Electron Microscopy  
ImmoMount media  Mounting media  9990402  Life Technologies  
4–15% Mini -PROTEAN® 
TGX™ Precast Protein 
Gels Polyacrylamide gel  4561083  Bio-Rad 
cOmplete™ ULTRA 
Tablets, Mini, EASYpack  Protease Inhibitor Cocktail  5892970001  Roche  
Transfermembran 
Amersham™ Protran® NC  Nitrocellulose membrane  4675.1  Carl Roth  
Color Prestained Protein 
Standard, Broad Range 
(11–245 kDa)  Molecular marker  P7712  New England 
BioLabs  
10x Tris/Glycine/SDS  Running Buffer  1610772  Bio-Rad 
4 x Laemmli Sample Buffer  Western blot  1610747  Bio-Rad 
DTT Western blot  A2948,0025  PanReac 
AppliChem  
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Product name  Application/specification  Article no.  Provider  
Fixable Viability Dye 
eFluor™ 450  FACS  65-0863 -14 eBioscience  
Fixation Buffer  FACS  420801  Biolegend  
Permeabilization Buffer 
(10X)  FACS  00-8333 -56 eBioscience  
Ethanol  Western blot  5054.4  Carl Roth  
Nonfat dried milk powder  Western blot  A0830,1000  AppliChem  
Tween -20 Western blot  9127.1  Carl Roth  
Pierce™ ECL Western 
Blotting Substrate  Chemiluminescent substrate  32209  Thermo Fisher 
Scientific  
Tris Western blot  3170.2  Carl Roth  
Glycin  Western blot  3790.2  Carl Roth  
SDS Western blot  0183.1  Carl Roth  
NaCl  Western blot  9265.2  Carl Roth  
Sodium deoxycholate  Western blot  S1827 -100G  Sigma Aldrich  
EDTA  Western blot  8040.3  Carl Roth  
 
Table  4: Antibodies  and recombinant protein controls    
Product name  Dilution  Article no.  Provider  
SARS -CoV Spike S1 Subunit Protein 
Antibody, Rabbit PAb  1:100 (IF); 
1:1,000 (WB)  40150 -RP01  Sino Biological  
SARS -CoV-2 (2019 -nCoV) Spike 
Antibody, Rabbit Mab  1:400 
(FACS)  40150 -R007  Sino Biological  
Alexa Fluor™ 647 Antibody Labeling Kit  N/A A20186  ThermoFisher  
Scientific  
Concanavalin A, Alexa Fluor™ 594 
Conjugate  1:100 (IF) C11253  Invitrogen  
Lectin GS -II From Griffonia simplicifolia, 
Alexa Fluor™ 594 Conjugate  1:100  L21416  Invitrogen  
Alexa Fluor® 488 AffiniPure Goat  
Anti-Rabbit IgG (H+L)  1:400 (IF)  111-545-003 Jackson 
ImmunoResearch  
Anti-Rabbit IgG (whole molecule) –
Peroxidase antibody produced in goat  1:2,000 (WB)  A0545  Sigma Aldrich  
NCP -CoV(2019 -nCoV) Spike Protein (S1 
Subunit, His Tag)  N/A 40591 -V08H  Sino Biological  
 
3.5 Methods  
Western blot and FACS assays were performed  to analyze antigen expression; 
immunofluorescence experiments were performed to assess  correct localization in 
cells.  
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3.5.1  Study Design  
The a im of  this study was to analyze the  express ion of BNT162b2  DS and DP  in 
HEK293T  cells as a surrogate for a mammalian cell culture system . HEK293T  cells 
were transfected with DS BNT162b2 -RNA using a commercial transfection reagent or 
with DP BNT162b2 to express the S protein of SARS -CoV-2 as the viral antigen. 
Transfected HEK293T cells were allowed to express the S protein for 18  h before 
analysis.  
Expression of DS BNT162b2 -RNA  was analyzed using Western blot  to confirm 
expression.  
FACS  analysis was performed in triplicates in permeabilized cells to assess 
transfection frequencies and viability of cells  transfected with either the DS BNT162b2 -
RNA, or with the DP BNT162b2 .  
Finally,  immunofluorescence microscopic analysis was used on cells transfected with 
the DS BNT162b2 -RNA to assess processing of the expressed protein in the 
endoplasmic reticulum ( ER). Since t he S protein contains a transmembrane domain it 
is expressed  on the cell surface, and therefore processing in the ER was p resumed . 
3.5.2  Transfection of RNA Constructs in HEK 293T  Cells 
HEK293T cells were seeded in 12 -well plates with a cell number of 2  × 105 per well  
one day before transfection or with a cell number of 4  × 105 per well 6  h before 
transfection in DMEM with 10% FBS. For immunofluorescence  experiments, HEK293T 
cells were seeded in 12 -well plates with cover slips previously coated in collagen with 
a cell number of 2  × 105 per well  one day before transfection  in DMEM with 10% FBS. 
Cells were transfected with DS BNT162b2 -RNA using Ribojuice according to the 
manufacturer’s protocol. As a transfection control, a  modRNA construct encoding GFP 
was used. Briefly, 1 µg of  RNA was diluted in Opti -MEM and mixed with transfection 
reagents. After an incubation of 4  min, 100  µL of the mixture was applied to the cells, 
mixed  gently , and incubated at 37°C/ 5% CO 2 for 18  h. For FACS analysis DP 
BNT162b2 was transfected by diluting 1 µg  of DP in 100 µl OptiMEM . The mixture was 
applied to the cells, mixed gently and centrifuged by 500 ×g for 5 min at room 
temperature before incubating at 37°C/5% CO 2 for 18  h. 
Before proceeding with subsequent analyses, c ells transfected with GFP were 
examined  microscopically for successful transfection. Cells transfected with DS or DP 
encoding for  the antigen were either harvested for Western blot analysis or prepared 
for subsequent immunofluorescence  or FACS analysis  
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3.5.3  Western Blot Analysis  
Western blot analyses were used to evaluate whether the designed constructs were 
expressed in HEK293T cells.  
HEK293T  cells were washed with PBS and detached from the well plate. Cells were 
collected in a 1.5  ml Eppendorf tube, centrifuged for 5  min at 300 ×g/4°C. Supernatants 
were discarded and the cell pellet was dissolved in 40  µL RIPA buffer (20  mM Tris, 
0 15 M NaCl, 1% Triton X 100, 1% odium deo ycholate, 0 1% SDS, 10  mM EDTA) 
with protease inhibitors and incubated for 30  min on ice. 13.3  µL 4x Laemmli sample 
buffer with 10% DTT was added to the Eppendorf tubes and samples were heated for 
5 min at 95°C. Recombinant protein controls were treated equally wit h 4x Laemmli 
sample buffer/10% DTT  diluted in PBS to achieve a 1x dilution. Afterwards, gels were 
loaded  with 25  µL of the samples and 3  µL of a marker. Gel electrophoresis was 
performed with Tris/ glycine/SDS running buffer at 120  V. Proteins were transferred on 
a nitrocellulose membrane for 30  min at 25  V (max. 1  A) using transfer buffer (43  mM 
Tris, 35  mM glycine, 10% ethanol). The membranes were subsequently washed with 
PBS/0.1% Tween -20, blocked for 1  h with blocking buffer (PBS, 0.1% Tween -20, 5% 
nonfat dried milk powder) and incubated with the primary antibody in blocking buffer 
overnight at 4°C.  
After incubation, m embranes were washed with PBS/0.1% Tween -20 before 
incubation with the secondary antibody for 1  h at room temperature, and washed again 
before developing with chemiluminescent substrate and subsequent analysis on a 
BioRad ChemiDoc system.  
3.5.4  FACS Analysis  
To assess transfection frequencies of DS BNT162b2 -RNA transfected cells using a 
commercial transfection reagent or DP BNT162b2  transfected cells , FACS analysis 
was performed. Cells were transferred to a 96 -well plate format and stained with 5 0 µl 
fixable viability dye eFluor™ 450 diluted 1:500 for 15 min at room temperature. To 
remove residual dye , cells were washed with FACS Buffer  (1xDPBS, 1% BSA, 1% 
0.5M EDTA) , centrifuged at 300xg for 5 min at 4°C and fixed with 100 µl Fixation Buffer 
(Biolegend)  for 12 minutes at room temperature. Cells were washed  with 1x 
Permeabilization Buffer (eBioscience)  by centrifuging  at 500xg for 5 min at 4°C and 
stained with 50 µl anti -S1 antibody labelled with AF647 diluted 1:400 in 1x 
permeabilization buffer fo r 30 min on ice. Afterwards, cells were washed twice with 1x 
permeabilization buffer, centrifuging at 500xg for 5 min at 4°C. Cells were resuspended 
in 100 µl FACS buffer before acquisition with a BD FACSCanto II.  
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3.5.5  Immunofluorescence  
Immunofluorescence staining of transfected cells was used to test whether the 
construct was processed within the endoplasmic reticulum (ER) towards the cell 
membrane leading to secretion or surface expression.  
HEK293T cells were washed twice in PBS and fixed in 4% PFA for 1 0 min. Afterwards, 
cells were washed three times for 5  min in PBS, permeabilized in PBS/0.2% Triton X -
100 for 5  min and blocked in PBS with 2% BSA and 5% goat sera for 30  min. Cells 
were then incubated for 1.5  h with the primary antibod y in PBS/2% BSA (ant i-S1 
antibody), washed three times in PBS for 5  min, and incubated with secondary 
antibodies and conjugated Concanavalin A and Lectin GS -II in PBS/2%BSA for 2  h. 
Afterwards, cells were stained with Hoechst for 3  min, washed three times in PBS for 
5 min and  were then mounted on slides and stored at 4°C until analysis. Cells were 
analyzed with a Leica SP8 confocal microscope.   
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4 TABLES AND FIGURES  
 
Figure  1: Western blot analysis for detection of BNT162b2 antigen expression  
Cells were transfected with DS BNT162b2 -RNA , and harvested after 18 h to allow antigen expression.  Cells were 
lysed and lysates were subjected  to a sodium dodecyl sulfate (SDS) –polyacrylamide gel electrophoresis (PAGE) 
system using a 4 –15% gradient polyacr ylamide gel followed by Western blot analysis . BNT162b2 has a predicted 
size of 141.14 kDa. A recombinant SARS -CoV-2 S1 Subunit protein (76.5 kDa) was used as a positive control.  
 
Figure  2: FACS analysis of transfect ion frequency and cell viability  
Cells were transfected with BNT162b2 -RNA or BNT162b2 . After 18  h in culture, cells were  stained with a viability 
dye, fixed , permeabilized  and stai ned with a monoclonal rabbit antibody recognizing the S1 protein  subdomain 
labelled with AF647. Non -transfected cells were used as a control.  
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Figure  3: Immunofluorescence staining of transfected cells  
Cells were transfected with BNT162b2 . After 18 h in culture,  cells were fixed and stained for : the ER  
(Concanavalin  A, Alexa Fluor™ 594 conjugate  and Lectin GS -II from Griffonia simplicifolia, Alexa Fluor™ 594 
conjugate , red) , the S1 protein subdomain using a polyclonal antibody  (anti-S1 antibody  and Alexa Fluor® 488, 
green)  and deoxyr bonucleic acid (DNA)  to define the nucleus  (Hoechst, blue) . The merged colored picture shows 
the co -localization of the two candidates within the ER  (scale: 10  µm). A control , using non -transfected cells , is 
shown in the bottom  row.  
 
  
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5 CONCLUSION  
Western blot analysis confirmed the expression and size of the BNT162b2 antigen  in 
cell lysates of HEK 293T  cells as a surrogate for  correct expression in a eukaryotic 
system . 
FACS analysis  was performed to assess transfection frequencies of HEK293T cells 
transfected with either BNT162b2  drug substance (BNT162b2 -RNA) or drug product 
(BNT162b2) . Both, BNT162b2 -RNA and BNT162b2  led to  high frequencies of cells 
being transfected, with BNT162b2 -transfected  cells showing slightly higher 
transfection frequencies compared to BNT162b2 -RNA transfect ed cells  using a 
commercial transfection reagent. There were no differences in cell viability after 
transfection with BNT162b2 -RNA or BNT162b2 when comparing to non -transfected 
cells.  
Furthermore, co -localization of the S protein  antigen  with an ER marker was detected  
by immunofluorescence experiments in HEK293T  cells expressing BNT162b2 -RNA . 
These result s show that the S protein  is processed within the ER for s urface  
expression . 
  
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6 DOCUMENT HISTORY  
Reasons for changes compared to previous version:  
Section  Version  Version  Reason for change  
2.6 01 02 Specification of lab book numbers  
3.4 01 02 Equipment was added  
3.4 01 02 Correction of IF staining  
3.5.5  01 02 Correction of IF staining  
4 01 02 Correction of IF staining  
 
  
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7 REFERENCES  
Not applicable.  
  
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8 APPENDIX  
Appendix  1: Certificate s of Analysis   
BNT162b2 -RNA  
 
  
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BNT162b2  
 
 
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(b) (6)
FDA-CBER-2021-5683-0709155
  
 
R&D Report R-20-0211  Version 0 2 Page 22 of 22 
  Strictly Confidential  
Appendix  2: FACS gating strategy  
 
090177e194fbdc19\Approved\Approved On: 23-Sep-2020 11:50 (GMT)
FDA-CBER-2021-5683-0709156