Jones Gyamfi

Background: Africa seemed to have had low SARS-CoV-2 infection and COVID-19 morbidity and mortality. While several studies reported high SARS-CoV-2 seropositivity among healthy Africans, others hypothesized that this could have resulted from pre-existing cross-reactive antibodies. Our study tracks trends in seropositivity across three West African countries during the Delta and Omicron pandemic waves using a validated test kit with 98.9% predictive accuracy, 97% sensitivity, and 99% specificity.Methods: Cross-sectional studies were conducted across three West African countries (Burkina Faso, Ghana, and Nigeria) with study sites conveniently selected in each country. Using the validated immunoassay kits, with already published validation procedures, SARS-CoV-2 antibodies were detected in peripheral blood during the ‘Delta’ and ‘Omicron’ waves. Participants' demographic and clinical data were obtained using a semi-structured questionnaire, and the primary outcome was the proportion of each population with SARS-CoV-2 antibodies.Findings: Across the 3 countries, 20,748 participants were recruited, and the results showed SARS-CoV-2 IgG seropositivity ranging between 24.1% to 77.0%, which increased during the Omicron wave. All sites showed low self-reported vaccination rates, delinking seropositivity and vaccination. While there was a significant positive association between seropositivity and age across all sites, the association with other demographic factors was country-dependent, and most participants expressed positive opinions of vaccination.Interpretation: This is one of the largest population-based SARS-CoV-2 seroepidemiology studies in Africa, confirming widespread mild SARS-CoV-2 infection in West Africa. This confirms a marked disconnect between high population exposure and low reported clinical burden, underscoring the need for strengthened community surveillance.

The majority of SARS-CoV-2 genomes obtained during the pandemic were derived by amplifying overlapping windows of the genome (‘tiled amplicons’), reconstructing their sequences and fitting them together. This leads to systematic errors in genomes unless the software is both aware of the amplicon scheme and of the error modes of amplicon sequencing. Additionally, over time, amplicon schemes need to be updated as new mutations in the virus interfere with the primer binding sites at the end of amplicons. Thus, waves of variants swept the world during the pandemic and were followed by waves of systematic errors in the genomes, which had significant impacts on the inferred phylogenetic tree. Here we reconstruct the genomes from all public data as of June 2024 using an assembly tool called Viridian ( https://github.com/iqbal-lab-org/viridian ), developed to rigorously process amplicon sequence data. With these high-quality consensus sequences we provide a global phylogenetic tree of 4,471,579 samples, viewable at https://viridian.taxonium.org . We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny.

Mosquito breeding habitats are ecosystems that comprise a complex, intimately associated micro-organism. This study aimed to determine the bacteria communities associated with Anopheles larval habitats and correlate their prevalence to the absence or presence of mosquito larvae. The 16S rRNA profiles of bacterial communities in Anopheles-positive breeding habitats (productive and semi-productive habitats) and negative habitats (non-productive) from Southern Ghana were analyzed using the Oxford Nanopore’s MinION platform with water and larval samples. A total of 15 bacterial taxa were identified across all habitats based on productivity. Significantly, mosquito-positive breeding habitats (productive and semi-productive) had more bacterial diversity compared to mosquito-negative habitats (non-productive). Comparison of the composition of bacteria in the different habitat types revealed that non-productive habitats had a higher prevalence of Epsilonproteobacteria (58.1%), while Gammaproteobacteria (33.2%) and Betaproteobacteria (30.5%) were dominant in the productive and semi-productive habitats. Gammaproteobacteria and Betaproteobacteria were the most abundant bacterial classes in Anopheles larvae. Comparing the water samples to larvae microbiomes revealed distinct composition. Betaproteobacteria (58.5%) and Cytophagia (10.7%) were predominately present in the water samples, whilst Betaproteobacteria (47.9%) and Gammaproteobacteria (21.6%) were dominant in the larval samples. This study revealed a higher bacterial composition may play a role in Anopheles mosquitoes’ attractiveness to a breeding habitat. These findings contribute to the understanding of which bacteria, directly or indirectly, can be linked to the absence or presence of mosquito larvae in breeding habitats and set the basis for the identification of specific bacterial taxa that could be harnessed for vector control in the future.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times 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 illuminate 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 reemerging 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.

Cancer has long been considered a genetic disease characterized by a myriad of mutations that drive cancer progression. Recent accumulating evidence indicates that the dysregulated metabolism in cancer cells is more than a hallmark of cancer but may be the underlying cause of the tumor. Most of the well-characterized oncogenes or tumor suppressor genes function to sustain the altered metabolic state in cancer. Here, we review evidence supporting the altered metabolic state in cancer including key alterations in glucose, glutamine, and fatty acid metabolism. Unlike genetic alterations that do not occur in all cancer types, metabolic alterations are more common among cancer subtypes and across cancers. Recognizing cancer as a metabolic disorder could unravel key diagnostic and treatments markers that can impact approaches used in cancer management.

SARS-CoV-2 across Africa: The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA

Adipocytes influence breast cancer behaviour via fatty acid release into the tumour microenvironment. Co-culturing human adipocytes and breast cancer cells increased CD36 expression, with fatty acid import into breast cancer cells. Genetic ablation of CD36 attenuates adipocyte-induced epithelial-mesenchymal transition (EMT) and stemness. We show a feedforward loop between CD36 and STAT3; where CD36 activates STAT3 signalling and STAT3 binds to the CD36 promoter, regulating its expression. CD36 expression results in metabolic reprogramming, with a shift towards fatty acid oxidation. CD36 inhibition induces de novo lipogenesis in breast cancer cells. Increased CD36 expression occurs with increased FABP4 expression. We showed that CD36 directly interacts with FABP4 to regulate fatty acid import, transport, and metabolism. CD36 and FABP4 inhibition induces apoptosis in tumour cells. These results indicate that CD36 mediates fatty acid import from adipocytes into cancer cells and activates signalling pathways that drive tumour progression. Targeting CD36 may have a potential for therapy, which will target the tumour microenvironment.

Background: Phenotypic characterization of antimicrobial resistance (AMR) in bacteria has remained the gold standard for investigation and monitoring of what resistance is present in an organism. However, the process is laborious and not attractive for screening multiple plasmids from a microbial community (plasmidomes). Instead, genomic tools are used, but a major bottle neck that presence of genes does not always translate into phenotypes. Methods: We designed the plasmidome AMR screening (PAMRS) workflow to investigate the presence of antibiotic resistant phenotypes in a plasmidome using Escherichia coli as a host organism. Plasmidomes were extracted from the faecal matter of chicken, cattle and humans using commercial plasmid extraction kits. Competent E. coli cells were transformed and evaluated using disk diffusion. Thirteen antibiotic resistant phenotypes were screened. Results: Here, we show that multiple antibiotic resistant phenotypes encoded by plasmids can be rapidly screened simultaneously using the PAMRS workflow. E. coli was able to pick up to 7, 5 or 8 resistant phenotypes from a single plasmidome from chicken, cattle or humans, respectively. Resistance to ceftazidime was the most frequently picked up phenotype in humans (52.6%) and cattle (90.5%), whereas in chickens, the most picked up resistant phenotype was resistance to co-trimoxazole, ceftriaxone and ampicillin (18.4% each). Conclusions: This workflow is a novel tool that could facilitate studies to evaluate the occurrence and expression of plasmid-encoded antibiotic resistance in microbial communities and their associated plasmid-host ranges. It could find application in the screening of plasmid-encoded virulence genes.