Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort

Abstract

Background: Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection.

Methods: Among healthy term infants we identified those with prolonged RSV infection and conducted (1) a human genome-wide association study (GWAS) to test the dependence of infection risk on host genotype, (2) a viral GWAS for association with prolonged RSV infection using RSV whole-genome sequencing, (3) an analysis of all viral public sequences, (4) an assessment of immunological responses, and (5) a summary of all major functional data. Analyses were adjusted for viral/human population structure and host factors associated with infection risk.

Results: We identified p.E123K/D and p.P218T/S/L in G protein that were associated with prolonged infection (Padj = .01). We found no evidence of host genetic risk for infection. The RSV variant positions approximate sequences that could bind a putative viral receptor, heparan sulfate.

Conclusions: Using analysis of both viral and host genetics we identified a novel RSV variant associated with prolonged infection in otherwise healthy infants and no evidence supporting host genetic susceptibility to infection. As the capacity of RSV for chronicity and its viral reservoir are not defined, these findings are important for understanding the impact of RSV on chronic disease and endemicity.

Keywords: GWAS; RSV; infection; population; prolonged; respiratory; viral.

Figure 1.

Genetic analyses of RSV infection in infancy. A, The Manhattan plot shows no genome-wide significant associations (P value threshold of 5e⁻⁸). B, The Q-Q plot demonstrates that the observed P values are congruent with those expected under the null hypothesis that RSV infection in infancy is independent of host genotype. C, The association between the 54 selected childhood asthma- or RSV lower respiratory tract infection-associated SNPs and RSV infection in infancy in our data. The solid diagonol identity line (shown in red), and the dashed grey lines are ±1 standard deviation around the expected −log₁₀ (P value). Abbreviations: RSV, respiratory syncytial virus; SNP, single nucleotide polymorphism.

Figure 2.

Viral population structure. A, Linear map of the RSV genome. B, Phylogenetic tree based on multiple sequence alignment of G protein amino acid sequences. Color indicates amino acids. C, Principal component analysis. PCs 1–3 with labels indicating prolonged infections from different phylogenetic clades. D, A summary of every pairwise genetic distance between every viral sequence is shown (above). Genetic invariance in prolonged infections separated by at least 15 days was compared to other genetic variation within the most closely related sequences (below left) and within all possible closely related pairs (below right). Jitter applied for visualization. Abbreviations: G, glycoprotein; M, matrix protein; PC, principal component; RSV, respiratory syncytial virus; SH, small hydrophobic protein; VE, variance explained.

Figure 3.

Viral genetic association with prolonged infection. A, Amino acid association with prolonged infection after multiple testing correction (significant threshold shown by dotted line). B, Variance explained within cohort. The effect of each variant on cohort structure is shown for PCs 1–2. The small percentage variance explained for a significantly associated lead variant supports a true positive. C, Variants in strong correlation were clumped for association testing using proxies for r² ≥ 0.8. One significant association was identified (shown in A); the r² values for all other variants show a single, highly correlated variant with the lead proxy (red), identifying p.E123K/D and p.P218T/S/L. D, Evidence for biological interpretation for every amino acid position is summarized. Dotted red lines indicate the positions at p.123 and p.218. Abbreviations: PC, principal component; SNP, single-nucleotide polymorphism.