Inter-Lineage Variation of Lassa Virus Glycoprotein Epitopes: A Challenge to Lassa Virus Vaccine Development

Abstract

Lassa virus (LASV), which causes considerable morbidity and mortality annually, has a high genetic diversity across West Africa. LASV glycoprotein (GP) expresses this diversity, but most LASV vaccine candidates utilize only the Lineage IV LASV Josiah strain GP antigen as an immunogen and homologous challenge with Lineage IV LASV. In addition to the sequence variation amongst the LASV lineages, these lineages are also distinguished in their presentations. Inter-lineage variations within previously mapped B-cell and T-cell LASV GP epitopes and the breadth of protection in LASV vaccine/challenge studies were examined critically. Multiple alignments of the GP primary sequence of strains from each LASV lineage showed that LASV GP has diverging degrees of amino acid conservation within known epitopes among LASV lineages. Conformational B-cell epitopes spanning different sites in GP subunits were less impacted by LASV diversity. LASV GP diversity should influence the approach used for LASV vaccine design. Expression of LASV GP on viral vectors, especially in its prefusion configuration, has shown potential for protective LASV vaccines that can overcome LASV diversity. Advanced vaccine candidates should demonstrate efficacy against all LASV lineages for evidence of a pan-LASV vaccine.

Keywords: epitopes; glycoprotein; lassa virus; lassa virus diversity; lassa virus vaccine.

Figure 1

Geographical distribution of Lassa virus (LASV) Lineages in West Africa. The shaded areas and symbols on the nap show the distribution of LASV lineage and sub-lineage infections as observed in West Africa, based on data from Ehichioya et al., 2019 and Wiley et al., 2019 [17,18]. The shaded areas depict administrative regions/states within LASV endemic countries, where each represented LASV lineage (II and III) or sub-lineage (IV.A and IV.B) has been reported. The symbols show the locations where LASV lineages I, V, VI, and VII have been observed. Note: Shaded areas and symbols do not represent the incidence or prevalence of LASV infections in each location or administrative region.

Figure 2

Maximum clade credibility tree of LASV Lineages’ glycoprotein (GP) gene. A phylogenetic analysis of the GP gene of members of confirmed and proposed (*) LASV lineages. The tree is rooted in Lineage I and each node shows the Bayesian posterior probabilities support. The tree tips are labelled to shown country, strain, year of collection, and GenBank accession numbers. Precursor glycoprotein (GPC) nucleotide sequences with greater than 60% coverage for the LASV GPC coding sequence (CDS) were retrieved from the GenBank, a maximum likelihood tree was generated in RAxML v8.2.12 [39] on CIPRES [40]. Bayesian phylogenetic inference was performed using BEAST v1.10.4 [41] with Generalized Time Reversible (GTR) plus gamma substitution model, uncorrelated relaxed clock model in lognormal distribution, SkyGrid coalescent tree prior setting, and the maximum likelihood tree as starting tree. Markov chain Monte Carlo (MCMC) chains were run for 250 million iterations, sampled every 10,000 states and 2500 trees were discarded as burn-in, to obtain an effective sample size (ESS) >200 for all parameters. Maximum clade credibility tree was drawn in Tree Annotator v1.10.4 [41].

Figure 3

GPC-B† quaternary structure epitope. The 25.6A and 37.7H monoclonal antibodies (mAbs) were raised to the LASV GPC-B conformational epitope. (a). (Top view) The LASV GP trimer is bound by three 25.6A Fabs, with each Fab binding two GP monomers near the trimer’s base. (b). (Front view rotated 60°) The GP trimer bound near its base by three 37.7H Fabs (two Fab in view) in a similar manner as above. Amino acid residues in the 37.7H epitope sites A and B highlighted in yellow to show the antibody footprint. GP monomers are shown as surface representations. LASV GP-mAb bound structures were retrieved from the Protein Database using PDB IDs 6P95 and 5VK2 for 25.6A mAb-bound GP and 37.7H mAb-bound GP respectively, image generated in EzMol 2.1 online program [60] and labelled manually.

Figure 4

Aligned GP precursor amino acid sequence of LASV confirmed and proposed lineages. Multiple sequence alignment of prototype LASV strains selected from the literature (see Table 1 for detailed description) created with Clustal Omega in Jalview 2.11.0 [61] and manually annotated. LASV lineages and strains: Lineage I—Pinneo 1969 Strain, Lineage II—Nig08-04 Strain, Lineage III—Nig08-A19 Strain, Lineage IV—Josiah Strain, proposed lineage V—Soromba-R strain, and proposed lineage VII—Alzey strain), and proposed lineage VI—KAK-428 strain. LASV GP B-cell epitopes include: 37.7H epitope site A (b & j) and site B (e & g), GPC-A (b & e), GP1-A (c), GP2-B (h), GP2-L1(f), GP2-L2 (i), and GP2-L3 (k). LASV GP T-cell epitopes include: GP1 epitope 42–50AA (a), GP1 epitope 60–68AA (b), and GP2 epitope 441–449AA (l).