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.

Clinical characteristics and outcomes of critically ill COVID-19 patients in Sfax, Tunisia.

BACKGROUND: Africa, like the rest of the world, has been impacted by the coronavirus disease 2019 (COVID-19) pandemic. However, only a few studies covering this subject in Africa have been published. METHODS: We conducted a retrospective study of critically ill adult COVID-19 patients-all of whom had a confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection- admitted to the intensive care unit (ICU) of Habib Bourguiba University Hospital (Sfax, Tunisia). RESULTS: A total of 96 patients were admitted into our ICU for respiratory distress due to COVID-19 infection. Mean age was 62.4±12.8 years and median age was 64 years. Mean arterial oxygen tension (PaO2)/fractional inspired oxygen (FiO2) ratio was 105±60 and ≤300 in all cases but one. Oxygen support was required for all patients (100%) and invasive mechanical ventilation for 38 (40%). Prone positioning was applied in 67 patients (70%). Within the study period, 47 of the 96 patients died (49%). Multivariate analysis showed that the factors associated with poor outcome were the development of acute renal failure (odds ratio [OR], 6.7; 95% confidence interval [CI], 1.75-25.9), the use of mechanical ventilation (OR, 5.8; 95% CI, 1.54-22.0), and serum cholinesterase (SChE) activity lower than 5,000 UI/L (OR, 5.0; 95% CI, 1.34-19). CONCLUSIONS: In this retrospective cohort study of critically ill patients admitted to the ICU in Sfax, Tunisia, for acute respiratory failure following COVID-19 infection, the mortality rate was high. The development of acute renal failure, the use of mechanical ventilation, and SChE activity lower than 5,000 UI/L were associated with a poor outcome.