Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses.

Mbayame Ndiaye Niang,Déborah Goudiaby,Sara Sy,Ndeye Sokhna Diop,Amary Fall,Ndongo Dia,Mamadou Aliou Barry,Davy E Kiori,Fatoumata Diene Sarr,Malick Fall,Oliver Schildgen

doi:10.1371/journal.pone.0174287

Abstract

BackgroundHuman adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases.Methodology and resultsFrom January 2012 to December 2015 swabs were collected from consenting ILI outpatients. Adenoviral detection is performed by rRT-PCR with the Anyplex™ II RV16 Detection kit (Seegene) and molecular characterization was performed using a partial hexon gene sequence. 6381 samples were collected. More than half of patients (51.7%; 3297/6381) were children of ≤ 5 years. 1967 (30.8%) were positive for HAdV with 1561 (79.4%) found in co-infection with at least one another respiratory virus. The most common co-detections were with influenza viruses (53.1%; 1045/1967), rhinoviruses (30%; 591/1967), enteroviruses (18.5%; 364/1967) and RSV (13.5%; 266/1967). Children under 5 were the most infected group (62.2%; 1224/1967; p <0.05). We noted that HAdV was detected throughout the year at a high level with detection peaks of different amplitudes without any clear seasonality. Phylogenetic analysis revealed species HAdV-C in majority, species HAdV-B and one HAdV- 4 genome type. The 9 HAdV-B species like strains from Senegal grouped with genome types HAdV-7, HAdV-55 and HAdV-11 as shown by a phylogenetic branch with a high bootstrap value of (88%).ConclusionIn conclusion, the results of the present study suggest strong year-round HAdV activity in Senegal, especially in children up to 5 years of age. Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B species. The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections.

Highlights

Human adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract
Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B
The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections

Summary

Methods

From January 2012 to December 2015 we collected specimens (nasal-pharyngeal and oral-pharyngeal swabs) and surveillance data for influenza and other viral respiratory pathogens from outpatients presenting with influenza-like-illness (ILI) at different sentinel sites in Senegal. Swabs are placed in 2-mL cryovials with viral transport medium (Universal Transport Medium; COPAN Diagnostics Inc., Murrieta, CA), and transported at a controlled temperature of 2 ̊C—8 ̊C to the laboratory. An ILI patient was defined as a person presenting with sudden onset of fever (>38 ̊C) or history of sudden onset of fever in the recent past ( 3 days) and either cough or sore throat and/or rhinorrhea in the absence of other diagnosis, according to the CDC case definition. Each sample is accompanied by a case report form collecting demographic and clinical data. Aliquots of samples were stored at −80 ̊C for additional analysis (isolation and/or molecular characterization)

Results

Discussion

Conclusion