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.
Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is essential for tracking the emergence and spread of AMR strains in local, national and international populations. This is crucial for developing or refining treatment guidelines. N. gonorrhoeae multiantigen sequence typing (NG-MAST) is beneficial for describing the molecular epidemiology of gonococci at national and international levels. Elucidation of AMR determinants to β-lactam drugs, is a means of monitoring the development of resistance. In Ghana, little is known about the current gonococcal AMR prevalence and no characterization of gonococcal isolates has been previously performed. In this study, gonococcal isolates (n = 44) collected from five health facilities in Ghana from 2012 to 2015, were examined using AMR testing, NG-MAST and sequencing of penA. High rates of resistance were identified to tetracycline (100%), benzylpenicillin (90.9%), and ciprofloxacin (81.8%). One isolate had a high cefixime MIC (0.75 μg/ml). Twenty-eight NG-MAST sequence types (STs) were identified, seventeen of which were novel. The isolate with the high cefixime MIC contained a mosaic penA-34 allele and belonged to NG-MAST ST1407, an internationally spreading multidrug-resistant clone that has accounted for most cefixime resistance in many countries. In conclusion, AMR testing, NG-MAST, and sequencing of the AMR determinant penA, revealed high rates of resistance to tetracycline, benzylpenicillin, and ciprofloxacin; as well as a highly diverse population of N. gonorrhoeae in Ghana. It is imperative to continue with enhanced AMR surveillance and to understand the molecular epidemiology of gonococcal strains circulating in Ghana and other African countries.
D engue virus (DENV), the causative agent of dengue fever, is a mosquitoborne single-stranded RNA virus from the genus Flavivirus, often defined as 4 related serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) (1). Globally, ≈4 billion persons in 128 countries are at risk for dengue fever (2). An estimated 390 million infections occur annually, of which 96 million are symptomatic (3), making DENV the most prevalent and rapidly spreading mosquitoborne viral disease of human beings (4). Clinical manifestations vary from a self-limited, potentially debilitating illness to hypovolemic shock; the mortality rate can be as high as 20% if left untreated ( 4).An estimated 750 million persons are at risk for acquiring DENV in Africa, and the disease burden is estimated to be nearly equivalent to that of the Americas (3,5). Many countries in Africa lack a national surveillance system and reporting mechanism (6), causing dengue fever cases to be misdiagnosed as malaria (7), which might explain why among the 34 countries in Africa to report dengue fever, 12 were not reported by the country where it occurred but by travelers returning to their country of origin (8). Travel, particularly to Africa, is emerging as a well-recognized mechanism of intercontinental DENV spread (9,10).Less than 1% of all global DENV envelope sequence data, key information for vaccine targets, come from isolates from Africa (11). A need exists for additional DENV sequencing, especially in Africa (12,13). The lack of genomic DENV data from Africa combined with complex transmission dynamics involving urban and sylvatic cycles impairs our understanding of DENV's evolutionary history, transmission and spread (13), molecular diagnostics (14), antiviral targets (15), vector susceptibility (16), human immune response (17), vaccine development (17), and DENV spillover events (18). Determining which contemporary genotypes are in circulation is crucial to ensuring effective diagnostics and developing preventive and therapeutic countermeasures (19).
Chikungunya viruses containing the A226V mutation detected retrospectively in Cameroon form a new geographical subclade,
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