Nature - USA (2020-06-25)

A A

AA AA

A

A

A

A

A

A

AAA

C

C

CC C C

C

C

C

C

CC

C

C

G

G

G

G

G

G

G

G

G

G

G

G

U

U

U

UUU

U

U

U

U

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UU

U

U

U

U

U

AAAU

A U U U U U

A

A

A

A

A

A

C

C

C

C

C

C

SL1

1

G

G

G

G

G

G

G

U

U

U

UU

N20

C

C

C

C

C

U

U U

U

GC

GC

10

20

30

40

50

90

100

110

120

SL2

SL4

AUU

U

A

U

AA

G

60

A

G

C

C

C

U

Base 10 20 30 40 50 60

* * * * * *

SARS-CoV-2 auuaaagguuuauaccuucccagguaacaaaccaaccaacuuucgaucucuuguagaucuguu

Clone 3.1 d..............................................................

Clone 6.2 r..............................................................

SARS-CoV ..auu......u.....a......--.a..g.........-c.....................

Clone 2.2 r.auu......u.....a......--.a..g.........-c.....................

Clone 5.2 r.auu......u.....a......--.a..g.........-c.....................

Bat SARS-related CoVs ..auu......u........................u....c.....................

Clone 1.1 r.auu..........................................................

Clone 4.1 r.auu..........................................................

Base 70 80 90 100 110 120

* * * * * *

SARS-CoV-2 cucuaaacgaacuuuaaaaucuguguggcugucacucggcugcaugcuuagugcacucacg

Clone 3.1 .............................................................

Clone 6.2 .............................................................

SARS-CoV ..........................a......g.............c........cu...

Clone 2.2 ..........................a......g.............c........cu...

Clone 5.2 ..........................a......g.............c........cu...

Bat SARS-related CoVs ...........................a........ua.......................

Clone 1.1 .............................................................

Clone 4.1 .............................................................

a b

20,000

15,000

10,000

5,000

0

0 10,000 20,000 30,000

20,000

15,000

10,000

5,000

0

0 10,000 20,000 30,000

20,000

15,000

10,000

5,000

0

0 10,000 20,000 30,000

rSARS-CoV-2

Clone 1.1

rSARS-CoV-2

Clone 2.2

rSARS-CoV-2-GFP

Clone 4.1

c d e

f

read count read counts

s

read counts

0 10,000 20,000 30,000

20,000

15,000

10,000

5,000

0

rSARS-CoV-2-GFP

Clone 6.2

read count

s

genome position

20,000

15,000

10,000

5,000

0

0 10,000 20,000 30,000

rSARS-CoV-2-GFP

Clone 5.2

read count

s

genome position genome position

genome position genome position

20,000

15,000

10,000

5,000

0

0 10,000 20,000 30,000

genome position

read counts

UUCUCUAAACGAACUUUAAAAT

UUCUCUAAACGAACAAUGUUUG

UUCUCUAAACGAACUUAUGGAU

UUCUCUAAACGAACUUAUGUAC

UUCUCUAAACGAACUAAAUAUU

UUCUCUAAACGAACGCUUUCUU

UUCUCUAAACGAACAUGAAAAU

UUCUCUAAACGAACAUGAAAUU

UUCUCUAAACGAACAAACUAAA

mRNAORF

1 2 3 4 5 6 7 8 9

1a/b

S 3 E M 6 7 8 N

Leader TRS Body

rSARS-CoV-2

Clone 3.1

5’ UTR nt 1 - 124: SARS-CoV-2

Constructs 3 and 6

5’ UTR nt 1 - 124: SARS-CoV

Constructs 2 and 5

5’ UTR nt 1 - 124: SARS-CoV-2 modified by 3 nt

Constructs 1 and 4

gh

Extended Data Fig. 2 | See next page for caption.