Introduction

In an age where viruses like SARS-CoV-2 and influenza pose significant public health risks, monitoring these pathogens has never been more critical.

Overview of ESIB-EQA

The 2023 European SARS-CoV-2 and Influenza Bioinformatics External Quality Assessment (ESIB-EQA) aimed to fortify the genomic epidemiology capabilities of laboratories across Europe, ensuring they are prepared for unpredictable health crises.

Assessment Details

The ESIB-EQA, conducted from March 1 to April 1, 2023, focused on enhancing both short-read and long-read sequencing technologies across 30 participating countries, including 27 member states from the European Union (EU), three from the European Economic Area (EEA), and several nations from the Western Balkans and Türkiye.

Evaluation Criteria

This rigorous assessment evaluated the quality of bioinformatics processes related to consensus sequence generation, genome clustering, and mutation analysis—essential tasks for understanding and responding to viral outbreaks.

Participation and Results

Out of the 30 invited laboratories, 25 EU/EEA countries and two Western Balkan countries participated, revealing a spectrum of capabilities. Notably, the fastest laboratories processed their samples within one to two working days.

Findings on Sample Classification

Most labs demonstrated proficiency in classifying samples based on expected quality standards, highlighting the robustness of their methodologies.

Challenges Identified

However, issues arose, particularly regarding the accuracy of consensus generation for SARS-CoV-2 genomes, where problems with insertions and deletions (commonly termed as 'indels') were identified.

Influenza Sequence Analysis

In the case of influenza sequences, many laboratories failed to generate complete consensus sequences, highlighting a gap in their analysis processes.

Genome Clustering Discrepancies

Furthermore, the assessment uncovered discrepancies in genome clustering methods, a critical component for tracking virus evolution and outbreak investigations, due to variations in mutation definition thresholds.

Mutation Analysis Results

While the mutation analysis for SARS-CoV-2 largely proved accurate, significant misclassifications emerged in influenza, especially concerning resistance to antiviral medications like oseltamivir, zanamivir, and baloxavir marboxil.

Recommendations for Improvement

The ESIB-EQA not only offered a snapshot of current laboratory practices but also laid the groundwork for improvements.

Standardization of Protocols

Standardizing protocols around primer sequences and flanking regions, along with well-defined guidelines for antiviral susceptibility predictions, could greatly enhance inter-laboratory consistency.

Educational Samples Inclusion

Moreover, the inclusion of novel viruses as educational samples could refine techniques for identifying reassortment and improving subtype determination, crucial for swift detection of health threats.

Conclusion

As Europe continues to navigate the complexities of viral pandemics, initiatives like the ESIB-EQA play a pivotal role in strengthening public health infrastructure and ensuring preparedness for future challenges.

The findings underline the importance of maintaining high standards in laboratory practices, ultimately safeguarding public health across the continent.