A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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.

Kalach 360 SL (KL) is a commercial herbicide which contains 360 g/l of glyphosate used in both agricultural and urban areas throughout the world including Tunisia. We aimed to evaluate the effects of KL on rats' renal system. Female Wistar rats were divided into three groups: group 1 (n = 6) received a standard diet and served as control, groups 2 and 3 (n = 12 each) received 0.07 ml (D1: 126 mg/kg), and 0.175 ml (D2: 315 mg/kg) of KL, respectively, for 60 d. The chronic exposure to KL induced a significant increase in plasma creatinine, urea, and uric acid levels. Creatinine clearance decreased in KL-treated groups, compared with controls. Several urine parameters, such as urine-specific gravity and urine osmolality, significantly decreased, while dieresis and urinary Na/K + ratio increased in KL-treated groups. These findings suggested a distal tubular damage caused by tubular necrosis. Moreover, the chronic exposure to KL induced an increase in lipid peroxidation (LPO) and a decrease in antioxidant status, enzymatic activities (superoxide dismutase and catalase) and non-enzymatic levels (vitamin C), which led to an oxidative stress. Histopathological studies showed a peritubular inflammatory reaction, nephrose, fragmented glomeruli, necrotic epithelial cells, and tubular dilatation. These results could have significant health implications for animal and human populations. Further data are necessary to investigate the potential consequences of chronic dose exposure during life.

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Objectives Since the onset of the COVID-19 pandemic, cases of reinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, raising additional public health concerns. SARS-CoV-2 reinfection was assessed in healthcare workers in Tunisia, as they are at the greatest exposure to infection by different variants. Methods We conducted whole-genome sequencing of the viral RNA from clinical specimens at the initial infection and suspected second infection from four healthcare workers, working at the Habib Bourguiba University Hospital (Sfax, Tunisia), who were retested positive for SARS-CoV-2 by RT-PCR after recovery from a first infection. A total of 8 viral RNAs from the patients’ respiratory specimens were obtained, which allowed us to characterize the differences between viral genomes from initial infection and positive retest. The serology status for total Ig, IgG, and IgM against SARS-CoV-2 was also determined and followed after the first infection. Results We confirmed by whole-genome sequencing of the viral samples that all four cases experienced a reinfection event. The interval between the two infection events ranged from 45 to 141 days and symptoms were milder in the second infection for two patients and more severe for the two remaining cases. Reinfection occurred for all four cases, despite the presence of antibodies for three of them. Conclusion This study adds to the rapidly growing evidence of COVID-19 reinfection, where viral sequences were used to confirm infection by distinct isolates of SARS-CoV-2 in healthcare workers. These findings suggest that individuals, who are exposed to different SARS-CoV-2 variants, might not acquire sufficiently protective immunity through natural infection and emphasis the necessity of their vaccination and the regular follow-up of their immune status both in quantitative and qualitative terms.