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MOLECULAR BASIS OF CORONAVIRUS
VIRULENCE AND VACCINE DESIGN TO
     PROTECT AGAINST SARS



             XRB. UNIVERSIDAD DE BARCELONA
                     13 JULIO 2012
                     LUIS ENJUANES
                   CNB-CSIC. MADRID
CORONAVIRUS
             TGEV & SARS-CoV


REPLICATION TRANSCRIPTION   PACKAGING   VIRULENCE




              VIRUS-HOST INTERACTION
CORONAVIRUS INDUCED DISEASES
                      MAN
   CENTRAL NERVOUS
            SYSTEM
                            ANIMALS
               EYE

  UPPER AND LOWER           AS IN HUMANS &
 RESPIRATORY TRACT          PERITONITIS

IMMUNE SYSTEM CELLS
                            HEPATITIS
                            NEPHRITIS
  GASTROINTESTINAL          CARDIOMIOPATHY
            TRACT
RNA VIRUS GENOME SIZE IN NUCLEOTIDES
NIDO_CORONAVIRUS
   NIDO_TOROVIRUS
  NIDO_RONIVIRIDAE
  CLOSTEROVIRIDAE
          BENYVIRUS
NIDO_ARTERIVIRIDAE
       SEQUIVIRIDAE
         POMOVIRUS
       TOGAVIRIDAE
       COMOVIRIDAE
       FLAVIVIRIDAE
          FUROVIRUS
        TOBRAVIRUS
         PECLUVIRUS
        CHERAVIRUS
       HORDEIVIRUS
        POTYVIRIDAE
           IFLAVIRUS
   DICISTROVIRIDAE
     MARMAVIRIDAE
     BROMOVIRIDAE
         IDAEOVIRUS
    PICORNAVIRIDAE
      CALICIVIRIDAE
       FLEXIVIRIDAE
      TETRAVIRIDAE
        HEPEVIRIDAE
      ASTROVIRIDAE
      TOBAMOVIRUS
      UNCLASSIFIED
       TYMOVIRIDAE
      LUTEOVIRIDAE
       NODAVIRIDAE
      SOBEMOVIRUS
        UMBRAVIRUS
    TOMBUSVIRIDAE
      BARNAVIRIDAE
         LEVIVIRIDAE
      NARNAVIRIDAE
MUTATION OF CORONAVIRUS EXON MOTIFS

 MHV                         REP 1a      REP 1b   nsp14   CPD HE   S   4a 4b 5a E   M       N   An
                                                                                        I




            C1         D89 E91        ZN F D242 D272                                    Q521




YEAST
               MUT 1
                    ..
              AIDAEFV-103-
                                      Zn F
                                                                                 .MUT 2.
                                                            VFVGHGLNNDFK-44-HDSIEDAHTAL
MHV-A59   GFDAEGA-111-VVCSVCTK-11-YGCWRHS-3-DYLYNPLIVDIQ-23-HVASSDAIMTR
SARS-CoV GFDVEGC-111-RTCCLCDK-11-YACWNHS-3-DYVYNPFMIDVQ-23-HVASCDAIMTR
HCoV-229E GMDVEGA-111-KHCQ-CGT-11-YCCFKHA-3-DYVYNPYVIDIQ-23-HVASGDAIMTR
TGEV          GFDVEGA-111-QKCE-CGK-11-YACFKHA-3-DYLYNPYCIDIQ-23-HVASGDAIMTR
IBV           GFDVEAT-111-QVCS-CGS-11-YACWKHC-3-DFVYNPLLVDIQ-23-HVASVDAIMTR



Eckerle et al., 2007, 2010
DISTRIBUTION OF MUTATIONS AFTER PASSAGE

MHV                         REP 1a   REP 1b   nsp14   CPD HE   S   4a 4b 5a E   M       N   An
                                                                                    I




WT          p5  c1
                c2
            p17 c1

MUT 1       p1
                       c1
            p5
                       c2
            p17 c1

MUT 2       p1
                       c1
            p5
                       c2
            p17 c2

Eckerle et al., 2007
CORONAVIRUS STRUCTURE AND GENE
          EXPRESSION

                                              3b
                    ORF 1a ORF 1b   S       3a E M          N 7 UTR
            + CAP                                                AAA
                                                                  mRNA
               +                                                AAA
                -                                               UUU
                                                                   G
                              +                                 AAA
                               -                                UUU   S
                                        +                       AAA
                                        -                       UUU   3a
                                            +                   AAA
                                            -                   UUU   3b
                                                +               AAA
                                                -               UUU   E
                                                    +           AAA
                                                    -           UUU   M
                                                        +       AAA
                                                        -       UUU   N
                                                            +   AAA
                                                            -   UUU   7
TRANSCRIPTION MECHANISM



   TEMPLATE SWITCH
   A HIGH FREQUENCY RECOMBINATION


ENGINEERED AN INFECTIOUS cDNA CLONE
REGULATION OF sgmRNA LEVELS


                     TRS-L                                    TRS-B

     gRNA 5’     L   CS-L                                      CS-B             An 3’




5’                                           An 3’ +   MULTIFACTOR REGULATION
                                                       1. TRS RNA STRUCTURE
3’      cL                    cCS-B          Un 5’ -
                                                       2. TRS PRIMARY SEQUENCE
                              cTRS-B
                                                       3. LONG DISTANCE INTERACTIONS
                                                       4. PROTEIN-RNA BINDING
           5’         cCS-B            3’   mRNA
                                                        .....................
TRANSCRIPTION AND LEADER-BODY CS IDENTITY




                     Gene 3a
 + 5’   L   CUAAAC   CUAAAC         An 3’   +

                     GAUUUG         Un 5’   -
TRANSCRIPTION AND LEADER-BODY CS IDENTITY




            TRS-L    Gene 3a
 + 5’   L   CUAAAC   CUAAAC         An 3’   +

            GAUUUG     5’ -
WILD TYPE TRS-L STRUCTURE PREDICTION

                U
            C16 17 A18      APICAL HEPTALOOP
           A15       A19
                            INCLUDING THE CS-L
           A14      A20
              G13 C21
              C12 G22
                            MICRO STEM
              U11 A23
           C10      A24
            A9        A25
                      U26
            A8              INTERNAL LOOP
                      A27
            C7
                      U28
            C6      U29
              A5 U30
              C4 G31
              A3 U32
              G2 C33
              G1 U34


                 WT
WT AND MUTANTS TRS-L STRUCTURES


                                                   U A        U        U A
   U A                     U A           U A    C         C  A       C
 C                       C             C        A     A             A     A
A     A          U A    A     A       A     A             A   A
               C                                A     A   A   A     A     A
A     A             A   A     A       A     A
              A                                 G     C       C       G C
  G C                     G C           G C               G
              A     A                           A     G       G
                                                          A          C G
    C G         G C         C G        C G            A       A
                                                A
                            U A                       A   U          U A
    U A         C G                     C G     C             A
C         A   A     A                 C     A         A   C   A      U A
                            C G                 A
A         A   C     A                 A     A         U   A U
                        A         A             A                    U A
          U   A     U                       U         A
A                       A         U   A         C         A U        A U
          A   A     A                       A         U
C                                 A   C
          U   C     U   C                   U   C     U   C G        C G
                                  U
C         U   C     U   C             C     U             C G
                                  U               A U                C G
    A U         A U                     A U
                         A U                     C G      A U        A U
    C G        C G                     C G                                 U
                            C G                  A U      C G
    A U                                A U                           C G
               A U       A U                              A U
                                                 G C                 A U
    G C        G C                     G C
                         G C                     G U      G C
    G U                                G U                           G C
               G U       G U                              G U
                                                                     G U



    WT         MS2          IL1        MS1       MS3          IL3     IL2
CONCLUSION


THE EXTENT OF sg mRNA SYNTHESIS:

  CORRELATES WITH TRS-L STABILITY
  WITH THE AVAILABILITY OF TRS-L
  REQUIRES A SPECIFIC SECONDARY
  STRUCTURE
TRANSCRIPTION MECHANISM



   TEMPLATE SWITCH
   A HIGH FREQUENCY RECOMBINATION


ENGINEERED AN INFECTIOUS cDNA CLONE
TRANSCRIPTION AND LEADER-BODY CS IDENTITY




                      Gene 3a
 + 5’   L   CUAAAC   CUACAC         An   3’ +


                     G A UG U G
                          U         Un   5’ -
TRANSCRIPTION AND LEADER-BODY CS IDENTITY




                        Gene 3a
 + 5’   L   CUAAAC      CUACAC      An   3’ +


            G AUG U G
                U
REQUIREMENT OF COMPLEMENTARITY BETWEEN
   CS-L AND cCS-B FOR sgmRNA SYNTHESIS

             CS-B MUTANTS                         CS-L MUTANTS
                             TITER*                               TITER*
           5’ C U A A A C 3’                    5’ C U A A A C 3’
     B-C1G G                  8x108        L-C1G G                   -
     B-U2G      G             1x107        L-U2G     G               -
     B-A3C        C           5x108        L-A3C       C             -
     B-A4C          C         6x108        L-A4C         C         2x104
     B-A5C            C       3x108        L-A5C           C       4x104
     B-C6G              G     4x108        L-C6G             G     2x103



  NON-WATSON-CRICK MUTANTS                COMPLEMENTARY MUTANTS
                                 TITER*                             TITER*
         5’ C U A A A C 3’                      5’ G U A A A C 3’
    L-C1U U                      2x103
                                          D-C1G                        -
                                                3’ C A U U U G 5’
      WT                         5x108                                 -
    L-A3U        U               3x103                                 -
                                 5x104                               2x105
    L-A4U            U
    L-A5U                U       2x104            5’ C U A A A G 3’ 4x105
                                          D-C6G
    L-C6U                    U   1x108            3’ G A U U U C 5’ 2x10
                                                                         3




  * pfu/ml
MAIN CONCLUSION



              Ξ”
BASE-PAIRING (Ξ”G) IS A DRIVING FORCE
IN CoV TRANSCRIPTION
COMPLEMENTARY AND SYNTHESIS OF sgmRNA
                                                                                                                                    mRNA CS2
  5’    CGAACUAAACGAAA   3’
                                                                  75




                                   POTENTIAL BASE-PAIRING SCORE
       CS1    ACUAAAC
       CS2     CUAAAC                                             65
       M1     ACUAAAC
       M2    AACUAAAC                                             55
       M3   GAACUAAAC                                                                       mRNA 3a.2
       M4  CGAACUAAAC                                             45
       M7      CUAAACG
       M8      CUAAACGA                                           35
       M9      CUAAACGAA
       M10     CUAAACGAAA                                         25
       M5  CGAACUAAACGA
       M6  CGAACUAAACGAAA                                         15




                                                                       24550


                                                                               24684



                                                                                           24685



                                                                                                   24710




                                                                                                               24734




                                                                                                                            24746
                                                                                       GENOME POSITION, nt



                                                                                         MUTANTS
              Mock CS1 CS2wt   1             2                         3       4           7       8       9           10   5        6
 506

                                                                                                                                               mRNA-3a.2
 220
                                                                                                                                               mRNA CS2
COMPLEMENTARITY BETWEEN NASCENT RNA AND TRS-L
         SEQUENCE AND mRNA LEVELS


                  14


                                                                     M4
                  10                             M3
  -Ξ”G, kcal/mol




                                   M2
                            M1
                  6
                           CS-S2
                                                           5’ TRS MUTANTS
   Ξ”




                  2

                       0           50   100      150       200      250     300
                                              mRNA, u.r.
mRNA LEVELS AND BASE-PAIRING SCORE

                 110


                 90        BASE-PAIRING
RELATIVE UNITS




                 70


                 50


                 30

                           mRNA
                 10

                       S    3a     E          M   N   7
                                       mRNA
REGULATION OF sg mRNA-N LEVELS


                   TRS-L                         TRS-N
                                                          N-GENE
gRNA 5’   L        CS-L    dE           pE       CS-N              An 3’
                                460nt          7nt




     5’


     3’       cL                   TAATGTATA


                                   ATTACATAT                   An 3’ +

                                                cCS-N          Un 5’ -
                                                 cTRS-N
COMPLEMENTARITY AND ENHANCER ACTIVITY
sgmRNA-N, RELATIVE UNITS




                           200


                           150


                           100


                            50



                                 0   5   10         15   20   25
                                          βˆ†G, Kcal/mol
REQUIREMENT OF pE AND dE FLANKING
          SEQUENCES


                                sgmRNA-N, %
MUTANT
             AD   dE   pE   0   50   100   150   200


E2-TRS-N

TRS-N

dE-113-158

dE-45-158

dE-173-20

pE-20
OPTIMIZED TRM


                      dE pE CS
ORF 1a                                   77
ORF 1a     ORF 1b
           ORF 1b                   N         AAA



               173      9 20 20 9   7   6 6




            Original TRM 642 nt     250 nt
ENHANCEMENT MECHANISM

   pE        CS-N
                         3’

  dE                     5’




        AD

                    5’
ENHANCEMENT MECHANISM

         CS-N
                     3’

                     5’




    AD

                5’
REQUIREMENT OF LONG DISTANCE INTERACTION

                             TRM
   MUTANT         AD dE                     pE CS-N   N
   REP-1

   TRS-N
                                       AD
   AD-TRS-N
                                       TRMopt
   TRMopt-N

              0    5           10             15
   REP-1
   TRS-N
   AD-TRS-N
   TRMopt-N

                       sgmRNA-N/gRNA
ENHANCEMENT MECHANISM

    pE        CS-N
                          3’

   dE                     5’




         AD

                     5’

 80% ENHANCEMENT
ACTIVE DOMAIN REGIONS REQUIREMENT


 A                                  25




         sgmRNA-N, RELATIVE UNITS
                                    20


 B                                  15


                                    10


                                     5
 C
                                     0   +
                                             -   Ξ”A   Ξ”B   Ξ”C
ACTIVE DOMAIN REGION C REQUIREMENT
        Ξ”A    Ξ”A-C’


                                                 25




                      sgmRNA-N, RELATIVE UNITS
B
                                                 20


                                                 15


                                                 10


C                                                5


                                                 0
                                                      Ξ”A   Ξ”A-C’   Ξ”[A-B]
ACTIVE DOMAIN REGION B REQUIREMENT
       βˆ†A                                   βˆ†A-B*2r        βˆ†A-B*1r        βˆ†A-B*1r4       βˆ†A-B*1r3


B




                                       25
            sgmRNA-N, RELATIVE UNITS




                                       20


                                       15


                                       10


                                       5


                                       0
                                            βˆ†A   βˆ†A-B*2r   βˆ†A-B*1r   βˆ†A-B*2r4 βˆ†A-B*1r3   (-)
INTRAGENOMIC RNA-RNA INTERACTIONS
        INVOLVING B RNA MOTIF




 cB-M                        B-M             cB-M                           B-M

nt 218-229                nt 26408 - 26421   nt 477-489                nt 26408 - 26421




             βˆ†G = -12.9                                   βˆ†G = -12.7
TGEV REPLICONS WITH MUTATED B AND cB RNA
                 MOTIFS

                      218-229   477-486   26,212-26,221
                 5’                                                3’
                                            B    dE       pE   N
 wt/B            5’                                                3’
                                                 dE       pE   N
    βˆ†
 wt/βˆ†B           5’                                                3’


                      cB-218                     dE       pE   N
                         *                  B
 cB-218*/B       5’                                                3’
                                                 dE       pE   N
         βˆ†
 cB-218*/βˆ†B      5’      *                                         3’

                         *                  B*   dE       pE   N
 cB-218*/B*      5’                                                3’



                                cB-477
                                            B    dE       pE   N
 cB-477*/B       5’               *                                3’
                                                 dE       pE   N
         βˆ†
 cB-477*/βˆ†B      5’               *                                3’
                                            B*   dE       pE   N
 cB-477*/B*      5’               *                                3’
                                            B*   dE       pE   N
 cB-477*/B*-14   5’               *                                3’
sgmRNA N, RELATIVE UNITS




                     0
                         5
                             10
                                  15
                                       20
                                            25
                                                 30
                                                      35
                                                           40
                                                                45
                                                                     5’

           w
               t/B
         w
             t/βˆ†
                 B
                                                                          218
                                                                          477




   cB
       -2
          18
  cB         * /B
     -2
        18
           */βˆ†
   cB           B
      -2
         18
            * /B
                 *



     cB
        47
           7*
   cB           /B
                                                                         B




      -4
                                                                      26,212




        77
            */βˆ†
   cB            B
                                                                      dE




      -4
cB      77
  -4        */ B
                                                                      pE




    77           *
       */ B
                                                                      N




           *-
                14
                                                                     3’
                                                                                TRANSCRIPTION AND COMPLEMENTARY LEVELS
EVOLUTION OF VIRUSES WITH MUTATED B AND cB RNA
                    MOTIFS
RELEVANCE OF THE INTERACTION BETWEEN B AND
  cB RNA MOTIFS ON sgmRNA AND VIRAL TITERS
MECHANISM OF DISCONTINUOUS TRANSCRIPTION

                            AD

                cB-M
                                  B-M
        TRS-L
                                      dE               pE      CS-N
5’(+)                                                                    3’(+)

                                 pE        CS-N
                                                             3’(+)

                                                             5’(-)
                             dE             cCS-N

                                                     5’(+)
                                              CS-L
                                      B-M
                                                      cB-M
                       AD
                                           cB-M
                                                               CS-L


                                                                      5’(+)
CoV TRANSCRIPTION IS REGULATED
       AT THREE LEVELS



TRS-L STABILITY AND SECONDARY STRUCTURE

COMPLEMENTARITY      BETWEEN   NASCENT
MINUS RNAs AND TRS-L

LONG DISTANCE RNA-RNA INTERACTIONS
TRM ACTIVITY WITHIN INFECTIOUS
           VIRUSES

               ORF 1a    ORF 1b          S   3a 3b    E    M         N 7
wt-TGEV                                         N                    N     A
                                                          dE pE

                                     0          2          4          6
                               CS
TRS-3a
                  AD    dE   pE CS
TRMopt-3a


TRMopt*-3a


TRMopt-19-3a


                                                    sgmRNA-3a/gRNA
GEOGRAPHICAL AREA ORIGIN OF SARS
SEVERE ACUTE RESPIRATORY SYNDROME




   Neumonia       High fever
   Lymphopenia    Death
SPREADING OF SARS

                            …JULY 5th, 03 END EPIDEMY BY WHO



NOV 02     JAN 03      FEB 03                      DEC03 to JAN04
FOSHAN     GUANGZHOU   HONG KONG



                                                   FOUR LABORATORY CASES
                       Dr. A     VIETNAM
                                 CANADA            FOUR NON-LABORATORY
MOST       FIRST       Nephro-                     ISOLATED CASES
                                 SINGAPORE
RECENT     MAJOR       logist    USA
COMMON     OUTBREAK              TWO ADDDITIONAL
ANCESTOR   HOSPITAL    HOTEL M   SSE IN HK          Beijin Apr F 26y, BSL-4
                                 (>100 CONTACTS)    Beijin Apr M 44y, BSL-4
RACOON




CIVET CAT
                     FERRETS
CORONAVIRUS EVOLUTION

          GENUS Ξ±




GENUS Ξ²              GENUS Ο’
ENGINEERING OF A SARS-CoV INFECTIOUS
        cDNA CLONE AS A BAC



             T by C   T by A
             10338    11163
                                                       8a
    L                                          3b M 7a 8b 9b
 CMV    REP 1a                 REP 1b   S   3a   E 6 7b N
                                                               An




                 pBAC-SARS-CoV-URB*
BASIS OF SARS-CoV VIRULENCE

                                            8a
                                     3b M 7a 8b 9b
L      REP 1a       REP 1b    S   3a   E 6 7b N
                                                     An




                DELETED GENE

     Structural:   E
     Accessory:    6, 7a, 7b, 8a, 8b, 9b
     Combinations: E, 6, 7a, 7b, 8a, 8b, 9b
BSL-3 CNB. CSIC. MADRID
GROWTH KINETICS OF SARS-CoV DELETION
                 MUTANTS

                                          VERO E6                         CaCo-2

                      107
                                                        wt
VIRUS TITER, pfu/ml




                                                     Ξ”6-9b
                      105

                                                        Ξ”E
                      103                           Ξ”E,6-9b



                      101


                            0        24        48      72       0         24       48   72
                                              TIME POST-INFECTION, HOUR
                                GENES: E, 6, 7a, 7b, 8a, 8b, 9b ARE NON ESSENTIAL
MORPHOGENESIS OF SARS-CoV IN ERGIC

     SARS-CoV            SARS-CoV-βˆ†E
                                  βˆ†
     SARS-CoV-βˆ† [6-9b]
              βˆ†          SARS-CoV-βˆ† [E,6-9b]
                                  βˆ†
ACTIVITY WHEEL USED TO QUANTIFY
        CLINICAL ILLNESS
βˆ†
SARS-CoV-βˆ†E-INFECTED HAMSTER WHEEL
              ACTIVITY
                                                         INFECTION

                  1200


                                                                         βˆ†E
                  1000
REVOLUTIONS/ hr




                  800
                              MOCK
                  600
                                                            wt
                  400

                  200

                    0
                         -7   -6   -5   -4   -3   -2   -1    0   1   2   3    4

                                                   DAY
ATTENUATION OF SARS-CoV DELETION MUTANTS
   IN TRANSGENIC MICE EXPRESSING hACE-2


                                                       12000 pfu intranasally

                                    CLINICAL DISEASE                                         LETHALITY
                       110                         Ξ”E                           100
 STARTTING WEIGHT, %




                                                                                                          Ξ”E,6-9b




                                                                  SURVIVAL, %
                                                                                                           Ξ”E
                       100                                                       75


                       90                            Ξ”E,6-9b                     50


                        80          wt       Ξ”6-9b                               25

                                                                                 0                       Ξ”6-9b
                        70
                                2        4     6        8                               2      4     6       8
                             TIME POSTINOCULATION, days
                                                                                      TIME POSTINOCULATION, days
SUMMARY



E GENE CONDITIONS TISSUE SPECIFIC TROPISM

         βˆ†
SARS-CoV-βˆ†E IS ATTENUATED


     GENE E IS A VIRULENCE FACTOR
MECHANISM OF E PROTEIN VIRULENCE




     E PROTEIN AND HOST GENE EXPRESSION

                                          8a
                                   3b M 7a 8b 9b
 L      REP 1a     REP 1b   S   3a   E 6 7b N
                                                   An


                                   Β±E
DIFFERENTIAL GENE EXPRESSION IN βˆ†E
DIFFERENTIAL GENE EXPRESSION IN Ξ”E AND WT
        AND WT INFECTED CELLS
                                                     INFECTED CELLS
                          wt vs mock                       Ξ”E vs mock                         Ξ”E vs wt
                 14

                 12

                 10
                                                                                                                    Vero E6
                 8

                 6                                                                                                  15 hpi
LOG EXPERIMENT




                 4

                 2




                 14

                 12

                 10
                                                                                                                    MA104
                 8

                 6                                                                                                  65 hpi
                 4

                 2


                      2   4   6   8   10   12   14     2   4   6   8   10   12   14   2   4    6   8   10   12 14

                                                           LOG CONTROL
Ξ”
GENES DIFFERENTIALLY EXPRESSED IN SARS-CoV-Ξ”E
     VS FULL-LENGTH VIRUS INFECTED CELLS
                   FOLD CHANGE                         FOLD CHANGE
 GENE               VERO MA-104     GENE               VERO MA-104

          STRESS RESPONSE                  IMMUNOREGULATION
 Hsp10 HspE1       + 3.3      --    FKBP4               + 4.7     + 5.5
 Hsp20 B5 CRYAB      --     + 3.2   RIPK2               + 2.3       --
 Hsp27 B1          +19.0      --    ZC3H12A               --      + 2.9
 Hsp40 DNAJB1      +14.8    +25.9
 Hsp40 DNAJA1      + 8.7    + 7.2
                                            INFLAMMATION
 Hsp40 DNAJB6      + 3.9    + 2.1
 Hsp40 DNAJA4        --     + 2.6   NFKBIZ             + 2.9        --
 Hsp40 DNAJB4        --     + 4.1   ADAMTS1            + 2.1        --
 Hsp47 SERPINH1    + 6.7    + 2.5   CCL2                --        - 3.2
 Hsp60 D1          + 4.1    + 4.7   CXCL2               --        - 2.2
 Hsp70 A1A         +22.3    +29.3
                                              APOPTOSIS
 Hsp70 A1B         +18.8       --
                                    DEDD2                 + 2.6   + 5.0
 Hsp70 A8          + 5.8    + 4.9
                                    CLU                   + 2.1   + 2.0
 Hsp70 A4L         --       + 2.3
                                    PHLDA1                + 3.2     --
 Hsp90 AA1         +15.1    + 6.5
                                    STK17B                  --    + 2.2
 Hsp90 AB1         + 6.1    + 2.7
 Hsp105/110        +35.3    +13.4         SIGNAL TRANSDUCTION
 UBB               + 3.9    + 4.4
                                    DSCR1              + 5.9    --
 UBC               + 2.3    + 2.7
                                    DUSP1              + 4.0    --
 BAG3              + 7.2    + 3.9
                                    DUSP10              --    + 2.7
 CCT4              + 3.3      --
                                    YWHAG              + 2.5    --
 CCT3              + 3.3      --
                                    WASL               + 2.5    --
 AHSA1             + 4.7      --
                                    MAP2K3             + 2.1    --
 CRYAB               --     + 3.2
                                    FOLR1                --  +15.6
 TCP1                --     + 2.3
                                    PDE4B                --   + 2.5
 STIP1               --     + 2.1
                                    K-RAS                --   - 2.6
UNFOLDED PROTEIN RESPONSE

         RE                                 CYTOPLASM                           NUCLEUS


                                                                                                 ACTIVATION
                                                                                                IN E VS WT-
                                                                                                 Ξ”
                GRP78 GRP78




                              PERK   eIF2       TRANSLATIONAL                                 INFECTED CELLS
                                                   BLOCK

                              PERK   eIF2
                                            P
                                                            ATF4
                                                                                TRANSLATION
                                                                                ATTENUATION          -
                                                                                CHOP

        GRP78

                                                                      GENE
                 GRP78




                                                   CLEAVED
GRP78




                                                                                CORRECT
                              ATF6
                                                     ATF6
                                                                   EXPRESSION
                                                                                PROTEIN
                                                                                FOLDING
                                                                                                     -
                                                                                CHOP
        GRP78
                GRP78 GRP78




                                      XBP1
                              IRE1    mRNA


                              IRE1    sXBP1
                                                      sXBP1
                                                                                PROTEIN
                                                                                DEGRADATION          +
                                                                                p58IPK
                                      mRNA
EFFECT OF E PROTEIN ON THE STRESS PRODUCED
                      Ξ”
          BY SARS-CoV-Ξ”E INFECTION

                                               E PROTEIN PROVIDED IN TRANS


                               12   HSP A1A HSP90 AA1 HSP H1   SERPIN H1     HSP E1   18S

                                               E+
 FOLD CHANGE, relative units




                               10              E-

                               8


                               6


                               4


                               2
SARS-CoV E PROTEIN AND STRESS PRODUCED
                         BY RSV INFECTION

                                                            E PROTEIN PROVIDED IN TRANS
                              350                                7
                                    HSP90 AA1         UBB                HSP H1        SERPIN H1         HSP E1            18S
                              300                                6


                                             E+
FOLD CHANGE, relative units




                              250                                5
                                             E-
                              200
                                                                 4


                              150
                                                                 3

                              100
                                                                 2

                              50
                                                                 1



                                    2   24   48   2    24   48       2    24      48   2   24   48   2    24      48   2    24   48

                                                                 TIME POST-INFECTION, hours
CONCLUSION


E PROTEIN REDUCED CELLULAR STRESS
INDUCED BY:
   SARS-CoV INFECTION
   RSV INFECTION
   THAPSIGARGIN     - Ca++
   TUNICAMYCIN      - GLYCOSYLATION
Ξ”
SARS-CoV-Ξ”E INFECTION AND INFLAMMATION




          STRESS        INFLAMMATORY
         RESPONSE         RESPONSE

 +E



  -E
MOUSE ADAPTED SARS-CoV

               SARS-CoV-MA15
High titers in lungs
Viremia, extrapulmonary spread

Neutrophilia
Pathological changes in lungs

Death
                                K. SUBBARAO AND R. BARIC LABS
CONSTRUCTION OF A MOUSE ADAPTED SARS-CoV


                                                          8a
                                                   3b M 7a 8b 9b
 L    REP 1a                 REP 1b     S       3a   E 6 7b N
                                                                   An

        nsp5       nsp9
        10384      12814
                           nsp13      S (RBD)         M
                           16117       22797        26428
               nsp5
               10793




               ENGINEERED MUTANTS       wt
                                        Ξ”[6-9b]
                                        Ξ”E
                                        Ξ”[E,6-9b]
CONCLUSION



              Ξ”
SARS-CoV-MA15-Ξ”E IS ATTENUATED AND
FULLY
PROTECTS BOTH YOUNG AND OLD MICE

THEREFORE IT IS A PROMISING VACCINE
                                 Ξ”
CANDIDATE, BETTER THAN SARS-CoV-Ξ”E
CNB. CSIC. MADRID              COLLABORATORS
REPLICATION                    PROTEOMICS
FERNANDO ALMAZAN               SILVIA JUAREZ. CNB-CSIC
AITOR NOGALES                  ALEXANDER AKOULICHEV. OXFORD
SILVIA MARQUEZ
                               GENOMICS
TRANSCRIPTION AND ASSEMBLY     IRENE LOPEZ-VIDRIERO
ISABEL SOLA                    MARTA GODOY
PEDRO A. MATEOS                JUAN CARLOS OLIVEROS
SONIA ZUΓ‘IGA
MARTINA BECARES
                               ANIMAL MODELS
                               KANTA SUBBARAO. NIH
VIRUS-HOST INTERACTION: SARS
                               STANLEY PERLMAN. UNIV. IOWA
MARTA L. DeDIEGO
JOSE LUIS NIETO
JOSE MANUEL JIMENEZ            ELECTRON MICROSCOPY
JOSE ANGEL REGLA               MARIA TERESA REJAS. CBM, CSIC
RAUL FERNANDEZ                 CRISTINA PATIΓ‘O. CNB. CSIC


                               CARLOS M. SANCHEZ
                               SARHAY ROS
LUIS ENJUANES                  MARGARITA GONZALEZ

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Molecular Basis of Coronavirus Virulence and Vaccine Design

  • 1. MOLECULAR BASIS OF CORONAVIRUS VIRULENCE AND VACCINE DESIGN TO PROTECT AGAINST SARS XRB. UNIVERSIDAD DE BARCELONA 13 JULIO 2012 LUIS ENJUANES CNB-CSIC. MADRID
  • 2. CORONAVIRUS TGEV & SARS-CoV REPLICATION TRANSCRIPTION PACKAGING VIRULENCE VIRUS-HOST INTERACTION
  • 3. CORONAVIRUS INDUCED DISEASES MAN CENTRAL NERVOUS SYSTEM ANIMALS EYE UPPER AND LOWER AS IN HUMANS & RESPIRATORY TRACT PERITONITIS IMMUNE SYSTEM CELLS HEPATITIS NEPHRITIS GASTROINTESTINAL CARDIOMIOPATHY TRACT
  • 4. RNA VIRUS GENOME SIZE IN NUCLEOTIDES NIDO_CORONAVIRUS NIDO_TOROVIRUS NIDO_RONIVIRIDAE CLOSTEROVIRIDAE BENYVIRUS NIDO_ARTERIVIRIDAE SEQUIVIRIDAE POMOVIRUS TOGAVIRIDAE COMOVIRIDAE FLAVIVIRIDAE FUROVIRUS TOBRAVIRUS PECLUVIRUS CHERAVIRUS HORDEIVIRUS POTYVIRIDAE IFLAVIRUS DICISTROVIRIDAE MARMAVIRIDAE BROMOVIRIDAE IDAEOVIRUS PICORNAVIRIDAE CALICIVIRIDAE FLEXIVIRIDAE TETRAVIRIDAE HEPEVIRIDAE ASTROVIRIDAE TOBAMOVIRUS UNCLASSIFIED TYMOVIRIDAE LUTEOVIRIDAE NODAVIRIDAE SOBEMOVIRUS UMBRAVIRUS TOMBUSVIRIDAE BARNAVIRIDAE LEVIVIRIDAE NARNAVIRIDAE
  • 5. MUTATION OF CORONAVIRUS EXON MOTIFS MHV REP 1a REP 1b nsp14 CPD HE S 4a 4b 5a E M N An I C1 D89 E91 ZN F D242 D272 Q521 YEAST MUT 1 .. AIDAEFV-103- Zn F .MUT 2. VFVGHGLNNDFK-44-HDSIEDAHTAL MHV-A59 GFDAEGA-111-VVCSVCTK-11-YGCWRHS-3-DYLYNPLIVDIQ-23-HVASSDAIMTR SARS-CoV GFDVEGC-111-RTCCLCDK-11-YACWNHS-3-DYVYNPFMIDVQ-23-HVASCDAIMTR HCoV-229E GMDVEGA-111-KHCQ-CGT-11-YCCFKHA-3-DYVYNPYVIDIQ-23-HVASGDAIMTR TGEV GFDVEGA-111-QKCE-CGK-11-YACFKHA-3-DYLYNPYCIDIQ-23-HVASGDAIMTR IBV GFDVEAT-111-QVCS-CGS-11-YACWKHC-3-DFVYNPLLVDIQ-23-HVASVDAIMTR Eckerle et al., 2007, 2010
  • 6. DISTRIBUTION OF MUTATIONS AFTER PASSAGE MHV REP 1a REP 1b nsp14 CPD HE S 4a 4b 5a E M N An I WT p5 c1 c2 p17 c1 MUT 1 p1 c1 p5 c2 p17 c1 MUT 2 p1 c1 p5 c2 p17 c2 Eckerle et al., 2007
  • 7. CORONAVIRUS STRUCTURE AND GENE EXPRESSION 3b ORF 1a ORF 1b S 3a E M N 7 UTR + CAP AAA mRNA + AAA - UUU G + AAA - UUU S + AAA - UUU 3a + AAA - UUU 3b + AAA - UUU E + AAA - UUU M + AAA - UUU N + AAA - UUU 7
  • 8. TRANSCRIPTION MECHANISM TEMPLATE SWITCH A HIGH FREQUENCY RECOMBINATION ENGINEERED AN INFECTIOUS cDNA CLONE
  • 9. REGULATION OF sgmRNA LEVELS TRS-L TRS-B gRNA 5’ L CS-L CS-B An 3’ 5’ An 3’ + MULTIFACTOR REGULATION 1. TRS RNA STRUCTURE 3’ cL cCS-B Un 5’ - 2. TRS PRIMARY SEQUENCE cTRS-B 3. LONG DISTANCE INTERACTIONS 4. PROTEIN-RNA BINDING 5’ cCS-B 3’ mRNA .....................
  • 10. TRANSCRIPTION AND LEADER-BODY CS IDENTITY Gene 3a + 5’ L CUAAAC CUAAAC An 3’ + GAUUUG Un 5’ -
  • 11. TRANSCRIPTION AND LEADER-BODY CS IDENTITY TRS-L Gene 3a + 5’ L CUAAAC CUAAAC An 3’ + GAUUUG 5’ -
  • 12. WILD TYPE TRS-L STRUCTURE PREDICTION U C16 17 A18 APICAL HEPTALOOP A15 A19 INCLUDING THE CS-L A14 A20 G13 C21 C12 G22 MICRO STEM U11 A23 C10 A24 A9 A25 U26 A8 INTERNAL LOOP A27 C7 U28 C6 U29 A5 U30 C4 G31 A3 U32 G2 C33 G1 U34 WT
  • 13. WT AND MUTANTS TRS-L STRUCTURES U A U U A U A U A U A C C A C C C C A A A A A A U A A A A A A A C A A A A A A A A A A A A A A G C C G C G C G C G C G A A A G G A C G C G G C C G C G A A A U A A U U A U A C G C G C A C A A A C A A C A U A C G A A A C A A A U A U A A A U A U A U U A A A U A C A U A U A A A A U C A C U C U C U C U C G C G U C U C U C C U C G U A U C G A U A U A U A U C G A U A U C G C G C G U C G A U C G A U A U C G A U A U A U G C A U G C G C G C G C G U G C G U G U G C G U G U G U G U WT MS2 IL1 MS1 MS3 IL3 IL2
  • 14. CONCLUSION THE EXTENT OF sg mRNA SYNTHESIS: CORRELATES WITH TRS-L STABILITY WITH THE AVAILABILITY OF TRS-L REQUIRES A SPECIFIC SECONDARY STRUCTURE
  • 15. TRANSCRIPTION MECHANISM TEMPLATE SWITCH A HIGH FREQUENCY RECOMBINATION ENGINEERED AN INFECTIOUS cDNA CLONE
  • 16. TRANSCRIPTION AND LEADER-BODY CS IDENTITY Gene 3a + 5’ L CUAAAC CUACAC An 3’ + G A UG U G U Un 5’ -
  • 17. TRANSCRIPTION AND LEADER-BODY CS IDENTITY Gene 3a + 5’ L CUAAAC CUACAC An 3’ + G AUG U G U
  • 18. REQUIREMENT OF COMPLEMENTARITY BETWEEN CS-L AND cCS-B FOR sgmRNA SYNTHESIS CS-B MUTANTS CS-L MUTANTS TITER* TITER* 5’ C U A A A C 3’ 5’ C U A A A C 3’ B-C1G G 8x108 L-C1G G - B-U2G G 1x107 L-U2G G - B-A3C C 5x108 L-A3C C - B-A4C C 6x108 L-A4C C 2x104 B-A5C C 3x108 L-A5C C 4x104 B-C6G G 4x108 L-C6G G 2x103 NON-WATSON-CRICK MUTANTS COMPLEMENTARY MUTANTS TITER* TITER* 5’ C U A A A C 3’ 5’ G U A A A C 3’ L-C1U U 2x103 D-C1G - 3’ C A U U U G 5’ WT 5x108 - L-A3U U 3x103 - 5x104 2x105 L-A4U U L-A5U U 2x104 5’ C U A A A G 3’ 4x105 D-C6G L-C6U U 1x108 3’ G A U U U C 5’ 2x10 3 * pfu/ml
  • 19. MAIN CONCLUSION Ξ” BASE-PAIRING (Ξ”G) IS A DRIVING FORCE IN CoV TRANSCRIPTION
  • 20. COMPLEMENTARY AND SYNTHESIS OF sgmRNA mRNA CS2 5’ CGAACUAAACGAAA 3’ 75 POTENTIAL BASE-PAIRING SCORE CS1 ACUAAAC CS2 CUAAAC 65 M1 ACUAAAC M2 AACUAAAC 55 M3 GAACUAAAC mRNA 3a.2 M4 CGAACUAAAC 45 M7 CUAAACG M8 CUAAACGA 35 M9 CUAAACGAA M10 CUAAACGAAA 25 M5 CGAACUAAACGA M6 CGAACUAAACGAAA 15 24550 24684 24685 24710 24734 24746 GENOME POSITION, nt MUTANTS Mock CS1 CS2wt 1 2 3 4 7 8 9 10 5 6 506 mRNA-3a.2 220 mRNA CS2
  • 21. COMPLEMENTARITY BETWEEN NASCENT RNA AND TRS-L SEQUENCE AND mRNA LEVELS 14 M4 10 M3 -Ξ”G, kcal/mol M2 M1 6 CS-S2 5’ TRS MUTANTS Ξ” 2 0 50 100 150 200 250 300 mRNA, u.r.
  • 22. mRNA LEVELS AND BASE-PAIRING SCORE 110 90 BASE-PAIRING RELATIVE UNITS 70 50 30 mRNA 10 S 3a E M N 7 mRNA
  • 23. REGULATION OF sg mRNA-N LEVELS TRS-L TRS-N N-GENE gRNA 5’ L CS-L dE pE CS-N An 3’ 460nt 7nt 5’ 3’ cL TAATGTATA ATTACATAT An 3’ + cCS-N Un 5’ - cTRS-N
  • 24. COMPLEMENTARITY AND ENHANCER ACTIVITY sgmRNA-N, RELATIVE UNITS 200 150 100 50 0 5 10 15 20 25 βˆ†G, Kcal/mol
  • 25. REQUIREMENT OF pE AND dE FLANKING SEQUENCES sgmRNA-N, % MUTANT AD dE pE 0 50 100 150 200 E2-TRS-N TRS-N dE-113-158 dE-45-158 dE-173-20 pE-20
  • 26. OPTIMIZED TRM dE pE CS ORF 1a 77 ORF 1a ORF 1b ORF 1b N AAA 173 9 20 20 9 7 6 6 Original TRM 642 nt 250 nt
  • 27. ENHANCEMENT MECHANISM pE CS-N 3’ dE 5’ AD 5’
  • 28. ENHANCEMENT MECHANISM CS-N 3’ 5’ AD 5’
  • 29. REQUIREMENT OF LONG DISTANCE INTERACTION TRM MUTANT AD dE pE CS-N N REP-1 TRS-N AD AD-TRS-N TRMopt TRMopt-N 0 5 10 15 REP-1 TRS-N AD-TRS-N TRMopt-N sgmRNA-N/gRNA
  • 30. ENHANCEMENT MECHANISM pE CS-N 3’ dE 5’ AD 5’ 80% ENHANCEMENT
  • 31. ACTIVE DOMAIN REGIONS REQUIREMENT A 25 sgmRNA-N, RELATIVE UNITS 20 B 15 10 5 C 0 + - Ξ”A Ξ”B Ξ”C
  • 32. ACTIVE DOMAIN REGION C REQUIREMENT Ξ”A Ξ”A-C’ 25 sgmRNA-N, RELATIVE UNITS B 20 15 10 C 5 0 Ξ”A Ξ”A-C’ Ξ”[A-B]
  • 33. ACTIVE DOMAIN REGION B REQUIREMENT βˆ†A βˆ†A-B*2r βˆ†A-B*1r βˆ†A-B*1r4 βˆ†A-B*1r3 B 25 sgmRNA-N, RELATIVE UNITS 20 15 10 5 0 βˆ†A βˆ†A-B*2r βˆ†A-B*1r βˆ†A-B*2r4 βˆ†A-B*1r3 (-)
  • 34. INTRAGENOMIC RNA-RNA INTERACTIONS INVOLVING B RNA MOTIF cB-M B-M cB-M B-M nt 218-229 nt 26408 - 26421 nt 477-489 nt 26408 - 26421 βˆ†G = -12.9 βˆ†G = -12.7
  • 35. TGEV REPLICONS WITH MUTATED B AND cB RNA MOTIFS 218-229 477-486 26,212-26,221 5’ 3’ B dE pE N wt/B 5’ 3’ dE pE N βˆ† wt/βˆ†B 5’ 3’ cB-218 dE pE N * B cB-218*/B 5’ 3’ dE pE N βˆ† cB-218*/βˆ†B 5’ * 3’ * B* dE pE N cB-218*/B* 5’ 3’ cB-477 B dE pE N cB-477*/B 5’ * 3’ dE pE N βˆ† cB-477*/βˆ†B 5’ * 3’ B* dE pE N cB-477*/B* 5’ * 3’ B* dE pE N cB-477*/B*-14 5’ * 3’
  • 36. sgmRNA N, RELATIVE UNITS 0 5 10 15 20 25 30 35 40 45 5’ w t/B w t/βˆ† B 218 477 cB -2 18 cB * /B -2 18 */βˆ† cB B -2 18 * /B * cB 47 7* cB /B B -4 26,212 77 */βˆ† cB B dE -4 cB 77 -4 */ B pE 77 * */ B N *- 14 3’ TRANSCRIPTION AND COMPLEMENTARY LEVELS
  • 37. EVOLUTION OF VIRUSES WITH MUTATED B AND cB RNA MOTIFS
  • 38. RELEVANCE OF THE INTERACTION BETWEEN B AND cB RNA MOTIFS ON sgmRNA AND VIRAL TITERS
  • 39. MECHANISM OF DISCONTINUOUS TRANSCRIPTION AD cB-M B-M TRS-L dE pE CS-N 5’(+) 3’(+) pE CS-N 3’(+) 5’(-) dE cCS-N 5’(+) CS-L B-M cB-M AD cB-M CS-L 5’(+)
  • 40. CoV TRANSCRIPTION IS REGULATED AT THREE LEVELS TRS-L STABILITY AND SECONDARY STRUCTURE COMPLEMENTARITY BETWEEN NASCENT MINUS RNAs AND TRS-L LONG DISTANCE RNA-RNA INTERACTIONS
  • 41. TRM ACTIVITY WITHIN INFECTIOUS VIRUSES ORF 1a ORF 1b S 3a 3b E M N 7 wt-TGEV N N A dE pE 0 2 4 6 CS TRS-3a AD dE pE CS TRMopt-3a TRMopt*-3a TRMopt-19-3a sgmRNA-3a/gRNA
  • 43. SEVERE ACUTE RESPIRATORY SYNDROME Neumonia High fever Lymphopenia Death
  • 44.
  • 45. SPREADING OF SARS …JULY 5th, 03 END EPIDEMY BY WHO NOV 02 JAN 03 FEB 03 DEC03 to JAN04 FOSHAN GUANGZHOU HONG KONG FOUR LABORATORY CASES Dr. A VIETNAM CANADA FOUR NON-LABORATORY MOST FIRST Nephro- ISOLATED CASES SINGAPORE RECENT MAJOR logist USA COMMON OUTBREAK TWO ADDDITIONAL ANCESTOR HOSPITAL HOTEL M SSE IN HK Beijin Apr F 26y, BSL-4 (>100 CONTACTS) Beijin Apr M 44y, BSL-4
  • 46. RACOON CIVET CAT FERRETS
  • 47. CORONAVIRUS EVOLUTION GENUS Ξ± GENUS Ξ² GENUS Ο’
  • 48. ENGINEERING OF A SARS-CoV INFECTIOUS cDNA CLONE AS A BAC T by C T by A 10338 11163 8a L 3b M 7a 8b 9b CMV REP 1a REP 1b S 3a E 6 7b N An pBAC-SARS-CoV-URB*
  • 49. BASIS OF SARS-CoV VIRULENCE 8a 3b M 7a 8b 9b L REP 1a REP 1b S 3a E 6 7b N An DELETED GENE Structural: E Accessory: 6, 7a, 7b, 8a, 8b, 9b Combinations: E, 6, 7a, 7b, 8a, 8b, 9b
  • 51. GROWTH KINETICS OF SARS-CoV DELETION MUTANTS VERO E6 CaCo-2 107 wt VIRUS TITER, pfu/ml Ξ”6-9b 105 Ξ”E 103 Ξ”E,6-9b 101 0 24 48 72 0 24 48 72 TIME POST-INFECTION, HOUR GENES: E, 6, 7a, 7b, 8a, 8b, 9b ARE NON ESSENTIAL
  • 52. MORPHOGENESIS OF SARS-CoV IN ERGIC SARS-CoV SARS-CoV-βˆ†E βˆ† SARS-CoV-βˆ† [6-9b] βˆ† SARS-CoV-βˆ† [E,6-9b] βˆ†
  • 53. ACTIVITY WHEEL USED TO QUANTIFY CLINICAL ILLNESS
  • 54. βˆ† SARS-CoV-βˆ†E-INFECTED HAMSTER WHEEL ACTIVITY INFECTION 1200 βˆ†E 1000 REVOLUTIONS/ hr 800 MOCK 600 wt 400 200 0 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 DAY
  • 55. ATTENUATION OF SARS-CoV DELETION MUTANTS IN TRANSGENIC MICE EXPRESSING hACE-2 12000 pfu intranasally CLINICAL DISEASE LETHALITY 110 Ξ”E 100 STARTTING WEIGHT, % Ξ”E,6-9b SURVIVAL, % Ξ”E 100 75 90 Ξ”E,6-9b 50 80 wt Ξ”6-9b 25 0 Ξ”6-9b 70 2 4 6 8 2 4 6 8 TIME POSTINOCULATION, days TIME POSTINOCULATION, days
  • 56. SUMMARY E GENE CONDITIONS TISSUE SPECIFIC TROPISM βˆ† SARS-CoV-βˆ†E IS ATTENUATED GENE E IS A VIRULENCE FACTOR
  • 57. MECHANISM OF E PROTEIN VIRULENCE E PROTEIN AND HOST GENE EXPRESSION 8a 3b M 7a 8b 9b L REP 1a REP 1b S 3a E 6 7b N An Β±E
  • 58. DIFFERENTIAL GENE EXPRESSION IN βˆ†E DIFFERENTIAL GENE EXPRESSION IN Ξ”E AND WT AND WT INFECTED CELLS INFECTED CELLS wt vs mock Ξ”E vs mock Ξ”E vs wt 14 12 10 Vero E6 8 6 15 hpi LOG EXPERIMENT 4 2 14 12 10 MA104 8 6 65 hpi 4 2 2 4 6 8 10 12 14 2 4 6 8 10 12 14 2 4 6 8 10 12 14 LOG CONTROL
  • 59. Ξ” GENES DIFFERENTIALLY EXPRESSED IN SARS-CoV-Ξ”E VS FULL-LENGTH VIRUS INFECTED CELLS FOLD CHANGE FOLD CHANGE GENE VERO MA-104 GENE VERO MA-104 STRESS RESPONSE IMMUNOREGULATION Hsp10 HspE1 + 3.3 -- FKBP4 + 4.7 + 5.5 Hsp20 B5 CRYAB -- + 3.2 RIPK2 + 2.3 -- Hsp27 B1 +19.0 -- ZC3H12A -- + 2.9 Hsp40 DNAJB1 +14.8 +25.9 Hsp40 DNAJA1 + 8.7 + 7.2 INFLAMMATION Hsp40 DNAJB6 + 3.9 + 2.1 Hsp40 DNAJA4 -- + 2.6 NFKBIZ + 2.9 -- Hsp40 DNAJB4 -- + 4.1 ADAMTS1 + 2.1 -- Hsp47 SERPINH1 + 6.7 + 2.5 CCL2 -- - 3.2 Hsp60 D1 + 4.1 + 4.7 CXCL2 -- - 2.2 Hsp70 A1A +22.3 +29.3 APOPTOSIS Hsp70 A1B +18.8 -- DEDD2 + 2.6 + 5.0 Hsp70 A8 + 5.8 + 4.9 CLU + 2.1 + 2.0 Hsp70 A4L -- + 2.3 PHLDA1 + 3.2 -- Hsp90 AA1 +15.1 + 6.5 STK17B -- + 2.2 Hsp90 AB1 + 6.1 + 2.7 Hsp105/110 +35.3 +13.4 SIGNAL TRANSDUCTION UBB + 3.9 + 4.4 DSCR1 + 5.9 -- UBC + 2.3 + 2.7 DUSP1 + 4.0 -- BAG3 + 7.2 + 3.9 DUSP10 -- + 2.7 CCT4 + 3.3 -- YWHAG + 2.5 -- CCT3 + 3.3 -- WASL + 2.5 -- AHSA1 + 4.7 -- MAP2K3 + 2.1 -- CRYAB -- + 3.2 FOLR1 -- +15.6 TCP1 -- + 2.3 PDE4B -- + 2.5 STIP1 -- + 2.1 K-RAS -- - 2.6
  • 60. UNFOLDED PROTEIN RESPONSE RE CYTOPLASM NUCLEUS ACTIVATION IN E VS WT- Ξ” GRP78 GRP78 PERK eIF2 TRANSLATIONAL INFECTED CELLS BLOCK PERK eIF2 P ATF4 TRANSLATION ATTENUATION - CHOP GRP78 GENE GRP78 CLEAVED GRP78 CORRECT ATF6 ATF6 EXPRESSION PROTEIN FOLDING - CHOP GRP78 GRP78 GRP78 XBP1 IRE1 mRNA IRE1 sXBP1 sXBP1 PROTEIN DEGRADATION + p58IPK mRNA
  • 61. EFFECT OF E PROTEIN ON THE STRESS PRODUCED Ξ” BY SARS-CoV-Ξ”E INFECTION E PROTEIN PROVIDED IN TRANS 12 HSP A1A HSP90 AA1 HSP H1 SERPIN H1 HSP E1 18S E+ FOLD CHANGE, relative units 10 E- 8 6 4 2
  • 62. SARS-CoV E PROTEIN AND STRESS PRODUCED BY RSV INFECTION E PROTEIN PROVIDED IN TRANS 350 7 HSP90 AA1 UBB HSP H1 SERPIN H1 HSP E1 18S 300 6 E+ FOLD CHANGE, relative units 250 5 E- 200 4 150 3 100 2 50 1 2 24 48 2 24 48 2 24 48 2 24 48 2 24 48 2 24 48 TIME POST-INFECTION, hours
  • 63. CONCLUSION E PROTEIN REDUCED CELLULAR STRESS INDUCED BY: SARS-CoV INFECTION RSV INFECTION THAPSIGARGIN - Ca++ TUNICAMYCIN - GLYCOSYLATION
  • 64. Ξ” SARS-CoV-Ξ”E INFECTION AND INFLAMMATION STRESS INFLAMMATORY RESPONSE RESPONSE +E -E
  • 65. MOUSE ADAPTED SARS-CoV SARS-CoV-MA15 High titers in lungs Viremia, extrapulmonary spread Neutrophilia Pathological changes in lungs Death K. SUBBARAO AND R. BARIC LABS
  • 66. CONSTRUCTION OF A MOUSE ADAPTED SARS-CoV 8a 3b M 7a 8b 9b L REP 1a REP 1b S 3a E 6 7b N An nsp5 nsp9 10384 12814 nsp13 S (RBD) M 16117 22797 26428 nsp5 10793 ENGINEERED MUTANTS wt Ξ”[6-9b] Ξ”E Ξ”[E,6-9b]
  • 67. CONCLUSION Ξ” SARS-CoV-MA15-Ξ”E IS ATTENUATED AND FULLY PROTECTS BOTH YOUNG AND OLD MICE THEREFORE IT IS A PROMISING VACCINE Ξ” CANDIDATE, BETTER THAN SARS-CoV-Ξ”E
  • 68. CNB. CSIC. MADRID COLLABORATORS REPLICATION PROTEOMICS FERNANDO ALMAZAN SILVIA JUAREZ. CNB-CSIC AITOR NOGALES ALEXANDER AKOULICHEV. OXFORD SILVIA MARQUEZ GENOMICS TRANSCRIPTION AND ASSEMBLY IRENE LOPEZ-VIDRIERO ISABEL SOLA MARTA GODOY PEDRO A. MATEOS JUAN CARLOS OLIVEROS SONIA ZUΓ‘IGA MARTINA BECARES ANIMAL MODELS KANTA SUBBARAO. NIH VIRUS-HOST INTERACTION: SARS STANLEY PERLMAN. UNIV. IOWA MARTA L. DeDIEGO JOSE LUIS NIETO JOSE MANUEL JIMENEZ ELECTRON MICROSCOPY JOSE ANGEL REGLA MARIA TERESA REJAS. CBM, CSIC RAUL FERNANDEZ CRISTINA PATIΓ‘O. CNB. CSIC CARLOS M. SANCHEZ SARHAY ROS LUIS ENJUANES MARGARITA GONZALEZ