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Journal of Virology, February 2000, p. 1393-1406, Vol. 74, No. 3
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Retargeting of Coronavirus by Substitution of the
Spike Glycoprotein Ectodomain: Crossing the Host Cell Species
Barrier
Lili
Kuo,1
Gert-Jan
Godeke,2
Martin J. B.
Raamsman,2
Paul S.
Masters,1,* and
Peter J. M.
Rottier2
David Axelrod Institute, Wadsworth Center for
Laboratories and Research, New York State Department of Health, Albany,
New York 12201,1 and Institute of
Virology, Department of Infectious Diseases and Immunology, Faculty of
Veterinary Medicine, and Institute of Biomembranes, Utrecht University,
3584 CL Utrecht, The Netherlands2
Received 8 July 1999/Accepted 25 October 1999
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ABSTRACT |
Coronaviruses generally have a narrow host range, infecting one or
just a few species. Using targeted RNA recombination, we constructed a
mutant of the coronavirus mouse hepatitis virus (MHV) in which the
ectodomain of the spike glycoprotein (S) was replaced with the highly
divergent ectodomain of the S protein of feline infectious peritonitis
virus. The resulting chimeric virus, designated fMHV, acquired the
ability to infect feline cells and simultaneously lost the ability to
infect murine cells in tissue culture. This reciprocal switch of
species specificity strongly supports the notion that coronavirus host
cell range is determined primarily at the level of interactions between
the S protein and the virus receptor. The isolation of fMHV allowed the
localization of the region responsible for S protein incorporation into
virions to the carboxy-terminal 64 of the 1,324 residues of this
protein. This establishes a basis for further definition of elements
involved in virion assembly. In addition, fMHV is potentially the ideal
recipient virus for carrying out reverse genetics of MHV by targeted
RNA recombination, since it presents the possibility of selecting
recombinants, no matter how defective, that have regained the ability
to replicate in murine cells.
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INTRODUCTION |
The family Coronaviridae
contains the causative agents of a number of significant respiratory
and enteric diseases affecting humans, other mammals, and birds
(55). One of the hallmarks of this family is that most of
its members exhibit a very strong degree of host species specificity,
the molecular basis of which is thought to reside in the particularity
of the interactions of individual viruses with their corresponding host
cell receptors.
Coronaviruses have positive-stranded RNA genomes, on the order of 30 kb
in length, that are packaged by a nucleocapsid protein (N) into helical
ribonucleoprotein structures (31). The nucleocapsid is
incorporated into viral particles by budding through the membrane of
the intermediate compartment between the endoplasmic reticulum and the
Golgi complex (26, 57). Subsequent to budding, it may
acquire a spherical, possibly icosahedral superstructure (43, 44). The virion envelope surrounding the nucleocapsid contains a
minimal set of three structural proteins: the membrane glycoprotein (M), the small envelope protein (E), and the spike glycoprotein (S). In
some coronaviruses, other proteins may also be present; these include a
hemagglutinin-esterase (HE) (34, 54) and the product of the
internal open reading frame of the N gene (I protein) (12,
53), neither of which is essential for virus infectivity.
M is the most abundant of the virion structural proteins. It spans the
membrane bilayer three times, having a short amino-terminal domain on
the exterior of the virus and a large carboxy terminus, containing more
than half the mass of the molecule, in the virion interior
(48). By contrast, E is a minor structural protein, in both
size and stoichiometry, and was only relatively recently identified as
a constituent of viral particles (17, 33, 62). The most
prominent virion protein, S, makes a single pass through the membrane
envelope, with almost the entire molecule forming an amino-terminal
ectodomain. Multimers of S make up the large peplomers, characteristic
of coronaviruses, that recognize cellular receptors and mediate fusion
to host cells.
Although the details of the coronavirus assembly process are not yet
understood, major progress in elucidating the molecular interactions
that determine the formation and composition of the virion envelope has
been made in the past few years. Much of this has been driven by the
demonstration that in the absence of viral infection, coexpression of
the M, E, and S proteins results in the assembly of coronavirus-like
particles (VLPs) that are released from cells (4, 60). The
VLPs produced in this manner form a homogeneous population that is
morphologically indistinguishable from normal virions. This finding,
i.e., that coronavirus assembly does not require the active
participation of the nucleocapsid, defined a new mode of virion
budding. Furthermore, the coexpression system was used to show that S
protein is also dispensable in the assembly process; only the M and E
proteins are required for VLP formation (4, 60). This
observation accorded well with earlier studies that noted the release
of spikeless, noninfectious virions from mouse hepatitis virus
(MHV)-infected cells treated with the glycosylation inhibitor
tunicamycin (21, 49).
The VLP assembly system has provided a valuable avenue to begin
exploring the roles of individual proteins in coronavirus morphogenesis
(2, 4, 5, 7, 8, 60), leading to conclusions that, in some
cases, have been complemented and extended by the construction of viral
mutants (7, 14). One of many critical questions to be
resolved is the nature of the apparently passive and optional
participation of S protein in the budding process. Clearly, the S
protein, although not required for virus assembly, is essential for
virus infectivity. Abundant evidence points to the existence of
specific interactions between the M and S proteins that are initiated
after successful folding of the latter in the endoplasmic reticulum
(36, 38, 39). S multimers must somehow fit specifically into
the interstices of the arrays of M (or M and E) monomers without
contributing much to their overall stability.
To investigate which residues of S are involved in this association,
VLPs were assembled from components of MHV and feline infectious
peritonitis virus (FIPV) (15a). MHV and FIPV belong to two
different groups of coronaviruses, and each is highly specific for its
corresponding host species. The S proteins of MHV and FIPV, with 1,324 and 1,452 residues, respectively, have only 26% overall amino acid
identity, with their greatest divergence occurring in the
amino-terminal half of each molecule (6). They recognize different receptors: members of the murine biliary glycoprotein family
for MHV (10) and feline aminopeptidase N (fAPN) for FIPV (19, 28, 58). Moreover, the locus of the receptor binding site varies for each, mapping in the amino-terminal 330 residues for
the MHV S protein (29) but within amino acids 600 to 676 for
the FIPV S protein, by analogy to the highly conserved S protein of
porcine transmissible gastroenteritis virus (16). An
additional point of difference is that during maturation the MHV S
protein is proteolytically cleaved into two moieties of roughly equal size whereas the FIPV S protein remains intact. It was learned from
experiments with the coexpression system that while the FIPV S protein
could assemble into homologous FIPV VLPs, it could not be incorporated
into heterologous VLPs formed by the MHV M and E proteins. By contrast,
a chimeric S protein, composed of the entire ectodomain of FIPV S
linked to the transmembrane domain and short carboxy-terminal
cytoplasmic tail of MHV S, was fully able to be incorporated into MHV
VLPs (15a). In addition, the reciprocal construct, having
the MHV S ectodomain linked to the FIPV transmembrane domain and
cytoplasmic tail, was incorporated into FIPV VLPs. From these results,
it could be concluded that the transmembrane and endodomains of a given
S protein contain sufficient information for assembly into VLPs of the
same species.
It remained to be resolved whether this principle would apply to the
complete MHV virion and whether a heterologous S ectodomain in this
context would still be functional in receptor binding and membrane
fusion. To determine this, we sought to obtain a viable MHV mutant
containing the equivalent FIPV-MHV chimeric S protein. Through targeted
RNA recombination (13, 27, 35) and selection on cells of the
heterologous species, we were able to construct such a recombinant. The
resulting chimeric virus (designated fMHV) had the host range
characteristics that would be predicted for this type of mutant: it was
able to grow in feline cells, and it was no longer able to grow in
murine cells. The availability of fMHV is an important first step
toward identification of the specific molecular interactions allowing S
protein participation in the viral assembly process and toward our
understanding of the principles governing viral particle formation.
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MATERIALS AND METHODS |
Virus, cells, and antibodies.
Wild-type MHV-A59 and MHV
mutants Alb4, Alb129, and Alb203 (all containing the wild-type MHV S
gene) were propagated in mouse 17 clone 1 (17Cl1) cells or Sac(
)
cells, and plaque assays and purifications were carried out with mouse
L2 cells. Alb4 is a temperature-sensitive N gene deletion mutant which
grows optimally at 33°C (27). Alb129, which contains a
phenotypically silent marker in gene 4 (13), and Alb203,
which contains a phenotypically silent mutation in the M gene
(7), were constructed from Alb4 by targeted recombination.
MHV was radiolabeled in a cell line derived from L cells transfected
with the MHV receptor, designated LR7, which was prepared in the same
manner as described previously (45). Selection, propagation,
plaque assay, radiolabeling, and neutralization of fMHV and FIPV
(strain 79-1146) were done with feline FCWF cells (American Type
Culture Collection). mTAL cells are mouse kidney medullary thick
ascending limb cells adapted to growth on a plastic support
(46). Usage of the fAPN receptor by fMHV was analyzed with
MKFA cells, a subline of mTAL cells constitutively expressing the fAPN gene.
Monoclonal antibody (MAb) J1.3 directed against the MHV M protein and
MAb WA3.10 against the MHV S protein (15) were provided by
J. Fleming (University of Wisconsin, Madison, Wis.). The production of
polyclonal antiserum K134 to MHV-A59 has been described previously (47). MAb 23F4.5 was kindly provided by Rhône
Mérieux (Lyon, France). This MAb recognizes the S protein of the
serotype II feline coronaviruses, to which FIPV strain 79-1146 belongs
(37). G73, a serum from an FIPV-infected cat (provided by H. Vennema), was used as a source of polyclonal antibodies to FIPV. MAb
R-G-4 directed against fAPN was obtained from T. Hohdatsu (Kitasato University, Towada, Aomori, Japan).
Plasmid constructs.
The progenitor for the donor RNA
transcription vector used in this study was pFV1 (see Fig. 1), which,
as described previously (13), encodes an RNA containing a
short 5' segment of the MHV genome fused via a polylinker to the S gene
and all of the 3' end of the MHV genome thereafter. The region of MHV
carried by pFV1 was enlarged in a series of steps that resulted in
pMH49 (see Fig. 1), a vector containing most of the upstream HE coding region as well as a new truncation cassette downstream of the poly(A)
tail, harboring the unique restriction sites PacI and SfiI. To facilitate replacement of the S gene in pMH49,
splicing overlap extension (SOE)-PCR (22) was used twice:
(i) to introduce an AvrII site into the
RsrII-SwaI segment (and concomitantly to repair a
point mutation generated in a previous PCR step) and (ii) to introduce
an Sse8387I site into the MluI-EcoRV segment.
The resulting plasmid, pMH54 (see Fig. 1), encodes a T7 RNA polymerase
transcript of 9,139 nucleotides (nt) followed by a poly(A) tail of
approximately 115 nt. This contains the 5' 467 nt of the MHV genome
(preceded by 2 G nucleotides) fused in frame, through a 72-nt linker,
to codon 28 of the HE pseudogene. From that point, its sequence exactly
follows the composition of the 3' end of the wild-type MHV genome
except for the following intentional alterations (see Fig. 1): (i)
coding-silent changes introduced into codons 28 and 29 of the HE
pseudogene, creating an RsrII site; (ii) coding-silent
changes introduced into codons 12 and 13 of the S gene, creating an
AvrII site; (iii) coding-silent changes made originally in
pFV1 (13) in codons 173 and 174 of the S gene, eliminating a
HindIII site and creating an AseI site; and
(iv) an Sse8387I site introduced 12 nt downstream of the S gene stop codon. We also note that in our laboratory strain of MHV-A59,
base 2132 of the previously reported gene 2a-HE sequence (34) (GenEMBL accession no. M23256) is not present:
TTTTTGAATGTTTT thus becomes TTTTTGATGTTTT.
The corrected carboxy terminus of the MHV-A59 HE gene product is
consequently longer and is homologous to that of MHV-JHM
(54).
In the final vector, a chimeric FIPV-MHV S gene was shuttled into pMH54
from the subclone pGTFMS (Godeke et al., unpublished), into which the
AvrII and Sse8387I sites had been introduced at positions corresponding to those in the MHV S gene construct. The FIPV
portion of the chimeric S gene was identical to that reported by de
Groot et al. (6) (GenEMBL accession no. X06170). The
resulting plasmid was designated pFM1 (see Fig. 1).
Manipulations of DNA were carried out by standard methods
(50). The compositions of all constructs were checked by
restriction analysis; all cloned cDNA precursors, PCR-generated
segments, and newly created junctions of each plasmid were verified by
DNA sequencing by the method of Sanger et al. (51) with
modified T7 DNA polymerase (Sequenase; U.S. Biochemicals) or by
automated sequencing with an Applied Biosystems 373A or 377 DNA sequencer.
Targeted recombination.
A chimeric FIPV-MHV S gene was
transduced into the MHV genome by targeted RNA recombination between
pFM1-generated donor RNA and the recipient virus, Alb4, essentially as
described previously (13, 35). Capped, runoff donor
transcripts were synthesized from PacI-truncated pFM1 with a
T7 RNA polymerase kit (Ambion) as specified by the manufacturer. Donor
RNA, without further purification, was transfected into Alb4-infected
L2 spinner culture cells, following a 2-h infection at 33°C, by using
two pulses at 960 µF and 0.3 kV in a Gene Pulser electroporation
apparatus (Bio-Rad). Infected and transfected cells were then plated
onto monolayers of FCWF cells. At 24 to 72 h after infection at
33°C, when syncytia could be detected in the FCWF monolayers, progeny
virus in the supernatant medium were harvested and candidate
recombinants were purified by two rounds of plaque titer determination
on FCWF cells at 37°C. Side-by-side controls, originating from
Alb4-infected L2 cells that had been mock transfected or transfected
with RNA from the parent vector pMH54, were treated identically.
Genomic analysis of candidate recombinants.
Independently
isolated and purified plaques of fMHV were used to infect
25-cm2 monolayers of FCWF cells at 37°C, and total
cellular RNA was harvested at 24 to 30 h postinfection and
purified either by a Nonidet P-40 gentle-lysis method (25)
or with Ultraspec reagent (Biotecx). Control RNA samples were purified
from MHV-infected 17Cl1 cell monolayers. RNA was reverse transcribed
under standard conditions (50) with a random primer,
p(dN)6 (Boehringer Mannheim), and cDNA was amplified by PCR
with various primer pairs to characterize candidate recombinants. PCR
amplifications were run for 30 cycles of 1 min at 94°C, 1 min at
48°C, and 2 min at 72°C with AmpliTaq DNA polymerase
(Perkin-Elmer), except for PCR amplifications of the entire S gene,
which were carried out with rTth DNA polymerase (Perkin-Elmer) for 30 cycles of 30 s at 94°C, 1 min at 50°C,
and 10 min at 68°C. Products were directly analyzed by agarose gel electrophoresis or were gel purified prior to restriction digestion and
analytical gel electrophoresis. Direct RNA sequencing was performed by
a modified dideoxy termination method (11, 40).
Intracellular viral protein analysis.
LR7 cells and FCWF
cells were grown in 35-mm dishes and infected with MHV-A59, fMHV, or
FIPV at a multiplicity of 10 PFU per cell. Before being labeled, the
cells were starved for 30 min in cysteine- and methionine-free minimal
essential medium containing 10 mM HEPES (pH 7.2) without fetal bovine
serum. The medium was then replaced by 600 µl of the same medium
containing 100 µCi of 35S in vitro cell-labeling mix
(Amersham) and, for FCWF cells, 25 µCi of [35S]cysteine
(ICN). MHV-A59-infected LR7 cells were labeled from 5 to 6 h
postinfection, and fMHV- and FIPV-infected FCWF cells were labeled from
7 to 8 h postinfection. After the labeling period, the cells were
washed with phosphate-buffered saline (PBS) and solubilized in 1 ml of
lysis buffer, consisting of TES (20 mM Tris HCl [pH 7.5], 100 mM
NaCl, 1 mM EDTA) containing 1% Triton X-100 and 2 mM
phenylmethylsulfonyl fluoride. Nuclei were removed from the cell
lysates by centrifugation at 12,000 × g for 10 min at
4°C.
For immunoprecipitations, 50-µl aliquots of lysate were diluted with
1 ml of detergent solution (50 mM Tris HCl [pH 8.0], 62.5 mM EDTA,
0.5% Nonidet P-40, 0.5% sodium deoxycholate) and 30 µl of 10%
sodium dodecyl sulfate (SDS) was added. Antibodies were then added: 3 µl of antiserum K134, 10 µl of MAb WA3.10, 3 µl of serum G73, or
3 µl of MAb 23F4.5. After an overnight incubation at 4°C, immune
complexes were adsorbed for 1 h to formalin-fixed Staphylococcus aureus cells (BRL Life Technologies) added as
45 µl of a 10% (wt/vol) suspension. Immune complexes were collected by centrifugation at 12,000 × g and washed three times
with RIPA buffer (20 mM Tris HCl [pH 7.5], 150 mM NaCl, 5 mM EDTA,
1% Triton X-100, 0.1% SDS, 1% sodium deoxycholate). Pellets were
resuspended in 30 µl of Laemmli sample buffer (30) and
were heated for 2.5 min at 95°C or, where indicated, were kept at
room temperature. Samples were analyzed by electrophoresis in an
SDS-12.5% polyacrylamide gel followed by fluorography.
Labeling, purification, and analysis of virion proteins.
Cells were infected and labeled as described above, except that
labeling periods were from 6 to 9 h postinfection for LR7 cells or
from 7 to 10 h postinfection for FCWF cells. At the end of the
labeling period, culture media (0.8 ml) were collected, cleared by
low-speed centrifugation, mixed with 2.3 ml of 67% sucrose in TM (10 mM Tris HCl [pH 7.0], 10 mM MgCl2), and transferred into
Beckman SW50.1 ultracentrifuge tubes. Each solution was overlaid with 1 ml of 48% sucrose, 0.5 ml of 40% sucrose, and 0.5 ml of 30% sucrose
in TM, and the gradients were centrifuged at 155,000 × g (36,000 rpm) for 43 h. After centrifugation, a fraction
consisting of the top 1 ml of each tube was collected. Virus particles
were affinity purified from 150 µl of this fraction by addition of 25 µl of MAb J1.3, 3 µl of MAb WA3.10, 3 µl of serum G73, or 3 µl
of MAb 23F4.5. Samples were processed and analyzed as above, except
that the S. aureus immune complexes were washed once with TM
instead of three times with RIPA buffer.
Neutralization of viral infectivity.
Comparable amounts of
infectivity (105 PFU) of MHV, fMHV, or FIPV were incubated
for 1 h at 37°C in 100 µl of PBS-DEAE to which was added 3 µl of polyclonal antibody K134 or 3 µl of serum G73. The viruses
were inoculated onto LR7 cells (MHV-A59) or FCWF cells (fMHV and FIPV)
grown on coverslips in 35-mm culture dishes. After 1 h, the cells
were washed and incubated in culture medium. At 6 h postinfection,
the cells were rinsed once with PBS and fixed with precooled (
20°C)
methanol for 10 min at
20°C. The cells were washed three times with
PBS and incubated with antibody K134 (1:300) or with serum G73 (1:200).
After 30 min at room temperature, the cells were rinsed three times
with PBS and stained with fluorescein isothiocyanate-conjugated or
tetramethylrhodamine isothiocyanate-conjugated goat anti-rabbit or goat
anti-cat immunoglobulin G antibody (Cappel), both diluted in PBS
(1:200). Finally, the cells were washed three times with PBS and
mounted in FluorSave reagent (Calbiochem). Fluorescence was viewed with
a Leica TCS4D confocal laser-scanning microscope.
Inhibition of infection by antireceptor antibodies.
MKFA
cells grown on glass coverslips in 35-mm culture dishes were
preincubated for 1 h at 37°C with undiluted MAb R-G-4 against the feline receptor (20) or with culture medium as a
control. They were then infected with MHV, fMHV, or FIPV at a
multiplicity of 5 PFU per cell as described above. At 6 h (MHV,
fMHV) or 7 h postinfection (FIPV), the cells were fixed and
stained as described above with antibody K134 (MHV, fMHV) or serum G73
(FIPV) and, as second antibodies, fluorescein isothiocyanate-conjugated
goat anti-rabbit or goat anti-cat immunoglobulin G antibodies.
 |
RESULTS |
Generation of an MHV mutant carrying a chimeric FIPV-MHV S
gene.
In previous work, we and others have created site-directed
point mutations in the MHV S gene by targeted recombination with donor
RNAs derived from pFV1 (13, 32). This transcription vector
contains the 3'-most 7.4 kb of the MHV genome, which consists of all
sequence distal to the start of the S gene (Fig.
1). For the present
work, in which we sought to completely replace the S gene, we
constructed a larger vector to provide sufficient material flanking the
5' end of the gene to enhance the probability of upstream homologous
crossover events between the donor RNA and the genome of the recipient
virus. The resulting enlarged vector, pMH54, contained almost all (1.2 kb) of the upstream HE pseudogene as well as two unique restriction
sites that were inserted to facilitate the exchange of S gene variants
(Fig. 1, sequences 2 and 4). The first of these, AvrII, was
generated by two coding-silent nucleotide changes in the 5'-proximal
portion of the S gene, which encodes the signal peptide. The second,
Sse8387I, was created by base changes 12, 15, and 17 nt
downstream of the stop codon of S. Both sites were expected to be
phenotypically silent when introduced into the MHV genome, an
assumption which later proved correct (42; L. Kuo
and P. S. Masters, unpublished results).

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FIG. 1.
Construction and composition of the donor RNA template
for incorporation of the FIPV S gene ectodomain into MHV. Transcription
vector pFM1 was derived from parent plasmid pFV1 (13) via
six intermediates, including pMH49 and pMH54, as described in Materials
and Methods. The chimeric FIPV-MHV S gene was shuttled into pFM1 from
the subclone pGTFMS. MHV and FIPV sequences are indicated,
respectively, by open and shaded rectangles. The arrow at the left end
of each vector indicates the T7 promoter; the solid circle represents
the polylinker between the 5'-end segment of the MHV genome (denoted
5'/1) and the 3' region containing the structural genes, the 3'
untranslated region (denoted 3'), and the polyadenylated segment
(denoted A). Restriction sites relevant to plasmid construction are
shown and, unless enclosed in parentheses, are unique in the plasmid in
which they appear. At the bottom are shown the sequences in pFM1: 1, between the polylinker and the HE gene fragment; 2, at the MHV-FIPV
junction in the signal peptide-encoding portion of the chimeric S gene
(with signal peptide residues boxed); 3, at the FIPV-MHV junction in
the transmembrane domain-encoding portion of the chimeric S gene; and
4, in the region immediately downstream of the S gene. Nucleotides
mutated to create restriction sites are underlined. The boundaries
between MHV and FIPV sequence are indicated by short vertical lines;
thicker horizontal bars between these indicate nucleotides or amino
acids common to both the MHV and FIPV sequences.
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A chimeric FIPV-MHV S gene was then incorporated into pMH54 from
pGTFMS, producing the vector pFM1 (Fig. 1). In the chimeric S gene, the
principal point of exchange was at a StyI site falling within the region encoding a 14-amino-acid stretch, YVKWPWYVWLLIGL, that borders the transmembrane domain and is common to both S proteins
(Fig. 1, sequence 3). The choice of this locus, which constitutes the
largest continuous segment of amino acid identity between the MHV and
FIPV sequences, was predicated on expression system results that
demonstrated that swapping of S protein ectodomains here allowed
incorporation of the chimeric S protein into MHV VLPs (15a).
A secondary MHV-FIPV junction was designed within a 3-amino-acid motif,
CIQ, that is common to both S proteins and follows the signal peptide
of each by 5 or 6 residues (Fig. 1, sequence 2). This was done to
preserve the MHV genomic region of some 70 nt immediately downstream of
the intergenic sequence preceding the S gene, in case this influenced
the transcription efficiency of the S mRNA. Thus, in the mature
chimeric S molecule, the entire ectodomain of the MHV S protein would
be replaced by the entire ectodomain of the FIPV S protein, except for
replacement of the first five residues of FIPV S with the first four
residues of MHV S.
Donor RNA transcribed in vitro from pFM1, or from pMH54 as a control,
was transfected into mouse L2 cells that had been infected with the
thermolabile MHV N gene deletion mutant Alb4 (27). Infected
and transfected cells were then overlaid onto monolayers of feline FCWF
cells to select for recombinants that, as a result of a crossover
upstream of the S genes of donor and recipient RNAs, had acquired the
ability to infect feline cells and simultaneously had lost the ability
to infect murine cells (Fig. 2). All FCWF monolayers that had received pFM1 RNA-transfected, Alb4-infected L2
cells unequivocally exhibited syncytium formation by 48 h
postinfection. By contrast, FCWF monolayers that had received
mock-transfected or pMH54 RNA-transfected, Alb4-infected L2 cells
showed no detectable syncytia by 96 h postinfection.

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FIG. 2.
Scheme for construction of fMHV by targeted
recombination between the MHV N gene deletion mutant, Alb4
(27), and donor RNA transcribed from the plasmid pFM1. The
deletion in the Alb4 N gene is shown as a discontinuity. A single
crossover event anywhere within the HE gene fragment of the donor RNA
should generate a recombinant, fMHV, containing both the
ectodomain-encoding region of the FIPV S gene (shaded) and the
wild-type MHV N gene. The recombinant should simultaneously lose the
ability to infect murine cells and gain the ability to infect feline
cells.
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Supernatant media from these infected and transfected cells were
harvested, clarified by centrifugation, and used in plaque titer
determinations on FCWF cells. At 48 and 72 h postinfection, plaques were clearly observed for samples derived from pFM1 RNA whereas
no detectable plaques were obtained from samples that had been mock
transfected or transfected with pMH54 RNA. Plaques of four independent
candidate recombinants derived from four separate transfections,
designated fMHV-A, fMHV-B, fMHV-C, and fMHV-D, were purified and
analyzed further.
Tissue culture growth phenotype of fMHV.
Consistent with
prediction, all four fMHV recombinants were unable to produce syncytia
or cytopathic effects in murine 17Cl1 cells or to give rise to plaques
in murine L2 cells. As shown in Fig.
3A, no plaques of any
size were evident on L2 cell monolayers by 66 h following
inoculation with fMHV-A or fMHV-C, in contrast to the large, clear
plaques generated by wild-type MHV on the same cells. Conversely, at
the same time postinfection, smaller plaques were obvious on FCWF
monolayers infected with the fMHV isolates but wild-type MHV was
absolutely unable to form plaques on these cells. This result confirmed
the expectation that the replacement of the MHV S protein with the
chimeric FIPV-MHV S protein completely switched the host species
specificity of the virus. The data shown in Fig. 3A were intentionally
obtained in a laboratory that has never held FIPV, to preclude the
possibility of cross-contamination.


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FIG. 3.
Growth of fMHV in feline cells. (A) Plaque-forming
ability of fMHV. Monolayers of murine L2 cells or feline FCWF cells
were mock infected or infected with wild-type MHV or either of two
independent isolates of fMHV. Plaques were visualized at 66 h
postinfection, after staining with neutral red. (B) Single-step growth
kinetics of fMHV-C and FIPV in FCWF cells. Viral infectivity in culture
medium at different times postinfection was determined by a quantal
assay on FCWF cells, and 50% tissue culture infective doses
(TCID50) were calculated.
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The fMHV recombinants grew efficiently in FCWF cells, exhibited similar
growth kinetics to FIPV (Fig. 3B), and caused extensive syncytia and
cytopathic effect comparable to that caused by FIPV. Stocks of the
recombinant virus typically reached titers an order of magnitude lower
than the titers obtained with FIPV. Thus, exchange of the S protein
ectodomain was sufficient to allow complete crossing of the host cell
species barrier by fMHV. However, this chimeric recombinant was not
entirely as fit as FIPV in its ability to grow in tissue culture.
Possible reasons for this observation are discussed below.
Genomic analysis of fMHV.
To ascertain the genomic structure
of the fMHV candidates, we purified RNA from feline cells infected with
four independent isolates of the recombinant as well as from murine
cells infected with MHV controls. Multiple sets of random-primed
reverse transcription followed by PCR (RT-PCR) were performed with the
primers listed in Table 1. First, to
determine whether the engineered FIPV-MHV S gene boundaries were indeed
present in the recombinants, primers specific for FIPV S gene regions
near both the 5' and 3' junctions were used together with MHV-specific
primers positioned on the opposite side of each junction. At the 5'
junction, when the FIPV S-specific primer LK68 was paired with the MHV
HE-specific primer FF29, a PCR product consistent with the expected
size of 995 bp was generated only from the fMHV isolates but not from
the MHV controls (Fig.
4A). Similarly, primers
LK56 and PM252, flanking the 3' FIPV-MHV junction, generated an
apparent 1,287-bp product from fMHV but not from the MHV controls (Fig.
4B). To ensure that the lack of signal from the control MHV strains,
Alb129 and Alb203, was not due to failure of the RT-PCR, RNA samples
were analyzed with a set of MHV S-specific primers, PM232 and FF50.
This produced a PCR fragment of 1,267 bp only for the MHV controls but
not for the fMHV isolates (Fig. 4C). This result not only verified the specific presence of FIPV S sequences in the fMHV isolates but also
indicated that they were devoid of any residual presence of the Alb4
parent.


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FIG. 4.
PCR analysis of fMHV recombinants. In each experiment,
RT-PCR was used to amplify regions of RNA isolated from cells infected
with each of four independent isolates of fMHV or two MHV controls. The
controls, Alb129 (13) and Alb203 (7), are MHV
mutants that were also obtained by targeted recombination between Alb4
and pFV1-related donor RNAs; both are phenotypically wild type and are
isogenic with wild-type MHV in the region under analysis. PCR products
were analyzed by electrophoresis in 0.8% agarose gels stained with
ethidium bromide. Sizes of relevant standard (std) marker DNA fragments
are indicated on the right or left of each gel. PCR primers (Table 1)
used in each experiment, their loci in the MHV or fMHV genomes, and the
predicted sizes of the PCR products or restriction fragments of the PCR
products are indicated on the right.
|
|
To rule out the possibility that FIPV S-specific RT-PCR products were
actually amplified from input pFM1 donor RNA that had somehow persisted
through plaque purification and passaging, a gene 2a-specific primer,
LK71, was paired with the FIPV S-specific primer LK69. This yielded a
1,950-bp product from fMHV RNA (and not from control MHV RNA) (Fig.
4D), which could not have originated from pFM1 RNA since the latter
does not contain any gene 2a sequence (Fig. 1). This finding, together
with the absence of any detectable MHV S-specific signal from fMHV RNA,
indicated that the FIPV S gene segment was indeed in the context of a
recombinant genome. In an additional control, the specificity of primer
LK71 was demonstrated by pairing it with the MHV S-specific primer CK1,
which produced a product consistent with the expected size of 1,618 bp
only with the MHV samples (Fig. 4E).
It seemed unlikely that additional homologous crossovers could have
occurred within the ectodomains of the MHV and the chimeric S genes of
the recipient and donor RNAs, owing to the low degree of sequence
homology between the two. However, this possibility could not be
excluded on the basis of the above data. Therefore, to examine whether
the whole chimeric S gene was present in the recombinants, the upstream
HE-specific primer FF29 and the downstream gene 4-specific primer PM252
were used to amplify the entire S gene region of the fMHV isolates and
MHV controls. This gave a single PCR product consistent with the
expected size of 4,089 bp for MHV and a larger single product,
predicted to be 4,461 bp, for fMHV (Fig. 4F). Moreover, digestion of
these products with HindIII (Fig. 4G), XbaI
(Fig. 4H), or SpeI (data not shown) yielded exactly the
predicted sets of restriction fragments for all the fMHV isolates and
the MHV controls. Since these enzymes differentially cleave the MHV S
gene and the chimeric S gene at intervals spanning their entire
lengths, we concluded that each fMHV strain contained the unaltered
chimeric FIPV-MHV S gene.
An additional RT-PCR, with primers flanking the locus of the 87-nt
deletion in the N gene in Alb4, as described previously (27,
40), revealed that all four independent fMHV isolates contained
the wild-type N gene (data not shown). The acquisition of this marker,
2.9 kb distant from the S gene and only 0.4 kb from the 3' end of the
genome, supports the notion that each of the fMHV mutants was generated
by a single crossover, as depicted in Fig. 2.
To further verify the presence of the chimeric S gene in the
recombinants, we directly sequenced the FIPV-MHV junctions in RNA
isolated from FCWF cells infected with fMHV-A or fMHV-C. At both the
upstream and the downstream boundaries, both recombinants exhibited the
expected transition between MHV S sequence and FIPV S sequence (Fig.
5). In addition, the RNA sequence of the
5' end of the HE genes of fMHV-A and fMHV-C revealed that no
heterologous region of the pFM1 RNA polylinker had been introduced by a
possible nonhomologous recombination event (data not shown). Since all the available evidence suggested that the independent isolates of fMHV
were identical, a single isolate, fMHV-C, was used for all subsequent
analyses.

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FIG. 5.
RNA sequence of the FIPV-MHV S gene junctions in fMHV.
RNA isolated from cells infected with independent recombinants fMHV-A
and fMHV-C was sequenced with a primer complementary to nt 118 to 141 of the FIPV S gene (left set, upstream junction) or a primer
complementary to nt 3817 to 3837 of the MHV S gene (right set,
downstream junction). For each junction, both the directly read
negative-strand cDNA sequence and the inferred positive-strand RNA
sequence are shown.
|
|
As a final confirmation of the composition of fMHV-C, we directly
sequenced RT-PCR products encompassing the entire S gene of this virus.
These products were obtained in the same manner as those shown in Fig.
4, except that specific, rather than random, primers were used for the
RT step. This analysis showed that the sequence of fMHV-C, from the end
of the HE gene through the start of gene 4, including both the FIPV and
MHV portions of the chimeric S gene, was identical to that of plasmid
pFM1, from which donor RNA had been transcribed. This result ruled out
the possibility that, in isolating fMHV, we had inadvertently selected
for additional mutations in the S gene that may have contributed to the
assembly or infectivity of this virus.
Analysis of viral proteins in fMHV-infected cells.
To
characterize the recombinant fMHV at the protein level, in particular
with respect to its S protein, we first analyzed the viral polypeptides
in infected cells. To this end, we infected FCWF cells with fMHV and
labeled the proteins for 1 h with 35S-amino acids. As
controls, we infected FCWF and L cells in parallel with FIPV and MHV,
respectively, and labeled them similarly. At the end of the labeling
period, cell lysates were prepared and immunoprecipitations were
carried out with the following antibodies: K134, a rabbit serum raised
against purified MHV; G73, a serum from an FIPV-infected cat; WA3.10, a
MAb against an epitope present in the MHV S ectodomain
(Sm); and 23F4.5, a MAb recognizing an epitope in the FIPV
S ectodomain (Sf). Before analysis by SDS-polyacrylamide gel electrophoresis, the immunoprecipitates were briefly heated, except
for samples containing the MHV M protein, which were also analyzed
unheated in view of the known aggregation of this protein at higher
temperatures (56). The electrophoretic patterns are shown in
Fig. 6. As expected, the anti-MHV serum
did not recognize any proteins in FIPV-infected cell lysates but
precipitated the major structural proteins M, N, and S from lysates of
MHV-infected cells. The same proteins were detected in the lysates from
fMHV-infected cells, except for the S protein, which was clearly
absent. This result was confirmed with the anti-Sm
antibodies, which recognized the S protein from MHV-infected cells but
nothing in the fMHV lysates. In contrast, both the anti-FIPV serum and
the anti-Sf MAb precipitated a protein that was
significantly larger than MHV S but comigrated with the FIPV S protein,
which these antibodies recognized in the FIPV-infected cell lysate.
These results indicate that a polypeptide with the expected
characteristics of the FIPV-MHV chimeric S protein, 1 residue shorter
than the mature FIPV S protein and 124 residues longer than the mature
MHV S protein, was synthesized in cells infected with fMHV.

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FIG. 6.
Viral proteins in fMHV-infected cells. FCWF cells
infected with fMHV and, for comparison, FIPV-infected FCWF cells and
MHV-infected LR7 cells were labeled for 1 h with
35S-amino acids. Immunoprecipitations were performed on
aliquots of cleared lysates of these cells by using the following
antibodies (Ab.): K134 rabbit serum against purified MHV-A59 ( MHV);
serum G73 from a FIPV-infected cat ( FIPV); and MAb WA3.10 and
23F4.5, recognizing the ectodomains of MHV S ( Sm) and
FIPV S ( Sf), respectively. As indicated, proteins were
heated at 95°C (+) or analyzed without heating ( ) in SDS-12.5%
polyacrylamide gels. The positions of the S, M, and N proteins in the
gel are indicated on the left for MHV and on the right for FIPV.
|
|
Analysis of fMHV structural proteins.
The protein composition
of fMHV virions was investigated and compared with those of MHV and
FIPV. Proteins synthesized in infected cells were labeled for 3 h
with 35S-amino acids, and viral particles released into the
culture medium were purified by floatation in sucrose gradients.
Virions were subsequently affinity purified by using the anti-FIPV,
anti-Sm, and anti-Sf antibodies described
above, as well as MAb J1.3, which recognizes an epitope in the MHV M
protein ectodomain (7). The fMHV proteins isolated with this
last antibody were the MHV M and N proteins and a protein distinctly
larger than MHV S but similar in electrophoretic mobility to the FIPV S
protein (Fig. 7). No fMHV particles were
selected with the anti-Sm MAb, indicating that they did not
display the MHV S epitope. They did, however, carry the FIPV S epitope,
since the anti-Sf MAb was able to select fMHV virions.
These observations are consistent with fMHV virions having the protein
composition of MHV, except with spikes composed only of the chimeric
FIPV-MHV S protein.

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FIG. 7.
Protein composition of purified fMHV.
35S-labeled fMHV and, for comparison, similarly labeled
FIPV and MHV were prepared and purified by floatation in sucrose
gradients. Virus particles were subsequently affinity purified with
specific antibodies and analyzed in an SDS-12.5% polyacrylamide gel.
Indications are as described in the legend to Fig. 6.
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|
Neutralization of fMHV by anti-FIPV but not by anti-MHV serum.
The chimeric virus was further characterized by studying its
sensitivity to neutralization of infectivity by MHV- and FIPV-specific antibodies. To this end, fMHV was incubated with antibodies before being inoculated onto FCWF cells. In parallel, samples of FIPV and MHV
were treated similarly and used for inoculation of FCWF and LR7 cells,
respectively. The effects of antibody pretreatment were evaluated by
analyzing the extent of infection through visualization of infected
cells in an immunofluorescence assay. Figure
8A shows that fMHV was neutralized
efficiently by G73, a serum obtained from an
FIPV-infected cat, but not by K134, a rabbit serum raised against
purified MHV-A59. This established that FIPV-specific epitopes are
exposed on the exterior of fMHV virions.


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FIG. 8.
Blocking of spike-receptor interactions. (A)
Neutralization of viral infectivity. fMHV, FIPV, and MHV were
preincubated with anti-MHV serum (K134) or anti-FIPV serum (G73) before
being inoculated on LR7 (MHV) or FCWF cells (fMHV and FIPV). Infection
was visualized at 6 h postinfection by immunofluorescence
microscopy. (B) Receptor dependence of infection. mTAL and MKFA cells
(mTAL cells expressing fAPN), the latter without or with treatment with
antibodies to the fAPN receptor, were inoculated with fMHV, MHV, and
FIPV, and infection was visualized by immunofluorescence analysis.
|
|
fAPN receptor-dependence of fMHV infection.
To confirm the
switch in receptor usage of fMHV as a result of the functional presence
of the FIPV spike ectodomain, we made use of a mouse cell line, mTAL
(46). These cells are susceptible to MHV but cannot be
infected by FIPV. As shown in the immunofluorescence analysis of Fig.
8B, these cells were also resistant to fMHV. However, MKFA cells, which
are mTAL cells that constitutively express the fAPN receptor gene, were
found to be susceptible to fMHV infection (Fig. 8B). Moreover, that
this infection was indeed mediated by the fAPN protein was corroborated
further by the observation that infection of MKFA cells could be
blocked by their preincubation with antibodies to the fAPN molecule.
These results demonstrated that fMHV cannot use the MHV receptor
present on these cells but can enter the cells by binding the FIPV
receptor fAPN.
 |
DISCUSSION |
Incorporation of S protein into coronaviruses.
This study was
initiated to localize the portion of the MHV S protein governing its
incorporation into mature virions. Although coronavirus assembly can
occur independently of S protein (4, 21, 49, 60), this
constituent is obviously pivotal to the biology of the virus. It will
thus be important to understand the basis of its selective inclusion
into particles, and, conversely, the reason why other proteins are
excluded. It has been previously shown that there are specific
associations between the M and S proteins while M is coalescing into
higher-order arrays, and these may be key to recruiting S into budding
viral particles (36, 38, 39). However, much remains to be
learned of the molecular details of this process, and an active role
for E protein cannot be ruled out.
In the work presented here, we were able replace the MHV S ectodomain
with that of FIPV, a representative of another of the three groups
within the coronavirus genus. The MHV and FIPV S proteins, although
ancestrally related, have diverged to the point where there is less
than 16% sequence identity between the amino-terminal half of each
molecule, and they have evolved to recognize different receptors with
different regions of their ectodomains. We have shown that the
resulting ectodomain-switched recombinant, fMHV, underwent a
corresponding switch of its host cell species specificity. Moreover, it
was clear that the chimeric FIPV-MHV S gene had replaced its purely MHV
counterpart in the viral genome and that the chimeric S protein product
was expressed in infected cells and was incorporated into virions. It
should be noted that both genomic analysis and immunochemistry
demonstrated that only the chimeric S gene was present and only the
chimeric S protein was expressed in fMHV-infected cells and fMHV
virions. Therefore, the altered host cell specificity was not the
result of phenotypic mixing of the MHV genome packaged into particles
containing the FIPV-MHV S chimera expressed from donor RNA.
The rationale for the ectodomain substitution that was made in fMHV was
derived from a more comprehensive series of chimeric gene expression
experiments involving the VLP assembly system (15a). We have
previously constructed MHV mutants by targeted recombination to extend
the results of VLP experiments that established the critical role of
the carboxy-terminal extremity of the M protein in virion formation
(7). The combined power of the two approaches has enabled us
to examine mutations of essential structural genes in order to probe
molecular interactions central to coronavirus assembly. In the present
work, incorporation of the chimeric FIPV-MHV S protein into fMHV
delimits the region of S required for inclusion into the virion
envelope to the carboxy-terminal 64 of its 1,324 amino acid residues
(Fig. 9). Common features between the
FIPV and MHV S proteins, a conserved transmembrane domain and a
cysteine-rich endodomain, were not sufficient for FIPV S protein to be
taken up into assembled VLPs formed by the MHV M and E proteins.
Therefore, further experiments will now be aimed toward determining
which subset of residues in this region that are unique to the MHV S protein interact specifically with MHV M protein and possibly E
protein.
Nature of the host range barrier for coronaviruses.
The
construction of fMHV is the first example of the complete, reciprocal
switch of the host cell specificity of a coronavirus. As such, it
contributes a well-defined element to the accumulating proof that the
interaction between S protein and receptor is the principal, and
perhaps only, determinant of species specificity for coronaviruses.
Other elements of this proof come from studies in which it was shown
that MHV could evolve, through high-passage persistent infection in
tissue culture, to have an expanded host range (1, 52). In
these cases, the resulting MHV mutants retained the ability to grow in
murine cells but could now also infect cells of a number of other
species, presumably via homologs of the murine MHV receptor.
Additionally, from the standpoint of the receptor rather than the
virus, there have been many demonstrations (including the experiment in
Fig. 8B) that expression of the receptor for a given coronavirus in
cells of a heterologous, nonpermissive species will render those cells
permissive to infection (9, 10, 18, 28, 45, 58, 61).
As mentioned above, fMHV did not appear to be entirely as fit as FIPV
with respect to growth in tissue culture (see Results). Although the
chimeric S protein allowed the entry of this virus into cells of a
heterologous species, it is conceivable that there were also less
stringent levels of host species restriction caused by interactions
between internal viral components and cytoplasmic host proteins.
However, an alternative possibility is that the level of expression of
the chimeric S protein was not optimal. Metabolic labeling of RNA
synthesis in FCWF cells infected with fMHV revealed that in addition to
the expected transcript (RNA3) containing the chimeric S gene, there
were at least two transcripts initiating within the chimeric S gene and
that these were of similar abundance to the full-length transcript
(data not shown). A complete analysis of these aberrant subgenomic RNAs
will be presented elsewhere, but their existence, plus the reduced
amount of RNA3 relative to that of the same species in MHV-infected
murine cells, is consistent with the notion that transcription of fMHV
S mRNA is rate limiting. We previously noted the local derangement of
MHV transcription caused by insertion of a heterologous gene into MHV
(13), and the observation of a similar effect in fMHV
suggests that even the introduction of related coronavirus genetic
material into the MHV genome is not entirely tolerated by the
transcription apparatus of the virus.
As a direct consequence of the reduced synthesis of RNA3 in
fMHV-infected cells, one would expect the relative amount of S protein
to be reduced as well. Unfortunately, due to the different efficiencies
with which the viral proteins were recognized in immunoprecipitation
reactions, we could not draw quantitative conclusions about the
relative amounts of S protein synthesis in cells infected by fMHV as
compared to MHV and FIPV. However, the relative amounts of
radioactivity in the structural proteins of the affinity-purified
viruses (Fig. 7) indicate that the chimeric S protein is indeed
underrepresented in fMHV. It remains to be established whether this is
simply because of the reduced availability of the protein in infected
cells or whether it reflects an impaired interaction of the S protein
with M, which would also result in less efficient incorporation into
viral particles. Obviously, infectivity of particles requires spikes,
but nothing is known about the relationship between infectivity and
spike content.
Another possible source of the apparent reduced fitness of fMHV may lie
in the functionality, rather than the amount, of the chimeric S
protein. Earlier expression studies with MHV S gene constructs have
indicated that changes in the transmembrane and endodomain can affect
the cell-to-cell fusion that this protein causes in susceptible cells
(3). Although the chimeric FIPV-MHV S protein clearly
exhibits this fusion activity when expressed in feline cells, the
efficiency of this process may well be decreased relative to that of
the parental wild-type S proteins. If so, this would probably give rise
to an inherently lower specific infectivity for fMHV.
Implications for reverse genetics of coronaviruses.
For
coronaviruses, the extremely large size of the RNA genome has been the
main obstacle to generating site-specific mutations for studies of gene
expression and function. To date, it has not been possible to construct
a full-length cDNA clone of any coronavirus for the production of
infectious RNA. Targeted RNA recombination has proved to be a
successful alternative approach to the reverse genetics of MHV, and it
has been used to generate mutations in the S (13, 32, 42), M
(7), E (14), and N (12, 40, 41, 59)
genes, gene 4 (13), and the 3' untranslated region (23,
24) of this virus. This method relies on the ability to select
against a temperature-sensitive and thermolabile parent virus in order
to identify recombinants that have acquired the mutation of interest
through recombination with a transfected donor RNA. In one case
(14), mutants were identified by screening rather than
selection, but generally, if a recombinant is to be obtained by
selection, it cannot be less fit than the recipient virus that is being
selected against.
Although fMHV was constructed to begin to answer questions about viral
assembly, we believe that this recombinant will also offer a tremendous
selective advantage as a recipient virus in targeted recombination.
Using a donor RNA containing the original MHV S gene, we expect now to
be able to isolate recombinants, no matter how defective, that have
regained the ability to grow in murine cells. This new basis for
selection should increase even further the strength of this genetic
system for MHV. Moreover, this approach should provide a general
blueprint for the generation of genomic mutations in the structural
genes of any coronavirus.
 |
ACKNOWLEDGMENTS |
We are grateful to Cheri Koetzner for expert technical
assistance and to Matthew Shudt and Tim Moran of the Molecular Genetics Core Facility of the Wadsworth Center for the synthesis of
oligonucleotides and automated DNA sequencing. We also thank John
Fleming, Wayne Corapi, and Tsutomu Hohdatsu for providing antibodies.
We are grateful to John Rossen, Harry Vennema, and Xander de Haan for their constructive support.
This work was supported in part by Public Health Service grant AI 39544 from the National Institutes of Health to P.S.M.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: David Axelrod
Institute, Wadsworth Center, NYSDOH, New Scotland Ave., P.O. Box 22002, Albany, NY 12201-2002. Phone: (518) 474-1283. Fax: (518) 473-1326. E-mail: masters{at}wadsworth.org.
 |
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