Whole Genome Sequencing and Genetic Diversity of Respiratory Viruses Detected in Children With Acute Respiratory Infections: A One-Year Cross-Sectional Study in Senegal

Abstract

Acute respiratory infections (ARI) are a health priority, especially in countries with limited resources. They are a major cause of morbidity and mortality, especially among children and the elderly. In Senegal, the endemic circulation of respiratory viruses other than influenza has been demonstrated. However, there is a paucity of data exploring the genetic diversity of these viruses based on whole-genome sequencing. In this study, we present data on the genetic diversity of respiratory viruses in children under 15 years old in Senegal, including an overview of the different pathogens detected. Between November 2022 and November 2023, we collected nasopharyngeal swabs from children seen in curative consultations for symptoms of acute respiratory infections. Of the 156 children included, 73.7% tested positive for at least one pathogen. The most frequently detected virus was rhinovirus (50.0%), followed by influenza B (41.6%) and human parainfluenza virus type 3 (7.6%). Combinations of rhinovirus/influenza B, human parainfluenza virus type 2/human parainfluenza virus type 4, and rhinovirus/influenza B/adenovirus were the most frequently identified. A statistically significant association was detected between some of the viruses detected. A high genetic diversity of respiratory viruses circulating in children was revealed. The strains were phylogenetically close to various strains circulating worldwide, suggesting a global circulation of respiratory viruses. Our study provides the first complete genome sequences of human parainfluenza viruses type 2, 3, 4 and human bocavirus from Senegal and thus contributes to the enrichment of international databases on sequences from Senegal and underlines the importance of sequencing in the dynamics of pathogen circulation.

Keywords: NGS; Senegal; acute respiratory infections; children; virus; whole genome.

Figure 1

Prevalence of detected pathogens. Number of different viruses detected. 156 children were tested; 1 child could be infected with several viruses at the same time. H1N1, hemagglutinin1 neuraminidase1; HPIV‐2, human parainfluenza virus 2; HPIV‐4, human parainfluenza virus 4; HPIV‐3, human parainfluenza virus 3; HMPV, human metapneumovirus; HRSV, human respiratory syncytial virus; HCoV, human coronavirus.

Figure 2

Proportion of single infections and co‐infections (n = 156). Rhinovirus, parainfluenza virus type 3, and adenovirus were the most frequently detected, while in co‐infections, rhinovirus and influenza B virus were the most common co‐infecting viruses. H1N1, hemagglutinin1 neuraminidase1; HPIV‐2, human parainfluenza virus 2; HPIV‐4, human parainfluenza virus 4; HPIV‐3, human parainfluenza virus 3; HMPV, human metapneumovirus; HRSV, human respiratory syncytial virus; HCoV, human coronavirus.