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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.

Typhoid fever is a significant public health concern in many parts of the world, particularly in developing countries with poor sanitation and hygiene conditions. In July 2016, an outbreak of typhoid fever occurred in Ghannouche, located in the south of Tunisia. This paper reports the results of a field investigation undertaken to identify possible transmission pathways and risk factors in order to propose control and preventive measures. A retrospective cohort study including a passive and active case finding, as well as an environmental and bacteriological investigation was conducted from July to September 2016. A case was defined as a person residing or having stayed in Ghannouche and having presented from the beginning of June clinical signs suggestive of typhoid fever, with, for a confirmed case, laboratory isolation of S.Tyhi, and for a probable case, an epidemiological link with a confirmed case. Attack rates were determined, and risk ratios were estimated with respect to exposures. Unadjusted and adjusted odds ratios were estimated using binary logistic regression. Among the 628 subjects investigated, 102 cases of typhoid fever were identified (74 confirmed and 28 probable) with an overall attack rate of 16.24%. Over 56% of cases were male and those under 10 years old were most affected (38.2%% of cases) with a median age of 12 years (interquartile range 5 to 25 years). The main clinical signs were fever (95%) and diarrhea (57%). Young age (adjusted OR = 0.95 and 95% CI = 0.93-0.97), low level of education (adjusted OR = 4.76 and 95% CI = 1.34-16.81), and the habitat type Arab or rudimentary house (adjusted OR = 4.93 and 95% CI = 2.61-8.27) were the socio-demographic factors independently associated with typhoid fever. Typhoid fever was found to be associated with drinking softened water (adjusted OR = 2.64 and 95% CI = 1.16-4.82), eating raw fruit and vegetables from family gardens (adjusted OR = 6.13 and 95% CI = 3.66-11.06), and using uncontrolled waste disposal (adjusted OR = 3.52 and 95% CI = 2.03-6.94). A total of 110 drinking water samples were analyzed; out of the 38 samples of softened water, 12 were non-compliant and 5 were positive for Salmonella . The screening activity identified two asymptomatic carriers, one of whom was a softened water seller. We concluded that drinking softened water from informal or unauthorized sale units, consuming fruit and vegetables from family gardens, uncontrolled dumping of household waste, and poor socio-economic conditions increase the risk of typhoid fever in this region. Many recommendations were implemented to stop this outbreak and to prevent further episodes.

The extent of the SARS-CoV-2 circulation and the COVID-19 epidemic in Tunisia three months after virus circulation was unknown. The aim of this study was to determine the extent of SARS-CoV-2 infection among household contacts of confirmed COVID-19 cases living in Hot spot areas of Great Tunis, Tunisia by estimating the seroprevalence of antibodies anti SARS-CoV-2 and to identify factors associated to seroprevalence at the first stage of the pandemic in order to guide decision making and to constitute a baseline for further longitudinal analysis of protective immunity to SARS-CoV-2. The National Observatory of New and Emerging Diseases (ONMNE), Ministry of Health Tunisia (MoH), with the support of the Office of the World Health Organization Representative in Tunisia and the WHO Regional Office for the Eastern Mediterranean (EMRO)), conducted a household cross-sectional survey on April 2020 in Great Tunis (Tunis, Ariana, Manouba and Ben Arous). The study was based on the WHO seroepidemiological investigation protocol for SARS-CoV-2 infection. SARS-CoV-2 specific antibodies (IgG and IgM) were qualitatively detected using a lateral immunoassay that detect SARS-CoV-2 nucleocapsid protein and administered by the interviewers. The included subjects were confirmed COVID-19 cases and their households contacts resided in hot spot areas (cumulative incidence rate ≥ 10 cases/100,000 inhabitants) of Great Tunis. Results: In total, 1165 subjects were enrolled: 116 confirmed COVID-19 cases (43 active cases and 73 convalescents cases) and 1049 household contacts resided in 291 households. The median age of participants was 39.0 with 31 years' interquartile range (Min = 8 months; Max = 96 years). The sex ratio (M/F) was 0.98. Twenty-nine per cent of participants resided in Tunis. The global crude seroprevalence among household contacts was 2.5% (26/1049); 95% CI 1.6-3.6%, 4.8%; 95% CI 2.3-8.7% in Ariana governorate and 0.3%; 95% CI 0.01%-1.8% in Manouba governorate. In multivariate analysis, the associated factors independently related to seroprevalence were age ≥25 years (aOR = 5.1; 95% CI 1.2-22.0), history of travel outside Tunisia since January 2020 (aOR = 4.6; 95% CI 1.7-12.9), symptomatic illness in the previous four months (aOR = 3.5; 95% CI 1.4-9.0) and governorate of residence ( p = 0.02). The low seroprevalence estimated among household contacts in Great Tunis reflect the effect of public health measures early taken (national lockdown, borders closed, remote work), the respect of non-pharmaceutical interventions and the efficacy of COVID-19 contact-tracing and case management at the first stage of the pandemic in Tunisia.

Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.