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Updated: Jun 4, 2026
High-throughput Detection Method for Influenza Virus
Published on: February 4, 2012
Microfluidic qPCR for detection of 21 common respiratory viruses in children with influenza-like illness
Thomas J Saville1,2, Hayley Colton3,4,5, Sheikh Jarju6
1Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK. t.j.saville@sheffield.ac.uk.
Insights
Global surveillance often overlooks viruses beyond influenza. This study used microfluidic quantitative polymerase chain reaction (qPCR) to detect multiple respiratory viruses in children, revealing frequent co-infections and highlighting the need for broader surveillance strategies.
Area of Science:
- Virology
- Epidemiology
- Public Health
Background:
- Global respiratory virus surveillance predominantly focuses on influenza, despite other viruses causing significant morbidity and mortality.
- The COVID-19 pandemic and advancements in vaccines for respiratory syncytial virus (RSV) underscore the need for comprehensive surveillance.
- Existing surveillance platforms may not adequately capture the diversity of respiratory pathogens.
Purpose of the Study:
- To establish and validate a microfluidic quantitative polymerase chain reaction (qPCR) assay for detecting multiple respiratory viruses.
- To assess the prevalence and co-detection of various respiratory viruses in young children with influenza-like illness in The Gambia.
- To demonstrate the utility of microfluidic qPCR for enhanced respiratory virus surveillance in resource-limited settings.
Main Methods:
- Upper respiratory tract swabs were collected from children aged 24-59 months presenting with influenza-like illness in The Gambia (2017-18).
- A microfluidic qPCR assay was developed to simultaneously detect 21 different respiratory viruses.
- Samples were analyzed to determine the frequency of individual and multiple viral detections.
Main Results:
- Over 76% of samples (121/158) tested positive for at least one respiratory virus.
- Rhinovirus (23.4%) and adenovirus (21.5%) were the most frequently detected viruses.
- A significant proportion of positive samples (33%) showed co-infection with two or more viruses, including parainfluenza virus 3, influenza B, and human metapneumovirus.
Conclusions:
- Microfluidic qPCR is an effective tool for high-throughput, comprehensive detection of multiple respiratory viruses in surveillance programs.
- The high prevalence of diverse respiratory viruses and co-infections necessitates broader surveillance approaches.
- Enhanced surveillance is crucial for responding to future epidemics and guiding the development and deployment of new preventive and therapeutic measures, especially in low-resource settings.
Abstract:
Multiple respiratory viruses lead to high morbidity and mortality, yet global surveillance platforms focus primarily on seasonal influenza viruses. The COVID-19 pandemic and new RSV vaccines highlight the importance of a broader approach. Upper respiratory tract swabs from children aged 24-59 months presenting with influenza-like illness in The Gambia were collected during follow-up of a live-attenuated influenza vaccine randomised controlled trial in 2017-18. A microfluidic quantitative polymerase chain reaction (qPCR) assay was established and used to detect 21 respiratory viruses. 76.6% of samples had one or more viruses detected (n = 121/158). The viruses detected most frequently were rhinovirus (n = 37/158, 23.4%) and adenovirus (n = 34/158, 21.5%), followed by parainfluenza virus 3, influenza B and human metapneumovirus B. A third of positive samples had multiple viruses detected (two n = 31/121, 25.6%; three n = 9/121, 7.4%). Our data demonstrates how microfluidic qPCR is a useful tool for high-throughput, comprehensive detection of multiple respiratory viruses in surveillance platforms. Rapidly changing epidemiology exemplifies the need for new, broader approaches to virus surveillance in low-resource settings to respond to future epidemics and to guide the need for and use of new prevention and therapeutic measures.
