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Objectives: In England, infectious syphilis diagnoses have reached the highest annual number since 1948. Fifty per cent of syphilis testing is now provided through online postal self-sampling sexually transmitted infection (STI) testing services (OPSS). To reduce the burden of syphilis, we need to understand the syphilis prevalence and transition to treatment rates among service users of OPSS. This report aims to estimate syphilis prevalence among people accessing Sexual Health London (SHL), a regional, National Health Service (NHS)-funded OPSS., Methods: Demographic, STI concurrency, sexual behaviour data and case outcomes were collected from SHL service users who received testing for syphilis between 8 March 2022 and 30 June 2023. Data were analysed to identify syphilis prevalence and transition to care rates., Results: 458 520 syphilis tests were performed for 267 780 service users. 12 870 (2.8%) results were reactive. Their assigned case outcomes comprised: 10 048 (78.1%) past adequately treated syphilis; 971 (7.5%) treated for active syphilis; 1293 (10.1%) SHL results did not subsequently confirm and 558 (4.3%) had an unknown final outcome. Of unique users, 0.4% (940/267 780) received syphilis treatment at least once. They were: 89.3% aged ≥25 years, 87.3% male, 83.7% gay/bisexual. Co-infections identified were: chlamydia (14%), gonorrhoea (13.3%) and previously undiagnosed HIV (1.5%). 36.1% (339) took pre-exposure HIV prophylaxis, 30.1% engaged in sex parties/group sex and 26.8% had sex under the influence of drugs/alcohol. Individuals aged ≥35 years, of non-female gender, gay/bisexual, from indices of multiple deprivation (1-5) and from certain racially minoritised communities were statistically more likely to require treatment for syphilis than the overall testing population (p<0.05)., Conclusion: Estimated syphilis prevalence (0.4%) was comparable to rates within national sexual health clinics and the demographic characteristics of those most affected by syphilis were also similar. Further work is required to improve the integration between NHS OPSS and sexual health clinics and to enable OPSS to more accurately input data on treatment and diagnoses towards national surveillance statistics., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)

There are concerns that sotrovimab has reduced efficacy at reducing hospitalisation risk against the BA.2 sub-lineage of the Omicron SARS-CoV-2 variant. We performed a retrospective cohort (n = 8850) study of individuals treated with sotrovimab in the community, with the objective of assessing whether there were any differences in risk of hospitalisation of BA.2 cases compared with BA.1. We estimated that the hazard ratio of hospital admission with a length of stay of 2 days or more was 1.17 for BA.2 compared with BA.1 (95%CI 0.74-1.86). These results suggest that the risk of hospital admission was similar between the two sub-lineages., (© 2023 Crown copyright. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd. This article is published with the permission of the Controller of HMSO and the King’s Printer for Scotland.)

The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

Background: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community., Objectives: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis., Methods and Results: Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training., Conclusions: For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa., (Copyright © 2017 World Heart Federation (Geneva). Published by Elsevier B.V. All rights reserved.)

In this study, we interpreted RNA-seq time-course data of three developmental stages of Plasmodium species by clustering genes based on similarities in their expression profile without prior knowledge of the gene function. Functional enrichment of clusters of upregulated genes at specific time-points reveals potential targetable biological processes with information on their timings. We identified common consensus sequences that these clusters shared as potential points of coordinated transcriptional control. Five cluster groups showed upregulated profile patterns of biological interest. This included two clusters from the Intraerythrocytic Developmental Cycle (cluster 4 = 16 genes, and cluster 9 = 32 genes), one from the sexual development stage (cluster 2 = 851 genes), and two from the gamete-fertilization stage in the mosquito host (cluster 4 = 153 genes, and cluster 9 = 258 genes). The IDC expressed the least numbers of genes with only 1448 genes showing any significant activity of the 5020 genes (~29%) in the experiment. Gene ontology (GO) enrichment analysis of these clusters revealed a total of 671 uncharacterized genes implicated in 14 biological processes and components associated with these stages, some of which are currently being investigated as drug targets in on-going research. Five putative transcription regulatory binding motifs shared by members of each cluster were also identified, one of which was also identified in a previous study by separate researchers. Our study shows stage-specific genes and biological processes that may be important in antimalarial drug research efforts. In addition, timed-coordinated control of separate processes may explain the paucity of factors in parasites., Competing Interests: No competing interests were disclosed.