Respiratory syncytial virus in pediatric patients with severe acute respiratory infections in Senegal: findings from the 2022 sentinel surveillance season

Abstract

In 2022, many regions around the world experienced a severe respiratory syncytial virus (RSV) epidemic with an earlier-than-usual start and increased numbers of paediatric patients in emergency departments. Here we carried out this study to describe the epidemiology and genetic characteristics of RSV infection in patients hospitalized with severe acute respiratory infections in 2022. Samples were tested for RSV by multiplex real time reverse transcription polymerase chain reaction. Subsequently, a subset of RSV positive samples was selected for NGS sequencing. RSV was detected in 16.04%, among which RSV-A was confirmed in 7.5% and RSV-B in 76.7%. RSV infection were more identified in infants aged ≤ 11 months (83.3%) and a shift in the circulation pattern was observed, with highest incidences between September-November. Phylogenetic analyses revealed that all RSV-A strains belonged to GA2.3.5 genotype and all RSV-B strains to GB5.0.5a genotype. Three putative N-glycosylation sites at amino acid positions 103, 135, 237 were predicted among RSV-A strains, while four N-linked glycosylation sites at positions 81, 86, 231 and 294 were identified in RSV-B strains. Globally, our findings reveal an exclusive co-circulation of two genetic lineages of RSV within the pediatric population in Senegal, especially in infants aged ≤ 11 months.

Figure 1

Weekly distribution of RSV among inpatients in Senegal from January to December 2022. Bars represent the proportions of RSV cases for each epidemiological week and the curve represent the positivity rates.

Figure 2

Phylogenetic tree of complete genomes of RSV-A subtype circulating among hospitalized patients in Senegal (January–December 2022). The tree was constructed using the maximum likelihood (ML) method using the IQ-TREE software version 1.6.12 and visualized using the Figtree software version 1.4.4. The statistical significance was tested by 1000 bootstrapping replicates, and the software was responsible for defining the correct model used. Sequences from Senegal are highlighted in red color. The scale bar represents the number of nucleotide substitutions per site.

Figure 3

Phylogenetic tree of complete genomes of RSV-B subtype circulating among hospitalized patients in Senegal (January-December 2022). The tree was constructed using the maximum likelihood (ML) method using the IQ-TREE software version 1.6.12 and visualized using the Figtree software version 1.4.4. The statistical significance was tested by 1000 bootstrapping replicates, and the software was responsible for defining the correct model used. Sequences from Senegal are highlighted in red color. The scale bar represents the number of nucleotide substitutions per site.

Figure 4

Deduced amino acid alignment and mutations in the second hypervariable region of the G protein of RSV-A (A) and RSV-B (B) strains from Senegal compared with prototype strain A2 (GenBank accession number M11486) and ON1 reference strain (GenBank accession number JN257693) for RSV-A, BA4128/99B strain (GenBank accession number AY333364) for RSV-B. The two copies of 23 amino acid regions in the RSV-A strains (A) and 20 amino acid regions in the RSV-B strains (B) are framed black, whereas potential N-glycosylation sites (NXT, where X is not proline) are indicated by red boxed areas. Identical amino acids are indicated by dot and asterisks represent stop codons.

Figure 5

Map of Senegal showing the different sentinel sites of the 4S network. Hospital sentinel sites, all located in the capital Dakar are represented by red dots, while blue dots represent the ILI community sentinel sites.