Mohamed Z. Alimohamed, Lennart F. Johansson, Ludolf G. Boven, Krista van Dijk, Paul van der Zwaag, Richard J. Sinke, Rolf H. Sijmons, Birgit Sikkema-Raddatz, Jan D H Jongbloed

Departments of Genetics, University Medical Center Groningen, Groningen, The Netherlands

Background:

Next generation sequencing is increasingly used for clinical evaluation of patients with cardiomyopathies because it allows for simultaneous evaluation of multiple genes known to be associated with the disease. However, the diagnostic yield is variable in routine clinical practice. Furthermore, analysis of copy number variations is still not routinely performed.

Objectives:

(1) To determine the diagnostic yield of our custom targeted NGS gene panel used in routine clinical diagnostics in a Dutch cohort of over 2000 cardiomyopathy patients. (2) Examine the impact on the yield of analyzing this cohort for single or multiple exon duplications and deletions.

Methods:

Up to 61 genes known to be implicated in cardiomyopathies were selected for enrichment and analysis on DNA isolated from peripheral blood from patients as a routine procedure. Patients directed for genetic testing to our clinical genetics laboratory having a referral diagnosis for various types of cardiomyopathies were included in this study [N=2002]. A written informed consent was obtained for all patients referred to our clinical genetics laboratory. Classification of variants was based on guidelines for variant interpretation recommended by the American College of Medical Genetics and Genomics. Diagnostic yield was calculated using cases where a likely pathogenic or pathogenic variant was detected. Putative exonic deletions/duplications were analyzed using CoNVaDING and XHMM tools using settings previously described.

Results and Conclusion:

An overall diagnostic yield of 23% was achieved. CNVs were detected in 16 patients. Variants of unknown clinical significance were identified in 39% patients. These results illustrate the need to further reassess disease variant classification.

Key words:

Cardiomyopathy, NGS-panel, Diagnostic-yield

Chiaka Anumudu1, Olugbenga Onile2, Adewale Adebayo1,3, Henrietta Awobode4, Raphael Isokpehi5

1Cellular Parasitology Programme, Department of Zoology, University of Ibadan, Ibadan Nigeria; 2Elizade University, Ilara Mokin, Ondo State Nigeria; 3King’s College London UK; 4Parasitology Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria; 5College of Engineering and Sciences, Bethune Cookman University, Daytona Beach, Florida, USA

Validated diagnostic markers are key to the early detection and treatment of cancer. Indeed, if these biomarkers can be readily extracted and detected in bodily fluids, a simple, diagnostic test can be developed that would be of extreme value to patients especially in rural and resource-poor settings. 

For urinary schistosomiasis, we are looking for such a marker, which can be used for the detection of Schistosoma associated bladder damage and schistosomiasis, in a low-tech-test. We have used proteomics and microbiome methods to search for such markers in our previous works, and identified a large number of targets. Using a cross sectional study design, we collected 371 blood and urine samples from adults resident in Eggua. The urine was screened by centrifugation for eggs of the parasite Schistosoma haematobium and later 49 samples by proteomics methods for molecules that could be uniquely indicative of schistosomiasis and bladder damage. Participants were also tested by ultrasound for bladder pathologies. Microbiome analysis was performed on 70 blood and urine samples using NGS and bioinformatics pipeline. A total of 1306 proteins, and 9701 unique peptides were observed, and 54 human proteins were found to be potential biomarkers for schistosomiasis and bladder pathologies. Due to the interesting biomarkers identified from these proteomic and microbiome studies, we are currently engaged in a research collaboration to repeat the studies and validate the results with a larger sample. Further work may be of interest in to make a comparative analysis of the usefulness of each of the 54 identified biomarkers for the diagnosis of schistosomiasis.

Vivien J Chebii1,3*, Emmanuel Mpolya1, Samuel O. Oyola3, Jean-Baka Domelevo Entfellner 3, J. Musembi Mutuku3, Morris Agaba1,4.

1Nelson Mandela Africa Institution of Science and Technology, Arusha, Tanzania, 3International Livestock Research Institute, Nairobi, Kenya , 4Sarissa Limited, Kampala, Uganda

Capra nubiana is a wild goat species inhabiting the Sahara and Arabia deserts characterized by extreme temperatures, scarcity of feed and water. The genetic basis of its' adaptation to these environments remains unknown. In this study, we explored the possible role of copy number variations in the evolution of Capra species with a focus in the adaptation of Capra nubiana to its' environments. Copy number variations (CNV) are gain or loss of genomic segments greater than 1,000 bp between genomes. CNV have been implicated in phenotypic variations between species and might have a role in species differentiation and adaptations.

Based on Capra nubiana paired-end Illumina Hiseq reads sequenced to a coverage of 30x, we detected CNV relative to the domestic goat reference genome using a combination of read depth and split read approach. We identified 1,622 CNV loci overlapping with 343 protein-coding genes. Functional annotation of the protein-coding genes overlapping with the CNV showed that majority of them were immune response, signal transduction, and metabolism genes. Interferons, major histocompatibility complex proteins, and UL16 binding protein 21 which confer resistance against microbial infections were high copy number variable and significantly enriched. Lower density lipoprotein receptor-related protein 11 (Lrp11) which plays a role in stress adaptation resulting from extreme temperatures, water deprivation, and starvation were also high copy number variable. We suggest that the copy number variations of the immune response genes and Lrp11 possibly have a role in Capra nubiana adaptation to their environments.

This study is the first to shed insights on the possible role of the CNV in Capra nubiana adaptation to its' environments. The candidate copy number variable genes identified could be used upon functional confirmation as markers in animal breeding studies aimed at improving livestock health and productivity.

Keywords: Capra nubiana, gene copy number variations, adaptations, harsh environments, whole genome sequencing, Read depth method

Jorge da Rocha2, Dr Zané Lombard1, Prof Michèle Ramsay2,

1Division of Human Genetics, University of the Witwatersrand; 2Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand

Cancer is a critical health burden in Africa, and mortality rates are rising rapidly. Treatments are severe and expensive, and often cause adverse-drug-reactions (ADRs). Pharmacogenomics (PGx) aims to increase drug safety and efficacy by aligning drugs to known responses based on genomic variants, but data is sparse for African populations. Thirteen genes linked with ADRs to medicines used for treating major cancer types were identified: ABCB1, DPYD, TYMS, CYP19A1, GSTP1, CYP1B1, CYP3A4, CYP3A5, ESR1, CYP2D6, SLC19A1 and XRCC1/5. Public domain whole-genome-sequencing data from the 1000-Genomes-Project and the African-Genome-Variation-Project were mined to assess variants in eight African populations. Functional annotation was performed with a series of bioinformatics-based scoring tools to assess potential likelihood of deleterious impact. Two key African specific variants were identified: the CYP3A5 frameshift variant, rs41303343, which is highly likely to knockout gene function, and the CYP2D6 missense variant rs59421388, which was scored highly likely deleterious by all tools. Both variants are common in Africans, but lack clinical investigation into their PGx impact. For missense variants with known PGx effects, such as CYP2D6 - rs1065852 and DPYD - rs2297595, intra-African frequencies are significantly distinct, with rs1065852 being more common in West Africans, while rs2297595 is more common in East Africans. Many known variants are less common in Africans than other populations. These data indicate that guidelines for cancer drug safety based on African data are essential for use in Africa, and novel region-specific guidelines should be developed to ensure that Africans could benefit from a precision medicine approach.

Irene Bassano1, Swee Hoe Ong2, Maximo Sanz-Hernandez3, Michal Vinkler4, Olivier Hanotte5, Ebele Onuigbo6, Paul Kellam1,7, Thomas Whitehead8, Mark Fife8

1Imperial College London, Department of Medicine, Division of Infectious Diseases, Wright Fleming Wing, St Mary's Campus, Norfolk Place, London, UK; 2Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; 3Imperial College London, Department of Life Sciences, South Kensington, London UK; 4Charles University, Faculty of Science, Department of Zoology, Prague, Czech Republic; 5 International Livestock Research Institute (ILRI), Ethiopia, Addis Ababa, Ethiopia; 6Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; 7Kymab Ltd, Babraham Research Campus, Cambridge; 8The Pirbright Institute, Woking, UK

The chicken IFITM (chIFITM) locus is clustered on chromosome 5 and contains five genes, of which three are known to be interferon stimulated genes (ISGs) with potent antiviral activity, namely chIFITM1, 2, 3. These proteins restrict viral infections by blocking fusion of the viral and host membranes, thereby interfering with viral entry and replication. Their biological activity is well documented in several animal species, but their genetic variation and biological mechanism is less well understood. Here we report the complete sequence of the IFITM locus from a wide variety of chicken breeds to examine the detailed pattern of genetic variation of the locus. We have generated chIFITM sequences from commercial breeds, indigenous chickens from Nigeria and Ethiopia, European breeds and inbred chicken lines from The Pirbright Institute, totalling of 211 chickens. Our data reveal that the chIFITM locus does not show structural variation across the populations analysed. However, SNPs in functionally important regions of the proteins were detected, in particular the European breeds and indigenous birds from Ethiopia and Nigeria, revealing some SNPs were simultaneously under positive selection. Together these data suggest that IFITM genetic variation may contribute to the capacities of different chicken populations to resist virus infection.

This research was supported by the BBSRC (Animal Health Research Club) grant Number BB/L003996/1 and BBSRC grant BBS/OS/GC/000015/2.

Keywords: variant calling, SNPs, INDELs, GATK, positive selection

Ijomanta, J.1,+, Asala, O.1, Bitrus, M.1, Musa, A.2, Shittu, I.1, Joannis, T.1, Nwosuh, C.1 and 1Meseko, C.*

1Regional Centre for Animal Influenza, National Veterinary Research Institute, Vom Nigeria; 2Veterinary Department, Plateau State Ministry of Agriculture, Jos Nigeria

+presenting author

*Corresponding author: cameseko@yahoo.com

Influenza virus A belongs to the family Orthomyxoviridae and is divided into subtypes H1-18. The virus affects a wide range of avian and mammalian hosts, subtypes H1; H3; H5; H7 and H9 have been reported to cause fatal infections that can adversely affect socio-economics and public health. In April 2009, WHO declared influenza pandemic when H1N1pdm09 spread to 214 countries and an estimated 151,700 –575 400 deaths were recorded. The virus was subsequently transmitted to pigs and had remained enzootic being detected in many countries including Nigeria.

In this study, a total of 143 tracheal swabs were collected during a targeted active surveillance of apparently healthy pigs in Jos abattoir, Plateau state from December 2017 through February 2018. The samples were analyzed for Influenza A by conventional One-step RT-PCR protocol targeting the matrix. To subtype the Influenza A viruses, multiplex RT-qPCR assays targeting the Hemagglutinin (H1pdm, H1avian, H1human and H3) and neuraminidase (N1, N2, N1pdm) were used. In all, 51 (35%) samples were positive for Influenza A while four of the ten selected samples for subtyping were identified as H1N1pdm09.

In a previous study carried out at the human-animal interface, circulation of H1N1pdm09 was reported in southwest Nigeria. Also, follow up studies revealed seroprevalence ranging from 20-60% in pigs. Here, we report a more recent and continuous circulation of the virus in pigs in North central Nigeria since it was first declared a pandemic in 2009. The virus in human is now seasonal and can easily be managed with vaccination. Currently, there is no vaccination programme for swine influenza in Nigeria therefore maintaining H1N1pdm09 in pigs poses great public health risk. Possible mutations and reassortments may result in emergence of novel virus with pandemic potential.

Keywords: surveillance; Influenza A virus; Nigeria; Pandemics; Pigs

Elizabeth Marincola

African Academy of Sciences, Nairobi, Kenya

Scientists everywhere in the world experience similar frustrations in disseminating the results of their research: delays of months or more; access constraints; bias resulting from opaque peer review; incomplete availability of data, and the tyranny of the Journal Impact Factor, which induces scientists to chase acceptance in a succession of journals, hoping to publish in the one with the highest possible JIF – exacerbating the delay problem. African scientists are subject to all these barriers, with amplified effects resulting from the status of many as relatively unknown, often from unknown institutions. This presents researchers in Africa and other low- and middle-income countries to an uneven playing field and thus even higher barriers to entry to compete in what is increasingly a global science landscape. Yet because of relative lack of legacy and the acceleration of quality research output on the Continent, African STM publishing is positioned to “leap frog” to a better global solution for science communication. These conditions have shown to lead to extraordinary leadership in Africa in other industries, such as mobile money and energy. We believe that open publishing platforms represent a welcome evolution to sharing knowledge and discovery without waste and unnecessary delay. African scientists are positioned to not just "catch up" with more developed countries, but to lead globe in enlightened science communication.

Farai C. Muchadeyi1, Khanyisile Hadebe1, Edgar F. Dzomba2

1Agricultural Research Council, Biotechnology Platform, Onderstepoort, South Africa; 2Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa

*Correspondence: MuchadeyiF@arc.agric.za

Local indigenous animal genetic resources play an important role in sustaining the livelihoods of rural and resource-limited farmers. These local breeds thrive on adaptation to unfavourable environment stressors such as extreme temperatures, worsening droughts and disease challenges that characterise most low input production systems. Livestock improvement programs strive to develop genotypes that are adapted to local conditions and are able to produce optimally and sustainably under constrained environments. Genetic mechanisms underlying biological traits for environmental adaptation are unclear but unravelling them would be essential when designing methods to improve and sustain these breeds. It is important to study the interaction between production environments and genetics of animal populations so as to establish selection priorities and develop suitable improvement strategies. Efforts to initiate improvement programs have historically been hindered by absence of performance data and pedigree records compounded by factors such as animals randomly mating within and between flocks on communal pastures. Landscape genomics merges the competing effects of the production system, geographical, and environment landscapes with adaptive genetic variation. Advances in livestock genomics have enabled production of large amounts of genetic data of genome-wide coverage which, when combined with environmental data, enables in-depth studies on the patterns of genetic diversity, identification of genes and elucidating processes underlying genetic adaptation in various indigenous animal populations. In this study, case studies are presented on the use of landscape genomics as a tool to understand the genetics of adaption in indigenous chickens and goat populations of Southern Africa.

Keywords: Livestock, rural farming communities, genetic adaptation; landscape genomics

*Nwosu Onyeka .K. and Ngozi Miracle

National Biosafety Management Agency (NBMA), Abuja, Nigeria

With African rising population and considering its commensurate demand for more food; deficiencies of vital dietary nutrients and vulnerability to the negative impacts of climate change, the continent’s full application of genetic diversity and modern biotechnology to mitigate against these impediments remains consequential. This review explains the current standpoint of Africa towards leveraging the genetic diversity, and application of modern biotechnology in agriculture and the effectiveness of biosafety regulation towards crop improvement and food security in the continent. Genetic diversity is the pillar of biodiversity and diversity within species, between species and of ecosystem aimed to serve as a cushion for the adaptation and resilience of plants in the face of environmental challenge. Therefore genomic projects for conserving plant genetic resources (PGR) in most of the stable food crops in Africa will be vital for crop improvement and food production and will provide tools for population monitoring and assessment that can be used for conservation planning and genetic engineering (Agro-Modern Biotechnology). The transfer of a desirable gene from one species to another has proved to be a way of agro revival and economic growth which benefits both the farmers and consumers in terms of yield and improved nutrition respectively. Genetically engineered (GE) maize grown in 2015 by just three countries generated US$ 8.1 billion and over 7000 peer reviewed studies has shown that GE crops has lower concentrations of toxins that are likely carcinogenic in human and animals and there was no significant differences in grain quality such as fiber, lipids and proteins when compared with non-GE plants. Despite all these benefits of agro-modern biotechnology, there are still ill-fated public perceptions of the technology centralized towards environmental, health and socio-economic concerns. However, biosafety regulation that involves the legal and technical efforts and thorough scientific evidence to eliminate the potential risks that may result from modern biotechnology, genetically modified organisms (GMOs) and products thereof which addresses the public concerns is the assurance of the safety. Africa should develop a thoughtful agenda for an effective germplasm for agro-modern biotechnology together with an efficient biosafety system that will meet human increasing demands and improve existing conditions prevalent in our environment.

Keywords: Genetic diversity, Modern biotechnology, Biosafety, Genetic engineering, Genetically modified organisms, Germplasm.

Oladipo E.K.*1,2, Adeniji J.A.3, Oloke J.K2

1Department of Microbiology, Laboratory of Molecular Biology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria; 2Department of Pure and Applied Biology (Microbiology / Virology Unit), Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; 3Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria

Introduction: Pigs are susceptible to infections with both avian and mammalian Influenza A viruses. Pigs play an important role in the ecology of influenza virus. The changing epidemiology of influenza has a significant implications for the circulation of viruses in pigs. Little is known about the circulating strains in this area. To understand the current the current situation regarding influenza viruses circulating among pigs in Ogbomoso, a surveillance study was conducted.

Methods: Viral isolation from nasal swabs collected from one hundred pigs was performed using egg inoculation, MDCK and haemagglutination assay. Reverse transcriptase polymerase chain reaction (RT-PCR) was carried out by amplifying the matrix gene for identification. The sequence was determined by Sanger dideoxy sequencing. The homology analysis was implemented by Influenza Research database (IRD) and phylogenetic analysis was performed by Maximum – Likelihood methods using MEGA 7.10 software package.

Results: Multiple sequence alignment showed that the matrix (M) genes of A/H5N1/Ogbomoso/2014 influenza virus showed highest nucleotide identity with A/Pigeon/Sichuan/NCXN29/2014(H5N1) and A/Duck/Sichuan/NCXN11/2014 (H5N1) {98% and 97% respectively}. The phylogenetic analysis of the matrix gene of A/H5N1/Ogbomoso/2014 indicated that this virus is closely related to H5N1 strains circulating in southwest China.

Conclusion: This is the first report of genetic characterization of influenza A virus H5N1 of swine origin isolate from Ogbomoso. The presented results can further promote Influenza A virus surveillance and epidemiology insight in this community. The potential role of pigs in interspecies transmission remains important.

Keywords: Pigs, H5N1, Ogbomoso, Influenza A, Genetic Characterization.