Convergent antibody signatures in human dengue

Abstract

Dengue is the most prevalent mosquito-borne viral disease in humans, and the lack of early prognostics, vaccines, and therapeutics contributes to immense disease burden. To identify patterns that could be used for sequence-based monitoring of the antibody response to dengue, we examined antibody heavy-chain gene rearrangements in longitudinal peripheral blood samples from 60 dengue patients. Comparing signatures between acute dengue, postrecovery, and healthy samples, we found increased expansion of B cell clones in acute dengue patients, with higher overall clonality in secondary infection. Additionally, we observed consistent antibody sequence features in acute dengue in the highly variable major antigen-binding determinant, complementarity-determining region 3 (CDR3), with specific CDR3 sequences highly enriched in acute samples compared to postrecovery, healthy, or non-dengue samples. Dengue thus provides a striking example of a human viral infection where convergent immune signatures can be identified in multiple individuals. Such signatures could facilitate surveillance of immunological memory in communities.

Figure 1. Antibody V_H clonality in peripheral blood as a surrogate for B cell expansion in human dengue

(A) Probability of observing identical V_H sequences in two or more independent PCR replicates (P(collision)) in acute and convalescent (Conv) phase samples (left panel, *P=0.0004, Wilcoxon Signed Rank test) or in acute and post-convalescent (P-Conv) phase samples (right panel, *P<0.0001, Wilcoxon Signed Rank test) from the same patients. Only convalescent samples that were taken 7–21 days post-symptom onset were considered for this analysis. (B) P(collision) measures for samples from healthy individuals and from individuals with acute, non-dengue febrile illness (febrile). *P=0.0486, Wilcoxon-Mann-Whitney test. (C) P(collision) in acute (left panel), convalescent (middle panel) or post-convalescent (right panel) phase samples from individuals presenting with primary or secondary DENV infections. Annotations to each plot show the 25th–75th percentiles (box), the 10th–90th percentiles (whiskers), and the median (horizontal line). *P=0.0409, Wilcoxon-Mann-Whitney test. See also Figure S1 and Table S2.

Figure 2. CDR3 prevalence in dengue and non-dengue samples

(A–B) Prevalence of selected CDR3s, measured as proportion of samples containing these CDR3s in various subsets of samples. (A) CDR3 prevalence in acute phase samples partitioned for cross-validation or by DENV serotype. (B) CDR3 prevalence in samples from 47 healthy individuals and 8 individuals with non-dengue febrile (non-dengue), and in post-convalescent phase samples partitioned either for cross-validation or by DENV serotype. See also Figure S2 and Table S3.

Figure 3. Diversity in sequences encoding for the ARLD(Y)₅GMDL CDR3

Nucleotide sequences encoding for the ARLD(Y)₅GMDL CDR3, segregated by patient identity and sample type (A, Acute; C, Convalescent; PC, Post-convalescent). #, count per sample; CON, Consensus; V, Variable region; D, Diversity region; N, non-templated additions; J, Joining region; *^identical sequences in multiple samples. See also Figure S3.

Figure 4. Sequence diversity in regions flanking the ARLD(Y)₅GMDL CDR3

Color-coded nucleotide diversity in FR regions flanking the ARLD(Y)₅GMDL CDR3 and its one-mismatch derivatives, with each row representing a unique sequence read within an individual. %mut, percent mutation in the V gene (which has been truncated to include 160 nucleotides at the 3’ terminus for direct comparison between sequences); V gene usage, V genes with evidence for usage in at least two samples; sample, sample of sequence origin. See also Figure S4.

Figure 5. Amino acid characteristics of coherent CDR3s

(A, B) Separation of CDR3 clusters in the spaces bounded by principal components (Prin) 1, 2 and 3, which represent residue-by-residue scores for hydrophilicity, molecular weight and isoelectric pH for all CDR3s with V_H usage and length identical to the convergent (A) 13-mer and (B) 10-mer CDR3s. All CDR3s that cluster with the (A) 13-mer and (B) 10-mer CDR3s identified by mismatch cross-validation are highlighted; members from all other clusters are faded. The top right quadrants are magnified images of the boxed graph areas. (C) Sequences and residue-specific characteristics of V_H CDR1 regions and CDR2 regions associated with the highlighted 13-mer (top panel) and 10-mer (bottom panel) convergent CDR3 clusters. Amino acids in black, consensus residues; amino acids in red, germline-encoded residues different from consensus; *junctional residues with undeterminable germline sequence. Colored circles indicate deviations in molecular weight, isoelectric pH or hydrophilicity scores from germline encodings for CDR1 and CDR2, or from median scores computed across all CDR3s with lengths identical to the corresponding CDR3s. See also Figure S5 and Table S4.