European SARS-CoV-2 and influenza Bioinformatics Exterior High quality Evaluation (ESIB-EQA), 2023

SARS-CoV-2 and influenza viruses are pathogens of main public well being influence. Surveillance has performed an important function in monitoring the COVID-19 pandemic in addition to seasonal influenza, together with public well being actions equivalent to updates on vaccines and antiviral medication.

The target of this Exterior High quality Evaluation (EQA) is to strengthen the capability for genomic epidemiology and public well being bioinformatics, which is essential for response throughout a pandemic or surprising main public well being occasion. 

The EQA was divided into SARS-CoV-2 and influenza and was composed of various elements that could possibly be carried out individually, collectively representing each brief learn and lengthy learn sequencing know-how, and included the bioinformatics processes related for public well being actions, i.e. consensus sequence technology and high quality management, clustering and classification of genomes and mutation evaluation for prediction of phenotypic properties. Laboratories from the 27 European Union (EU) and the three European Financial Space (EEA) nations in addition to the six Western Balkan nations and Türkiye had been invited to take part. The EQA was open between 1 March and 1 April 2023, and the correctness of the responses and throughput time was assessed.

The EQA had participation from 25 of 30 EU/EEA nations and two of six Western Balkan nations. The elements they participated in diverse. The quartile of the adjusted throughput time for these 4 elements, indicative of the extra performant laboratories, was within the vary of 1 to 2 working days. A big majority of
the laboratories accurately categorised the samples in response to their anticipated high quality standing. For the consensus technology of SARS-CoV-2 genomes, points had been largely associated to insertions or deletions (‘indels’) compared to the comparator sequence and for influenza, the problems had been largely associated to that consensus sequences weren’t generated of their full size and primer sequences weren’t thought-about synthetic sequences. For the genome clustering part, a course of essential for outbreak investigations and for following virus evolution, laboratories carried out effectively. For each SARS-CoV-2 and influenza, the most typical discrepancies had been on account of utilizing totally different thresholds of cluster definitions (variety of mutations). The mutation evaluation part for SARSCoV- 2 was generally correct, nonetheless for influenza there was important fraction of mutation-based misclassifications of resistance to antiviral medication oseltamivir, zanamivir and baloxavir marboxil. 

The problems recognized on this EQA could facilitate a number of enhancements within the laboratories’ bioinformatic processes. The instance of indels which can be both falsely assigned or missed could result in incorrect variant classification or delayed detection of an rising variant or that circumstances will not be assigned to an outbreak which they belong to. Moreover, for influenza, standardisation of parameters equivalent to flanking areas, primer sequence masking and antiviral susceptibility predictions can facilitate inter-laboratory comparisons. Novel viruses supplied as academic samples that doesn’t
have an effect on the rating could enhance detecting reassortment and willpower of subtype and origin. 

This EQA establishes a baseline that could possibly be used for future comparisons. The contributors obtained particular person suggestions with recommendations for enchancment and laboratories from three nations had been invited to and accomplished a five-day twinning coaching exercise. Moreover, normal suggestions are compiled on this report in an effort to enhance the laboratory practices and efficiency.