Due to the emergence of the SARS-CoV-2 B.1.1.7 (Alpha) variant in the UK in 2020 and its risk of increased transmission, the Ministry of Health in Tunisia implemented a sequencing surveillance strategy for SARS-CoV-2. The aim of this study was to analyze SARS-CoV-2 genomic surveillance data in Tunisia (January 2021–February 2022) and to assess the implementation of the sequencing strategy for SARS-CoV-2 in accordance with national recommendations and the guidance for SARS-CoV-2 genomic surveillance for public health goals. A descriptive study of all sequenced RT-PCR samples sequenced (January 2021–February2022). An internal audit was also done to assess the compliance against standards covering national recommendations and the Guidance for SARS-CoV-2 genomic surveillance for public health goals. A total of 12 simple or composite requirements related to the following areas were included in the audit standards: sampling (one requirements); data collection/analysis (six requirements); partnership (one requirement); and ethical considerations (one requirement). A total of 4819 samples were sent to laboratories and 4278 samples were sequenced. A total of 3648 samples were classified. Positive variants of concern (VOC) samples were 80.92%, differentiated as follows: Alpha, 40.24%; Beta, 0.24%; Gamma, 0.03%; Delta, 45.26%; and Omicron, 14.19%. Three principal phases of VOCs per ISO-week were shown: Alpha 3/2021–25/2021; Delta 26/2021–2/2022; and Omicron 3/2022–6/2022. Levels of compliance were identified; from a total of 12 requirements, 7 were considered as “not met”, 4 as “partially met”, and 1 as “fully met” but including not totally achieved objectives. In conclusion, the internal audit of the national SARS-CoV-2 sequencing strategy revealed an overall “not met” level of compliance. The results offered a trigger to collaborate with all stakeholders to develop a surveillance strategy for early detection and response to outbreaks caused by VOCs.

Background: Older adults experienced a disproportionate burden of COVID-19 mortality, but national evidence is limited. We described COVID-19 mortality among adults aged ≥65 years (March 2020–December 2022) and vaccination coverage among adults aged ≥60 years (March 2021–December 2022). Methods: We conducted a retrospective national descriptive and ecological study using ONMNE mortality surveillance and aggregated EVAX vaccination data. We calculated mortality, age-standardized, and proportional mortality rates; vaccination coverage; dropout proportions; and no-show rates. Results: Of 29,306 COVID-19 deaths, 20,467 (69.8%) occurred among adults aged ≥65 years; 8,725 (42.6%) were aged ≥80 years and 11,463 (56.0%) were male. Cumulative mortality was 1,809.9 per 100,000, with the highest period-specific rate during Delta predominance (750.1 per 100,000). Coverage among adults aged ≥60 years was 95.4% for at least one dose, 88.3% for primary-schedule completion, and 38.4% for a third dose; cumulative uptake was 215.1 doses per 100. Coverage varied by governorate; no-show rates increased in 2022. Conclusions: Mortality was concentrated among the oldest-old and during Delta predominance. Coverage was high nationally but uneven geographically, and booster uptake and attendance declined. Targeted outreach and equitable access remain priorities.

The first case of Coronavirus Disease 2019 (COVID-19) in Tunisia was reported on 2 March 2020. This study aimed to describe the epidemiological evolution of the COVID-19 pandemic in Tunisia from March 2020 to December 2022 and to assess changes in key transmission indicators across the different phases and epidemic waves. We conducted a nationwide longitudinal descriptive study based on prospectively collected surveillance data including all laboratory-confirmed COVID-19 cases reported through the national surveillance system between March 2020 and December 2022. Descriptive analyses were performed to estimate screening rates, test positivity rates, cumulative incidence rates, and the time-varying effective reproduction number (Rt). During the three-year study period, Tunisia reported a cumulative incidence of 9562.05 cases per 100,000 inhabitants. The mean daily screening rate was 38.23 tests per 100,000 inhabitants, while the average positivity rate reached 16.03%. The mean effective reproduction number was estimated at 1.14 (95% CI: 1.11–1.17). The epidemic evolved through two distinct transmission phases. The first phase, extending from 2 March to 17 August 2020, was characterized by limited community transmission mainly associated with imported cases. The second phase was marked by sustained autochthonous community transmission and comprised five epidemic waves. Between March and May 2021, genomic surveillance identified the predominance of the Alpha Variant of Concern (VOC). The fourth wave was dominated by the Delta VOC until December 2021, whereas the fifth wave, occurring in 2022, was associated with the Omicron VOC. Continuous monitoring of transmission indicators through the national surveillance system provided timely evidence to support risk assessment, guide public health decision-making, and adapt prevention and control measures throughout the different phases of the pandemic in Tunisia.