Background and objective:
Since emergent Variant Of Concern(VOC) has threatned public health and has impacted vaccination effectiveness, genomic surveillance of these variants was becoming a crucial approach allowing to monitor the evolution of SARS-CoV-2 variants and to guide COVID-19 pandemic response. The objective of this study was to describe the genomic epidemiology from January 2021 to December 2022.

Methods:
Sequences were performed on nasopharyngeal specimens With CT less than 25 tested in all Tunisian laboratories of clinical virology. The sample selection strategy was conducted in accordance with the Tunisian sequencing strategy of SARS-CoV-2 based on two approachs : First ,on a weekly randomly stratified sample by gouvernorate and second on a targeted sampling focusing on specific subsets: imported cases, vaccinated cases, reinfections, severe cases… SARS-CoV-2 genome sequencing methods applied during this study were�: whole-genome sequencing(wgs), partial s gene sequencing and variant-specific real-time rt-pcr tests. clinical virology laboratories involved were ➺ charles nicolle hospital, tunis➻ pasteur institute➻ habib bourguiba hospital sfax and fatouma bourguiba hospital, monastir.

Results:
During this study a total of 5999 nasopharyngeal samples have been sent to laboratories of clinical virology. Using the three sequencing methods a total of 4937(82 ;3%) lineages were assigned and 4105(83.15%) were classified as VOC : 1442 Omicron(35.2%) ;1418 Delta(34,6%),1230 Alpha(30%) ;7 Beta(0.2%) ; 1 Alpha and 1 coinfection Delta omicron. Periods of predominace of VOC were identified as following : Alpha variant was predominant from ISO week3/2021 to ISO week 25/2021 ; Delta variant from ISO week 26/2021 to ISO week 50/2021 and Omicron from ISO week 1/2022.

Conclusion:
This study was the first Tunisian national analysis of main lineages of SARS-CoV-2 circulating during two years . This Epidemiolgical genomic surveilance of SARS CoV 2 have contributed to implement preventive measurs in a timely manner.