Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Aug 18;17(8):1131.
doi: 10.3390/v17081131.

Detection of Influenza and Other Respiratory Pathogens by RT-qPCR and Characterization by Genomic Sequencing Using ILI/SARI Hospital-Based Sentinel Surveillance System

Charity A Nassuna  1 , Fahim Yiga  1 , Joweria Nakaseegu  1 , Esther Amwine  1 , Bridget Nakamoga  1 , Noel Ayuro  1 , Nicholas Owor  1 , David Odongo  1 , Jocelyn Kiconco  1 , Thomas Nsibambi  2 , Samuel Wasike  2 , Ben Andagalu  2 , Chelsea Harrington  2 , Adam W Crawley  2 , Julius Ssempiira  2 , Ray Ransom  2 , Amy L Boore  2 , Barnabas Bakamutumaho  1 , John T Kayiwa  1 , Julius J Lutwama  1
Affiliations

Detection of Influenza and Other Respiratory Pathogens by RT-qPCR and Characterization by Genomic Sequencing Using ILI/SARI Hospital-Based Sentinel Surveillance System

Charity A Nassuna et al. Viruses. .

Abstract

Limited surveillance and laboratory testing for non-influenza viruses remains a challenge in Uganda. The World Health Organization (WHO) designated National Influenza Center (NIC) tested samples from patients with influenza-like illness (ILI) and severe acute respiratory infections (SARIs) during August 2022-February 2023. We leveraged the influenza sentinel surveillance system to detect other respiratory viruses (ORVs). Samples were tested using the US Centers for Disease Control and Prevention (CDC) influenza and SARS-CoV-2 multiplex and the FTDTM Respiratory Pathogens 21 assays using real-time reverse transcription polymerase chain reaction (RT-qPCR). A total of 687 (ILI = 471 (68.6%) and SARI = 216 (31.4%) samples were tested. The median age was 2 years (IQR: 1-25) for ILI and 6 years (IQR: 1-18) for SARI case definitions (p-value = 0.045). One or more respiratory pathogens were detected in 38.7% (n = 266) of all samples; 33 (12.4%) were selected for metagenomics sequencing and 8 (3%) for SARS-CoV-2 targeted sequencing. Respiratory pathogens were detected by sequencing in 23 of 33 (69.7%) samples. Our study provides insight into the usefulness of this surveillance system in conducting virological testing for other viruses and provides tools and evidence to monitor patterns and characteristics of viruses causing ILI/SARI, which will guide public health decisions and interventions in Uganda.

Keywords: RSV; SARS-CoV-2; Uganda; influenza; metagenomic next-generation sequencing; other respiratory viruses.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Detection of single and mixed pathogens. (The round black dots denote the type of pathogen(s) detected on the Y-axis against single or co-infections on the horizontal axis.) The scale on the top shows the number of single or co-infection cases detected along the specific column.
Figure 2
Figure 2
Number of positive respiratory pathogens detected by year and month.
See this image and copyright information in PMC

References

    1. Shi T., McAllister D.A., O’Brien K.L., Simoes E.A., Madhi S.A., Gessner B.D., Polack F.P., Balsells E., Acacio S., Aguayo C., et al. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: A systematic review and modelling study. Lancet. 2017;390:946–958. doi: 10.1016/S0140-6736(17)30938-8. - DOI - PMC - PubMed
    1. Wang X., Li Y., O’brien K.L., Madhi S.A., Widdowson M.A., Byass P., Omer S.B., Abbas Q., Ali A., Amu A., et al. Global burden of respiratory infections associated with seasonal influenza in children under 5 years in 2018: A systematic review and modelling study. Lancet Glob. Health. 2020;8:e497–e510. doi: 10.1016/S2214-109X(19)30545-5. - DOI - PMC - PubMed
    1. Shi T., Denouel A., Tietjen A.K., Campbell I., Moran E., Li X., Campbell H., Demont C., Nyawanda B.O., Chu H.Y., et al. Global Disease Burden Estimates of Respiratory Syncytial Virus-Associated Acute Respiratory Infection in Older Adults in 2015: A Systematic Review and Meta-Analysis. J. Infect. Dis. 2020;222((Suppl. S7)):S577–S583. doi: 10.1093/infdis/jiz059. - DOI - PubMed
    1. Sarfo J.O., Amoadu M., Gyan T.B., Osman A.G., Kordorwu P.Y., Adams A.K., Asiedu I., Ansah E.W., Amponsah-Manu F., Ofosu-Appiah P. Acute lower respiratory infections among children under five in Sub-Saharan Africa: A scoping review of prevalence and risk factors. BMC Pediatr. 2023;23:225. doi: 10.1186/s12887-023-04033-x. - DOI - PMC - PubMed
    1. Manjarrez-Zavala M.E., Rosete-Olvera D.P., Gutiérrez-González L.H., Ocadiz-Delgado R., Cabello-Gutiérrez C. Respiratory Disease and Infection—A New Insight. InTech; London, UK: 2013. Pathogenesis of Viral Respiratory Infection. - DOI

LinkOut - more resources