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.

Objective. To determine the prevalence of metallo beta-lactamases (MBL) among carbapenem resistant strains of Acinetobacter baumannii in our hospital. Methodology. During a period of 12 months (January-December 2010), 47 isolates of Acinetobacter baumannii were collected from different clinical specimens of in-patients. Antimicrobial susceptibility was determined and interpreted using the disk diffusion method according to the Antibiogram Committee of the French Society for Microbiology guidelines. Imipenem nonsusceptible isolates were further screened for production of MBL. Results. All Acinetobacter baumannii' isolates were resistant to ticarcillin, ticarcilline/clavulanate, piperacillin, piperacillin/tazobactam, gentamicin, tobramycin, and cipro�oxacin, except an isolate that was sensitive to ceazidime and cefepime. In addition to that, amikacin and trimethoprim/sulfamethoxazole were, respectively, sensitive by 59.5% and 53%. Among 57,4% (27/47) imipenem non-susceptible isolates of Acinetobacter baumannii, 74% (20/27) were found to be MBL producers. Conclusion. Although the rate of imipenem nonsusceptible isolates of Acinetobacter baumanni seems to remain stable in 2005 (57%) and 2010 (57,5%), the prevalence of MBL producer strain is increasing (38% in 2005 versus 75% in 2010). e �ndings strongly suggest that there is a need to track the detection of MBL producers; moreover, a judicious use of carbapenems is necessary to prevent further spread of these organisms.

Background. RT-PCR is the gold standard for COVID-19 diagnosis, but the lack of standardization of assays, whose diagnostic performance may widely vary, complicates the interpretation of the discrepancies that may be encountered. Study design. We conducted a retrospective study over a ten-month period at the Central Laboratory of Virology of Ibn Sina University Hospital of Rabat. We included nasopharyngeal swabs, positive and negative for SARS-CoV-2 on FilmArray BioFire® Respiratory Panel 2.1 Plus, which were subjected to our laboratory’s reference test, MAScIR SARS-CoV-2 M kit 2.0, initially or after a freeze-thaw cycle. The results were compared, and each discrepant sample with sufficient volume underwent the third test, using ARGENE® SARS-CoV-2 R-GENE kit. Results. Of 80 SARS-CoV-2 negative samples on FilmArray, there were no discordant results, whereas of 80 SARS-CoV-2 positive samples on FilmArray, 21 had discordant results on MAScIR, and only 11 could be tested on ARGENE, revealing positive results in 6 cases. 12.7% and 76.5% correspond to the discordance rates for MAScIR (with one or both targets detected on FilmArray), while 14.3% and 100% correspond to those of ARGENE. As the estimated sensitivity and specificity of FilmArray, compared with MAScIR, were 100% and 79.2%, respectively, its lower limit of detection, and ARGENE assay results, made it difficult to distinguish between false positives on FilmArray and false negatives on MAScIR without further investigations. Conclusion. The implementation of a new assay in our laboratory revealed discrepancies suggesting a lack of sensitivity of our laboratory’s reference test, leading us consequently to retain the SARS-CoV-2 positive result of these discordant samples on FilmArray, regardless of the detection of one or both targets. Our study, which is, to our knowledge, the first comparing FilmArray RP2.1 and MAScIR 2.0 assays for SARS-CoV-2 detection, highlights the urgent need to standardize RT-PCR assays for COVID-19 diagnosis.

No abstract

Purpose: Despite the use of antiviral prophylaxis with valacyclovir, cytomegalovirus infection (CMV) can still occur in seropositive kidney transplant recipients. In this study, we aimed to assess the incidence of CMV DNAemia and its risk factors in Moroccan transplant recipients. Patients and Methods: Sixty kidney recipients with positive cytomegalovirus serostatus, receiving post-transplant prophylaxis were enrolled between 2013 and 2017. In total, 455 plasma samples were collected and tested for CMV DNAemia using PCR-based Abbott RealTime assays. Results: The incidence of CMV infection in seropositive patients was 63%. In patients with quantifiable DNAemia, the duration of CMV infection was significantly shorter than in those with detectable DNAemia (141.5 ± 96.9 vs 294.1 ± 112.6 days, P < 0.001). During prophylactic treatment, 14 of 30 patients (47.0%) experienced active replication with quantifiable DNAemia, whereas none of eight patients with detectable DNAemia did (P = 0.017). Patients with symptomatic DNAemia were significantly younger than those without symptoms (28.8 ± 5.12 vs 38.1 ± 12.34 years, P = 0.007). The peak viral loads were significantly associated with viral disease (odds ratio: 3.39, 95% confidence interval: 1.21-9.53, P = 0.02). The duration of DNAemia (21.2 vs 13.4 days, P = 0.028) was significantly longer in symptomatic patients. Significantly higher rates of acute rejection were exclusively observed in recipients with disease (4/8, 50% vs 0/22, 0%, P = 0.003). Conclusion:Patients with high-level DNAemia were at an increased risk of progression to disease and acute rejection. Monitoring the viral load during the first year posttransplantation is essential, to support current preventive strategies.