How to Cite: Yadav, S., Wagh, V., Pajai, S., Joseph, A. S. M., Jaganathan, R., & Banerjee, D. (2022). Detection of respiratory viruses in clinical samples: Exploring next generation sequencing and clinical metagenomics. International Journal of Health Sciences, 6(S6), 8264–8273. https://doi.org/10.53730/ijhs.v6nS6.12062 International Journal of Health Sciences ISSN 2550-6978 E-ISSN 2550-696X © 2022. Manuscript submitted: 9 April 2022, Manuscript revised: 18 June 2022, Accepted for publication: 27 July 2022 8264 Detection of respiratory viruses in clinical samples: Exploring next generation sequencing and clinical metagenomics Shubham Yadav Department of Microbiology, Jawaharlal Nehru Medical College, Belagavi (KLE Deemed to be University) Email: yadavshubham835@gmail.com Vaishnav Wagh Department of Multidisciplinary Research Unit, AFMC, Pune Email: vaishnavwagh04@gmail.com Sakshi Pajai Department of Biochemistry, AIIMS Nagpur Email: Sakshipajai27@gmail.com Anto Simon Joseph M. Department of Biotechnology, Sri Krishna Arts and Science College, Coimbatore Email: simonbscbt@gmail.com Ravindran Jaganathan Preclinical Department, Royal College of Medicine Perak, University of Kuala Lumpur Email: jravimicro@gmail.com Durba Banerjee Department of Biotechnology, University of Gautam Buddha Email: banerjeedurba24@gmail.com Abstract---Respiratory viral infections accounts for more than 4.25 million fatalities each year, making them the third most common cause of death worldwide. Although the majority of acute respiratory infections are assumed to be caused by viruses, the exact cause is often unknown. Comprehensive mapping of viral genomic sequencing is done, which also shows a significant degree of viral heterogeneity that contributes to the early diagnosis of respiratory illness. The development of next-generation sequencing (NGS), particularly for the detection of unidentified respiratory viruses, has revolutionized the field of novel viral genome detection. This review focusses on different