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Viral metagenomics analysis of stool specimens from children with unresolved gastroenteritis in Qatar
Ghina Hijazi1, Fatima Dakroub1, Pierre Khoueiry2
1Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.
Insights
Viral metagenomics identified the cause of acute gastroenteritis (AGE) in children when standard tests failed. This approach detected various human viruses, aiding in diagnosing undiagnosed AGE cases.
Area of Science:
- Virology
- Pediatric Infectious Diseases
- Genomics
Background:
- Acute gastroenteritis (AGE) causes significant global illness and death, particularly in young children.
- Viruses are primary causes of AGE, especially in developing nations, yet many cases remain undiagnosed.
- Advances in molecular diagnostics have not fully resolved the etiology of a substantial proportion of AGE cases.
Purpose of the Study:
- To investigate the viral etiology of undiagnosed acute gastroenteritis in children under five years old in Qatar.
- To implement a viral metagenomics pipeline for identifying causative agents of AGE.
- To determine the utility of viral metagenomics in cases where routine diagnostics are insufficient.
Main Methods:
- Collected 89 stool specimens from children under five with undiagnosed AGE.
- Enriched viral genomes from specimens.
- Generated approximately 1.3 billion sequences using Illumina HiSeq platform.
- Mapped sequences to viral genomes to identify viral pathogens.
Main Results:
- Viral genomes were detected in 7% of the generated sequences.
- Human viruses were identified in 34 out of 89 specimens (38.2%).
- Detected viruses included adenovirus, coxsackievirus A16, rotavirus (G9P[8], G4P[8]), norovirus (GII), influenza A virus (H3), and respiratory syncytial virus A (RSVA).
Conclusions:
- Viral metagenomics is an effective tool for diagnosing the etiology of AGE when conventional molecular assays are unsuccessful.
- This approach successfully identified a range of human viruses contributing to undiagnosed AGE in the studied pediatric population.
- The findings highlight the importance of advanced sequencing techniques in understanding the full spectrum of viral infections causing gastroenteritis.
Abstract:
Acute gastroenteritis (AGE) is associated with significant global morbidity and mortality, especially among children under five years of age. Viruses are well established as etiologic agents of gastroenteritis since they are the most common pathogens that contribute to the disease burden in developing countries. Despite the advances in molecular diagnosis, a substantial proportion of AGE etiology remain unresolved. We implemented a viral metagenomics pipeline to determine the potential viral etiology associated with AGE among children under the age of five years in Qatar with undiagnosed etiology. Following enriching for the viral genome, ∼1.3 billion sequences were generated from 89 stool specimens using the Illumina HiSeq platform, of which 7% were mapped to viral genomes. Human viruses were detected in 34 specimens (38.2%); 14 were adenovirus, nine coxsackievirus A16, five rotavirus (G9P[8] and G4P[8]), four norovirus (GII), one influenza A virus (H3), and one respiratory syncytial virus A (RSVA). In conclusion, the viral metagenomics approach is useful for determining AGE's etiology when routine molecular diagnostic assays fail.
