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


RESULTS
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.


CONCLUSIONS
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.
Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal.
Amary
A
Fall
Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal.
Ndongo
N
Dia
Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal.
El Hadj Abdel Kader
el HA
Cisse
Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal.
Davy E
DE
Kiori
Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, Dakar, Sénégal.
Fatoumata Diene
FD
Sarr
Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal.
Sara
S
Sy
Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal.
Debora
D
Goudiaby
Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, Dakar, Sénégal.
Vincent
V
Richard
Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal.
Mbayame Ndiaye
MN
Niang
D000293:Adolescent; D000328:Adult; D000595:Amino Acid Sequence / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D005260:Female; D005838:Genotype; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D010865:Pilot Projects; D018357:Respiratory Syncytial Virus Infections / Q000453:epidemiology* / Q000235:genetics* / Q000473:pathology / Q000821:virology; D018113:Respiratory Syncytial Virus, Human / Q000235:genetics* / Q000472:pathogenicity; D012621:Seasons; D012675:Senegal; D016415:Sequence Alignment