JVI Accepted Manuscript Posted Online 24 February 2016 J. Virol. doi:10.1128/JVI.02861-15 Copyright © 2016, American Society for Microbiology. All Rights Reserved.
1
Recovery of West Nile Virus Envelope Protein Domain III Chimeras with
2
Altered Antigenicity and Mouse Virulence
3 4
Alexander J McAuley 1,2, Maricela Torres 1, Jessica A Plante 2,3*, Claire Y-H Huang 4,
5
Dennis A Bente 1,2,5,6, and David W C Beasley 1,2,5,6#
6 7
1Department
8
77555
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2Institute
of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas,
for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
10
Texas, 77555
11
3Department
12
4Arbovirus
13
Prevention, U.S. Department of Health and Human Services, Fort Collins, Colorado, 80521
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5Center
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Galveston, Texas, 77555
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6Sealy
17
77555
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#Corresponding
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*Current Address: Gillings School of Global Public Health, University of North Carolina, Chapel Hill,
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NC, 27599
of Pathology, University of Texas Medical Branch, Galveston, Texas, 77550
Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and
for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch,
Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas,
Author: [email protected]
21 22
Running Title: Flavivirus Receptor-Binding Domain Chimeras
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Word Count (Abstract): 191
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Word Count (Text): 6773
1
25
Abstract
26
Flaviviruses are positive-sense, single-stranded RNA viruses responsible for millions of
27
human infections annually. The envelope (E) protein of flaviviruses comprises three
28
structural domains, of which domain III (EIII) represents a discrete subunit. EIII typically
29
encodes epitopes recognized by virus-specific, potently neutralizing antibodies and is
30
believed to play a major role in receptor binding. In order to assess potential interactions
31
between EIII and the remainder of the E protein, and to assess effects of EIII sequence
32
substitutions on antigenicity, growth, and virulence of a representative flavivirus, chimeric
33
viruses were generated using the West Nile virus (WNV) infectious clone, into which EIIIs
34
from nine flaviviruses of varying genetic diversity from WNV were substituted. Of the
35
constructs tested, chimeras containing EIIIs from Koutango virus (KOUV), Japanese
36
encephalitis virus (JEV), St Louis encephalitis virus (SLEV), and Bagaza virus (BAGV) were
37
successfully recovered. Characterization of the chimeras in vitro and in vivo revealed
38
differences in growth and virulence between the viruses, with in vivo pathogenesis often
39
not correlated to in vitro growth. Taken together, the data demonstrate that substitutions
40
of EIII can allow for the generation of viable chimeric viruses with significantly altered
41
antigenicity and virulence.
42 43 44 45 46 47
2
48
Importance
49
The envelope (E) glycoprotein is the major protein present on the surface of flavivirus
50
virions, and is responsible for mediating virus binding and entry into target cells. Several
51
viable West Nile virus (WNV) variants were recovered with chimeric E proteins in which
52
the putative receptor-binding domain (EIII) sequences of other mosquito-borne
53
flaviviruses were substituted in place of the WNV EIII, although substitution of several
54
more divergent EIII sequences were not tolerated. The differences in virulence and tissue
55
tropism observed with the chimeric viruses indicate a significant role for this sequence in
56
determining the pathogenesis of the virus within the mammalian host. Our studies
57
demonstrate that these chimeras are viable, and suggest that such recombinant viruses
58
may be useful to investigate domain-specific antibody responses and to more extensively
59
define the contributions of EIII to tropism and pathogenesis of WNV or other flaviviruses.
60 61 62 63 64 65 66 67 68 69 70
3
71
Introduction
72
The flaviviruses are a large genus of viruses with positive-sense, single-stranded RNA
73
genomes, responsible for significant global morbidity and mortality (1). The fact that the
74
majority are vector-borne, carried by either by ticks or mosquitoes, allows for a wide
75
geographical distribution and ready transmission to humans. The clinical manifestations of
76
flavivirus infections in humans vary considerably, with many causing non-specific febrile
77
illnesses that may progress to more severe syndromes including hemorrhagic fever or
78
encephalitis (1).
79 80
The surface of mature flavivirus virions is primarily comprised of 180 copies of the
81
envelope (E) glycoprotein (2). As a result, the E protein is involved in the major steps of
82
virus entry into susceptible cells, including the mediation of receptor binding and fusion
83
between the viral envelope and host endosomal membranes allowing for the release of the
84
viral genomic RNA into the cell cytoplasm for replication (3-6). These roles require
85
considerable rearrangement of the E proteins on the surface of the mature virion, with
86
important intra- and intermolecular interactions occurring at each stage (3, 7). Structurally,
87
E may be divided into three major domains: EI, which in many WNV strains includes the
88
single glycosylation motif; EII, which contains the flavivirus-conserved fusion loop; and
89
EIII, the putative receptor-binding domain (8). Although all three domains of the E protein
90
appear to contribute to interactions with target cell ligands in different experimental
91
systems, data that support a significant role for EIII in receptor binding come from
92
investigations into competition between recombinant EIII molecules and infectious virions
93
for adsorption to cell surfaces (9-11), immunological studies using neutralizing monoclonal
4
94
antibodies targeting EIII (12), the generation of mutant viruses containing particular amino
95
acid substitutions in EIII (13-19), and DENV E fusion proteins (6). Studies of EIII protein
96
subunits derived from different mosquito and tick-borne flaviviruses have identified virus-
97
specific differences in antigenicity, surface biochemistry, and structure, which further
98
support a role for EIII as a key determinant of ligand binding and cell tropism for individual
99
flavivirus types (20-28).
100 101
Construction of chimeric flaviviruses, whereby segments of genome from one virus are
102
substituted into the genome of a different flavivirus, has been used to investigate the roles
103
of individual viral proteins in virulence or other phenotypes, or to develop candidate
104
vaccines and diagnostic reagents. Previous structural protein chimeric flaviviruses have
105
involved the substitution of the coding sequences for complete structural proteins, usually
106
prM and E, from a donor virus into a backbone virus (29-56). These chimeric viruses have
107
the antigenic characteristics of the donor structural proteins, and characterization of
108
several has also identified significant shifts in in vitro growth and/or in vivo virulence
109
phenotypes, consistent with the importance of the structural proteins, and E in particular,
110
in those phenotypes. For example, the substitution of prM-E from TBEV into DENV-4
111
significantly affected the behavior of the virus both in vitro and in vivo, with growth in LLC-
112
MK2 cells resulting in higher peak titers with the chimeric virus compared to the DENV-4
113
control and increased neurovirulence following i.c. administration compared to infections
114
with the equivalent dose of DENV-4 (30). Similar prM-E chimeras comprised of TBEV and
115
OHFV as donor and backbone virus, respectively, showed significantly earlier
5
116
neuroinvasion by the chimera compared to the OHFV control, further indicating that the
117
structural proteins can affect the behavior of the virus (52).
118 119
To date, few studies have attempted to generate chimeric proteins (i.e. containing
120
domains/regions derived from two or more different flaviviruses) and incorporate them
121
into a viable virus. Given the discrete nature of EIII within the flavivirus E protein, as well
122
as its role in receptor binding and as a target for virus-specific neutralizing antibodies, we
123
hypothesized that substitution of EIII sequences between some flaviviruses would yield
124
viable viruses, but would likely be associated with significant changes in growth, virulence,
125
and/or antigenicity of the resulting chimeras. Therefore, the aims of this study were (1) to
126
determine whether viable chimeras could be generated via the substitution of the EIII
127
protein domain alone (i.e. chimerization of the E protein), and (2) to assess the effects of
128
EIII substitutions on the in vitro growth and in vivo pathogenesis of these chimeras. West
129
Nile virus (WNV), an encephalitic, mosquito-borne flavivirus, was used as the backbone
130
virus for these initial investigations due to the availability of a well-characterized infectious
131
clone system (57) and small animal neuroinvasive disease models.
132 133
Materials and Methods
134
WNV NY99 Infectious Clone and EIII Donor Viruses
135
For the generation of chimeric viruses, a previously-described WNV infectious clone
136
system was employed (57, 58). Briefly, the infectious clone consisted of two plasmids:
137
pWN-AB, which contained the 5’ UTR and the structural protein coding region; and pWN-
138
CG, which contained the non-structural protein coding region and the 3’ UTR. For virus
6
139
recovery, the two plasmids were digested with XbaI and NgoMIV (New England Biolabs,
140
Ipswich, MA) and ligated together after purification. The ligated full-length plasmid was
141
linearized with XbaI, and full-length genome-equivalent RNA was produced by in vitro
142
transcription from a T7 promoter upstream of the coding sequence using an Ampliscribe
143
T7-Flash in vitro Transcription kit (Epicentre Biotechnologies, Madison, WI). Virus
144
recovery was carried out by electroporating the in vitro transcribed RNA in to Vero cells
145
(ATCC, Manassas, VA) using an Invitrogen Neon Transfection System (Life Technologies,
146
Waltham, MA).
147 148
Four unique restriction sites (SalI at nt1829-1834; PstI at nt1859-1864; StuI at nt2183-
149
2188; and BamHI at nt2251-2256) were engineered into the pWN-AB plasmid by site-
150
directed mutagenesis using the QuikChange XL and Multi kits (Agilent Technologies, Santa
151
Clara, CA). The locations of the sites were chosen based upon the strongly conserved amino
152
acid sequences in these regions amongst many of the flaviviruses. Three of the four
153
mutations were silent at the amino acid level; however, the SalI site resulted in a
154
conservative V290L amino acid substitution in E. This substitution has been identified in
155
natural, pathogenic isolates of WNV, including the T2 strain from Turkey (59). Nine EIII
156
donor viruses were used of increasing genetic diversity from WNV (Table 1). cDNA for all
157
but one of the viruses was derived from isolated viral RNA obtained from the World
158
Reference Center for Emerging Viruses and Arboviruses (WRCEVA) at UTMB. The ZIKV EIII
159
sequence was amplified from a synthetic construct purchased from Bio Basic (Bio Basic
160
Inc., Markham, ON) based upon the published accession number NC_012532.
161
7
162
Construction of Chimeric Plasmids
163
Viral RNA was extracted from culture supernatant samples of each donor virus using
164
TRIzol (Thermo Fisher Scientific, Waltham, MA), with RNA purification performed using
165
the Zymo Direct-Zol RNA purification kit (Zymo Research Corp., Irvine, CA). Reverse
166
transcription to generate viral cDNA was performed using NEB AMV Reverse Transcriptase
167
(New England Biolabs, Ipswich, MA). EIII inserts were amplified from cDNA generated from
168
viral genomic RNA or synthetic plasmid using the Roche High Fidelity PCR Master Mix
169
(Roche, Indianapolis, IN). The PCR products were separated by agarose gel electrophoresis
170
and purified using a Qiagen QIAquick Gel Extraction kit (Qiagen, Germantown, MD). Both
171
the purified PCR products and backbone plasmids were digested with the appropriate
172
restriction enzyme pairs (New England Biolabs, Ipswich, MA).
173 174
For seven of the EIII donor virus, four chimera versions were generated using each
175
combination of the up- and downstream restriction sites, denoted A, B, C, and D (Figure 1a).
176
For YFV and DTV, only the A- and B-form chimeric plasmids were generated. Based on the
177
location of the restriction sites, the B-form (PstI-StuI) had the smallest insert, consisting
178
solely of EIII, whereas the A-form (SalI-BamHI) was the largest substitution, containing
179
part of EI upstream of the EI/EIII linker region, and the first stem-helix region downstream.
180
The C- and D-forms (SalI-StuI and PstI-BamHI, respectively) had the additional upstream
181
and downstream sequences, respectively. For the B-forms, an infectious clone AB plasmid
182
containing just PstI and StuI sites was used, thereby allowing for chimeras to be generated
183
without the SalI-associated V290L substitution.
184
8
185
The digested plasmids and inserts were gel purified and ligated overnight at 4°C using T4
186
DNA ligase (New England Biolabs, Ipswich, MA). The ligated plasmids were sequenced to
187
confirm identity, and were transformed into DH5α E. coli, from which glycerol stocks were
188
generated for storage. Chimeric viruses were recovered following ligation of full-length
189
genomic cDNA, in vitro transcription and electroporation of the RNA into Vero cells as
190
described above.
191 192
Construction of EIII chimeras using the WNV infectious clone was approved by the
193
University of Texas Medical Branch Institutional Biosafety Committee. Only EIII sequences
194
derived from viruses of the same or lower biosafety level were used for attempts at
195
chimerization, and all transfected cell cultures were handled under BSL-3 conditions. All
196
subsequent experimentation with viable chimeric viruses occurred under BSL-3/ABSL-3
197
conditions.
198 199
Nucleotide Sequencing
200
Chimeric infectious clone plasmids and PCR-amplified viral cDNA generated from TRIzol-
201
extracted RNA from cell culture supernatant were submitted to the UTMB Molecular
202
Genomics core facility for sequence determination using an Applied Biosystems 3130xl
203
DNA Sequencer (Applied Biosystems, Waltham, MA). Whole genome sequences for
204
recovered and serially-passaged chimeric viruses were determined from purified viral RNA
205
samples at the UTMB Next Generation Sequencing core facility using an Illumina HiSeq
206
1500 Next Generation sequencer (Illumina Inc., San Diego, CA).
207
9
208
Plaque, Immunofocus, and Temperature Sensitivity Assays
209
Virus titration was carried out in Vero cells grown in minimal essential medium (MEM;
210
Corning,
211
Penicillin/Streptomycin (Corning, Manassas, VA), 1x Non-Essential Amino Acids (Corning,
212
Manassas, VA), and 1x L-glutamine (Life Technologies, Waltham, MA). Cells were plated in
213
6-well plates, and grown until approximately 90% confluence. Virus culture supernatant
214
samples, sera, or homogenized organs were serially 10-fold diluted (typically 10-2 to 10-7
215
dilutions) in MEM containing 2% FCS. The diluted samples were transferred to the plated
216
cells, and the viruses allowed to incubate with the cells for 30mins at 37°C. After the
217
incubation, the cells were overlaid with 4ml per well of MEM/agar (1:1 ratio of 2% agar
218
and 2x MEM (Quality Biological, Gaithersburg, MD) with 4% FCS and 2x supplements). The
219
plates were incubated for 48hrs at 37°C with 5% CO2, after which 2ml of MEM/agar
220
containing 2% neutral red (Sigma Aldrich, St Louis, MO) was added to each well. The plates
221
were incubated for a further 24hrs before plaques were counted. For crystal violet staining
222
and immunostaining, the cells were fixed on Day 3 post infection with 10% buffered
223
formalin (Fisher Scientific, Waltham, MA) before the agar plugs were removed. Cells were
224
crystal violet stained using 0.25% crystal violet solution (Sigma Aldrich, St Louis, MO).
225
Immunostaining was carried out by permeabilizing the cells using 70% ethanol per well,
226
followed by incubation at -20°C for 30mins. The cells were blocked using PBS containing
227
0.5% I-Block (Thermo Scientific, Pittsburgh, PA). The primary antibody used was an anti-
228
WNV MIAF (T-35345) obtained from the WRCEVA. An HRP-conjugated anti-mouse
229
secondary antibody (Sigma Aldrich, St Louis, MO) was used with True Blue HRP substrate
230
(KPL, Gaithersburg, MD).
Manassas,
VA)
containing
8%
10
FCS
(HyClone,
Logan,
UT),
1x
231
Temperature sensitivity (TS) assays, which have previously been used as a marker of
232
possible attenuation of naturally-occurring and recombinant WNV variants (60-62), were
233
carried out as described above for the plaque assays. Duplicate plates were prepared for
234
each sample and, following the first MEM/agar overlay, one of the plates was incubated at
235
37°C, while the other was incubated at 41°C. Comparison of plaque count and morphology
236
at the two temperatures following the 72hrs total incubation and neutral red overlay was
237
used to determine temperature sensitivity.
238 239
Virus Stability
240
To compare the relative particle stability of the chimeric viruses, 1.2ml 1:20 dilutions of
241
each virus stock was prepared in MEM containing 2% FCS, with duplicate samples placed at
242
37°C and 4°C. 150μl of each duplicate sample was harvested after thorough vortexing at
243
0hr, 12hr, 24hr, 36hr, 48hr, and 72hr timepoints. The harvested samples were titrated in
244
12-well plates as described above for the plaque assays. The virus titers at each timepoint
245
were determined and normalized to the 0hr values to give a “percent remaining” value for
246
each sample. The normalized data were plotted using GraphPad Prism v6.0g (GraphPad, La
247
Jolla, CA), and fitted with a one-phase decay non-linear regression to determine particle
248
half lives with 95% confidence intervals.
249 250
Growth Kinetics
251
Vero and C6/36 cells were plated in T-25 tissue culture flasks. Cells in triplicate flasks for
252
each virus were infected with 1,000pfu virus, an MOI of 5x10-4, to allow for determination
253
of minor differences in growth kinetics. Inoculating doses were confirmed by back titration.
11
254
500μl aliquots of supernatant were removed daily on Days 0, 1, 2, 3, 4, and 5 post infection,
255
and were clarified by centrifugation prior to storage at -80°C until titration. Virus titers in
256
the samples were determined by plaque assay.
257 258
Western Blots
259
Cell lysates were prepared from the Vero cells used for the growth kinetics on Day 5 post
260
infection. Lysates were prepared using Invitrogen NuPAGE LDS sample buffer (Life
261
Technologies, Waltham, MA) and were heat inactivated at 95°C for 30mins before being
262
stored at -20°C until use. The non-reduced protein samples were run on 15-well NuPAGE
263
Novex 4-12% Bis-Tris protein gels (Life Technologies, Waltham, MA) using an XCell
264
SureLock Mini-Cell gel tank (Life Technologies, Waltham, MA), with loading volume
265
normalized by the band intensity with the flavivirus EII-reactive 4G2 monoclonal antibody
266
(EMD Millipore, Billerica, MA). Proteins were transferred to a nitrocellulose membrane (GE
267
Healthcare Life Sciences, Pittsburgh, PA) using an XCell II blot module (Life Technologies,
268
Waltham, MA). Following transfer, the blots were processed using a WesternBreeze
269
Chemiluminescent Mouse kit (Life Technologies, Waltham, MA) following the
270
manufacturers instructions. Anti-WNV EIII-specific monoclonal antibody 3A3 (BioReliance
271
Corp., Rockville, MD) and anti-JEV EIII monoclonal antibody ab81193 (Abcam, Cambridge,
272
MA) were used to determine EIII antigenic specificity. Mouse immune ascitic fluids (MIAF)
273
raised against WNV Lineage I, WNV Lineage II, JEV Nakayama, SLEV Parton, and BAGV
274
DakAr B209 were acquired from the WRCEVA collection. Previously described human sera
275
from WNV-infected patients were also used (63). For the human sera, an HRP-conjugated
276
anti-human IgG (Sigma Aldrich, St Louis, MO) was used with Pierce SuperSignal West
12
277
Femto (Thermo Fisher, Waltham, MA). Antibody binding was detected via exposure of
278
membranes to Amersham Hyperfilm ECL x-ray films (GE Healthcare Life Sciences,
279
Pittsburgh, PA) that were developed using a Kodak X-OMAT 2000 x-ray film processor
280
(Kodak, Rochester, NY).
281 282
Neutralization Assays
283
Vero cells were plated in 12-well plates and grown until approximately 90% confluent.
284
Once ready, serial 2-fold dilutions of MIAF and serum samples in duplicate were prepared
285
in 96-well plates in MEM containing 2% FCS to a total volume of 60μl per well. One well in
286
each dilution series contained MEM/2% FCS only as a negative control. Previously-titrated
287
virus stocks were diluted to a final concentration of 1,000pfu/ml with 60μl added to each
288
well, giving approximately 60pfu per well. The virus/antibody mixtures were incubated at
289
room temperature for an hour to allow for neutralization to occur. After the incubation,
290
100μl of the duplicate virus/antibody mixtures were added to each well on the 12-well
291
plate, with each plate also containing duplicate MEM/virus-only wells as a control. Plates
292
were incubated at room temperature for 30mins, before 2ml of MEM/agar overlay was
293
applied to each well. The plates were then incubated at 37°C with 5% CO2 for 48hrs, before
294
being fixed with 10% buffered formalin and immunostained as described above. Fifty
295
percent neutralization titer (NT50) values were determined for each virus/antibody
296
combination by identifying the dilutions of antibody that lead to a 50% reduction in focus
297
number in the well compared to the virus-only control wells.
298 299
13
300
Mouse Virulence Studies
301
3-4 week-old female Swiss Webster mice (Harlan, Indianapolis, IN) were used as the
302
animal model for WNV neuroinvasive disease, due to their susceptibility to infection with
303
the WNV NY99 strain following inoculation via various routes (64, 65). All of the mice were
304
housed in HEPA-filtered enclosures within the ABSL-3 facilities at UTMB, and were
305
provided with an unlimited supply of food and water. All animal studies were conducted in
306
accordance with protocols approved by the UTMB IACUC.
307 308
Virulence of the viable chimeric viruses compared to WNV NY99 was determined following
309
infection via the i.p. or i.c. route of groups of 5 or 10 mice with 10pfu (i.c.) and 100pfu (i.p.
310
and i.c.). The inocula were tested by back titration to confirm the virus dose. Mice were
311
checked daily for 21 days post infection for signs of infection, with checks increasing to
312
twice-daily once clinical signs started to develop.
313 314
Assessment of Virus Distributions in Infected Mice
315
Prior to infection, groups of five mice were anaesthetized and injected with subcutaneous
316
IPTT-300 transponders (BMDS, Seaford, DE) to allow for identification and temperature
317
measurements. Temperature and weight data was recorded daily throughout the course of
318
the experiment. On Day 0, five chipped mice, and an additional 15 unchipped mice, were
319
inoculated i.p. with 100pfu of WNV NY99 or viable chimeric viruses. The virus titer in the
320
inocula was confirmed by back titration. On Days 1, 3, 5, 7, and 9 post infection, groups of
321
three unchipped mice were selected at random for each virus and euthanised to collect
322
blood, via cardiac puncture, and tissues. Blood samples were dispensed into EDTA-
14
323
containing tubes (Sarstedt, Nümbrecht, Germany). Hematological analysis was carried out
324
on the whole blood using a Hemavet 950 instrument (Drew Scientific, Miami Lakes, FL).
325
Liver, spleen, kidney, lung, and brain samples were removed and deposited in pre-weighed
326
2ml homogenization tubes containing Lysing Matrix D (MP Biomedicals, Santa Ana, CA).
327 328
The anti-coagulated blood samples were centrifuged at room temperature for 5mins at
329
10,000g to recover out plasma, which was removed and stored at -80°C until needed. The
330
organ-containing tubes were weighed before and after addition of the tissue to determine
331
tissue weights. Organ weights were converted to volume equivalents (1mg≈1μl), with MEM
332
containing 2% FCS and 2x Penicillin/Streptomycin added to each homogenization tube to
333
reach a total volume of 500μl. Samples were homogenized using a Qiagen TissueLyser II
334
(Qiagen, Germantown, MD) set to full speed for two 90sec cycles. The samples were spun
335
down, and a further 500μl of medium was added to each tube for a total volume of 1ml. The
336
brain samples were frozen at -80°C until needed, while the other organs were further
337
homogenized for two 120sec cycles at full speed. The samples were centrifuged again and
338
stored at -80°C until needed. Virus titers in the plasma and organs were determined by
339
plaque assay starting at a 10-1 dilution, with titers reported per ml of plasma and per
340
100mg of tissue.
341 342
Statistical Analyses
343
Statistical analysis of growth kinetics, plaque sizes, organ titer, and hematology data was
344
performed by ANOVA with Bonferroni post-hoc analysis using Stata 14 (StataCorp, College
345
Station, TX). Survival curve analysis was performed using a Log-rank (Mantel-Cox) test
15
346
with GraphPad Prism v6.0g (GraphPad, La Jolla, CA). Comparison of average survival times
347
was performed using a two-tailed Student’s t-test with Microsoft Excel (Microsoft,
348
Redmond, WA).
349 350
Results
351
Viability of Chimeric Viruses
352
Of the 30 EIII chimeras generated using the WNV infectious clone plasmids, 16 resulted in
353
recoverable viruses: all four versions of the four donor viruses most similar to WNV (KOUV,
354
JEV, SLEV, and BAGV). Deep sequencing of the viable, recovered Passage 0 viruses revealed
355
only one non-synonymous mutation present at a frequency over 20%: an N222Y
356
substitution present at >80% frequency in each of the SLEV C/D and BAGV B/C chimeras.
357
Cells transfected with the inviable chimeric constructs failed to release infectious particles
358
into
359
Immunostaining of the electroporated cell monolayers revealed staining of individual cells
360
when an anti-WNV MIAF was used, but not when the anti-flavivirus EII mAb 4G2 was used
361
(data not shown), suggesting that E protein folding was impaired.
the
supernatant
following
electroporation
(as
determined
by
RT-PCR).
362 363
Antigenicity of Chimeric Viruses
364
Western blots performed using whole cell lysates prepared from Vero cells infected with
365
the A- or B-forms of the chimeras, as well as WNV NY99, showed similar reactivity with the
366
anti-flavivirus EII 4G2 mAb (Figure 2a). The anti-WNV EIII mAb 3A3 had slightly reduced
367
reactivity with the KOUV chimeras, and was not reactive with any of the other chimeras.
368
The anti-JEV EIII mAb (ab81193) was reactive with the JEV EIII A/B chimeras only. Specific
16
369
antibodies against the EIIIs of the other donor viruses were not available, so instead, mouse
370
immune ascitic fluids (MIAFs) raised against the donor viruses were used to compare
371
antigenicity changes associated with EIII substitutions (Figure 2b). Two anti-WNV MIAFs,
372
one against a Lineage I WNV strain and another against a Lineage II WNV strain, showed
373
strong binding with all the chimeras, most likely due to antibodies targeting epitopes in
374
domains I and II of the E protein that are retained in the chimeras. The JEV MIAF also
375
showed significant cross-reactivity, with band intensities for the JEV chimeras similar to
376
the other viruses, consistent with the closer antigenic relatedness of WNV and JEV. The
377
SLEV and BAGV MIAFs showed much less cross-reactivity. The BAGV MIAF only reacted
378
with the BAGV chimeras, in agreement with its grouping in the Ntaya, rather than the JE,
379
serocomplex.
380 381
Due to the higher recovery titers, greater apparent tolerance of the B-form EIII
382
substitutions, and the lack of distinct antigenic differences between the A- and B-forms, the
383
B-forms were utilized for further comparative characterization, and will henceforth be
384
referred to as WNV/JEV-EIII, WNV/KOUV-EIII, WNV/SLEV-EIII, and WNV/BAGV-EIII.
385 386
Plaque Morphology of Recovered Chimeric Viruses
387
Distinct and statistically significant differences were observed in plaque sizes between
388
WNV NY99 and some of the chimeras (Figure 3a,b). Ten representative plaques were
389
measured for each virus and compared by one-way ANOVA with Bonferroni correction. For
390
WNV NY99, plaques in Vero cells after 72hrs were large and distinct (3.60±0.52mm).
391
WNV/JEV-EIII had a mean plaque size 0.45mm smaller than WNV NY99 (3.15±0.47mm),
17
392
although this difference was not statistically significant (p>0.05). By contrast, WNV/KOUV-
393
EIII had a significantly smaller plaque size compared to WNV NY99 (2.30±0.42mm;
394
p
1
Recovery of West Nile Virus Envelope Protein Domain III Chimeras with
2
Altered Antigenicity and Mouse Virulence
3 4
Alexander J McAuley 1,2, Maricela Torres 1, Jessica A Plante 2,3*, Claire Y-H Huang 4,
5
Dennis A Bente 1,2,5,6, and David W C Beasley 1,2,5,6#
6 7
1Department
8
77555
9
2Institute
of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas,
for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
10
Texas, 77555
11
3Department
12
4Arbovirus
13
Prevention, U.S. Department of Health and Human Services, Fort Collins, Colorado, 80521
14
5Center
15
Galveston, Texas, 77555
16
6Sealy
17
77555
18
#Corresponding
19
*Current Address: Gillings School of Global Public Health, University of North Carolina, Chapel Hill,
20
NC, 27599
of Pathology, University of Texas Medical Branch, Galveston, Texas, 77550
Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and
for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch,
Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas,
Author: [email protected]
21 22
Running Title: Flavivirus Receptor-Binding Domain Chimeras
23
Word Count (Abstract): 191
24
Word Count (Text): 6773
1
25
Abstract
26
Flaviviruses are positive-sense, single-stranded RNA viruses responsible for millions of
27
human infections annually. The envelope (E) protein of flaviviruses comprises three
28
structural domains, of which domain III (EIII) represents a discrete subunit. EIII typically
29
encodes epitopes recognized by virus-specific, potently neutralizing antibodies and is
30
believed to play a major role in receptor binding. In order to assess potential interactions
31
between EIII and the remainder of the E protein, and to assess effects of EIII sequence
32
substitutions on antigenicity, growth, and virulence of a representative flavivirus, chimeric
33
viruses were generated using the West Nile virus (WNV) infectious clone, into which EIIIs
34
from nine flaviviruses of varying genetic diversity from WNV were substituted. Of the
35
constructs tested, chimeras containing EIIIs from Koutango virus (KOUV), Japanese
36
encephalitis virus (JEV), St Louis encephalitis virus (SLEV), and Bagaza virus (BAGV) were
37
successfully recovered. Characterization of the chimeras in vitro and in vivo revealed
38
differences in growth and virulence between the viruses, with in vivo pathogenesis often
39
not correlated to in vitro growth. Taken together, the data demonstrate that substitutions
40
of EIII can allow for the generation of viable chimeric viruses with significantly altered
41
antigenicity and virulence.
42 43 44 45 46 47
2
48
Importance
49
The envelope (E) glycoprotein is the major protein present on the surface of flavivirus
50
virions, and is responsible for mediating virus binding and entry into target cells. Several
51
viable West Nile virus (WNV) variants were recovered with chimeric E proteins in which
52
the putative receptor-binding domain (EIII) sequences of other mosquito-borne
53
flaviviruses were substituted in place of the WNV EIII, although substitution of several
54
more divergent EIII sequences were not tolerated. The differences in virulence and tissue
55
tropism observed with the chimeric viruses indicate a significant role for this sequence in
56
determining the pathogenesis of the virus within the mammalian host. Our studies
57
demonstrate that these chimeras are viable, and suggest that such recombinant viruses
58
may be useful to investigate domain-specific antibody responses and to more extensively
59
define the contributions of EIII to tropism and pathogenesis of WNV or other flaviviruses.
60 61 62 63 64 65 66 67 68 69 70
3
71
Introduction
72
The flaviviruses are a large genus of viruses with positive-sense, single-stranded RNA
73
genomes, responsible for significant global morbidity and mortality (1). The fact that the
74
majority are vector-borne, carried by either by ticks or mosquitoes, allows for a wide
75
geographical distribution and ready transmission to humans. The clinical manifestations of
76
flavivirus infections in humans vary considerably, with many causing non-specific febrile
77
illnesses that may progress to more severe syndromes including hemorrhagic fever or
78
encephalitis (1).
79 80
The surface of mature flavivirus virions is primarily comprised of 180 copies of the
81
envelope (E) glycoprotein (2). As a result, the E protein is involved in the major steps of
82
virus entry into susceptible cells, including the mediation of receptor binding and fusion
83
between the viral envelope and host endosomal membranes allowing for the release of the
84
viral genomic RNA into the cell cytoplasm for replication (3-6). These roles require
85
considerable rearrangement of the E proteins on the surface of the mature virion, with
86
important intra- and intermolecular interactions occurring at each stage (3, 7). Structurally,
87
E may be divided into three major domains: EI, which in many WNV strains includes the
88
single glycosylation motif; EII, which contains the flavivirus-conserved fusion loop; and
89
EIII, the putative receptor-binding domain (8). Although all three domains of the E protein
90
appear to contribute to interactions with target cell ligands in different experimental
91
systems, data that support a significant role for EIII in receptor binding come from
92
investigations into competition between recombinant EIII molecules and infectious virions
93
for adsorption to cell surfaces (9-11), immunological studies using neutralizing monoclonal
4
94
antibodies targeting EIII (12), the generation of mutant viruses containing particular amino
95
acid substitutions in EIII (13-19), and DENV E fusion proteins (6). Studies of EIII protein
96
subunits derived from different mosquito and tick-borne flaviviruses have identified virus-
97
specific differences in antigenicity, surface biochemistry, and structure, which further
98
support a role for EIII as a key determinant of ligand binding and cell tropism for individual
99
flavivirus types (20-28).
100 101
Construction of chimeric flaviviruses, whereby segments of genome from one virus are
102
substituted into the genome of a different flavivirus, has been used to investigate the roles
103
of individual viral proteins in virulence or other phenotypes, or to develop candidate
104
vaccines and diagnostic reagents. Previous structural protein chimeric flaviviruses have
105
involved the substitution of the coding sequences for complete structural proteins, usually
106
prM and E, from a donor virus into a backbone virus (29-56). These chimeric viruses have
107
the antigenic characteristics of the donor structural proteins, and characterization of
108
several has also identified significant shifts in in vitro growth and/or in vivo virulence
109
phenotypes, consistent with the importance of the structural proteins, and E in particular,
110
in those phenotypes. For example, the substitution of prM-E from TBEV into DENV-4
111
significantly affected the behavior of the virus both in vitro and in vivo, with growth in LLC-
112
MK2 cells resulting in higher peak titers with the chimeric virus compared to the DENV-4
113
control and increased neurovirulence following i.c. administration compared to infections
114
with the equivalent dose of DENV-4 (30). Similar prM-E chimeras comprised of TBEV and
115
OHFV as donor and backbone virus, respectively, showed significantly earlier
5
116
neuroinvasion by the chimera compared to the OHFV control, further indicating that the
117
structural proteins can affect the behavior of the virus (52).
118 119
To date, few studies have attempted to generate chimeric proteins (i.e. containing
120
domains/regions derived from two or more different flaviviruses) and incorporate them
121
into a viable virus. Given the discrete nature of EIII within the flavivirus E protein, as well
122
as its role in receptor binding and as a target for virus-specific neutralizing antibodies, we
123
hypothesized that substitution of EIII sequences between some flaviviruses would yield
124
viable viruses, but would likely be associated with significant changes in growth, virulence,
125
and/or antigenicity of the resulting chimeras. Therefore, the aims of this study were (1) to
126
determine whether viable chimeras could be generated via the substitution of the EIII
127
protein domain alone (i.e. chimerization of the E protein), and (2) to assess the effects of
128
EIII substitutions on the in vitro growth and in vivo pathogenesis of these chimeras. West
129
Nile virus (WNV), an encephalitic, mosquito-borne flavivirus, was used as the backbone
130
virus for these initial investigations due to the availability of a well-characterized infectious
131
clone system (57) and small animal neuroinvasive disease models.
132 133
Materials and Methods
134
WNV NY99 Infectious Clone and EIII Donor Viruses
135
For the generation of chimeric viruses, a previously-described WNV infectious clone
136
system was employed (57, 58). Briefly, the infectious clone consisted of two plasmids:
137
pWN-AB, which contained the 5’ UTR and the structural protein coding region; and pWN-
138
CG, which contained the non-structural protein coding region and the 3’ UTR. For virus
6
139
recovery, the two plasmids were digested with XbaI and NgoMIV (New England Biolabs,
140
Ipswich, MA) and ligated together after purification. The ligated full-length plasmid was
141
linearized with XbaI, and full-length genome-equivalent RNA was produced by in vitro
142
transcription from a T7 promoter upstream of the coding sequence using an Ampliscribe
143
T7-Flash in vitro Transcription kit (Epicentre Biotechnologies, Madison, WI). Virus
144
recovery was carried out by electroporating the in vitro transcribed RNA in to Vero cells
145
(ATCC, Manassas, VA) using an Invitrogen Neon Transfection System (Life Technologies,
146
Waltham, MA).
147 148
Four unique restriction sites (SalI at nt1829-1834; PstI at nt1859-1864; StuI at nt2183-
149
2188; and BamHI at nt2251-2256) were engineered into the pWN-AB plasmid by site-
150
directed mutagenesis using the QuikChange XL and Multi kits (Agilent Technologies, Santa
151
Clara, CA). The locations of the sites were chosen based upon the strongly conserved amino
152
acid sequences in these regions amongst many of the flaviviruses. Three of the four
153
mutations were silent at the amino acid level; however, the SalI site resulted in a
154
conservative V290L amino acid substitution in E. This substitution has been identified in
155
natural, pathogenic isolates of WNV, including the T2 strain from Turkey (59). Nine EIII
156
donor viruses were used of increasing genetic diversity from WNV (Table 1). cDNA for all
157
but one of the viruses was derived from isolated viral RNA obtained from the World
158
Reference Center for Emerging Viruses and Arboviruses (WRCEVA) at UTMB. The ZIKV EIII
159
sequence was amplified from a synthetic construct purchased from Bio Basic (Bio Basic
160
Inc., Markham, ON) based upon the published accession number NC_012532.
161
7
162
Construction of Chimeric Plasmids
163
Viral RNA was extracted from culture supernatant samples of each donor virus using
164
TRIzol (Thermo Fisher Scientific, Waltham, MA), with RNA purification performed using
165
the Zymo Direct-Zol RNA purification kit (Zymo Research Corp., Irvine, CA). Reverse
166
transcription to generate viral cDNA was performed using NEB AMV Reverse Transcriptase
167
(New England Biolabs, Ipswich, MA). EIII inserts were amplified from cDNA generated from
168
viral genomic RNA or synthetic plasmid using the Roche High Fidelity PCR Master Mix
169
(Roche, Indianapolis, IN). The PCR products were separated by agarose gel electrophoresis
170
and purified using a Qiagen QIAquick Gel Extraction kit (Qiagen, Germantown, MD). Both
171
the purified PCR products and backbone plasmids were digested with the appropriate
172
restriction enzyme pairs (New England Biolabs, Ipswich, MA).
173 174
For seven of the EIII donor virus, four chimera versions were generated using each
175
combination of the up- and downstream restriction sites, denoted A, B, C, and D (Figure 1a).
176
For YFV and DTV, only the A- and B-form chimeric plasmids were generated. Based on the
177
location of the restriction sites, the B-form (PstI-StuI) had the smallest insert, consisting
178
solely of EIII, whereas the A-form (SalI-BamHI) was the largest substitution, containing
179
part of EI upstream of the EI/EIII linker region, and the first stem-helix region downstream.
180
The C- and D-forms (SalI-StuI and PstI-BamHI, respectively) had the additional upstream
181
and downstream sequences, respectively. For the B-forms, an infectious clone AB plasmid
182
containing just PstI and StuI sites was used, thereby allowing for chimeras to be generated
183
without the SalI-associated V290L substitution.
184
8
185
The digested plasmids and inserts were gel purified and ligated overnight at 4°C using T4
186
DNA ligase (New England Biolabs, Ipswich, MA). The ligated plasmids were sequenced to
187
confirm identity, and were transformed into DH5α E. coli, from which glycerol stocks were
188
generated for storage. Chimeric viruses were recovered following ligation of full-length
189
genomic cDNA, in vitro transcription and electroporation of the RNA into Vero cells as
190
described above.
191 192
Construction of EIII chimeras using the WNV infectious clone was approved by the
193
University of Texas Medical Branch Institutional Biosafety Committee. Only EIII sequences
194
derived from viruses of the same or lower biosafety level were used for attempts at
195
chimerization, and all transfected cell cultures were handled under BSL-3 conditions. All
196
subsequent experimentation with viable chimeric viruses occurred under BSL-3/ABSL-3
197
conditions.
198 199
Nucleotide Sequencing
200
Chimeric infectious clone plasmids and PCR-amplified viral cDNA generated from TRIzol-
201
extracted RNA from cell culture supernatant were submitted to the UTMB Molecular
202
Genomics core facility for sequence determination using an Applied Biosystems 3130xl
203
DNA Sequencer (Applied Biosystems, Waltham, MA). Whole genome sequences for
204
recovered and serially-passaged chimeric viruses were determined from purified viral RNA
205
samples at the UTMB Next Generation Sequencing core facility using an Illumina HiSeq
206
1500 Next Generation sequencer (Illumina Inc., San Diego, CA).
207
9
208
Plaque, Immunofocus, and Temperature Sensitivity Assays
209
Virus titration was carried out in Vero cells grown in minimal essential medium (MEM;
210
Corning,
211
Penicillin/Streptomycin (Corning, Manassas, VA), 1x Non-Essential Amino Acids (Corning,
212
Manassas, VA), and 1x L-glutamine (Life Technologies, Waltham, MA). Cells were plated in
213
6-well plates, and grown until approximately 90% confluence. Virus culture supernatant
214
samples, sera, or homogenized organs were serially 10-fold diluted (typically 10-2 to 10-7
215
dilutions) in MEM containing 2% FCS. The diluted samples were transferred to the plated
216
cells, and the viruses allowed to incubate with the cells for 30mins at 37°C. After the
217
incubation, the cells were overlaid with 4ml per well of MEM/agar (1:1 ratio of 2% agar
218
and 2x MEM (Quality Biological, Gaithersburg, MD) with 4% FCS and 2x supplements). The
219
plates were incubated for 48hrs at 37°C with 5% CO2, after which 2ml of MEM/agar
220
containing 2% neutral red (Sigma Aldrich, St Louis, MO) was added to each well. The plates
221
were incubated for a further 24hrs before plaques were counted. For crystal violet staining
222
and immunostaining, the cells were fixed on Day 3 post infection with 10% buffered
223
formalin (Fisher Scientific, Waltham, MA) before the agar plugs were removed. Cells were
224
crystal violet stained using 0.25% crystal violet solution (Sigma Aldrich, St Louis, MO).
225
Immunostaining was carried out by permeabilizing the cells using 70% ethanol per well,
226
followed by incubation at -20°C for 30mins. The cells were blocked using PBS containing
227
0.5% I-Block (Thermo Scientific, Pittsburgh, PA). The primary antibody used was an anti-
228
WNV MIAF (T-35345) obtained from the WRCEVA. An HRP-conjugated anti-mouse
229
secondary antibody (Sigma Aldrich, St Louis, MO) was used with True Blue HRP substrate
230
(KPL, Gaithersburg, MD).
Manassas,
VA)
containing
8%
10
FCS
(HyClone,
Logan,
UT),
1x
231
Temperature sensitivity (TS) assays, which have previously been used as a marker of
232
possible attenuation of naturally-occurring and recombinant WNV variants (60-62), were
233
carried out as described above for the plaque assays. Duplicate plates were prepared for
234
each sample and, following the first MEM/agar overlay, one of the plates was incubated at
235
37°C, while the other was incubated at 41°C. Comparison of plaque count and morphology
236
at the two temperatures following the 72hrs total incubation and neutral red overlay was
237
used to determine temperature sensitivity.
238 239
Virus Stability
240
To compare the relative particle stability of the chimeric viruses, 1.2ml 1:20 dilutions of
241
each virus stock was prepared in MEM containing 2% FCS, with duplicate samples placed at
242
37°C and 4°C. 150μl of each duplicate sample was harvested after thorough vortexing at
243
0hr, 12hr, 24hr, 36hr, 48hr, and 72hr timepoints. The harvested samples were titrated in
244
12-well plates as described above for the plaque assays. The virus titers at each timepoint
245
were determined and normalized to the 0hr values to give a “percent remaining” value for
246
each sample. The normalized data were plotted using GraphPad Prism v6.0g (GraphPad, La
247
Jolla, CA), and fitted with a one-phase decay non-linear regression to determine particle
248
half lives with 95% confidence intervals.
249 250
Growth Kinetics
251
Vero and C6/36 cells were plated in T-25 tissue culture flasks. Cells in triplicate flasks for
252
each virus were infected with 1,000pfu virus, an MOI of 5x10-4, to allow for determination
253
of minor differences in growth kinetics. Inoculating doses were confirmed by back titration.
11
254
500μl aliquots of supernatant were removed daily on Days 0, 1, 2, 3, 4, and 5 post infection,
255
and were clarified by centrifugation prior to storage at -80°C until titration. Virus titers in
256
the samples were determined by plaque assay.
257 258
Western Blots
259
Cell lysates were prepared from the Vero cells used for the growth kinetics on Day 5 post
260
infection. Lysates were prepared using Invitrogen NuPAGE LDS sample buffer (Life
261
Technologies, Waltham, MA) and were heat inactivated at 95°C for 30mins before being
262
stored at -20°C until use. The non-reduced protein samples were run on 15-well NuPAGE
263
Novex 4-12% Bis-Tris protein gels (Life Technologies, Waltham, MA) using an XCell
264
SureLock Mini-Cell gel tank (Life Technologies, Waltham, MA), with loading volume
265
normalized by the band intensity with the flavivirus EII-reactive 4G2 monoclonal antibody
266
(EMD Millipore, Billerica, MA). Proteins were transferred to a nitrocellulose membrane (GE
267
Healthcare Life Sciences, Pittsburgh, PA) using an XCell II blot module (Life Technologies,
268
Waltham, MA). Following transfer, the blots were processed using a WesternBreeze
269
Chemiluminescent Mouse kit (Life Technologies, Waltham, MA) following the
270
manufacturers instructions. Anti-WNV EIII-specific monoclonal antibody 3A3 (BioReliance
271
Corp., Rockville, MD) and anti-JEV EIII monoclonal antibody ab81193 (Abcam, Cambridge,
272
MA) were used to determine EIII antigenic specificity. Mouse immune ascitic fluids (MIAF)
273
raised against WNV Lineage I, WNV Lineage II, JEV Nakayama, SLEV Parton, and BAGV
274
DakAr B209 were acquired from the WRCEVA collection. Previously described human sera
275
from WNV-infected patients were also used (63). For the human sera, an HRP-conjugated
276
anti-human IgG (Sigma Aldrich, St Louis, MO) was used with Pierce SuperSignal West
12
277
Femto (Thermo Fisher, Waltham, MA). Antibody binding was detected via exposure of
278
membranes to Amersham Hyperfilm ECL x-ray films (GE Healthcare Life Sciences,
279
Pittsburgh, PA) that were developed using a Kodak X-OMAT 2000 x-ray film processor
280
(Kodak, Rochester, NY).
281 282
Neutralization Assays
283
Vero cells were plated in 12-well plates and grown until approximately 90% confluent.
284
Once ready, serial 2-fold dilutions of MIAF and serum samples in duplicate were prepared
285
in 96-well plates in MEM containing 2% FCS to a total volume of 60μl per well. One well in
286
each dilution series contained MEM/2% FCS only as a negative control. Previously-titrated
287
virus stocks were diluted to a final concentration of 1,000pfu/ml with 60μl added to each
288
well, giving approximately 60pfu per well. The virus/antibody mixtures were incubated at
289
room temperature for an hour to allow for neutralization to occur. After the incubation,
290
100μl of the duplicate virus/antibody mixtures were added to each well on the 12-well
291
plate, with each plate also containing duplicate MEM/virus-only wells as a control. Plates
292
were incubated at room temperature for 30mins, before 2ml of MEM/agar overlay was
293
applied to each well. The plates were then incubated at 37°C with 5% CO2 for 48hrs, before
294
being fixed with 10% buffered formalin and immunostained as described above. Fifty
295
percent neutralization titer (NT50) values were determined for each virus/antibody
296
combination by identifying the dilutions of antibody that lead to a 50% reduction in focus
297
number in the well compared to the virus-only control wells.
298 299
13
300
Mouse Virulence Studies
301
3-4 week-old female Swiss Webster mice (Harlan, Indianapolis, IN) were used as the
302
animal model for WNV neuroinvasive disease, due to their susceptibility to infection with
303
the WNV NY99 strain following inoculation via various routes (64, 65). All of the mice were
304
housed in HEPA-filtered enclosures within the ABSL-3 facilities at UTMB, and were
305
provided with an unlimited supply of food and water. All animal studies were conducted in
306
accordance with protocols approved by the UTMB IACUC.
307 308
Virulence of the viable chimeric viruses compared to WNV NY99 was determined following
309
infection via the i.p. or i.c. route of groups of 5 or 10 mice with 10pfu (i.c.) and 100pfu (i.p.
310
and i.c.). The inocula were tested by back titration to confirm the virus dose. Mice were
311
checked daily for 21 days post infection for signs of infection, with checks increasing to
312
twice-daily once clinical signs started to develop.
313 314
Assessment of Virus Distributions in Infected Mice
315
Prior to infection, groups of five mice were anaesthetized and injected with subcutaneous
316
IPTT-300 transponders (BMDS, Seaford, DE) to allow for identification and temperature
317
measurements. Temperature and weight data was recorded daily throughout the course of
318
the experiment. On Day 0, five chipped mice, and an additional 15 unchipped mice, were
319
inoculated i.p. with 100pfu of WNV NY99 or viable chimeric viruses. The virus titer in the
320
inocula was confirmed by back titration. On Days 1, 3, 5, 7, and 9 post infection, groups of
321
three unchipped mice were selected at random for each virus and euthanised to collect
322
blood, via cardiac puncture, and tissues. Blood samples were dispensed into EDTA-
14
323
containing tubes (Sarstedt, Nümbrecht, Germany). Hematological analysis was carried out
324
on the whole blood using a Hemavet 950 instrument (Drew Scientific, Miami Lakes, FL).
325
Liver, spleen, kidney, lung, and brain samples were removed and deposited in pre-weighed
326
2ml homogenization tubes containing Lysing Matrix D (MP Biomedicals, Santa Ana, CA).
327 328
The anti-coagulated blood samples were centrifuged at room temperature for 5mins at
329
10,000g to recover out plasma, which was removed and stored at -80°C until needed. The
330
organ-containing tubes were weighed before and after addition of the tissue to determine
331
tissue weights. Organ weights were converted to volume equivalents (1mg≈1μl), with MEM
332
containing 2% FCS and 2x Penicillin/Streptomycin added to each homogenization tube to
333
reach a total volume of 500μl. Samples were homogenized using a Qiagen TissueLyser II
334
(Qiagen, Germantown, MD) set to full speed for two 90sec cycles. The samples were spun
335
down, and a further 500μl of medium was added to each tube for a total volume of 1ml. The
336
brain samples were frozen at -80°C until needed, while the other organs were further
337
homogenized for two 120sec cycles at full speed. The samples were centrifuged again and
338
stored at -80°C until needed. Virus titers in the plasma and organs were determined by
339
plaque assay starting at a 10-1 dilution, with titers reported per ml of plasma and per
340
100mg of tissue.
341 342
Statistical Analyses
343
Statistical analysis of growth kinetics, plaque sizes, organ titer, and hematology data was
344
performed by ANOVA with Bonferroni post-hoc analysis using Stata 14 (StataCorp, College
345
Station, TX). Survival curve analysis was performed using a Log-rank (Mantel-Cox) test
15
346
with GraphPad Prism v6.0g (GraphPad, La Jolla, CA). Comparison of average survival times
347
was performed using a two-tailed Student’s t-test with Microsoft Excel (Microsoft,
348
Redmond, WA).
349 350
Results
351
Viability of Chimeric Viruses
352
Of the 30 EIII chimeras generated using the WNV infectious clone plasmids, 16 resulted in
353
recoverable viruses: all four versions of the four donor viruses most similar to WNV (KOUV,
354
JEV, SLEV, and BAGV). Deep sequencing of the viable, recovered Passage 0 viruses revealed
355
only one non-synonymous mutation present at a frequency over 20%: an N222Y
356
substitution present at >80% frequency in each of the SLEV C/D and BAGV B/C chimeras.
357
Cells transfected with the inviable chimeric constructs failed to release infectious particles
358
into
359
Immunostaining of the electroporated cell monolayers revealed staining of individual cells
360
when an anti-WNV MIAF was used, but not when the anti-flavivirus EII mAb 4G2 was used
361
(data not shown), suggesting that E protein folding was impaired.
the
supernatant
following
electroporation
(as
determined
by
RT-PCR).
362 363
Antigenicity of Chimeric Viruses
364
Western blots performed using whole cell lysates prepared from Vero cells infected with
365
the A- or B-forms of the chimeras, as well as WNV NY99, showed similar reactivity with the
366
anti-flavivirus EII 4G2 mAb (Figure 2a). The anti-WNV EIII mAb 3A3 had slightly reduced
367
reactivity with the KOUV chimeras, and was not reactive with any of the other chimeras.
368
The anti-JEV EIII mAb (ab81193) was reactive with the JEV EIII A/B chimeras only. Specific
16
369
antibodies against the EIIIs of the other donor viruses were not available, so instead, mouse
370
immune ascitic fluids (MIAFs) raised against the donor viruses were used to compare
371
antigenicity changes associated with EIII substitutions (Figure 2b). Two anti-WNV MIAFs,
372
one against a Lineage I WNV strain and another against a Lineage II WNV strain, showed
373
strong binding with all the chimeras, most likely due to antibodies targeting epitopes in
374
domains I and II of the E protein that are retained in the chimeras. The JEV MIAF also
375
showed significant cross-reactivity, with band intensities for the JEV chimeras similar to
376
the other viruses, consistent with the closer antigenic relatedness of WNV and JEV. The
377
SLEV and BAGV MIAFs showed much less cross-reactivity. The BAGV MIAF only reacted
378
with the BAGV chimeras, in agreement with its grouping in the Ntaya, rather than the JE,
379
serocomplex.
380 381
Due to the higher recovery titers, greater apparent tolerance of the B-form EIII
382
substitutions, and the lack of distinct antigenic differences between the A- and B-forms, the
383
B-forms were utilized for further comparative characterization, and will henceforth be
384
referred to as WNV/JEV-EIII, WNV/KOUV-EIII, WNV/SLEV-EIII, and WNV/BAGV-EIII.
385 386
Plaque Morphology of Recovered Chimeric Viruses
387
Distinct and statistically significant differences were observed in plaque sizes between
388
WNV NY99 and some of the chimeras (Figure 3a,b). Ten representative plaques were
389
measured for each virus and compared by one-way ANOVA with Bonferroni correction. For
390
WNV NY99, plaques in Vero cells after 72hrs were large and distinct (3.60±0.52mm).
391
WNV/JEV-EIII had a mean plaque size 0.45mm smaller than WNV NY99 (3.15±0.47mm),
17
392
although this difference was not statistically significant (p>0.05). By contrast, WNV/KOUV-
393
EIII had a significantly smaller plaque size compared to WNV NY99 (2.30±0.42mm;
394
p
