Difference between revisions of "Team:Wageningen UR/Results/Viral Antigens"

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<h4>Viral Antigens</h4>
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<a href="#Intro">Introduction</a>
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<a href="#VLP">Virus Like Particles</a>
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<li>Viral Antigens</li>
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<h1>Production of Viral Antigens</h1> </div>
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<p>In order to safely produce viral antigens for phage display, two different approaches were taken. The first focuses on the production of enveloped Virus-Like-Particles (VLPs) for chikungunya (CHIKV), Zika (ZIKV) and Mayaro (MAYV). These particles are noninfectious and widely used as vaccines for various viral diseases. The second approach is to produce secreted Strep-tagged antigens for alphaviruses. These antigens can be purified easier and can be directly linked to Strep-tactin beads for antigen display in the <a href="https://2017.igem.org/Team:Wageningen_UR/Results/Phage_Display" target="_blank">phage-panning.</a>
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Three viruses were chosen for the production of antigens; two alphaviruses (CHIKV and MAYV) and one flavivirus (ZIKV). The VLPs were produced using the Invitrogen<sup>TM</sup> Bac-to-Bac<sup>®</sup> Baculovirus Expression System [1]. The baculovirus expression system is widely used in biotechnology for high yield recombinant protein expression by exploiting the life cycle of the virus in insect cells [2,3]. The advantage of using insect cells is the accurate post-translational modifications (phosphorylation, chaperone-assisted folding, glycosylation etc.) which cannot be achieved in <i>E. coli.</i>. To generate the CHIKV, ZIKV and MAYV VLPs, the genes encoding the viral structural proteins for the specific virus were placed downstream of the very strong polyhedrin promotor of the baculovirus, in this case <i>Autographa californica</i> multicapsid nucleopolyhedrovirus (AcMNPV). The recombinant baculovirus DNA is then used to transfect a <i>Spodoptera frugiperda (Sf-21)</i> cell line in order to produce recombinant baculoviruses expressing the VLPs. </p><p>
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Wageningen University & Research has constructs available for ZIKV and CHIKV [4], but not for MAYV. As the generation of such virus-like particles is similar, only the generation of MAYV VLPs will be described below.
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MAYV genomic RNA was isolated from a Trizol sample. After the integrity and yield of the MAYV RNA was checked, cDNA was generated using Superscript RTII according to the <a href="https://static.igem.org/mediawiki/2017/6/6c/Cloning_and_DNA_Manipulation.pdf" target="_blank">cDNA generation protocol.</a> Gene-specific primers were ordered to amplify the structural polyprotein gene with attB1/2 overhangs (Gateway), after which Phusion PCR was used to generate the MAYV amplicon.<br>
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A BP Gateway reaction was used to insert the MAYV amplicon in a pDONR207 vector, followed by an LR Gateway reaction to move the fragment to the pDEST8 baculovirus expression vector. In parallel the fragment was directly cloned into pFastBacDual (pFBD), another baculovirus expression vector used in the Bac-to-Bac® system. Both vectors (pFBD and pDEST8) place the MAYV polyprotein gene downstream the strong polyhedrin promotor. The plasmids were checked using restriction analysis, colony PCR and sequencing. The resulting expression clones are abbreviated MAYV-D (pDEST8 derived) and MAYV-F (pFBD derived). Both constructs were used in the Bac-to-Bac® system, the resulting 136kb bacmids (plasmids containing AcMNPV DNA) were confirmed using colony PCR and isolated using the <a href="https://static.igem.org/mediawiki/2017/3/32/VLP_Generation.pdf" target="_blank">bacmid isolation protocol.</a><br>
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Bacmids of MAYV-D and MAYV-F were used to transfect an <i>Sf-21</i> at cell-line using ExpreS2 transfection reagent in a 6 wells plate, a healthy cell line was used as control/mock. The baculovirus infection was observed for 72 hours. The medium was then replaced, and the cells were moved to a T25 flask. After 48 hour the infection was clearly visible, as can be observed in Figure A.
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<b>Figure A: </b> Transfection of <i>Sf</i>-21 with bacmid containing MAYV structural casette. T=48 hour, prior to harvesting.
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The infected cells are enlarged, and show some degree of capsid bodies in the nucleus, which might indicate the presence of MAYV capsids. The AcMNPV-MAYV-D and AcMNPV-MAYV-F baculoviruses were harvested, titrated, and the passage 0 (P0) stock was used to infect <i>Sf21</i> cells in a T25 flask at 50% confluency with an multiplicity of infection (MOI) of 5. Six days post infection the cells and medium were harvested.
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<b>Figure B: </b> Western blot of <i>Sf/</i>-21 cells infected with AcMNPV-MAYV, cell fraction and medium fraction, 5.5D11 Alphavirus capsid antibody. Expected size: 35kDa. Blot on right is a repead due to overloading of CHIKV lane (positive control). The coloring reaction was performed using secondary antibodies with alkaline phosphatase.
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Western blot with specific antibody (<a href="https://static.igem.org/mediawiki/2017/3/32/VLP_Generation.pdf" target="_blank">Semi-dry blotting protocol</a>) was used to determine the presence of the alphavirus capsid, as seen in Figure B. Furthermore, 10 ml of medium was precipitated and VLP's were purified using ultracentrifugation (UC) accoding to the <a href="https://static.igem.org/mediawiki/2017/3/32/VLP_Generation.pdf" target="_blank">UC protocol</a>. The isolated fraction was analyzed using Transmission Electron Microscopy, as can be seen in Figure 1.
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<b>Figure 1: </b>Transmission Electron Microscopy of MAYV VLP samples, stained with uranyl acetate. Pictures taken using JEOL JEM1400.
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Figure 1 shows the particles in the purified VLP fractions. The particle are spherical and sized approximately 70nm in diameter. Immunogold staining could be used to confirm this hypothesis. Virus-Like Particles for chikungunya and Zika virus were produced in a similar fashion.
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Next to producing VLPs, strep-tagged surface glycoproteins of CHIKV were also produced. The benefit of these proteins is the ease of purification compared to VLPs, whilst offering comparable antigenic properties. The schematic structure of the surface glycoproteins is depicted in Figure 2 [5]. The native CHIKV polyprotein is cleaved into the individual E1 and E2 glcyoproteins, which are transported to the plasma membrane. There, they are taken up by budding nucleocapsids, resulting in mature, enveloped virions [6]. The introduction of a linker between E2 and E1 as well as the instruction of a strep-tag bypasses the need for membrane anchoring and yields secreted proteins, which are easily purified. The constructs for CHIKV secreted glycosylated trimeric E-protein were produced by a MSc student at the Wageningen University & Research. As with the production of the VLPs, the production of the Strep-tagged CHIKV-E uses the Bac-to-Bac<sup>®</sup> system as well.
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<b>Figure 2: </b> Schematic overview of CHIKV-E protein membrane organization of native and recombinant surface proteins, adapted from Voss <i>et al.</i> (2010).
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                            <p>In order to fully implement the point of care nature of our diagnostic, we developed a small battery powered device, which is easily brought into the field. The device is capable of measuring the fluorescence produced by our bacterial diagnostic system. The addition of a GPS sensor tags the location of the measurement for epidemiological analysis. By using 3D printing as well as the open source Arduino system, we were capable of producing an affordable product.
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                                                    Brainstorming and initial designs
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An AcMNPV clone containing the Strep-tagged CHIKV-E was available at the Laboratory of Virology at Wageningen University & Research. <i>Sf21</i> cells were infected with a MOI of 5. The infection was observed for 7 days, after which the infection was harvested. As the CHIKV-E spikes are secreted, the medium fraction could be used directly. The binding of the CHIKV-E protein was tested using Sepharose-Strep-Tactin beads. 2ml of 50% resin beads suspension was added to 10ml harvested medium and incubated for 1 hour at 4C. The beads were washed and eluted using biotin in an empty column. Various fractions were loaded on an SDS gel and subsequently semi-dry-blotted. Western blot analysis with a specific antibody for CHIKV-E was used to detect the CHIKV-E protein.
  
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                                            Working off the idea that we wanted a portable device quickly led us to a consumer 3D printer allowing us to do rapid prototyping. The printer we used is an Ultimaker 2+ provided to us by Ultimaker. We wanted a device that could show a fluorescent signal so we came we came up with our first designs. The fluorescent molecules produced by our system are excited by UV-LED’s with a specific wavelength. The emission spectrum is visible by the naked eye and this is how we planned to read out the signal. The membrane sealed sample vials containing our bacterial system are placed in the device from the top. Initially we started off with a device which fits one sample. However we soon realised that adding a positive and negative control makes out device more reliable. Once the button is pressed the UV-LED’s are turned on and the signal can be compared to the positive and negative control in order to determine the result. This approach was problematic since lighting conditions, background signal and observers are not a set variable. This prompted us rethink the way the device works and version 2 was on the way.
 
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                                                    The first prototype
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<b>Figure 3: </b>Western blot of Sepharose-Strep-Tactin beads with CHIKV-E spikes. Fractions: pre, first flow through, last flow trough, last wash, elution 1-5.
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                                            The first working prototype included space for 3 membrane sealed sample vials, a positive control, the sample and a negative control. In order to take out the variables of the lighting conditions, background signal and observers we wanted to use cheap and simple electronics in order to read off the signal. This led to the removal of the ‘windows’ in the front and a bulkier design to accommodate the electronics. The improved computational approach to read off the signal was based on Light Depended Resistors (LDR). This component changes its resistance according to the amount of light that it receives. This resistance can be measured via a simple circuit (See Figure) and processed by the arduino microprocessor. Once the button is pressed the device excites the sample vials with UV light and the emission spectrum is detected by the LDR’s. The signal of the sample is compared to the positive and negative control and the final result is displayed on an integrated OLED display on the front. Although this is a mayor improvement over trying to detect the signal by eye, this way of detecting the light is unreliable.
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As can be seen in Figure 3, the strep-tactin sepharose beads are capable of catching the strep-tagged CHIKV-E proteins. The experiment was repeated to cover a total of 6ml strep-tactin sepharose beads to be used in <a href="https://2017.igem.org/Team:Wageningen_UR/Results/Phage_Display" target="_blank">phage-panning</a> later on.
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The production of the secreted CHIKV-E construct is defined by Voss <i>et al.</i> and can be applied to Mayaro as well, as this virus is similar to chikungunya. For Zika, a different approach can be taken where the E protein present in the surface of the virion can be tagged [7]. Due to time constraints we chose not to pursue such methods and focus on the CHIKV-E proteins.
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                                            <br> To improve the measurement capability of the system, various components were exchanged. First we chose to calibrate our device using fluorescein, as this circumvents the use of recombinant bacteria in this part of the prototyping faze. The UV-LED were exchanged for 475nm blue Cree LED’s, which will excite fluorescein provided in the InterLab study kit. This wavelength is much safer too use as it is not harmful to the retina. Second, circuit containing LDR’s was replaced. Whilst cheap, LDR’s are not very suitable of taking precise measurements. To improve on this we chose to implement photodiodes, a semiconductor which converters light into electrical current. However, this signal needs amplification, for which small transimpedance amplifier (TIA) circuit containing an operational amplifier was used (figure X). Furthermore, a small piece of orange filter paper was placed in between the photodiode and the sample. The filter paper blocks much of the blue, thereby reducing the amount of background signal. These parts were combined in a prototype setup as seen in figure X. Measurements were taking using a fluorescein dilution series, the results of which are shown in figure X..
 
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References
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                                            The resulting graphs show a very nice calibration curve in the range of 0 to 2 mM of fluorescein. In order to check repeatability the whole setup was built again and the results are shown in Figure Xb. The results show the same very nice calibration curve and proves that this system is reliable and reproducible.
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<ol>
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<li>Invitrogen. Bac-to-Bac<sup>®</sup> Baculovirus Expression System, User Guide. A.0. Life Technologies Corporation; 2010.</li>
                                </div>
+
<li>Kost TA, Condreay JP, Jarvis DL. Baculovirus as versatile vectors for protein expression in insect and mammalian cells. Nat Biotechnol. 2005;23(5):567-575. doi:10.1038/nbt1095.</li>
                            </div>
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<li>Rohrmann GF. Baculovirus Molecular Biology. 3rd ed. Bethesda (MD): National Center for Biotechnology Information (US); 2013. doi:NBK114593.</li>
                        </div>
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<li>Metz SW, Gardner J, Geertsema C, et al. Effective Chikungunya Virus-like Particle Vaccine Produced in Insect Cells. PLoS Negl Trop Dis. 2013;7(3). doi:10.1371/journal.pntd.0002124.</li>
                    </section>
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<li>Voss JE, Vaney M-C, Duquerroy S, et al. Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography. Nature. 2010;468(7324):709-712. doi:10.1038/nature09555.</li>
                    <section class="device">
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<li>Rashad AA, Mahalingam S, Keller PA. Chikungunya Virus : Emerging Targets and New Opportunities for Medicinal Chemistry. 2013. doi:10.1021/jm400460d.</li>
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<li>Barba-Spaeth, Giovanna, et al. "Structural basis of potent Zika–dengue virus antibody cross-neutralization." Nature 536.7614 (2016): 48-53.</li>
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Latest revision as of 15:20, 1 November 2017

Production of Viral Antigens

In order to safely produce viral antigens for phage display, two different approaches were taken. The first focuses on the production of enveloped Virus-Like-Particles (VLPs) for chikungunya (CHIKV), Zika (ZIKV) and Mayaro (MAYV). These particles are noninfectious and widely used as vaccines for various viral diseases. The second approach is to produce secreted Strep-tagged antigens for alphaviruses. These antigens can be purified easier and can be directly linked to Strep-tactin beads for antigen display in the phage-panning.

Virus-Like Particles

Three viruses were chosen for the production of antigens; two alphaviruses (CHIKV and MAYV) and one flavivirus (ZIKV). The VLPs were produced using the InvitrogenTM Bac-to-Bac® Baculovirus Expression System [1]. The baculovirus expression system is widely used in biotechnology for high yield recombinant protein expression by exploiting the life cycle of the virus in insect cells [2,3]. The advantage of using insect cells is the accurate post-translational modifications (phosphorylation, chaperone-assisted folding, glycosylation etc.) which cannot be achieved in E. coli.. To generate the CHIKV, ZIKV and MAYV VLPs, the genes encoding the viral structural proteins for the specific virus were placed downstream of the very strong polyhedrin promotor of the baculovirus, in this case Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV). The recombinant baculovirus DNA is then used to transfect a Spodoptera frugiperda (Sf-21) cell line in order to produce recombinant baculoviruses expressing the VLPs.

Wageningen University & Research has constructs available for ZIKV and CHIKV [4], but not for MAYV. As the generation of such virus-like particles is similar, only the generation of MAYV VLPs will be described below.

MAYV genomic RNA was isolated from a Trizol sample. After the integrity and yield of the MAYV RNA was checked, cDNA was generated using Superscript RTII according to the cDNA generation protocol. Gene-specific primers were ordered to amplify the structural polyprotein gene with attB1/2 overhangs (Gateway), after which Phusion PCR was used to generate the MAYV amplicon.
A BP Gateway reaction was used to insert the MAYV amplicon in a pDONR207 vector, followed by an LR Gateway reaction to move the fragment to the pDEST8 baculovirus expression vector. In parallel the fragment was directly cloned into pFastBacDual (pFBD), another baculovirus expression vector used in the Bac-to-Bac® system. Both vectors (pFBD and pDEST8) place the MAYV polyprotein gene downstream the strong polyhedrin promotor. The plasmids were checked using restriction analysis, colony PCR and sequencing. The resulting expression clones are abbreviated MAYV-D (pDEST8 derived) and MAYV-F (pFBD derived). Both constructs were used in the Bac-to-Bac® system, the resulting 136kb bacmids (plasmids containing AcMNPV DNA) were confirmed using colony PCR and isolated using the bacmid isolation protocol.
Bacmids of MAYV-D and MAYV-F were used to transfect an Sf-21 at cell-line using ExpreS2 transfection reagent in a 6 wells plate, a healthy cell line was used as control/mock. The baculovirus infection was observed for 72 hours. The medium was then replaced, and the cells were moved to a T25 flask. After 48 hour the infection was clearly visible, as can be observed in Figure A.

Figure A: Transfection of Sf-21 with bacmid containing MAYV structural casette. T=48 hour, prior to harvesting.

The infected cells are enlarged, and show some degree of capsid bodies in the nucleus, which might indicate the presence of MAYV capsids. The AcMNPV-MAYV-D and AcMNPV-MAYV-F baculoviruses were harvested, titrated, and the passage 0 (P0) stock was used to infect Sf21 cells in a T25 flask at 50% confluency with an multiplicity of infection (MOI) of 5. Six days post infection the cells and medium were harvested.

Figure B: Western blot of Sf/-21 cells infected with AcMNPV-MAYV, cell fraction and medium fraction, 5.5D11 Alphavirus capsid antibody. Expected size: 35kDa. Blot on right is a repead due to overloading of CHIKV lane (positive control). The coloring reaction was performed using secondary antibodies with alkaline phosphatase.

Western blot with specific antibody (Semi-dry blotting protocol) was used to determine the presence of the alphavirus capsid, as seen in Figure B. Furthermore, 10 ml of medium was precipitated and VLP's were purified using ultracentrifugation (UC) accoding to the UC protocol. The isolated fraction was analyzed using Transmission Electron Microscopy, as can be seen in Figure 1.

Figure 1: Transmission Electron Microscopy of MAYV VLP samples, stained with uranyl acetate. Pictures taken using JEOL JEM1400.

Figure 1 shows the particles in the purified VLP fractions. The particle are spherical and sized approximately 70nm in diameter. Immunogold staining could be used to confirm this hypothesis. Virus-Like Particles for chikungunya and Zika virus were produced in a similar fashion.

Strep-tagged surface proteins

Next to producing VLPs, strep-tagged surface glycoproteins of CHIKV were also produced. The benefit of these proteins is the ease of purification compared to VLPs, whilst offering comparable antigenic properties. The schematic structure of the surface glycoproteins is depicted in Figure 2 [5]. The native CHIKV polyprotein is cleaved into the individual E1 and E2 glcyoproteins, which are transported to the plasma membrane. There, they are taken up by budding nucleocapsids, resulting in mature, enveloped virions [6]. The introduction of a linker between E2 and E1 as well as the instruction of a strep-tag bypasses the need for membrane anchoring and yields secreted proteins, which are easily purified. The constructs for CHIKV secreted glycosylated trimeric E-protein were produced by a MSc student at the Wageningen University & Research. As with the production of the VLPs, the production of the Strep-tagged CHIKV-E uses the Bac-to-Bac® system as well.

Figure 2: Schematic overview of CHIKV-E protein membrane organization of native and recombinant surface proteins, adapted from Voss et al. (2010).

An AcMNPV clone containing the Strep-tagged CHIKV-E was available at the Laboratory of Virology at Wageningen University & Research. Sf21 cells were infected with a MOI of 5. The infection was observed for 7 days, after which the infection was harvested. As the CHIKV-E spikes are secreted, the medium fraction could be used directly. The binding of the CHIKV-E protein was tested using Sepharose-Strep-Tactin beads. 2ml of 50% resin beads suspension was added to 10ml harvested medium and incubated for 1 hour at 4C. The beads were washed and eluted using biotin in an empty column. Various fractions were loaded on an SDS gel and subsequently semi-dry-blotted. Western blot analysis with a specific antibody for CHIKV-E was used to detect the CHIKV-E protein.


As can be seen in Figure 3, the strep-tactin sepharose beads are capable of catching the strep-tagged CHIKV-E proteins. The experiment was repeated to cover a total of 6ml strep-tactin sepharose beads to be used in phage-panning later on.

The production of the secreted CHIKV-E construct is defined by Voss et al. and can be applied to Mayaro as well, as this virus is similar to chikungunya. For Zika, a different approach can be taken where the E protein present in the surface of the virion can be tagged [7]. Due to time constraints we chose not to pursue such methods and focus on the CHIKV-E proteins.

References

  1. Invitrogen. Bac-to-Bac® Baculovirus Expression System, User Guide. A.0. Life Technologies Corporation; 2010.
  2. Kost TA, Condreay JP, Jarvis DL. Baculovirus as versatile vectors for protein expression in insect and mammalian cells. Nat Biotechnol. 2005;23(5):567-575. doi:10.1038/nbt1095.
  3. Rohrmann GF. Baculovirus Molecular Biology. 3rd ed. Bethesda (MD): National Center for Biotechnology Information (US); 2013. doi:NBK114593.
  4. Metz SW, Gardner J, Geertsema C, et al. Effective Chikungunya Virus-like Particle Vaccine Produced in Insect Cells. PLoS Negl Trop Dis. 2013;7(3). doi:10.1371/journal.pntd.0002124.
  5. Voss JE, Vaney M-C, Duquerroy S, et al. Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography. Nature. 2010;468(7324):709-712. doi:10.1038/nature09555.
  6. Rashad AA, Mahalingam S, Keller PA. Chikungunya Virus : Emerging Targets and New Opportunities for Medicinal Chemistry. 2013. doi:10.1021/jm400460d.
  7. Barba-Spaeth, Giovanna, et al. "Structural basis of potent Zika–dengue virus antibody cross-neutralization." Nature 536.7614 (2016): 48-53.