Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

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.

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.