Caractéristiques cliniques et épidémiologiques des décès COVID-19 en Tunisie avant l'émergence des VOCs (mars 2020-février 2021) Clinical and epidemiological features of COVID-19-related deaths in Tunisia before the emergence of VOCs (March 2020-February 2021)

Introduction les objectifs de ce travail étaient de décrire le profil clinique et épidémiologique des décès COVID-19 en Tunisie notifié à l´ONMNE (Observatoire National des Maladies Nouvelles et Émergentes) entre le 02 mars 2020 et le 28 février 2021 et de comparer la mortalité COVID-19 enregistrée en Tunisie aux données internationales. Méthodes nous avons mené une étude nationale descriptive longitudinale prospective auprès des données colligées à travers le système national de surveillance de l´infection au SARS-CoV-2 de l´ONMNE, Ministère de la Santé. Tous les décès COVID-19 survenus en Tunisie entre mars 2020 et février 2021 ont été inclus dans cette étude. Les données ont été colligées auprès des structures hospitalières, des municipalités et des directions régionales de la santé. Les notifications des décès ont été collectées à travers différentes sources d´information (méthode de triangulation): les directions régionales de santé, Le ShocRoom (Strategic Health Operations Center ou Centre stratégique d´opérations sanitaires), les structures sanitaires publiques et privés, la Cellule de Crise de la Présidence du Gouvernement, La Direction d´Hygiène et de protection de l´Environnement, le Ministère des Affaires Locales et de l´Environnement, dans le cadre de suivi des cas confirmés par l´équipe de l´ONMNE, les résultats RT-PCR/TDR positifs en post mortem. Résultats durant la période de l´étude, 8051 décès ont été enregistrés soit une mortalité proportionnelle de 10,4%. L´âge médian était de 73 ans avec un intervalle interquartile de 17 ans. Le sex-ratio (M/F) était de 1,8. Le taux brut de mortalité était de 69,1/100 000 habitants et la létalité était de 3,5%. L´étude de la courbe épidémique a montré 2 pics de décès le 29 octobre 2020 et le 22 janvier 2021 avec respectivement 70 et 86 décès notifiés. La distribution spatiale des décès a montré que la région du Sud tunisien avait enregistré le taux de mortalité le plus élevé. Les patients âgés de 65 ans et plus étaient les plus concernés (73,7% des cas) avec un taux brut de mortalité de 570,9/100 000 habitants et une létalité de 13,7%. Conclusion la stratégie de prévention basée sur les mesures de santé publique doit être renforcées par le déploiement rapide de la vaccination anti-COVID-19 surtout pour les populations à risque de décès.

[Clinical and epidemiological features of COVID-19-related deaths in Tunisia before the emergence of VOCs (March 2020-February 2021)]. / Caractéristiques cliniques et épidémiologiques des décès COVID-19 en Tunisie avant l'émergence des VOCs (mars 2020-février 2021).

Introduction: the purpose of this study was to describe the clinical and epidemiological features of COVID-19-related deaths in Tunisia notified at the ONMNE (National Observatory of New and emerging Diseases) between 2nd March 2020 and 28th February 2021 and to compare COVID-19-related deaths recorded in Tunisia with the international data. Methods: we conducted a national prospective longitudinal descriptive study of data collected from the National Surveillance System of SARS-CoV-2 infection of the ONMNE, Ministry of Health. All COVID-19-related deaths that occurred in Tunisia between March 2020 and February 2021 were included in this study. Data were collected from hospitals, municipalities and regional health departments. Death notifications were collected from multiple data sources (triangulation): The Regional Directorate of Basic Health Care, the ShocRoom (Strategic Health Operations Center), public and private health facilities, the Crisis Unit of the Presidency of the Government, the Directorate for Hygiene and Environmental Protection, the Ministry of Local Affairs and the Environment, as part of the follow-up of confirmed cases by the ONMNE team, positive RT-PCR / TDR post mortem results. Results: during this study, 8051 deaths were recorded, corresponding to a proportional mortality of 10.4%. The median age was 73 years, with an interquartile range of 17 years. Sex-ratio (M/F) was 1.8. The crude death rate was 69.1/100 000 inhabitants and fatality rate was 3.5%. The analysis of the epidemic curve showed 2 peaks of deaths on 29th October 2020 and 22nd January 2021, with 70 and 86 deaths notified respectively. The spatial distribution of mortality showed that the southern Tunisian region had the highest mortality rate. Patients aged 65 and over were most affected (73.7% of cases) with a crude mortality rate of 570.9/100,000 inhabitants and a fatality rate of 13.7%. Conclusion: prevention strategy based on public health measures must be reinforced by the rapid deployment of anti-COVID-19 vaccination, especially for people at risk of death.

The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage.

Introduction: The Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated. Methods: Viral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs. Results: The age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country. Discussion: This study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.

Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia.

Since the beginning of the Coronavirus disease-2019 pandemic, there has been a growing interest in exploring SARS-CoV-2 genetic variation to understand the origin and spread of the pandemic, improve diagnostic methods and develop the appropriate vaccines. The objective of this study was to identify the SARS-CoV-2s lineages circulating in Tunisia and to explore their amino acid signature in order to follow their genome dynamics. Whole genome sequencing and genetic analyses of fifty-eight SARS-CoV-2 samples collected during one-year between March 2020 and March 2021 from the National Influenza Center were performed using three sampling strategies.. Multiple lineage introductions were noted during the initial phase of the pandemic, including B.4, B.1.1, B.1.428.2, B.1.540 and B.1.1.189. Subsequently, lineages B1.160 (24.2%) and B1.177 (22.4%) were dominant throughout the year. The Alpha variant (B.1.1.7 lineage) was identified in February 2021 and firstly observed in the center of our country. In addition, A clear diversity of lineages was observed in the North of the country. A total of 335 mutations including 10 deletions were found. The SARS-CoV-2 proteins ORF1ab, Spike, ORF3a, and Nucleocapsid were observed as mutation hotspots with a mutation frequency exceeding 20%. The 2 most frequent mutations, D614G in S protein and P314L in Nsp12 appeared simultaneously and are often associated with increased viral infectivity. Interestingly, deletions in coding regions causing consequent deletions of amino acids and frame shifts were identified in NSP3, NSP6, S, E, ORF7a, ORF8 and N proteins. These findings contribute to define the COVID-19 outbreak in Tunisia. Despite the country's limited resources, surveillance of SARS-CoV-2 genomic variation should be continued to control the occurrence of new variants.

Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19.

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.

Identification of transmission chains and clusters associated with COVID-19 in Tunisia.

BACKGROUND: The aim of this study was to characterize the transmission chains and clusters of COVID-19 infection in Tunisia. METHODS: All cases were confirmed by Reverse Transcriptase Polymerase Chain Reaction of a nasopharyngeal specimen. Contact tracing is undertaken for all confirmed cases in order to identify close contacts that will be systematically screened and quarantined. Transmission chains were identified based on field investigation, contact tracing, results of screening tests and by assessing all probable mode of transmission and interactions. RESULTS: As of May 18, 2020, 656 cases out of a total of 1043 confirmed cases of Coronavirus disease 2019 belong to 127 transmission chains identified during the epidemic (mean age 42.36 years, Standard deviation 19.56 and sex ratio 0.86). The virus transmission is the most concentrated in the governorate of Tunis (31.5%), Ariana (10.2%) and Ben Arous (10.2%). Virus transmission occurred 50 times (9.72% of secondary transmission events) between two different governorates. A maximum of seven generations of secondary infection was identified, whereas 62% of these secondary infections belong the first generation. A total of 11 "super spreader" cases were identified in this investigation. Four large clusters have been identified. The evolution of secondary cases highlighted two peaks: one in 2nd April and a second in 16 th April whereas imported cases caused local transmission of virus during the early phase of the epidemic. CONCLUSION: Correct contact tracing and early active case finding is useful to identify transmission chains and source of infection in order to contain the widespread transmission in the community.

Characteristics and prognostic factors of COVID-19 among infected cases: a nationwide Tunisian analysis.

BACKGROUND: The outbreak of coronavirus disease (COVID-19) continues to constitute an international public health concern. Few data are available on the duration and prognostic factors of the disease. We aimed to study the recovery time among a Tunisian cohort of COVID-19 confirmed patients and identify the prognostic factors. METHODS: A retrospective, nationwide study was conducted from March 2 to May 8, 2020, recruiting all patients who were diagnosed with COVID-19, by RT-PCR methods, in Tunisia. Data were collected via phone call interview. Kaplan-Meir Methods and Cox proportional hazards regression models were, respectively, used to study the recovery time and estimate its prognostic factors. RESULTS: One thousand and thirty patients with COVID-19 (aged 43.2 ± 18.2 years, 526 female (51.1%)) were enrolled. Among them 141 (14.8%) were healthcare professionals. Out of 173 patients (17.8%) admitted to the hospital, 47 were admitted in an intensive care unit. Among 827 patients who didn't require specialized care, 55.5% were self-isolated at home, while the rest were in specialized centers. Six hundred and two patients were symptomatic. A total of 634 (61.6%) patients have recovered and 45 (4.4%) patients died. The median duration of illness was estimated to be 31 days (95% CI: [29-32]). Older age (HR = 0.66, CI:[0.46-0.96], P = 0.031) and symptoms (HR = 0.61, CI:[0.43-0.81], P = 0.021) were independently associated with a delay in recovery time. Being a healthcare professional (HR = 1.52, CI: [1.10-2.08], P = 0.011) and patients in home isolation compared to isolation centers (HR = 2.99, CI: [1.85-4.83], P < 10¯3) were independently associated with faster recovery time. CONCLUSION: The duration of illness was estimated to be 1 month. However, this long estimated duration of illness may not equate to infectiousness. A particular attention must to be paid to elderly and symptomatic patients with closer monitoring.

Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: a statistical analysis in Tunisia from February 29 to May 5, 2020.

BACKGROUND: Describing transmission dynamics of the outbreak and impact of intervention measures are critical to planning responses to future outbreaks and providing timely information to guide policy makers decision. We estimate serial interval (SI) and temporal reproduction number (Rt) of SARS-CoV-2 in Tunisia. METHODS: We collected data of investigations and contact tracing between March 1, 2020 and May 5, 2020 as well as illness onset data during the period February 29-May 5, 2020 from National Observatory of New and Emerging Diseases of Tunisia. Maximum likelihood (ML) approach is used to estimate dynamics of Rt. RESULTS: Four hundred ninety-one of infector-infectee pairs were involved, with 14.46% reported pre-symptomatic transmission. SI follows Gamma distribution with mean 5.30 days [95% Confidence Interval (CI) 4.66-5.95] and standard deviation 0.26 [95% CI 0.23-0.30]. Also, we estimated large changes in Rt in response to the combined lockdown interventions. The Rt moves from 3.18 [95% Credible Interval (CrI) 2.73-3.69] to 1.77 [95% CrI 1.49-2.08] with curfew prevention measure, and under the epidemic threshold (0.89 [95% CrI 0.84-0.94]) by national lockdown measure. CONCLUSIONS: Overall, our findings highlight contribution of interventions to interrupt transmission of SARS-CoV-2 in Tunisia.

Characteristics, onset, and evolution of neurological symptoms in patients with COVID-19.

BACKGROUND: A wide range of neurological manifestations has been described in COVID-19. METHODS: In this nationwide retrospective observational study, patients in Tunisia diagnosed with COVID-19 between the 2nd of March and the 16th of May 2020 were contacted by telephone. We collected demographic and clinical data and specified characteristics and evolution of main neurological symptoms. RESULTS: Of 1034 confirmed COVID-19 patients, 646 were included (mean age 42.17 years old) and 466 (72.1%) had neurological symptoms. Neurological symptoms were isolated 22.7% (n = 106). Headache was the most frequent neurological symptom (n = 279, 41.1%): mainly frontotemporal (n = 143, 51.1%) and mild or moderate (n = 165, 59.1%). When associated with fever (n = 143, 51.3%), headache was more likely to be severe and present at onset. Recovery was reported in 83.2%. Smell and taste impairment were found in 37.9% (n = 245) and 36.8% (n = 238) respectively. Among them, 65.3% (156/239) were anosmic and 63.2% (146/231) were ageusic. A complete improvement was found in 72.1% (174/240) of smell impairment and in 76.8% (179/233) of taste impairment. Myalgia (n = 241, 37.3%) and sleep disturbances (n = 241, 37.3%) were also frequent. Imported cases had more neurological symptoms (p = 0.001). In 14.5%, neurological symptoms preceded the respiratory signs (RS). RS were associated with more frequent (p = 0.006) and numerous (p < 0.001) neurological symptoms. CONCLUSIONS: Neurological symptoms in COVID-19 are frequent, can be isolated and present at onset. A total recovery is the most recorded outcome. RS are predictive of neurological symptoms. Studies in to virus and host genetics should be considered to understand the different phenotypes.

Assessment of sample pooling for SARS-CoV-2 molecular testing for screening of asymptomatic persons in Tunisia.

The aim of this study is to test a pooling approach for the RT-PCR test to detect low viral loads of SARS-CoV-2. We found that a single positive specimen can still be detected in pools of up to 10. Each laboratory should conduct its own evaluation and validation of pooling protocols according to its specific context.