Strengthening surveillance: lessons from evaluating Finland’s SARS-CoV-2 genomic system, 2023

Abstract Background Effective genomic surveillance is essential for detecting emerging variants and informing timely public health actions. Yet, formal evaluations of such systems remain rare. We evaluated Finland's SARS-CoV-2 genomic surveillance in 2023 to assess its representativeness, completeness, and timeliness, aiming to identify strengths and areas for improvement. Methods We conducted a descriptive evaluation using 2023 data from the Laboratory Information System, the National Infectious Disease Register (NIDR), and the Global Initiative on Sharing All Influenza Data (GISAID). Representativeness was assessed by comparing the demographic characteristics of sequenced and PCR-confirmed cases in NIDR; completeness via laboratory submission rates and metadata availability; and timeliness by calculating turnaround times from sample collection to sequencing results, including sending, processing, and international reporting delays. Results The system showed high representation of older age groups (median age 74; IQR 54-84) and high data completeness. However, most laboratories did not consistently meet the requested weekly sample numbers, with submission compliance ranging from 2% to 53%. Turnaround times also varied by laboratory (median 13-22 days), mainly due to differences in sample transfer times (median 3-8 days; overall median 5). The evaluation highlighted the value of integrated laboratory and epidemiological databases, and flexible guidelines that adapt to changing contexts. Conclusions This study demonstrated how comprehensive evaluations of genomic surveillance systems can reveal operational gaps and guide improvements. In our evaluation, improving communication with clinical laboratories and optimising sample logistics were identified as key actions. As SARS-CoV-2 genomic surveillance is integrated with that of other respiratory viruses, such evaluations are vital to ensure health system resilience and preparedness, and inform effective public health responses. Key messages • Evaluations of surveillance systems are critical tools to identify gaps, guide improvements, and ensure they remain effective, responsive, and fit for evolving public health needs. • The evaluation of the Finnish SARS-CoV-2 surveillance system revealed strong data quality, while highlighting the need to improve sampling compliance and logistics through targeted actions.