Background:
Tunisia SARS-CoV-2 genomic surveillance strategy (SARS-CoV-2 GSS) is based on two approaches: randomized sampling and targeted sampling focusing on specific subsets of cases associated with public health risks.

Objective:
To evaluate the implementation of the SARS-CoV-2 GSS in accordance with the national recommendations and guidelines.

Methodology:
We initially performed a descriptive study to describe the components and operation of the strategy and to analyze data transmitted to the National observatory of new and emerging diseases from January 2021 to February 2022. An internal audit assessing the compliance to the national recommendations and guidelines was conducted covering12 requirements related to sampling, data collection and analysis, notification, usefulness and ethical considerations.

Results:
Among a total of 4819 samples only 4278 (88,8%) were sequenced with 3648 (80.92%) were classified VOC : Alpha 40.24%, Beta 0.24 %, Gamma 0.03%, Delta 45.26%, and Omicron 14.19%. The Alpha variant was already dominant from the ISO week 3-2021 to ISO week 25-2021. The Delta variant was predominant from the ISO week 26-2021 to the ISO week 2-2022 and the Omicron from the ISO week 3-2022 to the ISO week 6-2022. The levels of compliance were considered as ‘not met’ for 7 components; as ‘partially met’ for 4, and ‘fully met’ for one. The usefulness of the result of genomic surveillance is considered very low since the results are communicated after three weeks from the date of the sample.

Conclusion:
Although the SARS-CoV-2 GSS in Tunisia has a relative advantage to draw up the profile and the dates of circulation of VOCs, the strategy suffers from several limitations related to the low level of compliance and delay to identify VOCs. This evaluation offered a trigger to revise the current strategy and enhance national capacities for early detection and rapid response to new VOCs.