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PF-073020 48: Qualificati on of the SARS -CoV -2 mNeon Green Virus Micron eutralization Assay
VR-MQR -1021 4, Ver. 2.0
PFIZER CONFIDENTIAL
Page 1
Title: Qualification of the SARS- CoV -2 mNeonGreen Virus Microneutralization Assay
Study Number: N/A
Parent Compound Number(s): PF-07302048
Alternative Compound Identifiers: N/A
Pfizer Vacc ine Research and Development
401 N. Mi ddletow n Rd.
Pearl River, NY
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PF-073020 48: Qualificati on of the SARS -CoV -2 mNeon Green Virus Micron eutralization Assay
VR-MQR -1021 4, Ver. 2.0
PFIZER CONFIDENTIAL
Page 2Title: Qualification of the SARS- CoV -2 mNeonGreen Virus Microneutralization Assay
PRINCIPAL INVESTIGATOR(S) :Ingrid L. Scully , Senior Director
Mark W. Cutler, Director
Pei-Yong Shi , PhD,I.H.Kempner Professor of Human
Genetic s
CONTRIBUTI NG SCIE NTIST(S): Camil a R. Fontes -Garfias, Antonio E.Muruato,
TylerGarretson,
PREPARED BY:
Ingrid L . Scully
Senior Director , Clinical and Diagnostic Assay Development
APPROVED BY:
Michael W. Pri de
Exec utive Director , Clinical a nd Diagnostic Assay Development
David Cooper
Executive Director and Head , High -throughput Immunoassay s &Diagnostics
Charles Tan
Senior Direc tor, Earl y Clinica lDevelop ment Biostatist ics
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Page 3Title: Qualification of the SARS- CoV -2 mNeonGreen Virus Microneutralization Assay
SYNOPSIS
This report documents the qualification of the SA RS-CoV-2 mNeon Green virus
microneutra lizatio n assay(SARS -CoV -2 mN G NT) . The SARS -CoV-2 mNG NTmeasures
funct ional antibodies present in serum capable of neutralizing SARS -CoV -2. Twoassay
endpoints were examined : 50% and 90% viral neutralization . The 9 0% neutralization titer
analyses were prepar edfor int ernal purposes only; in routine clinic al testing onl y the 50%
neutralization titers will be reported. The data provided in this repor tindicate the
SAR S-CoV -2 mN G NT has the precision expecte d of a cell-based biofunctional manual
assay , acceptab le performance near the assa y LOD (l ow false negative and false positive
rates), and quality control sera are perform ing as exp ected. Together, the data confirm that
the assay issuitabl e for itsintended us e wh en performed in accordanc ewith stand ard
operating procedures b y qualifie d personnel.
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Page 4TABLE OF CO NTENTS
SYNOPSI S................................ ................................ ................................ ................................ .3
LIST OF TABLES ................................ ................................ ................................ ..................... 5
LIST OF FIGURES ................................ ................................ ................................ ................... 5
1.OBJECTI VE................................ ................................ ................................ .......................... 6
2.INTRODUCTION ................................ ................................ ................................ ................. 6
3.GLOSSARY ................................ ................................ ................................ .......................... 7
4.MATERIAL S AND METHO DS................................ ................................ ........................... 7
4.1.Materials ................................ ................................ ................................ .................... 7
4.1.1. Precision Sample Pa nel................................ ................................ ................. 8
4.1.2. Quality Control Samples...............................................................................9
4.2.Methods ................................ ................................ ................................ ..................... 9
4.2.1. Assay Methods..............................................................................................9
4.2.2. Precision Assessment Experimental Design ................................ ................. 9
4.3.Statistical Methods ................................ ................................ ................................ ..10
4.3.1. Precision ................................ ................................ ................................ .....10
4.3.2. Intermediate Precision ................................ ................................ ................ 10
4.3.3. Assessment of Assay Performance Near the LOD ................................ .....11
4.3.4. Assessment of Performance ................................ ........... 11
5.RESUL TS AND DI SCUSSION ................................ ................................ .......................... 12
5.1.Precision Assessment ................................ ................................ .............................. 12
5.1.1. Precision ................................ ................................ ................................ .....12
5.1.2. Intermediate Precision ................................ ................................ ................ 12
5.2.Assessment of Assay Performance Near the LOD ................................ .................. 13
5.3.Assessment of Performance ................................ ........................ 13
5.4.Infection Rati o Consistency ................................ ................................ .................... 16
6.CONCL USION ................................ ................................ ................................ .................... 17
7.SUPPORTING DOCUMENTATION ................................ ................................ ................. 17
8.SUPPL EMENTAL INFORMATI ON................................ ................................ ................. 18
9.SUPPORTIVE TABLES ................................ ................................ ................................ .....19
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Page 5LIST OF TABLES
Table 1. Terms and Definit ions................................ ................................ ................ 7
Table 2. SARS -CoV -2 mNG NT Assay Critical Reagents ................................ ......7
Table 3. Precision Sample Panel ................................ ................................ ............... 8
Table 4. Precision Assessm ent Run Schedule ................................ .......................... 9
Table 5. ................................ ................................ 12
Table 6. Database Prof ile for the SARS -CoV -2 Control Data Baseline b y
Control Serum Descriptive Information ................................ ................... 13
Table 7. Control Data Profile for SARS -CoV -2 mNG NT Assay b y QC
Serum Process (Day , Residual) ............................... 14
Table 8. Specification Limits for SARS- CoV -2 mNG NT by Control Serum
............................... ................................ ................................ .......14
LIST OF FIGURES
Figure 1. ................................ ........................... 15
Figure 2. ................................ ........................... 16
Figure 3. Infection Rati o Chart ................................ ................................ ................ 17
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Page 6Title: Qualification of theSARS-CoV- 2 mNeonGre en Virus Micro neutraliza tionAssay
Study N umber: N/A
Functional Are a:Vaccine Research an dDevelopme nt
Test Facility:Univer sity of Texas Medica l Branc h, 224 11th St reet, Galveston, TX 77555
Stud y Initiation Date: 30-May-2020
Study Completion Date: 03-Jun-2020
1.OBJEC TIVE
This reportsummarize sthemethodology , statistical analysis and results of the qualification
of theSARS -CoV -2 mNeonGr eenMicron eutralization Assay (SARS -CoV-2 mNG NT),
including assay precision, assay performance near the L OD, and assessment of qua lity
control sample (QCS) performance.
2. INTRODU CTION
The SARS -CoV-2 mNG NT is abiofunctional assay thatmeasures neutraliz ing antibodies
againstSARS -CoV -2.The SARS -CoV -2 mNG virus is derived from the USA -WA1/ 2020
strain that had bee n rescued by reverse ge netics and e nginee red to containa mNe onGreen
(mNG) reporter gene into op en reading frame 7 of the vira l genome thatproduces green
fluores cence upon productive infection of cells (Xieet al,2020 ).1This report er virus
generates similar plaque morphologies and indistinguishable gr owth cur ves fro m wild -type
virus (Muruato et al, 2020).2
This assay is descri bed in the test method SHI-SOP-10011 (see Section 7).Briefly, the
SARS -CoV-2 mNG NT is a t hreeday manual 96-w ellassay . On Day 0, Vero CCL -81 cells
areseeded into 96-well tissue -culture treated read -out pl ates (R OPs). On Day 1, serial
dilutions of heat-inactivated testsera are inc ubated with theSARS -CoV-2 mNG virus to
allow an y virus -specific antibodies to bind to the virus. The serum -virus mixture is then
transferred onto the Verocell monolay erand incubated for 16-24hours to allo wforinfectio n
by non-neutralized virus. On Day 2, productiv e viral i nfection is enumerated by visualiz ing
fluorescent viral foci on a C ytation-7 Cell Imag ingMulti-Mode Reade r. Total number of
cells per well is cal culated by visualizing Hoechst 33342 stained Vero cel l nuclei , which ar e
blue. An infe ction ratio i s then c alculated fo r each wel l, whereb y the totalnumb er of virus
infected ( green )cells is divid edby the t otal n umber of cells present (blue nuclei ). A sample
titeris defined as the recipro cal se rum dilution at which a specific pe rcentage of the virus is
neutralized : 50% o r90% of t he virus (termed “TiterDetermi ning Value”, T DV)
(seeSection 4.2.1 ).
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Page 7Thequalification is being conducted to demonstr ate that theSARS -CoV -2 mNG NT yields
consi stent a ndacceptable results for the test ingof clinica l samples . This rep ort documen ts
the pr ecision assessment exper imental design ,as well as the statistical a nalysis of the
precisionassessment data, perf ormance near the assay LOD and QCS performance.
3.GLOSSA RY
Table 1.Terms and De finitions
Term Definition
IR Infection Ratio
GMT Geom etric Mean Titer
LOD Limit of Detection
QCS Quality Control Sample
ROP Read O ut Plate
RSD Relative Standard D eviation
SARS -CoV- 2 mNG NT 96-wellmanual microneutralizat ion assay for the detection of functional antibo dies to
SARS -CoV-2using themNe onGreen reporter virus
SOP Standard Operatin g Procedure
TDV Titer Determining Val ue; the threshol d value in percen tof measured viral green
particl e counts that is used to report sample ti ters. Titers may be report ed at 5 0%or
90% TDV.
Vero African green monk ey kid ney epithelial cell line
4.MATERIALS AND METHODS
4.1.Mate rials
Reagents, s uppliesand equipment used in the precisi on assessment are listed in the t est
method , SHI-SOP-10 011 ( see Section 7 ). Thecritical reagents used in these precision
assessment runs are listed in Table2.The viral bank is aliquote dinsingle-use vials and is at
a concentration o f . The Vero ce lls w ere purchased f rom ATCC .A Vero
cellbank was prepared and each cell bankvialis used f or up to 35 passages.
Table2.SARS -CoV -2 mNG NT Assay Critic al Reage nts
Reagent Nam e/Lot #
SARS -CoV-2 mNGvirus SAR S-CoV-2- mNEON
P1Vero E6
04.21.20 AM
Cell Line Vero cells;ATCC CC L81, used from pas sage 1to35
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Page 84.1.1. Precision Sample Panel
The precision panel iscomprised of non-immunized SARS -CoV -2positive huma n serum
samples or SARS -CoV -2 negative sample s( and pre -SARS -CoV -2 outbreak
samples, res pectively ) with a range of virus neutralizing titers fr om<20(presumed negative
to a titer of , see Section 9). There were low tite red sampl es (tit er medium
titer samples (titer ) and high titer ed samples (titer )availabl e for
analysis. Serumsample s from SARS -CoV -2 donor s were obtained from
.
Inaddition, in-house antibody -depleted serum samples (prepared from pre -SARS -CoV-2
outbr eak sera) and presumed neg ative serum samples (pre-SARS -CoV -2 outbreak) were
also includ ed. nested repl icates were also included in the study(Table 3). All precis ion
samples we reheat-inactivated (30min at 56°C ) and tested neat.
Table 3. Precision Sample Panel
PP Barcode Source Sample ID Sourc eBarcode
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Page 94.1.2. Q uality Con trol S amples
4.2.Methods
4.2.1. Assay Methods
SARS -CoV -
2 mNG NT assays were performed as described in SHI-SOP-10011
(see Section 7).
Sampl eswere prepared for testin g manually .
A sample ti ter is calculat ed as the reci procal s erum dilut ion a t whic h aspecific percentage of
thevirus isneutralized (eg, 50% or 90% of the virus). This value is referred to as the titer
determinin gvalue (TDV). To calculate this percentage, an infectio nrate m ust first be
determined b y dividing the number of vi ral fo ci(green) by live cells (blue )in any given well.
The number of Vero cells per well i s targeted between and and the amo unt of
virus ad ded is expected to y ield a .Infection rates are p lotted i n
Figure 3. The percent ne utralization is then determined by comparing the infect ion rates of
the serum contai ning wells to that of the contr olwells without serum samples. A titer is
calculated fo reach of the two replicates of a sample on a plate and the geo metric mean titer
(GMT) of the tw o is reported as the final samp le titer.
4.2.2. Precision Assessment Experimen tal Design
Precision describes the variabi lity of repeated indepen dent mea suremen ts(repli cates) for
samplestestedmultipletimes. This experiment cons isted of assay runs. To acco unt for
known sources of va riability , the r uns were performed over testing days, by analysts
(T
able4). Eachassayrun consist edofplates .
Table4.Precision Assessm ent Run Sch edule
Run Day Analyst
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Page 104.3.Statistical Me thods
Sample level titers are o nly reported when the repli catetiter ratio is . During the precision
experiment, only observations yielded a replicate titer ratio . Samples
that y ield a replicate titer ratio and have titers above the assay LOD (20) during clinical
testing are repeate d to yielda valid tite r resul t.Titerswere before stat istical
analysis.All statistical analy seswere performe d using SAS version 9.4. Analy ses
describ ed her ein we reperformed on data co llected duri ng the precision a ssessment
experimen ts.Presumednegative serum sample s normal human sera and
pre-2019 samples) and samples with a geometric mean titer <20 (LOD) were excluded
from analyses as descr ibedinthe following sections .
4.3.1. Precisi on
4.3.2. I ntermediate Precision
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Page 114.3.3. Assessment of Assay Performance Near the LOD
The LOD of the SARS- CoV -2 mNG NT assay is defined as the reciprocal of the lowest
serum dilution run in the a ssay, 20. To deter mine the perf ormance o f the assay near the
LOD, the number of times a presumed negative sample returned
a positive titer was
calculated and expressed a s a ratio and as a percentage (false positive rate) . Similarly , the
number of times a presumed positive low titer sample (samples with a n expected titer
but greater than )yielded a negative result was al so calculated an d expressed
as a ratio and as a percentage (false negative rate) .
4.3.4. Assessment of Perfor man ce
specificatio nlimits were calculated according to the following method and
the result sare shown in Table 5.
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Page 125. RESULTS AND DISC USSION
5.1. P recision Assessment
Precision assessment runs were performed by qualified anal ystsbetween 30-May-2020 and
03-Jun-2020 , inclusive. The raw SARS -CoV -2-mNG NT data for the precision experiment
is liste d inVR-MQR -1021 4-ATT01 (Section 7).
5.1.1. P recisi on
Descriptive sta tistics for each serum sampl eare tabulat ed inSupportive Table 9.1. These
include the for eac h serum
sample for the 50 %and 9 0% TDVs . were ca lcula ted as des cribed in
Section 4.3.1 .
5.1.2. I ntermediate Precision
The inte rmediate p recisio n of the assay was evaluated usi ng the as descri bed in
Section 4.3.2 and the results are summa rized in Table 5.The fi rst serum dilutio n in the assay
is 1:20 . Thus a titer of 20 hasbeen defined as the assay ’sLOD.
Overal l,the precision of the SARS -CoV -2mNG NTwas acceptable for a manua lly
performe d biofunctional ass ayat the 50% and 90% TDV.
Table 5.
TDV
50%
90%
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Page 135.2.Assessm ent of Assay Performance Near the LOD
5.3.Assessment of Perfo
rmance
To monitor for as say variabili tyover time, a baseline database w as establish ed by inclu ding
data collec tedfrom 23- Jun-2020 through 07-July-2020, inclusive . QCS
data f or the SARS- CoV -2-mNG NT is listed in VR -MQR -10214 -ATT02 (see Section 7).
Descriptive infor mation such as the number of data points ( N) and the dates of the first and
last runs included in the database a re sho wn in Table 6.
Table 6. Database Profile for the SARS -CoV-2Contr ol Data Baseline by Cont rol
Serum Descript ive Informa tion
Assay Control DaysaNbMin
TitercMax
TiterdFirst
DateeLast
Datef
SARS -CoV-2 mNG
NT23JUN2020 07JUL2020
23JUN2020 07JUL2020
a.Days, Num ber of Days .
b.N, N umber of observations .
c.Min Ti ter, Low estobserved t itervalue .
d.Max Titer, Highest observed t iter value .
e.First Date, Earliest run d ate..
f.Last Date, Las t run d ate
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Page 14Table 7.Control Data Profi le for SARS -CoV-2 mNG NT Assay by QC Serum
Proce ss
Assay Cont rol NaDaysb
SARS-CoV-
2mNG NT
a.N, Nu mber of observations .
b.Days, Nu mber of days .
Specification limits were set as descr ibed in Section 4.3.4 and the results are sho wn in
Table 8. As additional dat a become ava ilable, the s pecification limits may be reset toreflect
routin e assay performance.
Table 8.Spec ification Limits f or SARS -CoV -2 mNG NT by Control Serum
Assay Control DaysaNbLow er
Spec
Limit
(LSL)cGeometric
MeanUppe r
Spec
Limit
(USL)d
SARS -CoV-2
mNG NT
a.Days, Numb
b.N, Number of observations .
c.Lower Spec Li mit,
d.Upper S pec Limit,
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Page 165.4.Infection Ratio Consistency
The number of Vero cells p lated per well and the amount of v irusadded aretargeted to yield
a
n infection ratio (IR) between 10- 30%. IRdata f or the SA RS-CoV -2-mNG NT is listed in
VR-MQR -10214 -ATT0 3(Section 7).Scatter pl ots of IR are sh own in Figure 3. Thisplot
indicate sthattheIR consistently falls between
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Page 17Figure 3.Infection Ratio Chart
6. CO NCLUSION
TheSARS-CoV -2 mNG NT demonstrated acceptable pre cision at the 50% and 90% TDV for
the detecti onof functional antibodies to SARS -CoV-2in test serum . The ass ay is performing
acceptabl y near the LO D,with low observed false negative a nd false posi tive rates.
Inaddition, the qua lity control sera fallwithin the spe cification limi ts andserve to control
assay performance. TheSARS -CoV-2mNG NT assay isthus deem ed qualified to support
both preclinica l and clinical studies.
7.SUPPORTING DOCU MENTATION
1.SHI-SOP-10011 , Manual 96-well Ne utralization Assay for the D etection of Functiona l
Antibodies to SA RS-CoV -2 in Test Serum u sing Cy tation7 Image Read er.
2.VR-MQR -10214-ATT01: Precision Experiment Data L isting .
3.VR-MQR -10214 -ATT02: QCS Data L isting .
4.VR-MQR -1021 4-ATT03: QCS I nfection Ratio Data Listing .
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Page 188. SUPPLEMENTAL INFORMA TION
1. X ie X, Mur uato M, Lokugamage KG et al. A n Infec tious cDNA Clone of SA RS-CoV -2.
Cell Host & Microbe 2020 , 27(5):841-848.
2.Muruato AE, Fontes -Garfias CR, Ren P, et al. A high- throughput neutralizing antibody
assay for COVID- 19 diagnosis and vaccine evaluation. Preprint. bioRxiv. 2020 May
22:2020.05.21.109546. doi: 10.1101/2020.05.21.109546 .
3.
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Page 199.SUPPORT IVE TABLES
The descriptive stati stics of the precision sam ples are found in Supportive Table 9.1.
9.1.Descript ive Stat istics of Precis ion Samples
TDV Samp le
50%
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Page 209.1.Descript ive Stat istics of Precis ion Samples
TDV Samp le
90%
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Document Approval Record
Document Name:
Document Title: !
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090177e194a57b00\Approved\Approved On: 18-Aug-2020 17:57 (GMT)
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FDA-CBER-2021-5683-1072900