Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses

Abstract

Animal viruses frequently cause zoonotic disease in humans. As these viruses are highly diverse, evaluating the threat that they pose remains a major challenge, and efficient approaches are needed to rapidly predict virus-host compatibility. Here, we develop a combined computational and experimental approach to assess the compatibility of New World arenaviruses, endemic in rodents, with the host TfR1 entry receptors of different potential new host species. Using signatures of positive selection, we identify a small motif on rodent TfR1 that conveys species specificity to the entry of viruses into cells. However, we show that mutations in this region affect the entry of each arenavirus differently. For example, a human single nucleotide polymorphism (SNP) in this region, L212V, makes human TfR1 a weaker receptor for one arenavirus, Machupo virus, but a stronger receptor for two other arenaviruses, Junin and Sabia viruses. Collectively, these findings set the stage for potential evolutionary trade-offs, where natural selection for resistance to one virus may make humans or rodents susceptible to other arenavirus species. Given the complexity of this host-virus interplay, we propose a computational method to predict these interactions, based on homology modeling and computational docking of the virus-receptor protein-protein interaction. We demonstrate the utility of this model for Machupo virus, for which a suitable cocrystal structural template exists. Our model effectively predicts whether the TfR1 receptors of different species will be functional receptors for Machupo virus entry. Approaches such at this could provide a first step toward computationally predicting the "host jumping" potential of a virus into a new host species.

Importance: We demonstrate how evolutionary trade-offs may exist in the dynamic evolutionary interplay between viruses and their hosts, where natural selection for resistance to one virus could make humans or rodents susceptible to other virus species. We present an algorithm that predicts which species have cell surface receptors that make them susceptible to Machupo virus, based on computational docking of protein structures. Few molecular models exist for predicting the risk of spillover of a particular animal virus into humans or new animal populations. Our results suggest that a combination of evolutionary analysis, structural modeling, and experimental verification may provide an efficient approach for screening and assessing the potential spillover risks of viruses circulating in animal populations.

FIG 1

New World arenaviruses and the species that they infect. A phylogeny of clade B New World arenaviruses is shown (12). The rodent species that are known to be endemically infected with each virus are listed to the right, along with an indication of the country where the rodent/virus pair is found. Asterisks identify zoonotic viruses known to infect humans.

FIG 2

An extended region of TfR1 determines species specificity of Machupo virus entry. (A) An alignment of one portion of the TfR1 apical domain is shown for host and nonhost species. The amino acid numbering corresponds to human TfR1. The three residues experiencing recurrent positive selection, as previously defined (28), are highlighted in yellow. In blue type, a strategy is summarized that was previously used to map the Machupo virus-binding interface on TfR1 (19). In that previous work, this region was swapped from the human TfR1 (RLVYL) into the house mouse (M. musculus) TfR1, replacing the corresponding 4 residues (NLDP). In the present work, residues in the C. callosus TfR1 were swapped into the rat TfR1 to create the rat-short (red type) and rat-long (red plus green type) chimeric TfR1s shown in the bottom two lines. Also shown is the position of the L212V human SNP discussed in this study. (B) The cocrystal structure shows the interaction between Machupo virus GP1 (blue) and the human TfR1 apical domain (gray) (PDB code 3KAS) (18). The residue positions mutated in the rat-short TfR1 chimera are shown in brown. The residue positions mutated in the rat-long chimera are shown in green and brown. (C) Canine D17 cells were transduced to stably express the wild-type and chimeric TfR1s with C-terminal FLAG tags. Cells were infected with increasing volumes of Machupo pseudovirus (GFP-encoding retrovirus pseudotyped with Machupo virus glycoprotein [GP]). Cells were monitored for GFP expression to determine the percentage of infected cells. Error bars indicate standard deviations from three technical replicates. The experiment was performed 3 times with similar results seen in all experiments; the graph represents data from one experiment. A t test was performed to determine if differences between mean values were statistically significant (*, <1e−8). Cell surface expression of TfR1 was monitored with a FLAG antibody via flow cytometry (inset) concurrently with measurement of GFP signal. Expression is given as mean fluorescence intensity (MFI). C.c, C. callosus; r-l, rat-long; r-s, rat-short; r, rat. (D) A Coomassie blue-stained SDS-PAGE gel shows purified Machupo virus GP1 fused to the human IgG1 Fc fragment. (E) Coomassie blue-stained SDS-PAGE gels show the five purified TfR1 proteins. (F) ELISA comparing the relative binding affinities of Machupo virus GP1 to each of the purified TfR1s. Purified TfR1 was bound to wells, and then GP1 was incubated at decreasing concentrations to determine the relative binding affinities. Error bars indicate standard deviations from three technical replicates. The experiment was performed 2 times with similar results seen in the two experiments; the graph represents data from one experiment. Curves were fitted using 4-parameter nonlinear regression.

FIG 3

Virus-specific effects on entry through TfR1. (A) The Chapare virus GP1 (blue) was homology modeled on the Machupo virus GP1 crystal structure (magenta; PDB code 3KAS). The Machupo virus GP1 loop 10 and surrounding residues are shown in light pink where divergence in structure is seen in the Chapare virus GP1. Similar results were seen with Sabia and Junin virus models (data not shown). (B) An alignment illustrates the C-terminal region of GP1 from Machupo, Junin, Sabia, Chapare, and Guanarito arenaviruses. Residues identical to those in Machupo virus have been replaced with dots. Machupo virus GP1 sites that make contact with TfR1 (18) are indicated with red asterisks. They fall in loop 7, loop 10, and two upstream regions which are not shown. Loop 10 is longer in Machupo virus than in all other viruses. The numbering scheme is based on the Machupo virus protein. Note that the alignment differs somewhat from a similar alignment shown in reference . The differences in these alignments concern the exact placement of insertions and deletions but are within the range to be expected from different alignment approaches. This alignment was generated using MAFFT (47, 48). (C and D) Canine D17 cells were transduced to stably express the wild-type and chimeric TfR1s with C-terminal FLAG tags. Cells were infected with increasing volumes of GFP-encoding retrovirus pseudotyped with Sabia (C) or Chapare (D) virus glycoprotein (GP). Cells were monitored for GFP expression to determine the percentage of infected cells. Error bars indicate standard deviations from three technical replicates. Experiments were performed 2 times, with similar results seen in the two experiments; the graph represents data from one experiment. A t test was performed to determine if differences between mean values were statistically significant (*, <1e−5; **, <1e−10). Cell surface expression of TfR1 was monitored with a FLAG antibody via flow cytometry (inset) concurrently with measurement of GFP signal. Expression is given as mean fluorescence intensity (MFI). See legend to Fig. 2C for definitions of abbreviations.

FIG 4

Human TfR1 L212V SNP has an opposite effect on the entry of related arenaviruses. (A) The L212 residue in TfR1 contacts loop 10 in the Machupo virus GP1 (PDB code 3KAS) (18). (B) Canine D17 cells were transduced to stably express the human TfR1 either with L212 or bearing the human SNP mutation, L212V, both with a C-terminal FLAG tag. Cells were infected with increasing volumes of a GFP-encoding retrovirus pseudotyped with Machupo virus glycoprotein. Cells were monitored for GFP expression to determine the percentage of infected cells. Error bars indicate standard deviations from three technical replicates. The experiment was performed 2 times with similar results seen in the two experiments; the graph represents data from one experiment. A t test was performed to determine if differences between mean values were statistically significant (*, <1e−3). Cell surface expression of TfR1 was monitored with a FLAG antibody via flow cytometry (right) concurrently with measurement of GFP signal. Expression is given as mean fluorescence intensity (MFI). (C) ELISA comparing the relative binding affinities of the purified human L212 and L212V TfR1s to Machupo virus GP1. Purified TfR1 was bound to wells. GP1 was then incubated at decreasing concentrations to determine the relative binding affinities. Error bars indicate standard deviations from three technical replicates. The experiment was performed 2 times with similar results seen in the two experiments; the graph represents data from one experiment. Curves were fitted using 4-parameter nonlinear regression. pbs, phosphate-buffered saline. (D) ELISA comparing the relative binding affinities of the purified human L212 and L212V TfR1 to iron-loaded human transferrin. For the ELISA, purified TfR1 was bound to wells. Iron-loaded TfR1 was incubated at decreasing concentrations to determine the relative binding affinities. Error bars indicate standard deviations from three technical replicates. The experiment was performed 2 times with similar results seen in the two experiments; the graph represents data from one experiment. Curves were fitted using 4-parameter nonlinear regression. (E and F) The experiment is the same as that in panel B. In this case, cells were infected over increasing volumes with a GFP-encoding retrovirus pseudotyped with Junin (E) or Sabia (F) virus glycoprotein.

FIG 5

Computational modeling of Machupo virus GP1 binding to different TfR1 variants. (A) The computational pipeline consisted of homology modeling of variant TfR1 to the template cocrystal of the TfR1-GP1 interaction, followed by structural refinement and redocking. The redocking procedure yields a characteristic “binding funnel” of low-energy conformations at around an 8-Å root mean square deviation (RMSD) relative to the starting position before docking. We use the 10 best (i.e., lowest) scores to compare predicted binding strengths, as shown in the graph in the final panel. (B) Binding funnels for the eight models that we analyzed. Each dot shows the Rosetta interface score and the RMSD from the undocked configuration for one of the 10,000 docked models that we generated. (C) Comparison of the 10 best scores across all models considered for each variant TfR1. Each box plot shows the distribution of the interface scores for the 10 best docked conformations for each model. The red, yellow, and green color coding refers to the ability of each TfR1 to act as a receptor for Machupo virus, based on experimental results presented here, or elsewhere for mouse TfR1 (19, 28) and mouse-human TfR1 (19). (One note should be made regarding the color coding of mouse-human TfR1 as green. In the previously published work, the mouse-human TfR1 became fully functional for virus entry only when another mutation, K348N, was also included [19]. On the other hand, K348N alone did not change the functionality of TfR1 for entry [19].)