Chapter 3 Conservation analysis of dengue virus epitopes reveal robust targets for a cross-serotypic vaccine

Abstract

The rise in global incidence of dengue virus (DENV) infections and the resulting rise in mortality rate necessitates an effective universal vaccine against it. Since infection from one DENV serotype makes a person vulnerable to severe disease upon infection from another serotype, an effective vaccine should protect against all DENV serotypes. Increasing experimental evidence suggests that T cells are important for protecting against DENV. In this chapter, we comprehensively analyzed the extensive publicly-available data on DENV and revealed a distinct pattern of epitope conservation for several of the DENV T cell epitopes leading to a set of epitopes that are highly conserved across at least three DENV serotypes. We identified a potentially robust set of epitopes as targets for a prospective universal T cell-based vaccine that maximizes global population coverage.

3.1 Introduction

Dengue is a mosquito-borne viral infection that mostly causes febrile illness, but in some cases progresses into a life-threatening disease (Sheets, 2019). It is caused by the dengue virus (DENV) which exists as four genetically and antigenically distinct serotypes (Katzelnick et al., 2015; Wilder-Smith et al., 2019). Global incidence of dengue has increased more than 6-fold over the last two decades (Stanaway et al., 2016) with an estimated 400 million new infections occurring annually (Bhatt et al., 2013). Dengue is now endemic in at least 100 countries with multiple DENV serotypes co-circulating in various parts of the world (Messina et al., 2014) and it is estimated that 3.9 billion people are at risk of being infected by DENV (Brady et al., 2012). Despite several efforts, there is currently no safe and effective vaccine that protects against dengue (Low et al., 2017). The only licensed dengue vaccine, Dengvaxia, does not completely protect against all DENV serotypes and, more importantly, increases the risk of severe disease among young children who are already most vulnerable to DENV infections (Guzman and Harris, 2015; Sridhar et al., 2018).

One of the main hindrances in the development of an effective DENV vaccine is its complicated pathogenesis: primary DENV infections are mostly asymptomatic but secondary infection with a different serotype (i.e., heterologous infection) can cause clinical complications and lead to severe forms of disease (Wilder-Smith et al., 2019). Severe dengue has been associated with immunopathology where an aberrant immune response exacerbates the disease outcome (Screaton et al., 2015). Although both arms of the adaptive immune response—antibodies and T cells—have been investigated, the sub-neutralizing antibodies seem to play a major role in progression to severe dengue during secondary infection via a phenomenon known as antibody-dependent enhancement (ADE) of disease (Zellweger et al., 2010; Elong Ngono and Shresta, 2018). In contrast, there is no explicit evidence for the role of T cells in progression to severe dengue as of yet (Yauch et al., 2009; Elong Ngono et al., 2016). In fact, increasing evidence suggests a protective role of T cells against DENV infection (Yauch et al., 2009; Elong Ngono et al., 2016; Wen and Shresta, 2017; Elong Ngono and Shresta, 2018; Rivino, 2016; Roth et al., 2019). Moreover, ADE as well as the lack of a DENV-specific T cell response following Dengvaxia vaccination have been suggested to be the main factors leading to an increased risk of severe dengue among vaccine recipients (Sridhar et al., 2018). These recent developments suggest the potential importance of a vaccine designed to induce protective T cell responses.

Most of the vaccines against DENV that are currently in advanced stages of development are based on live-attenuated viruses (LAVs) comprising variant chimeric forms of DENV serotypes (Chu et al., 2015; Whitehead, 2016; Torresi et al., 2017; Elong Ngono and Shresta, 2019). These vaccines are expected to induce strong T cell responses against the vaccine-strain-specific immunodominant epitopes, but may not be protective against multiple DENV serotypes (Holtappels et al., 2008; Duangchinda et al., 2010; Piazza et al., 2014; Alwis et al., 2016). The immunodominance hierarchy of DENV T cell epitopes is complex and has been shown to depend upon the serotypes of current and past infecting strains. That is, for primary and subsequent homologous infections, T cell responses are dominant towards serotype-specific epitopes, while for secondary heterologous infections the responses skew towards epitopes that are conserved across multiple DENV serotypes (Weiskopf et al., 2014; Weiskopf, Cerpas, et al., 2015; Grifoni et al., 2017). This expansion of T cell responses towards conserved epitopes following heterologous secondary infection is thought to play a protective role, resulting in a low incidence rate of symptomatic tertiary infections (Gordon et al., 2013; Weiskopf, Cerpas, et al., 2015). Notably, cross-reactive CD8+ T cells that target conserved epitopes in multiple DENV serotypes have been shown to mediate protection in heterologous secondary infections (Yauch et al., 2009; Weiskopf et al., 2013; Elong Ngono et al., 2016; Wijeratne et al., 2018). Experiments using mice have shown that cross-reactive CD8+ T cells provide protection from DENV even in the presence of disease-enhancing antibodies (Zellweger et al., 2014; Lam et al., 2017). These recent findings strongly suggest that a vaccine eliciting a T cell response specifically targeting epitopes conserved across serotypes is likely to enable protection against DENV, as highlighted in a recent review (Elong Ngono and Shresta, 2018).

Thus far, only a few studies have attempted to identify protein regions (peptides) conserved across multiple DENV serotypes that may be targeted by T cell-based vaccines (Khan et al., 2008; Olsen et al., 2011; Nascimento et al., 2013; Roth et al., 2019). Specifically, in one such study (Khan et al., 2008), conservation of overlapping peptides across sequence data of multiple serotypes was used to identify 44 pan-DENV conserved peptides of varying lengths (9 to 22 residues). In another study (Olsen et al., 2011), a block entropy based method was employed to identify 1,551 pan-DENV conserved blocks of 9-mer peptides from sequence data available at the time of study. The selection of conserved peptides in this study was not strict as it allowed for variants (i.e., peptides that differ from each other at few residues either within a single serotype or across serotypes). Similar to (Olsen et al., 2011), studies (Nascimento et al., 2013) and (Roth et al., 2019) allowed for variants and reported 46 and 11 conserved epitopes, respectively. Although all these studies (Khan et al., 2008; Olsen et al., 2011; Nascimento et al., 2013; Roth et al., 2019) reported multiple conserved regions/epitopes within the DENV proteome, they did not consider other factors that are important for the design of a cross-serotypic dengue vaccine. First, the conserved peptides/blocks predicted exclusively from DENV sequences (as in (Khan et al., 2008; Olsen et al., 2011)) may not represent T cell epitopes that are actually presented on HLA molecules of DENV-infected cells. Second, training the immune system using variants of peptides/epitopes (Olsen et al., 2011; Roth et al., 2019; Nascimento et al., 2013), especially those which are serotype-specific, may result in sub-optimal T cell responses in subsequent heterotypic infections (Weiskopf et al., 2014). These issues may be addressed respectively by exclusively using data on experimentally-determined DENV T cell epitopes (a large number of which have been determined over the past few years), and by selecting conserved epitopes based on a strict criterion that discounts variants. Thus, using the available immunological data, together with a strict approach to determine epitope conservation (i.e., which considers each variant as a separate epitope) based on the publicly-available patient-derived DENV sequence data, could enable the identification of cross-serotypically conserved T cell epitopes that can aid the rational design of a potentially effective universal vaccine against dengue.

In this chapter, we take an epitope-centric approach by focusing on all available data of experimentally-determined DENV T cell epitopes that are derived from human hosts and carry associated HLA information. This makes our approach distinct from previous related studies as the T cell epitopes that we consider are not only known to be processed and presented by the infected cells, but they also elicit positive/protective T cell responses within humans in the context of cognate HLA alleles. By examining the conservation of each available T cell epitope in the protein sequence data for each DENV serotype, our analysis reveals a striking near-binary pattern of conservation across serotypes for multiple epitopes. That is, epitopes are often highly conserved in particular serotypes and nearly absent from the remaining ones. We employ a conservative approach for mapping the epitopes onto sequences, which excludes non-conserved epitope variants from the analysis. This is important as mutation of even a single epitope residue is known to potentially abrogate HLA-epitope binding and significantly weaken the T cell response (Sloan-Lancaster and Allen, 1996; Kalergis and Nathenson, 2000; Ogishi and Yotsuyanagi, 2019). Based on the determined conservation profile of the epitopes, we identify a set of 55 epitopes that are strictly conserved in at least three of the four DENV serotypes. The majority of these epitopes are derived from functionally important regions of DENV non-structural proteins (NS3 and NS5), highlighting their potential as effective vaccine targets. Incorporating the HLA information associated with the identified cross-serotypically conserved epitopes, we propose a set of robust epitopes as targets for a prospective T cell-based universal vaccine against DENV that can potentially protect a large percentage of the global population. Moreover, to demonstrate the further applicability of our approach, we also propose country-specific vaccine targets for three dengue-endemic countries (Thailand, Brazil and Philippines), that are experiencing a significant recent rise in number of DENV infections (prevention and Control, 2019).

3.2 Acquisition and pre-processing of data

We downloaded all available DENV protein sequences derived from human hosts from the NIAID ViPR database²⁵ (Pickett et al., 2012). The downloaded sequences were aligned separately for each DENV protein (E, prM, C, NS1, NS2a, NS2b, NS3, NS4a, NS4b, and NS5) and each serotype (DENV1-4) using the MAFFT multiple sequence alignment program (Katoh and Standley, 2013). Sequences that had less than 15% gaps within the alignment were retained for further analysis, which resulted in a total of 56,496 protein sequences (Fig. 3.1). Most of these sequences are from DENV1 and DENV2. The fewest are from DENV4, for which reporting of sequences has increased the least rapidly over the past several years (Messina et al., 2014). Among DENV proteins, a large number of envelope protein (E) sequences are reported as compared to other proteins. This is expected, with envelope being a major focus of dengue research as it is the main target of antibodies.

Figure 3.1: Summary of the analyzed DENV sequences.

We also downloaded data of all available DENV T cell epitopes from the NIAID ViPR database²⁶ (Pickett et al., 2012) that were derived from human hosts. This data comprises both HLA class I and class II restricted epitopes, including those associated with the recently characterized class II loci (HLA-DP, DQ, and DRB3/4/5) (Grifoni et al., 2019). These were grouped according to protein by separately filtering the epitope data for each protein. For this, the starting and ending protein positions were defined based on the following reference sequences: NP_059433.1 (DENV1), NP_056776.2 (DENV2), YP_001621843.1 (DENV3) and NP_073286.1 (DENV4). Of all the obtained epitopes, we retained only those that were reported to be positive in at least one T cell assay, and for which HLA information was available. This procedure resulted in a total of 1,768 (674 HLA class I and 1,094 HLA class II restricted) DENV T cell epitopes (Fig. 3.2A and HTML table deposited in online repository²⁷).

3.3 Methods

3.3.1 Computing conservation of epitopes

We measured the conservation of each epitope for each serotype as the fraction of protein sequences within that serotype that comprised the exact “epitope sequence”. That is, to compute the conservation of an epitope, we used an exact mapping procedure (Fig. 3.2B) that screened each epitope against all protein sequences within each serotype and mapped the epitope onto a particular sequence only when it matched identically to the corresponding region of that sequence. The fraction of sequences to which the epitope was mapped represented its conservation in the respective serotype. This strict approach ensured that (variant) epitopes differing from each other at one or more residues were considered separately.

3.3.2 Computing epitope coverage of DENV proteome

We defined the epitope coverage at any position of a protein as the number of epitopes that covered that position. To compute it, we first mapped all the T cell epitopes onto all sequences of the corresponding proteins for each serotype using the exact mapping procedure explained above (Fig. 3.2B). The epitope coverage of a protein was then computed after accounting for all epitopes that mapped onto at least one sequence of that protein. We found the coverage of DENV proteins to be qualitatively similar across all serotypes (Fig. 3.2C, Figs. 3.3, 3.4, 3.5).

Statistics and coverage of experimentally-determined DENV T cell epitopes. (A) Number of DENV epitopes derived from different proteins across the serotypes. (B) Procedure for the exact mapping of an epitope to a protein sequence. (C) Coverage of T cell epitopes across DENV proteins (locations determined with reference to DENV1 sequences). Similar patterns of epitope coverage were observed for most proteins when the epitopes were mapped onto sequences of DENV2/3/4 (see Figs. 3.3, 3.4, 3.5).

Figure 3.2: Statistics and coverage of experimentally-determined DENV T cell epitopes. (A) Number of DENV epitopes derived from different proteins across the serotypes. (B) Procedure for the exact mapping of an epitope to a protein sequence. (C) Coverage of T cell epitopes across DENV proteins (locations determined with reference to DENV1 sequences). Similar patterns of epitope coverage were observed for most proteins when the epitopes were mapped onto sequences of DENV2/3/4 (see Figs. 3.3, 3.4, 3.5).

Figure 3.3: Coverage of DENV T cell epitopes across the primary structure of DENV2 proteins.

Coverage of DENV T cell epitopes across the primary structure of DENV3 proteins. The locations of epitopes were determined by mapping them onto all DENV3 sequences. The color scales indicate the HLA class restriction of the epitopes.

Figure 3.4: Coverage of DENV T cell epitopes across the primary structure of DENV3 proteins. The locations of epitopes were determined by mapping them onto all DENV3 sequences. The color scales indicate the HLA class restriction of the epitopes.

Coverage of DENV T cell epitopes across the primary structure of DENV4 proteins. The locations of epitopes were determined by mapping them onto all DENV4 sequences. The color scales indicate the HLA class restriction of the epitopes.

Figure 3.5: Coverage of DENV T cell epitopes across the primary structure of DENV4 proteins. The locations of epitopes were determined by mapping them onto all DENV4 sequences. The color scales indicate the HLA class restriction of the epitopes.

3.3.3 Estimating population coverage of epitopes

Population coverage is an estimate of the percentage of individuals in a target population that are likely to be able to mount a T cell response against a given epitope. We computed the population coverage of a T cell epitope based on the associated HLA alleles in the ViPR database that were reported together with the positive T cell assay data. We only considered alleles with at least 4-digit resolution (e.g., A*02:01). The (accumulated) population coverage of a set of epitopes is defined as the percentage of individuals in a target population that are likely to be able to respond to at least one T cell epitope within the set. We adopted a greedy approach to identify the set of epitopes from among the highly conserved ones which maximized the accumulated population coverage. The steps of the approach were as follows: (i) we initialized the set with the epitope that had the highest individual population coverage; (ii) added to the set another epitope which maximized the accumulated population coverage; and (iii) continued adding epitopes until we obtained a set of epitopes for which the accumulated population coverage did not increase further by adding any of the remaining highly conserved epitopes. If at any step the same increase in accumulated population coverage resulted from adding multiple epitopes, then only the most conserved epitope among them was added to the set.

The Python code of the tool for computing the population coverage was downloaded from the IEDB Analysis Resource²⁸ (Vita et al., 2019) and run locally. This tool uses the population-specific HLA allele genotypic frequencies from the Allele Frequency database²⁹ (González-Galarza et al., 2015).

3.4 Results

3.4.1 Mapping T cell epitopes onto the DENV proteome reveals their broad and non-uniform coverage

We first mapped the downloaded experimentally-determined HLA class I and II restricted T cell epitopes (summarized in Fig. 3.2A) onto the protein sequences for each DENV serotype by using an exact mapping criterion; i.e., no mismatch was allowed between the epitope sequence and the corresponding region of the protein sequence (Fig. 3.2B). We then determined the coverage of the mapped epitopes in each DENV serotype (see section 3.3.2 for details). We found that for most DENV proteins the epitope coverage was broad, with at least 70% of C, NS2a, NS3, NS4a and NS4b residues being covered by at least one T cell epitope (Figs. 3.2C, Figs. 3.3, 3.4, 3.5). Among the remaining proteins, coverage of E, NS1, NS2b and NS5 was moderate (40-70%), while prM was the least covered (less than 40%). This suggests that all DENV proteins are targeted by natural T cell responses, and that a large part of the DENV proteome is potentially immunogenic.

The mapping of epitopes onto the DENV proteome further revealed that the epitope coverage is distributed non-uniformly across different proteomic regions (Fig. 3.2C, Figs. 3.3, 3.4, 3.5). Interestingly, specific “immunologically dense” regions, defined as regions covered by multiple epitopes, were observed in some proteins, including C (residues 50-100), NS2a (residues 150-180) and NS3 (residues 200-250). Moreover, most of the protein regions were covered by both HLA class I and II restricted epitopes, while some were covered by only one type of epitope. For example, both HLA class I and class II restricted epitopes covered most regions of NS2a, NS4b and NS5 proteins, while most of the C-terminal region of NS3 was covered only by HLA class I restricted epitopes and that of the C protein was covered only by HLA class II restricted epitopes. Epitope coverage is important to understand the proteomic regions accessible to T cells. It is also important, however, to examine their conservation across DENV serotypes in order to identify specific cross-serotypically conserved epitopes that may serve as potentially effective targets for T cells.

3.4.2 Conservation profiles of epitopes reveal a near-binary pattern across serotypes

In order to compute the conservation profiles of the T cell epitopes, we first mapped them onto all available protein sequences for each serotype (see section 3.3.1). Similar to above, we used an exact mapping criterion such that no mismatch was allowed between the epitope and any protein sequence (Fig. 3.2B). This conservative mapping precluded one- or multiple-residue variants of an epitope from spuriously inflating its conservation profile. This is important from the perspective of identifying vaccine targets since single residue substitutions have been demonstrated to influence epitope presentation, weaken or completely abrogate epitope-HLA molecule binding, and result in insufficient T cell responses (Sloan-Lancaster and Allen, 1996; Kalergis and Nathenson, 2000; Ogishi and Yotsuyanagi, 2019). Furthermore, it is particularly important to avoid training the immune system against epitope variants in the case of DENV, as targeting these can lead to weakened T cell responses (i.e., T cell responses to the variant epitopes may be weakly cross-reactive), and such effects have been implicated in offering a lack of protection and progression to severe disease (Weiskopf et al., 2013; Weiskopf and Sette, 2014; Tian et al., 2019).

Following the exact mapping of epitopes, we found 13 highly conserved epitopes, representing less than 1% of all available DENV epitopes across all four DENV serotypes. All of these epitopes were derived from non-structural proteins, with the majority (8 out of 13) from NS5 (Fig. 3.6). The conservation profiles of the remaining epitopes revealed a distinct pattern: a large number of epitopes were highly conserved in 3 serotypes and nearly absent (almost zero conservation) in the fourth serotype. For the conservation profile of all available (1,768) T cell epitopes see file deposited in online repository³⁰.

This unique near-binary pattern apparently resulted from the presence of serotype-specific residues within these epitopes. For example, the NS5 epitope LEFEALGFL was highly conserved (>99%) within each of DENV2, DENV3 and DENV4 but absent in DENV1 where, in the last epitope position, Leucine (L) was substituted by Methionine (M). Similarly, the envelope epitope QEGAMHTAL was highly conserved in DENV1, DENV2 and DENV3 but not in DENV4 where the variant QEGAMHSAL was highly conserved (see Figs. 6.2, 6.3 and 6.4). This distinct pattern of epitope conservation extended beyond the top epitopes and several other epitopes were found to be highly conserved within only two or one DENV serotype while being absent from the remaining serotypes (HTML table deposited in online repository³¹).

Top cross-serotypically conserved DENV T cell epitopes exhibit near-binary conservation. Of the 1,768 experimentally-determined epitopes, 55 mapped exactly onto at least 90% of sequences in at least 3 of the 4 DENV serotypes. The cells adjacent to each epitope represent its conservation within each DENV serotype. The number of donors and assays that have tested positive and the response frequency (RF) as reported in IEDB (Vita et al., 2019) are shown for each epitope. RF percentile score shows the response frequencies of each epitope compared to those reported for all DENV epitopes in IEDB. Epitopes are arranged according to their mean conservation (in descending order) and colored according to the protein from which they were derived. The number of epitopes within the set derived from each protein is shown within parentheses in the legend.

Figure 3.6: Top cross-serotypically conserved DENV T cell epitopes exhibit near-binary conservation. Of the 1,768 experimentally-determined epitopes, 55 mapped exactly onto at least 90% of sequences in at least 3 of the 4 DENV serotypes. The cells adjacent to each epitope represent its conservation within each DENV serotype. The number of donors and assays that have tested positive and the response frequency (RF) as reported in IEDB (Vita et al., 2019) are shown for each epitope. RF percentile score shows the response frequencies of each epitope compared to those reported for all DENV epitopes in IEDB. Epitopes are arranged according to their mean conservation (in descending order) and colored according to the protein from which they were derived. The number of epitopes within the set derived from each protein is shown within parentheses in the legend.

To identify robust T cell targets against multiple DENV serotypes, we excluded epitopes that are highly conserved in only one or two serotypes ($\sim 42\%$ and $\sim 6\%$ of all DENV epitopes respectively), and instead focused only on epitopes that are expected to be protective against a majority of serotypes. Based on the conservation profile, we identified a set of 55 DENV epitopes that had a minimum conservation level above a high threshold (0.9) within at least 3 of the 4 serotypes (Fig. 3.6). This set of epitopes was found to be robust to the specific choice of threshold used for defining the minimum conservation level (Fig. 3.7).

Histogram of minimum conservation of epitopes among 3 DENV serotypes. Minimum conservation of epitopes across sets of 3 out of 4 DENV serotypes. The conservation for each epitope within each serotype of DENV was determined after mapping the epitopes onto the corresponding protein sequences, as shown in Fig. 3.2B. A threshold of 0.9 was used that resulted in the set of 55 top epitopes (i.e., epitopes that mapped exactly onto at least 90% of sequences in at least 3 of the 4 DENV serotypes were selected), shown in Fig 3.6. The histograms show that the selection of epitopes is robust to the choice of threshold.

Figure 3.7: Histogram of minimum conservation of epitopes among 3 DENV serotypes. Minimum conservation of epitopes across sets of 3 out of 4 DENV serotypes. The conservation for each epitope within each serotype of DENV was determined after mapping the epitopes onto the corresponding protein sequences, as shown in Fig. 3.2B. A threshold of 0.9 was used that resulted in the set of 55 top epitopes (i.e., epitopes that mapped exactly onto at least 90% of sequences in at least 3 of the 4 DENV serotypes were selected), shown in Fig 3.6. The histograms show that the selection of epitopes is robust to the choice of threshold.

While the identification of epitopes that are conserved across multiple serotypes is critical to select targets for a prospective vaccine, examining the immunodominance of these epitopes across multiple individuals is also important. Measuring the immunodominance of epitopes, in general, is complicated and varies across studies (Tian et al., 2019; Raué and Slifka, 2009). Here, we used two approaches to quantitatively compare the immunodominance of epitopes. First, we extracted from IEDB the information about the number of positive assays and donors reported for each of the top 55 conserved epitopes (Fig. 3.6). Half of these epitopes (28/55) were reported positive in multiple assays while nearly two-thirds (35/55) were reported positive in multiple donors, suggesting that these can be considered as immunodominant epitopes (Tian et al., 2019). Second, we compared the response frequencies reported for each of these epitopes in the IEDB database (Fig. 3.6). The median of the response frequencies for these epitopes was 0.09. Comparing this against the distribution of the reported response frequencies for all DENV T cell epitopes in IEDB, we found that all 55 identified epitopes scored above $\sim 43\%$ of all DENV T cell epitopes (Fig. 3.6). In addition, many of our identified epitopes were reported to have very strong affinities with cognate HLA molecules (Fig. 3.8 and HTML table deposited in online repository³²); a factor considered important for eliciting a strong T cell response (Yauch et al., 2009). Moreover, we found that several of our identified epitopes were listed as being immunodominant in multiple previous studies (Weiskopf et al., 2013; Alwis et al., 2016; Tian et al., 2019) (see Table 7.4).

Reported epitope-HLA binding affinity for the top 55 conserved epitopes (Fig. 3.6) in the context of cognate HLA alleles. The quantitative measure, IC50 values, of epitope-MHC binding was extracted from positive MHC assays corresponding to these epitopes in the IEDB database. Color of the cells represent the strength of the binding affinity. White cells represent epitope-HLA complexes for which no binding measurements were reported.

Figure 3.8: Reported epitope-HLA binding affinity for the top 55 conserved epitopes (Fig. 3.6) in the context of cognate HLA alleles. The quantitative measure, IC50 values, of epitope-MHC binding was extracted from positive MHC assays corresponding to these epitopes in the IEDB database. Color of the cells represent the strength of the binding affinity. White cells represent epitope-HLA complexes for which no binding measurements were reported.

So far, we have focused only on epitopes determined from human hosts. However, we can also use our framework to analyze all the (213) experimentally-determined T cell epitopes from HLA transgenic mice reported in the ViPR database (Pickett et al., 2012) (HTML table deposited in online repository³³). Using our strict criteria, we found only 9 epitopes from HLA transgenic mice to be conserved (conservation greater than 0.9) in at least 3 serotypes (Fig. 3.9). Five of these epitopes (namely, APTRVVAAEM, ELMRRGDLPV, RVIDPRRCL, SRAIWYMWLGARFLE, and LPAIVREAI) were also reported from human hosts and are thus present in our top 55 conserved epitopes (Fig. 3.6).

Figure 3.9: Cross-serotypically-conserved DENV T cell epitopes from HLA-transgenic mice. Of the 213 experimentally-determined HLA-transgenic mice epitopes, 9 mapped exactly onto at least 90% of sequences in at least 3 of the 4 DENV serotypes. Five of these epitopes—APTRVVAAEM, ELMRRGDLPV, RVIDPRRCL, SRAIWYMWLGARFLE, and LPAIVREAI—were also reported from human hosts (Fig. 3.6). Cells adjacent to each epitope represents its conservation within each DENV serotype. The conservation of an epitope within a serotype was determined using the exact mapping procedure (Fig. 3.2B). All epitopes are colored according to the protein from which they are derived.

To complement these results, we developed a software tool that filters all available DENV epitopes based on any choice of threshold for the minimum conservation level of epitopes within each serotype. This easy-to-use tool presents the conservation profiles of all 1,768 experimentally-determined DENV T cell epitopes considered in the study presented in this chapter and is provided as a standalone HTML file (deposited in online repository³⁴) which can also help to quickly identify the most conserved epitopes from any DENV protein. Thus, this tool may serve as a useful reference for future research on DENV epitopes.

3.4.3 Top conserved DENV T cell epitopes in NS3 and NS5 are located in functionally important regions

Most of the identified conserved epitopes (45 out of 55) were derived from NS5 and NS3 (25 and 20, respectively) (Fig. 3.6), highlighting the potential biological importance of targeting these non-structural proteins. Both NS5 and NS3 are large DENV proteins, comprising about 900 and 618 residues respectively (lengths slightly vary across serotypes), which are multi-functional enzymes playing a critical role in viral replication (Swarbrick et al., 2017; Teramoto et al., 2017; Patil et al., 2019). The high conservation of the identified NS5 and NS3 epitopes across serotypes (Fig. 3.6) indicates that the protein regions associated with them may be structurally/functionally important for DENV. To investigate this, we mapped these epitopes to the available protein crystal structures of these proteins. These top conserved epitopes were found to lie deep within the protein tertiary structures and generally in the proximity of functionally important regions such as RNA binding sites and known flavivirus motifs.

Among the top conserved NS5 epitopes, two of them (SRNSTHEMY and LSRNSTHEM) contained an active site (E216) of the enzymatic tetrad of methyltransferase (MTAse) domain known to be critical for viral replication (Klema et al., 2016). Four of the top conserved NS5 epitopes (DTTPFGQQR, TPFGQQRVF, KTWAYHGSY and GPGHEEPIPM) contained residues that are known to be involved in interactions that provide overall stability to the NS5 quaternary structure (Fonseca et al., 2017). Some residues involved in these epitopes are known to be functionally critical as well (Klema et al., 2016); for example, mutations in epitopes DTTPFGQQR (F349D) and SRNSTHEMY (E216A) were shown to severely impair viral replication. Four other epitopes among the top conserved NS5 epitopes (WSIHAHHQW, TWSIHAHHQW, PTSRTTWSIH and CVYNMMGKREKKLGE) were found to overlap with the priming loop, which is important for stabilizing the RNA-dependent RNA-polymerase (RdRp) initiation complex (Patil et al., 2019); and motif F, which mediates conformational changes between the thumb and fingers domains of NS5 to provide stability to the RdRp domain (Lim et al., 2015) (Fig. 3.10A). Furthermore, two of the top conserved epitopes of NS5 (GPGHEEPIPM and KVRKDIPQW) contained residues involved at the NS5 inter-dimer interface (Klema et al., 2016) (Fig. 3.11).

$Mapping of top conserved DENV NS5 and NS3 epitopes onto the protein primary and tertiary structures. (A) (Left panel) Coverage of the top conserved NS5 epitopes (Fig. 3.6) along the protein sequence, and (right panel) their locations in the corresponding tertiary structure (PDB ID: 5DTO). Most of the residues within these epitopes are located in regions that provide stability to the polymerase complex (Patil et al., 2019). (B) (Left panel) Coverage of the top conserved NS3 epitopes (Fig. 3.6) along the protein sequence, and (right panel) their locations in the corresponding tertiary structure (PDB ID 5XC6) (Swarbrick et al., 2017). Although these epitopes are spread out in the primary structure, they localize near the RNA binding groove of the helicase domain (Luo et al., 2008). Right panels show side views of the protein structure, rotated by $180^{0}$. Residues that belong to conserved epitopes are shown as green spheres while the RNA, interacting with helicase of NS3 (A) and methyltransferase of NS5 (B), is shown in red.$

Figure 3.10: Mapping of top conserved DENV NS5 and NS3 epitopes onto the protein primary and tertiary structures. (A) (Left panel) Coverage of the top conserved NS5 epitopes (Fig. 3.6) along the protein sequence, and (right panel) their locations in the corresponding tertiary structure (PDB ID: 5DTO). Most of the residues within these epitopes are located in regions that provide stability to the polymerase complex (Patil et al., 2019). (B) (Left panel) Coverage of the top conserved NS3 epitopes (Fig. 3.6) along the protein sequence, and (right panel) their locations in the corresponding tertiary structure (PDB ID 5XC6) (Swarbrick et al., 2017). Although these epitopes are spread out in the primary structure, they localize near the RNA binding groove of the helicase domain (Luo et al., 2008). Right panels show side views of the protein structure, rotated by $180^{0}$. Residues that belong to conserved epitopes are shown as green spheres while the RNA, interacting with helicase of NS3 (A) and methyltransferase of NS5 (B), is shown in red.

Among the top conserved NS3 epitopes, one epitope (KPGTSGSPI) comprised an active site (S135) of the catalytic triad, mutations at which have been shown to completely abolish the protease activity (Li et al., 2017). All remaining top conserved NS3 epitopes were found to lie within the conserved flavivirus motifs and map to the helicase domain (Luo et al., 2015). Remarkably, while these NS3 epitopes were located far from each other in the primary structure (Fig. 3.10B), they localized in the tertiary structure around the groove that is important for interacting with viral RNA and facilitating its unwinding (Luo et al., 2008; Swarbrick et al., 2017).

Some top epitopes are putatively involved in the inter-dimer interface in the quaternary structure proposed for DENV NS5. The NS5 dimer structure (PDB ID: 5CCV) proposed in (Klema et al., 2016) is shown where one monomer is colored blue and the other green. The residues of two top NS5 epitopes (GPGHEEPIPM and KVRKDIPQW) that are involved in the inter-dimer interface are shown as spheres.

Figure 3.11: Some top epitopes are putatively involved in the inter-dimer interface in the quaternary structure proposed for DENV NS5. The NS5 dimer structure (PDB ID: 5CCV) proposed in (Klema et al., 2016) is shown where one monomer is colored blue and the other green. The residues of two top NS5 epitopes (GPGHEEPIPM and KVRKDIPQW) that are involved in the inter-dimer interface are shown as spheres.

Overall, this analysis suggested that the identified top conserved epitopes of NS5 and NS3 are derived from functionally/structurally important regions of these proteins. These results provide biological reasoning, complementary to the statistical analysis, to further suggest that training T cells to recognize the identified top conserved epitopes through vaccination may potentially be helpful in eliciting a robust T cell response against DENV.

3.4.4 Identifying epitopes that can serve as targets for a universal T cell-based dengue vaccine

We sought to identify a robust set of epitopes as targets for a potential universal T cell-based dengue vaccine that would maximize chances of eliciting a T cell response against the conserved regions of DENV in a large percentage of the population. To address this, we used the global prevalence data of the HLA alleles (González-Galarza et al., 2015) that are associated with the identified top 55 cross-serotypically conserved DENV epitopes (Fig. 3.6).

We first estimated the population coverage of each of the top epitopes and ranked them accordingly. We then sought to determine sets of epitopes that provided maximum global population coverage. We started by considering the epitope (LEFEALGFLNEDHWF) that had the highest individual population coverage (52.92%), and then progressively added epitopes such that the accumulated population coverage was maximized (see section 3.3.3 for details). We continued this procedure until we obtained a set of epitopes for which the accumulated population coverage saturated. This procedure identified a set of 17 epitopes, from the top 55 epitopes (Fig. 3.6), which provided an accumulated global population coverage of 99.23% (Fig. 3.12A). Three epitopes in this set were highly conserved across all DENV serotypes, while the remaining were highly conserved in three of the four serotypes. Of these, DENV2 is covered by the greatest number of epitopes (16), followed by DENV3 (14), DENV4 (13) and DENV1 (11), respectively.

Candidate for a universal DENV T-cell-based vaccine. (A) Proposed set comprising 17 epitopes, selected from the set of top 55 DENV epitopes (Fig. 3.6), that maximizes the global population coverage (left panel). The population coverage of each epitope individually (middle panel) and the accumulated population coverage (right panel) of all epitopes up to and including the current one was calculated based on the information of the associated HLA alleles. Epitopes are ranked in increasing order of the accumulated coverage, which reached the maximum of 99.23%. (B) Population coverage by country of the proposed set of epitopes. Countries for which the population coverage could not be computed due to the lack of country-specific HLA information or if no sequences were reported from them, are colored as grey.

Figure 3.12: Candidate for a universal DENV T-cell-based vaccine. (A) Proposed set comprising 17 epitopes, selected from the set of top 55 DENV epitopes (Fig. 3.6), that maximizes the global population coverage (left panel). The population coverage of each epitope individually (middle panel) and the accumulated population coverage (right panel) of all epitopes up to and including the current one was calculated based on the information of the associated HLA alleles. Epitopes are ranked in increasing order of the accumulated coverage, which reached the maximum of 99.23%. (B) Population coverage by country of the proposed set of epitopes. Countries for which the population coverage could not be computed due to the lack of country-specific HLA information or if no sequences were reported from them, are colored as grey.

Coverage is high in most countries, especially those with high incidence rate of dengue infections (prevention and Control, 2019) such as Thailand (98.25%), Brazil (98.8%) and Philippines (96.73%). Incorporating more epitopes within the set did not result in further increase of coverage (see Fig. 6.1).

Based on our analysis we recommend these 17 epitopes (8 HLA class I and 9 HLA class II restricted) as potentially robust targets for a universal T cell-based vaccine against DENV. Interestingly, three epitopes within this set (LEFEALGFLNEDHWF, LPAIVREAI, and RVIDPRRCLK) together provided a global population coverage of greater than 80% due to their known associations with multiple distinct HLA alleles (Vita et al., 2019). It is encouraging that the proposed set has a high population coverage within individual populations across multiple DENV-endemic countries spread across South-East Asia, Central and South Americas and the Western Pacific (Brady et al., 2012; Bhatt et al., 2013; Sheets, 2019) (Fig. 3.12B). Importantly, the estimated population coverage of the proposed set of epitopes is high within most countries that have recently experienced a high incidence of dengue (Control, 2019), such as Thailand (98.25%), Brazil (98.8%) and Philippines (96.73%). To further demonstrate the applicability of our approach, we also proposed separate sets of epitopes as potentially robust targets for vaccines specifically targeting populations within these dengue-endemic countries by identifying the smallest sets of epitopes that achieved the maximum population coverages. These sets comprised 12, 13 and 5 epitopes, respectively (Figs. 3.13 and 3.14). With the exception of two epitopes (KGSRAIWYMW and YLAGAGLAF) in the Thailand-specific set, and one epitope (RTLILAPTRVVAAEM) in the Brazil-specific set, all the epitopes within the three country-specific target sets are also part of our proposed set for a universal dengue vaccine (Fig. 3.12).

Proposed immunogens for country-specific populations: (A) Thailand, and (B) Philippines. For (A-B): (Left panel) Proposed immunogens comprising epitopes selected from the set of top 55 DENV epitopes (Fig. 3.6), that maximized the country-specific population coverages. The epitopes are ranked in increasing order of the accumulated coverage which reached the maximum of: (A) 98.25%, and (B) 96.73%. Incorporating more top epitopes within these immunogens did not result in further increase of coverage.

Figure 3.13: Proposed immunogens for country-specific populations: (A) Thailand, and (B) Philippines. For (A-B): (Left panel) Proposed immunogens comprising epitopes selected from the set of top 55 DENV epitopes (Fig. 3.6), that maximized the country-specific population coverages. The epitopes are ranked in increasing order of the accumulated coverage which reached the maximum of: (A) 98.25%, and (B) 96.73%. Incorporating more top epitopes within these immunogens did not result in further increase of coverage.

Proposed immunogens for country-specific populations: Brazil. (Left panel) Proposed immunogens comprising epitopes selected from the set of top 55 DENV epitopes (Fig. 3.6), that maximized the country-specific population coverage. The epitopes are ranked in increasing order of the accumulated coverage which reached the maximum of 98.8%. Incorporating more top epitopes within these immunogens did not result in further increase of coverage.

Figure 3.14: Proposed immunogens for country-specific populations: Brazil. (Left panel) Proposed immunogens comprising epitopes selected from the set of top 55 DENV epitopes (Fig. 3.6), that maximized the country-specific population coverage. The epitopes are ranked in increasing order of the accumulated coverage which reached the maximum of 98.8%. Incorporating more top epitopes within these immunogens did not result in further increase of coverage.

3.5 Discussion

Incidence of infections from all serotypes of DENV continue to rise across the world, affecting more countries than ever before. Despite various efforts there is still no safe and effective vaccine that protects against dengue. Increasing experimental evidence indicates the potential protective role of T cell-based immune responses against DENV (Elong Ngono and Shresta, 2018). As all four serotypes of DENV are known to co-circulate in endemic regions and with increased risk of severe dengue from heterotypic infections, an effective vaccine should elicit protective T cell responses against most, if not all, serotypes. A fundamental question in designing such a cross-serotype vaccine is whether there exist parts of the DENV proteome that are: (i) highly conserved across a majority of the four DENV serotypes, and (ii) immunogenic so that T cells can be trained to recognize them. Our study presented in this chapter has sought to address this question. We analyzed the conservation profile of all experimentally-determined DENV T cell epitopes derived from human hosts within each serotype and identified 55 T cell epitopes that are highly conserved within at least three serotypes. Their high conservation is apparently driven by functional/structural constraints imposed by the corresponding residues. Training T cells against these epitopes is expected to elicit robust responses against at least three DENV serotypes which may potentially be difficult to escape. Based on the identified top conserved epitopes, we also proposed a set of epitopes as recommended targets for a universal T cell-based dengue vaccine. This was chosen to maximize the global population coverage using HLA information associated with each epitope.

Most vaccine design efforts rely upon the use of LAVs to train the immune system for defending against DENV. However, LAVs pose multiple concerns. This includes mutation of the vaccine strain to virulent form, and the possibility of leading to severe dengue through ADE upon subsequent infection. In contrast, T cell-based vaccines are safer alternatives (Reginald et al., 2018) as they not only eliminate the risks associated with LAVs, but they also provide the opportunity to explicitly train the immune system to target more precise regions of the viral proteome. Importantly, strong T cell responses against more conserved regions of DENV proteins have been correlated with protection from progression to severe disease (Elong Ngono et al., 2016).

Vaccination strategies targeting specifically the conserved epitopes are expected to develop cross-reactive T cell responses which would be expanded upon subsequent natural infection by any DENV serotype. However, this has not yet been demonstrated and further experimental studies are needed to examine the T cell responses elicited upon challenge with different serotypes following such vaccination. Encouragingly, there is evidence that T cell responses can be elicited against “conserved” epitopes among dengue/flavivirus-naïve individuals vaccinated with monovalent as well as tetravalent LAVs, namely TV003 and TAK-003 vaccines (Weiskopf, Angelo, et al., 2015; Waickman et al., 2019), which are in advanced stages of clinical trials. Detectable T cell responses targeting some of the top 55 conserved epitopes identified in this study (Fig. 3.6) have been reported in naïve individuals following immunization with these LAVs. Specifically, following vaccination with monovalent or tetravalent LAV TV003 (Weiskopf, Angelo, et al., 2015) and with tetravalent LAV TAK-003 (Waickman et al., 2019), T cell responses have been reported against 9 and 11 of the 55 identified epitopes, respectively (see Table 7.5). Moreover, there is evidence that a pre-existing T cell response against conserved epitopes is expanded in secondary infection (Weiskopf et al., 2013; Weiskopf et al., 2014). Therefore, focusing the T cell response towards cross-serotypically conserved regions and away from serotype-specific regions, as proposed in this chapter, through properly designed T cell-based vaccines appears to be a promising vaccination strategy against DENV.

Various vaccine platforms (e.g., based on modified vaccinia Ankara (MVA) viral vector, polypeptide mixtures, fusion proteins and nanoparticles) which have been studied in clinical trials for T cell-based influenza vaccines (Berthoud et al., 2011; Atsmon et al., 2012; Pleguezuelos et al., 2015) may be utilized for designing prospective T cell-based dengue vaccines employing the set of epitopes identified in our study. However, the T cell responses elicited against the combined set of (17) identified epitopes need to be examined experimentally to determine their strength and the resulting immunodominance pattern of the epitopes. This is important because the sequence context in which the epitopes are delivered influences the intra-cellular processing and presentation of the T cell epitopes (Martinez et al., 2009; Welsh et al., 2010) and affects their immunodominance hierarchy (Weiskopf et al., 2014). Specifically, DENV epitopes are reported to have different immunodominance hierarchies depending upon the serotype as well as the order (primary vs secondary) of natural infection (Weiskopf et al., 2014). Furthermore, the presence of other antigenic peptides (i.e., potential epitopes) with respect to the cognate HLA molecules and the peptide-HLA binding affinity also affects epitope immunodominance (Weiskopf et al., 2013; Feltkamp et al., 1994). Thus, while immunodominant epitopes are likely to elicit strong responses, precisely determining the immunodominance hierarchy of T cell epitopes is complex and beyond the scope of this study. This would require carefully designed experimental studies to examine the immune responses elicited following immunization with the proposed set of identified epitopes upon challenge with each DENV serotype.

There is evidence that by priming through vaccination, the immunodominance hierarchy can be altered and the immune response can be directed towards otherwise weakly immunodominant epitopes (Welsh et al., 2010; Im et al., 2011; Remakus et al., 2012). In fact, targeting such weakly immunodominant epitopes has been shown to even confer protection (Holtappels et al., 2008; Ruckwardt et al., 2010; Frahm et al., 2006). Thus, while a few of the 55 identified cross-serotypically conserved epitopes appear to be weakly immunodominant (Fig. 3.6), we considered all of them when finding the subset of epitopes for recommending as vaccine targets (Fig. 3.12).

The cross-serotypically conserved epitopes identified in our study differ from those obtained in previous related studies (Khan et al., 2008; Olsen et al., 2011; Nascimento et al., 2013). Specifically, 44 pan-DENV conserved peptides (9 to 22 residues long) were identified in (Khan et al., 2008), 78 conserved regions (9 to 139 residues long) were identified in (Olsen et al., 2011), and 46 peptides (15 to 18 residues long) were identified in (Nascimento et al., 2013). None of these matched exactly with the 55 top conserved epitopes identified in our study. We note, however, that some of the conserved regions/peptides reported in the previous studies (10 peptides from (Khan et al., 2008) and 12 peptides from (Nascimento et al., 2013)), overlap partially with the top conserved epitopes identified in our study (Fig. 6.5). We identify three main reasons for these differences. First, there is a larger amount of immunological and sequence data available now compared with past years when the previous studies were conducted, and this would affect the conservation profile of the epitopes. Second, our procedure is epitope-centric, which focuses on the conservation of precise DENV-specific T cell epitopes which have been experimentally-determined from human hosts, while the previous studies (Khan et al., 2008; Olsen et al., 2011) predicted conserved (large) regions/peptides from the sequence data alone which may not represent the precise epitope sequences processed and presented by the HLA molecules, and may not be immunogenic. Third, our definition of epitope conservation based on an “exact mapping” criterion is stricter and potentially more robust than the criteria used in previous studies. This strict criterion is important for identifying robust vaccine targets because T cells trained against epitopes may not cross-react with even single residue variants of those epitopes (e.g., as reported for DENV epitope variants EENMDVEIW and EENMEVEIW (Piazza et al., 2014)) .

While we have recommended a set of target epitopes for a prospective T cell-based dengue vaccine that seeks to target a large proportion of the global population, the proposed framework also provides a template for identifying robust vaccine target recommendations for any specific population. The only additional information required is the HLA distribution of the specific population being targeted, which can be seamlessly incorporated with the accompanying source software. We demonstrated this by identifying country-specific sets that maximize the individual population coverages for three dengue-endemic countries. This shows the promise of the proposed approach in identifying sets of epitopes for prospective vaccines targeting specific populations that are most adversely affected by dengue. It is worthwhile to note that although the strategy adopted in this work to maximize population coverage takes into account HLA distribution, it does not factor in the co-expression of certain HLAs in individuals. Multiple HLAs are co-expressed at different loci (e.g. loci A, B and C for HLA class I) and their expression may be correlated, which might lead to overestimation of the population coverage using the current strategy. However, with sufficient data to estimate the frequency of co-expressed HLAs in a target population, the optimization framework can be modified to select epitopes that collectively maximize the population coverage. Here, instead of HLA allele frequencies, the HLA haplotype frequency data (i.e., frequency of multiple HLAs co-occurring in a population) can be incorporated to guide epitope selection.

Moreover, the developed framework can also be extended to perform a systematic study for identifying conserved epitopes across the flavivirus genus, particularly since there is evidence of cross-reactive T cell epitopes across different flaviviruses (Slon Campos et al., 2018; Rathore and St. John, 2020). Similar approaches have been employed recently to identify potential immune targets for viruses belonging to other genera, e.g., SARS-CoV-2, the virus causing the ongoing COVID-19 pandemic (Grifoni et al., 2020; Ahmed et al., 2020b, 2020a).

We have also provided a comprehensive list of conservation profiles of 1,768 experimentally-determined DENV T cell epitopes with their associated HLAs (HTML table deposited in online repository³⁵) which could serve as a reference for future studies. This comprehensive list can aid in reinterpreting earlier results. For example, the epitope NIQTAINQV was previously understood as being conserved across multiple DENV serotypes (Testa et al., 2012). However, using the provided list one can observe that this epitope is only conserved in DENV2. Furthermore, it would be interesting to investigate the functional/structural importance of all the top cross-serotypically conserved epitopes identified in this study to better understand molecular determinants of their conservation.