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Journal of Virology, October 2004, p. 10628-10635, Vol. 78, No. 19
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.19.10628-10635.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Retroviruses Pseudotyped with the Severe Acute Respiratory Syndrome Coronavirus Spike Protein Efficiently Infect Cells Expressing Angiotensin-Converting Enzyme 2
Michael J. Moore,1 Tatyana Dorfman,1 Wenhui Li,1 Swee Kee Wong,1 Yanhan Li,2 Jens H. Kuhn,1,3 James Coderre,4 Natalya Vasilieva,5 Zhongchao Han,2 Thomas C. Greenough,4 Michael Farzan,1* and Hyeryun Choe5*
Partners AIDS Research Center, Brigham and Women's Hospital, and Department of Medicine (Microbiology and Molecular Genetics),1
Perlmutter Laboratory, Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston,5
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,4
State Key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China,2
Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany3
Received 3 February 2004/
Accepted 28 May 2004

ABSTRACT
Infection of receptor-bearing cells by coronaviruses is mediated
by their spike (S) proteins. The coronavirus (SARS-CoV) that
causes severe acute respiratory syndrome (SARS) infects cells
expressing the receptor angiotensin-converting enzyme 2 (ACE2).
Here we show that codon optimization of the SARS-CoV S-protein
gene substantially enhanced S-protein expression. We also found
that two retroviruses, simian immunodeficiency virus (SIV) and
murine leukemia virus, both expressing green fluorescent protein
and pseudotyped with SARS-CoV S protein or S-protein variants,
efficiently infected HEK293T cells stably expressing ACE2. Infection
mediated by an S-protein variant whose cytoplasmic domain had
been truncated and altered to include a fragment of the cytoplasmic
tail of the human immunodeficiency virus type 1 envelope glycoprotein
was, in both cases, substantially more efficient than that mediated
by wild-type S protein. Using S-protein-pseudotyped SIV, we
found that the enzymatic activity of ACE2 made no contribution
to S-protein-mediated infection. Finally, we show that a soluble
and catalytically inactive form of ACE2 potently blocked infection
by S-protein-pseudotyped retrovirus and by SARS-CoV. These results
permit studies of SARS-CoV entry inhibitors without the use
of live virus and suggest a candidate therapy for SARS.

INTRODUCTION
A distinct coronavirus (SARS-CoV) has been identified as the
etiological agent of severe acute respiratory syndrome (SARS),
an acute pulmonary syndrome characterized by an atypical pneumonia
that results in progressive respiratory failure and death in
close to 10% of infected individuals (
8,
11,
14,
15). SARS-CoV
is not closely related to any of the three previously defined
genetic and serological coronavirus groups, although it may
be distantly related to group 2 coronaviruses (
21); the SARS-CoV
spike (S) protein, a surface glycoprotein that mediates coronavirus
entry into receptor-bearing cells, is also distinct from those
of other coronaviruses (
18,
20). Reflecting this difference,
SARS-CoV does not utilize any previously identified coronavirus
receptors to infect cells. Rather, as our group have recently
demonstrated, angiotensin-converting enzyme 2 (ACE2) serves
as a functional receptor for this coronavirus (
16,
24,
25).
A quantitative system utilizing a well-characterized retroviral vector (1) for measuring SARS-CoV S-protein-mediated infection would obviate the need for specialized biosafety facilities for many studies, including those assessing humoral responses to potential vaccines. Here we show that simian immunodeficiency virus (SIV) pseudotyped with several codon-optimized S-protein variants could efficiently infect Vero E6 cells and HEK293T cells transiently or stably expressing ACE2. One such variant, truncated at its cytoplasmic tail and bearing instead a region of the tail of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (17), was especially efficient at mediating infection. Murine leukemia virus (MLV) pseudotyped with this S-protein variant also infected ACE2-expressing cells more efficiently than MLV pseudotyped with other S-protein variants. We used this system to show quantitatively that the enzymatic activity of ACE2 does not contribute to S-protein-mediated infection. We also show that a catalytically inactive form of soluble ACE2 can potently inhibit infection by S-protein-pseudotyped virus and by SARS-CoV and therefore may be useful in the treatment of SARS.

MATERIALS AND METHODS
Plasmids encoding ACE2 and S-protein variants.
A gene encoding the entire SARS-CoV S protein, except its signal
sequence (residues 12 to 1255), was constructed de novo by recursive
PCR and subcloned into a previously described pcDM8-derived
vector that encodes the signal sequence of CD5 and a nine-residue
C-terminal tag (C9; amino acid sequence, TETSQVAPA) recognized
by the mouse monoclonal antibody 1D4 (National Cell Culture
Center) (
5,
19,
20). Three additional variants of this gene
(S-C9) were generated by the QuikChange method (Stratagene).
The first was modified to exclude the C9 tag. The second and
third were modified to include the eight most membrane-proximal
residues of the HIV-1 envelope glycoprotein cytoplasmic domain
(amino acid sequence, NRVRQGYS) (
17) after residue 1216 (S-H1)
or 1228 (S-H2) of the S protein. Plasmids encoding S-C9, S protein,
S-H1, and S-H2 were sequenced within their entire coding regions.
The codon-optimized S-protein gene was also subcloned into the
vector pcDNA3.1 (Invitrogen) for direct comparison with the
virally encoded S-protein gene (also in this vector; generously
provided by Dimiter Dimitrov) (
25). ACE2-Ig was generated by
ligating the PCR product encoding the ectodomain of ACE2 into
a previously described vector encoding the Fc domain of human
immunoglobulin G1 (IgG1) (
10). ACE2-NN-Ig was generated from
ACE2-Ig by altering the codons of ACE2 active-site histidines
374 and 378 to those of asparagines, using the QuikChange method.
Plasmids encoding ACE2-Ig and ACE2-NN-Ig were fully sequenced
in their coding regions.
Comparison of native and codon-optimized S-protein gene expression.
HEK293T cells were transfected, using Polyfect transfection reagent (QIAGEN), with a plasmid encoding codon-optimized S protein or virally encoded (native) S protein or with vector only. Four hours posttransfection, cells were infected, or not, with recombinant vaccinia virus VTF7.3 encoding T7 polymerase and incubated at 31°C (9, 25). Two hours later, the cells were washed, radiolabeled with [35S]cysteine and -methionine, and incubated for 20 h at 31°C. The cells were washed and lysed with phosphate-buffered saline (PBS) containing 0.5% NP-40 and a protease inhibitor cocktail (Sigma). S protein was precipitated from cell lysates by using ACE2-Ig and ACE2-NN-Ig bound to protein A-Sepharose beads and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Relative expression of codon-optimized and virally encoded S proteins was quantified by phosphorimaging.
Surface expression of S-protein variants.
HEK293T cells were transfected by the calcium phosphate method with a plasmid encoding S, S-C9, S-H1, or S-H2 or with vector alone. Forty-eight hours posttransfection, cells were detached with PBS containing 5 mM EDTA, split into two aliquots of approximately 106 cells each, and incubated for 45 min with 10 µg of S1(12-327)-Ig per ml, previously shown not to bind ACE2 (16), or of ACE2-NN-Ig. Cells were washed once in PBS containing 0.5% bovine serum albumin (BSA), stained with goat anti-human IgG-fluorescein isothiocyanate conjugate, and analyzed by flow cytometry.
Generation of cells stably expressing ACE2.
HEK293T cells were cotransfected by the calcium phosphate method with a pcDNA3.1 plasmid encoding ACE2 and pcDNA3.1-puro, which expresses a puromycin resistance gene. Transfected cells were selected in growth medium containing 0.75 µg of puromycin per ml. Puromycin-resistant clones were expanded, and a clone with a high level of expression of ACE2 (HEK293T-ACE2) was compared with Vero E6 and HEK293T cells for ACE2 expression by flow cytometry using goat anti-ACE2 antibody (R&D Systems) and S1-Ig, which contains S-protein residues 12 to 672 fused to the Fc domain of human IgG1 (16).
Production of and infection by S-protein-pseudotyped retroviruses.
S-protein-pseudotyped lentiviral stocks were produced by cotransfecting HEK293T cells with a plasmid encoding S-protein variants or vesicular stomatitis virus protein G (VSV-G) or with vector alone, together with a previously described plasmid (1) containing the SIV genome with the env gene deleted and the nef gene replaced by that for green fluorescent protein (GFP). Forty-eight hours posttransfection, viral supernatants were harvested, cleared of cell debris by centrifugation and filtration through a 0.45-µm-pore-size filter, and concentrated by ultracentrifugation to one-fifth their original volume. Viral stocks were quantified by measuring reverse transcriptase activity in the concentrated supernatant (4). Stocks were aliquoted and frozen at 80°C for later use. Vero E6 cells, HEK293T-ACE2 cells, or HEK293T cells transiently transfected by the calcium phosphate method with ACE2 or ACE-NN plasmid or with vector alone were incubated with pseudotyped SIV-GFP, normalized to 8 x 105 cpm of [32P] reverse transcriptase activity in a total volume of 2 ml in 12-well plates. Cells were photographed 48 h postinfection and then detached with trypsin, washed once with PBS, and fixed in PBS containing 2% formaldehyde. GFP fluorescence was measured by flow cytometry.
MLVs pseudotyped with S-protein variants were generated by cotransfecting the pQCXIX vector (BD Sciences) expressing GFP and plasmids encoding the indicated S-protein variants or pcDNA3.1 vector into the retroviral packaging cell line GP2-293 (BD Sciences). Forty-eight hours posttransfection, unconcentrated cell supernatants were normalized for reverse transcriptase activity and incubated with HEK293T-ACE2 cells. Forty-eight hours postincubation, GFP fluorescence of infected cells was measured as described above.
S-protein incorporation into virions.
HEK293T cells were transfected as described above to produce S-, S-C9-, S-H1-, S-H2-, and VSV-G-pseudotyped SIV-GFP, as well as SIV-GFP lacking an envelope glycoprotein. Transfected cells were radiolabeled with [35S]cysteine and -methionine 1 day after transfection. Forty-eight hours posttransfection, viral supernatants were harvested, cleared of cell debris by centrifugation and filtration, and layered over a 20% sucrose cushion in PBS. Viral particles were pelleted by ultracentrifugation. The supernatant was removed, and virions were lysed in buffer containing 1% NP-40, 0.2% sodium deoxycholate, and 0.05% SDS and analyzed by SDS-PAGE.
ACE2-NN-Ig and patient serum inhibition of S-protein-mediated infection.
HEK293T cells stably expressing ACE2 were plated in 24-well plates and infected with S-H2- and VSV-G-pseudotyped SIV-GFP normalized to 2 x 105 cpm of [32P] reverse transcriptase activity in the presence of various concentrations of ACE2-NN-Ig or S1(12-327)-Ig or in the presence of various dilutions of a mixture of antisera from 12 patients who had recovered from SARS. At 72 h postinfection cells were detached, washed, and analyzed by flow cytometry. In some cases MLV-GFP was used instead of SIV-GFP. In parallel, Vero E6 cells were infected with 2,100 tissue culture infective doses of SARS-CoV per ml or with medium alone preincubated for 30 min at 37°C at neutral pH with various concentrations of ACE2-NN-Ig or of BSA and washed at 1 h postinfection (16). Three days postinfection, SARS-CoV-induced cytopathicity was measured by reading absorbance at 492 nm of cells incubated with CellTiter96 (Promega).

RESULTS
Codon optimization enhances S-protein expression.
The gene encoding the S protein of SARS-CoV contains many codons
used infrequently in mammalian genes for efficiently expressed
proteins (
12,
18,
20). We therefore generated a codon-optimized
form of the S-protein gene and compared its expression with
the S-protein gene of the native viral sequence. S protein was
readily detected in HEK293T cells transfected with a plasmid
encoding the codon-optimized S protein (Fig.
1). No S protein
was detected in cells transfected with a plasmid encoding the
native S-protein gene. When transfected cells were infected
with recombinant vaccinia virus expressing T7 polymerase, which
can transcribe message in the cytoplasm, S protein was efficiently
produced from plasmids containing either codon-optimized or
native genes (
9,
25). However, the codon-optimized gene expressed
more than twice as much S protein as the native viral sequence.
Because S protein could be efficiently expressed from the codon-optimized
plasmid without T7 polymerase, we used this plasmid in our subsequent
studies.
Infection with SIV pseudotyped with S-protein variants.
HEK293T cells transfected with a plasmid encoding ACE2, but
not mock-transfected HEK293T cells, form large multinucleated
syncytia with cells expressing SARS-CoV S protein and support
efficient replication of SARS-CoV (
16). We investigated whether
an SIV variant (SIV-GFP) whose
nef gene has been replaced by
that for GFP, lacking a functional
env gene, and pseudotyped
with S protein could infect ACE2-expressing cells (
1). SIV was
initially chosen because it readily infects Vero E6 cells, commonly
used to propagate SARS-CoV, whereas HIV-1 does not (
2). The
complete S protein and three additional S-protein variants,
differing in their cytoplasmic domains, were assayed (Fig.
2A).
One variant, S-C9, includes at its C terminus nine amino acids
derived from the rhodopsin C terminus and recognized by the
antibody 1D4 (
19). Two additional variants, truncated after
S-protein residue 1216 (S-H1) or 1228 (S-H2), were also studied.
In both these variants, an additional eight residuesthe
most membrane-proximal of the HIV-1 envelope glycoprotein cytoplasmic
domainwere included. An HIV-1 envelope glycoprotein truncated
after these residues has been shown to be better expressed on
the cell surface and better incorporated into MLV and HIV-1
virions than is wild-type HIV-1 envelope glycoprotein (
17).
HEK293T cells were transfected with a plasmid encoding SIV-GFP
and with plasmids encoding each of the S-protein variants or
VSV-G or with vector alone. Cell supernatants were concentrated,
normalized for reverse transcriptase activity, and incubated
with HEK293T cells transfected with ACE2 or with vector alone.
Fluorescent cells were observed in cultures of all ACE2-transfected
cells infected with SIV-GFP pseudotyped with S-protein variants
or with VSV-G (Fig.
2B and C). No fluorescence was observed
in cultures of ACE2-transfected cells infected with SIV-GFP
lacking a fusion protein (Fig.
2B, right panel, middle row),
nor was any observed in cultures of mock-transfected HEK293T
cells infected with virus pseudotyped with any S-protein variants
(Fig.
2B, left panel, bottom row, and results not shown). SIV-GFP
pseudotyped with S-H2, consistently the most efficient of the
S-protein variants (Fig.
2B, left panel, middle row), also infected
Vero E6 cells (Fig.
2B, bottom right panel). Figure
2D shows
that HEK293T cells stably expressing ACE2 were more efficiently
infected by S-H2-pseudotyped SIV-GFP than were Vero E6 cells,
consistent with higher ACE2 levels in the former cells. Again,
no infection was observed in HEK293T cells lacking exogenous
ACE2.
S-H2 incorporates efficiently into retroviral virions.
We investigated possible reasons for the substantially higher efficiency of infection observed with SIV-GFP pseudotyped with S-H2 compared to virus pseudotyped with the other S-protein variants. Total expression, cell surface expression, and virion incorporation of these variants were compared (Fig. 3). Lysates of metabolically labeled HEK293T cells transfected with plasmids encoding S-protein variants were precipitated with the ectodomain of ACE2 fused to human IgG1 (ACE2-Ig) or with a catalytically inactive variant of ACE2-Ig whose active-site histidines have been replaced by asparagines (ACE2-NN-Ig). Substantially more S-C9 and S-H2 than S protein or S-H1 were precipitated by both forms of ACE2-Ig (Fig. 3A). No significant differences were observed in the ability of ACE2-Ig and ACE2-NN-Ig to precipitate S-protein variants, indicating that modification of the ACE2 active site did not detectably alter the ACE2 affinity for S protein. We therefore used the catalytically inactive ACE2-NN-Ig for subsequent studies. The amount of each S-protein variant precipitated from cell lysates was also reflected in its cell surface expression, as measured by flow cytometry using ACE2-NN-Ig (Fig. 3B). In contrast, incorporation of each S-protein variant into the SIV virion did not correlate with its total or surface expression levels (Fig. 3C). Rather, those variants (S-H1 and S-H2) with shorter cytoplasmic domains and containing residues from the cytoplasmic tail of the HIV-1 envelope glycoprotein were preferentially incorporated. We conclude that the greater efficiency with which S-H2-pseudotyped virions infect ACE2-expressing cells compared to virions pseudotyped with S protein or S-C9 is likely due to preferential incorporation of S-H2. The observed difference between S-H1 and S-H2 may be due to the absence in S-H1 of cysteines critical to the function of the S proteins of other coronaviruses (3).
ACE2 enzymatic activity does not contribute to S-protein-mediated fusion.
We then investigated whether the enzymatic activity of ACE2
contributes to its ability to promote S-protein-mediated infection.
HEK293T cells were transfected with a plasmid expressing full-length
ACE2 or a variant thereof (ACE2-NN) altered as described for
ACE2-NN-Ig so as to be catalytically inactive. This full-length
variant was expressed on HEK293T cells as efficiently as wild-type
ACE2 (Fig.
4). Various amounts of each plasmid or a control
plasmid were transfected, and expression of ACE2 and ACE2-NN
was measured with S1-Ig, using flow cytometry, 24 h posttransfection.
An aliquot of each set of transfected cells was also incubated
at 24 h posttransfection with SIV-GFP pseudotyped with S-H2,
and infection was measured by flow cytometry 60 h posttransfection.
A plot of receptor expression against S-protein-mediated infection
is shown in Fig.
4. Infection was dependent on receptor expression
levels but was independent of the ACE2 variant used. These data
indicate that the enzymatic activity of ACE2 makes no detectable
contribution to S-protein-mediated infection.
ACE2-NN-Ig potently inhibits infection.
We also investigated whether S-H2-pseudotyped virions could
be useful in evaluating inhibitors of S-protein-mediated fusion.
We have previously shown that a protein [S1(12-327)-Ig] bearing
an amino-terminal fragment of the S protein does not bind ACE2
(
16). As expected, this protein had no effect on the efficiency
of S-H2-mediated infection of HEK293T cells stably expressing
ACE2 (Fig.
5A). In contrast, ACE2-NN-Ig potently blocked infection,
with a 50% inhibitory concentration of approximately 2 nM. In
parallel, neutralization assays were performed in which SARS-CoV
(400 TCID
50s per well) was preincubated with various concentrations
of ACE2-NN-Ig or BSA for 1 h before infection of Vero E6 cells
(5,000 per well). Three days postinfection, SARS-CoV-induced
cytopathicity was measured and half-maximal cell viability was
consistently observed at less than 19 nM ACE2-NN-Ig. These data
show that quantitative measurements of infection are possible
using S-H2-pseudotyped virus and that ACE2-NN-Ig may be a potent
inhibitor of SARS-CoV infection.
MLV can be pseudotyped with S-protein variants.
Finally, we explored whether MLV pseudotyped with S-protein
variants could infect ACE2-HEK293T cells. As shown in Fig.
6,
MLV expressing GFP and pseudotyped with S protein, S-H2, or
an S-H2 molecule lacking residues derived from HIV-1 (S-TR)
could infect ACE2-expressing cells whereas MLV made in the absence
of any S-protein variant could not. As with SIV-GFP, MLV pseudotyped
with S-H2 infected cells more efficiently than that pseudotyped
with S protein. MLV pseudotyped with S-H2 was slightly more
efficient than MLV pseudotyped with S-TR, implying that truncation
of the S protein makes a substantial contribution to the efficiency
of pseudotyping whereas residues derived from HIV-1 may contribute
modestly. MLV-GFP pseudotyped with S-H2 was used to assay the
potency of a mixture of antisera from individuals who had recovered
from SARS (Fig.
6C). These antisera efficiently blocked infection
by S-H2-pseudotyped MLV at the highest dilution assayed. Figure
6C also demonstrates that ACE2-NN-Ig blocked MLV-GFP infection
with an efficiency comparable to that observed with SIV-GFP.
These data show that S-protein-mediated fusion can be studied
with convenient vectors and packaging cell lines expressing
MLV.

DISCUSSION
Here we developed and utilized a system for studying S-protein-mediated
infection using commonly used retroviral vectors, thereby making
accessible studies of S-protein entry to many investigators
without access to Biosafety Level 3 facilities. This system
uses multiple approaches to make more efficient and quantitative
what might otherwise be prohibitively inefficient. First, we
used a codon-optimized form of the S protein, which simplifies
its efficient expression. Second, we modified the cytoplasmic
tail of the S protein to allow more efficient incorporation
into the SIV and MLV virions. This modification likely reduces
steric interaction with the retroviral matrix protein and may
facilitate S-protein expression on the cell surface, where retroviral
but not coronaviral budding occurs. Third, cells stably expressing
high levels of the SARS-CoV receptor ACE2 were used for infection.
We anticipate that these or similar approaches will be useful
in the quantitative assessment of inhibitors of S-protein-mediated
infection and of antisera from vaccinated animals (
22,
23,
26).
Using this system, we demonstrated quantitatively that the enzymatic activity of ACE2 does not make even a small contribution to the ability of ACE2 to support S-protein-mediated infection. Similar observations have been made for the group 1 coronavirus transmissible gastroenteritis virus, which utilizes the zinc metalloprotease aminopeptidase N (CD13) as a receptor (7). Our data imply that the S-protein-binding site of ACE2 is distinct from its catalytic site and that small molecules screened for their ability to block ACE2 catalysis (6, 13) may not slow viral replication.
We also used this system to document the potency of a soluble form of a catalytically inactive ACE2 in blocking infection. Infection of SIV-GFP pseudotyped with S-H2 was inhibited with a 50% inhibitory concentration of 2 nM ACE2-NN-Ig. Similar concentrations of ACE2-NN-Ig were required to block replication of live SARS-CoV. It is not yet clear whether the soluble receptor irreversibly inactivates the S protein or whether its potency derives from its high affinity for S protein, measured at 1.7 nM by surface plasmon resonance (23). Regardless, these studies suggest that soluble ACE2 may be useful as a therapy for SARS and perhaps that soluble receptors of other coronaviruses can be used to control replication of these viruses in infected animals.

FOOTNOTES
* Corresponding authors. Mailing address for Michael Farzan: Partners AIDS Research Center, 65 Landsdowne St., Cambridge, MA 02139. Phone: (617) 768-8372. Fax: (617) 768-8738. E-mail:
farzan{at}mbcrr.harvard.edu. Mailing address for Hyeryun Choe: Perlmutter Laboratory, Children's Hospital, 300 Longwood Ave., Boston, MA 02115. Phone: (617) 355-7586. Fax: (617) 730-0240. E-mail:
hyeryun.choe{at}tch.harvard.edu.


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Journal of Virology, October 2004, p. 10628-10635, Vol. 78, No. 19
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.19.10628-10635.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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