Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya

Journal article

Background: Pandemic preparedness is critical to respond effectively to existing and emerging/new viral pathogens. Important lessons have been learned during the last pandemic at various levels. This revision discusses some of the major challenges and potential ways to address them in the likely event of future pandemics. Objectives: To identify critical points of readiness that may help us accelerate the response to future pandemics from a clinical microbiology laboratory perspective with a focus on viral diagnostics and genomic sequencing. The potential areas of improvement identified are discussed from the sample collection to information reporting. Sources: Microbiologists and researchers from five countries reflect on challenges encountered during the COVID-19 pandemic, review published literature on prior and current pandemics, and suggest potential solutions in preparation for future outbreaks. Content: Major challenges identified in the pre-analytic and post-analytic phases from sample collection to result reporting are discussed. From the perspective of clinical microbiology laboratories, the preparedness for a new pandemic should focus on zoonotic viruses. Laboratory readiness for scalability is critical and should include elements related to material procurement, training personnel, specific funding programmes, and regulatory issues to rapidly implement "in-house" tests. Laboratories across various countries should establish (or re-use) operational networks to communicate to respond effectively, ensuring the presence of agile circuits with full traceability of samples. Implications: Laboratory preparedness is paramount to respond effectively to emerging and re-emerging viral infections and to limit the clinical and societal impact of new potential pandemics. Agile and fully traceable methods for sample collection to report are the cornerstone of a successful response. Expert group communication and early involvement of information technology personnel are critical for preparedness. A specific budget for pandemic preparedness should be ring-fenced and added to the national health budgets

Authors: Phan, MVT; Agoti, CN; Munywoki, PK; Otieno, GP; Ngama, M

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Scientific Reports
• Volume: 12
• Issue: 1
• Pages: 202-202
• Article number: 202
• Publication date: 2022-01-07
• DOI: 10.1038/s41598-021-03987-1
• EISSN: 2045-2322
• ISSN: 2045-2322
• Language: English
• Keywords: Biology; Coronavirus disease 2019 (COVID-19); Metapneumovirus; Internal medicine; Bioinformatics; Human metapneumovirus; Respiratory tract infections; Human bocavirus; Enterovirus; Respiratory system; Polymerase chain reaction; Virus; Genetics; Medicine; Virology; Primer (cosmetics); Viral pneumonia; Rhinovirus; Molecular diagnostics; Gene; Pneumonia