Epidemiology and Molecular Characterization of Human Respiratory Syncytial Virus in Senegal after Four Consecutive Years of Surveillance, 2012-2015.

The burden of respiratory syncytial virus (RSV) infection remains poorly defined in Africa. To address this, we carried out a descriptive and retrospective pilot study, with a focus on the epidemiology of RSV in Senegal after 4 years of surveillance.From January 2012 to October 2015 swabs were collected from consenting ILI outpatients. Viral detection was performed using RV16 kit enabling direct subtyping of RSV-A and B. For the molecular characterization of HRSV, the second hypervariable region of the Glycoprotein (G) gene was targeted for sequencing. We enrolled 5338 patients with 2803 children younger than five years of age (52.5%). 610 (11.4%) were positive for RSV infection: 276 (45.2%) were group A infections, 334 (54.8%) were group B infections and 21 (3.4%) were A/B co-infections. RSV detection rate is significantly higher (P < 0.0001) in children below 5 years. We noted that the annual distribution of RSV varied substantially by season and for the predominant subtype. Globally, results show a clear circulation pattern in the second half of each year; between June and September and possibly extended into November. The majority of RSV-A strains from Senegal clustered with strains that were previously assigned NA1 and novel ON1 genotype sequences. RSV-B sequences from Senegal clustered with the BA9 genotype. At the amino acid level, RSV-A strains from Senegal show proximity with the genotype ON1 characterized by a 72 nt insertion in G, resulting in 24 extra amino acids of which 23 are duplications of aa 261-283.Globally our results show a clear circulation pattern of RSV in the second half of each year, between June and September and possibly extending into November, with children under 5 being more susceptible. Molecular studies identified the novel strains ON1 and BA9 as the major genotypes circulating in Senegal between 2012 and 2015

Comparison of the distribution of VRS-positive cases into children under 5 years old age groups.

<p>Comparison of the distribution of VRS-positive cases into children under 5 years old age groups.</p

Detection rates of human RSV infection in patients with ILI per sub-group and year from 2012 to 2015 in Senegal and comparison of the distribution into the different age groups.

<p>Detection rates of human RSV infection in patients with ILI per sub-group and year from 2012 to 2015 in Senegal and comparison of the distribution into the different age groups.</p

Phylogenetic tree for RSV-B nucleotide sequences strains between 2012 and 2015 based on the second variable region of the G protein.

<p>We used the neighbor-joining method with 1000 bootstrap replicates with MEGA 6 version. Senegal isolates are highlighted in different colors for each year and reference strains from Genbank are in black. Only bootstrap values over 70 are shown.</p

Monthly distribution of RSV A and RSV B infections in patients with ILI in Senegal, over the years of the study (2012–2015).

<p>In green is represented the rainfall during the period of study. Temperatures (mean values of the maxima and the minima ones per month) are also represented.</p

Demographical characteristics and symptoms.

<p>Demographical characteristics and symptoms.</p

Deduced amino acid alignments of the second variable region of the G protein gene from RSV-A strains from Senegal (in black).

<p>Alignments are shown relative to the sequences of prototype strain A2 (GenBank accession number M11486). The amino acid numbering corresponds to strain A2 G protein positions 220 to 308 for the HRSV-A viruses. Identical residues are indicated by dashes. Potential N-glycosylation sites (NXT) in the reference sequence are indicated in red amino acid. Amino acid in blue indicated a duplicated block in strains from Senegal (we voluntary included an isolate from Ontario with the same inserted amino acid block).</p