Association of disease severity and genetic variation during primary Respiratory Syncytial Virus infections

Abstract

Background: Respiratory Syncytial Virus (RSV) disease in young children ranges from mild cold symptoms to severe symptoms that require hospitalization and sometimes result in death. Studies have shown a statistical association between RSV subtype or phylogenic lineage and RSV disease severity, although these results have been inconsistent. Associations between variation within RSV gene coding regions or residues and RSV disease severity has been largely unexplored.

Methods: Nasal swabs from children (< 8 months-old) infected with RSV in Rochester, NY between 1977-1998 clinically presenting with either mild or severe disease during their first cold-season were used. Whole-genome RSV sequences were obtained using overlapping PCR and next-generation sequencing. Both whole-genome phylogenetic and non-phylogenetic statistical approaches were performed to associate RSV genotype with disease severity.

Results: The RSVB subtype was statistically associated with disease severity. A significant association between phylogenetic clustering of mild/severe traits and disease severity was also found. GA1 clade sequences were associated with severe disease while GB1 was significantly associated with mild disease. Both G and M2-2 gene variation was significantly associated with disease severity. We identified 16 residues in the G gene and 3 in the M2-2 RSV gene associated with disease severity.

Conclusion: These results suggest that phylogenetic lineage and the genetic variability in G or M2-2 genes of RSV may contribute to disease severity in young children undergoing their first infection.

Keywords: Genetic variation; RSV; Respiratory infection; Severe disease; Whole-genome.

Fig. 1

Genomic Variation of the RSV Genome. Sequence genotyping resulted in 7 genotypes (3 RSVA, 4 RSVB). Subtype A contained 93 total sequences falling into 3 different genotypes colored Red(GA1), Cyan(GA2), and Purple(GA3). Subtype B contained 67 total sequences and the 4 different genotypes are colored Green(GB1), Blue(GB2), Orange(GB3), and Pink(GB4). Each sequence name contains metadata representing the subtype, year, and severity (name.subtype.year.severity). Severity is colored Black (Mild) and Red (Severe)

Fig. 2

Comparison of Amino Acid Variation in Across RSV Proteins. The number of amino acid substitution between each gene coding region of the whole-genome RSV sequence was calculated. A Boxplot of the number of amino acid substitutions for each gene within subtype for each RSV gene coding region. B Boxplot of the percentage of number of amino acid substitutions divided by the amino acid length of the coding sequence within subtype for each RSV gene coding region

Fig. 3

Amino Acid Variability Among RSV G and M2-2 Proteins. Protein sequences for G and M2-2 proteins from RSVA and RSVB subtypes were aligned separately. The number of amino acid substitutions were calculated between all strains and Principal Coordinate Analysis was performed to demonstrate amino acid variability in reduced dimensional space. Ellipses are centered on centroids with 1 standard deviation. Points are colored by disease severity status; red = mild, black = severe. When points contain multiple sequences and from patients of both disease types, points are colored by the more numerous disease type