Development of Bioinformatics Infrastructure for Genomics Research in H3Africa

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

Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates

Women's sexual control within conjugal union: Implications for HIV/AIDS infection and control in a metropolitan city

This study attempts to examine the extent to which women have control over their sexuality within marriage and its implication for the spread of HIV/AIDS. The survey was carried out in metropolitan Lagos. The study shows that women have some control over their sexuality especially during certain occasions such as during menstruation, breastfeeding, pregnancy and when they are sick. However, only few women could negotiate with their husbands especially by insisting on safe sexual practices. The study therefore shows that women need to be educated on the need for safer sex practices, especially in this era of HIV/AIDS. They should also be economically empowered so as to practice safer sex. Again, men should be educated on the safer sex practices in other to control the spread of HIV/AIDS

Environmental Considerations toward the Provision of Conducive Learning Environments in Nigerian Schools

Learning, which is the expected outcome of any educational institution, can be influenced by many factors that include environmental factors. This study is aimed at comparing the learning environment of junior secondary schools, in a North-western state of Nigeria, with established standards in some other countries. Four government-owned and four private owned schools participated in the study. Environmental variables such as classroom temperature, noise level, lighting and classroom size were all evaluated using standard equipment. Using statistical analytical tools, such as descriptive and comparison of means, the result shows that classroom lighting, noise and temperature do not meet the established standards. The noise level in all the schools was above the recommended maximum comfort noise level of 40 dB(A) but still below noise harmfulness level of 85dB. The lighting in the classes was also not sufficient based on international recommendations of 300 Lux. The temperature in the classrooms is significantly higher than the acceptable level of 18-28°C. Although public schools have significantly larger classrooms than private schools, they have a smaller space/pupil ratio because of larger population. There is need to improve the building design of schools so that they might aid learning among the children