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1. Molecular characterization of non-aureus staphylococci and Mammaliicoccus from Hipposideros bats in Southwest Nigeria

Author

Adesoji, Tomiwa O., George, Uwem E., Sulayman, Taofiq A., Uwanibe, Jessica N., Olawoye, Idowu B., Igbokwe, Joseph O., Olanipekun, Tobi G., Adeleke, Richard A., Akindoyin, Akintayo I., Famakinwa, Temitope J., Adamu, Andrew M., Terkuma, Christabel A., Ezekiel, Grace O., Eromon, Philomena E., Happi, Anise N., Fadare, Taiwo O., Shittu, Adebayo O., and Happi, Christian T.

Published
2024
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2. Immunological insights into COVID-19 in Southern Nigeria

Author

Chinedu A. Ugwu, Oluwasina Alao, Oluwagboadurami G. John, Blossom Akinnawo, Israel Ajayi, Ooreofe Odebode, Ifeoluwa Bejide, Allan Campbell, Julian Campbell, Jolly A. Adole, Idowu B. Olawoye, Kazeem Akano, Johnson Okolie, Philomena Eromon, Peter Olaitan, Ajibola Olagunoye, Ibukun Adebayo, Victor Adebayo, Elizabeth Babalola, Omowumi Abioye, Nnennaya Ajayi, Emeka Ogah, Kingsley Ukwaja, Sylvanus Okoro, Ogbonnaya Oje, Ojide Chiedozie Kingsley, Matthew Eke, Venatius Onyia, Olivia Achonduh-Atijegbe, Friday Elechi Ewah, Mary Obasi, Violet Igwe, Olufemi Ayodeji, Abejegah Chukwuyem, Sampson Owhin, Nicholas Oyejide, Sylvester Abah, Winifred Ingbian, Moyosoore Osoba, Ahmed Alebiosu, Angalee Nadesalingam, Ernest T. Aguinam, George Carnell, Nina Krause, Andrew Chan, Charlotte George, Rebecca Kinsley, Paul Tonks, Nigel Temperton, Jonathan Heeney, and Christian Happi

Subjects
COVID-19, SARS-CoV-2, immunity, vaccine, Nigeria, pre-pandemic, Immunologic diseases. Allergy, RC581-607
Abstract

IntroductionOne of the unexpected outcomes of the COVID-19 pandemic was the relatively low levels of morbidity and mortality in Africa compared to the rest of the world. Nigeria, Africa's most populous nation, accounted for less than 0.01% of the global COVID-19 fatalities. The factors responsible for Nigeria's relatively low loss of life due to COVID-19 are unknown. Also, the correlates of protective immunity to SARS-CoV-2 and the impact of pre-existing immunity on the outcome of the COVID-19 pandemic in Africa are yet to be elucidated. Here, we evaluated the natural and vaccine-induced immune responses from vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria throughout the three waves of the COVID-19 pandemic in Nigeria. We also examined the pre-existing immune responses to SARS-CoV-2 from samples collected prior to the COVID-19 pandemic.MethodsWe used spike RBD and N- IgG antibody ELISA to measure binding antibody responses, SARS-CoV-2 pseudotype assay protocol expressing the spike protein of different variants (D614G, Delta, Beta, Omicron BA1) to measure neutralizing antibody responses and nucleoprotein (N) and spike (S1, S2) direct ex vivo interferon gamma (IFNγ) T cell ELISpot to measure T cell responses. ResultOur study demonstrated a similar magnitude of both binding (N-IgG (74% and 62%), S-RBD IgG (70% and 53%) and neutralizing (D614G (49% and 29%), Delta (56% and 47%), Beta (48% and 24%), Omicron BA1 (41% and 21%)) antibody responses from symptomatic and asymptomatic survivors in Nigeria. A similar magnitude was also seen among vaccinated participants. Interestingly, we revealed the presence of preexisting binding antibodies (N-IgG (60%) and S-RBD IgG (44%)) but no neutralizing antibodies from samples collected prior to the pandemic. DiscussionThese findings revealed that both vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria make similar magnitude of both binding and cross-reactive neutralizing antibody responses. It supported the presence of preexisting binding antibody responses among some Nigerians prior to the COVID-19 pandemic. Lastly, hybrid immunity and heterologous vaccine boosting induced the strongest binding and broadly neutralizing antibody responses compared to vaccine or infection-acquired immunity alone.

Published
2024
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5. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Author

Olawoye, Idowu B., Oluniyi, Paul E., Oguzie, Judith U., Uwanibe, Jessica N., Kayode, Tolulope A., Olumade, Testimony J., Ajogbasile, Fehintola V., Parker, Edyth, Eromon, Philomena E., Abechi, Priscilla, Sobajo, Tope A., Ugwu, Chinedu A., George, Uwem E., Ayoade, Femi, Akano, Kazeem, Oyejide, Nicholas E., Nosamiefan, Iguosadolo, Fred-Akintunwa, Iyanuoluwa, Adedotun-Sulaiman, Kemi, Brimmo, Farida B., Adegboyega, Babatunde B., Philip, Courage, Adeleke, Richard A., Chukwu, Grace C., Ahmed, Muhammad I., Ope-Ewe, Oludayo O., Otitoola, Shobi G., Ogunsanya, Olusola A., Saibu, Mudasiru F., Sijuwola, Ayotunde E., Ezekiel, Grace O., John, Oluwagboadurami G., Akin-John, Julie O., Akinlo, Oluwasemilogo O., Fayemi, Olanrewaju O., Ipaye, Testimony O., Nwodo, Deborah C., Omoniyi, Abolade E., Omwanghe, Iyobosa B., Terkuma, Christabel A., Okolie, Johnson, Ayo-Ale, Olubukola, Ikponmwosa, Odia, Benevolence, Ebo, Naregose, Grace O., Patience, Akhilomen E., Blessing, Osiemi, Micheal, Airende, Jacqueline, Agbukor, Aiyepada, John O., Ebhodaghe, Paulson, Racheal, Omiunu, Rita, Esumeh, Rosemary, Giwa E., Solomon, Ehikhametalor, Anieno, Ekanem, Edna, Yerumoh, Chris, Aire O., Donatus, Adomeh I., Ogbaini-Emovon, Ephraim, Tatfeng, Mirabeau Y., Omunakwe, Hannah E., Bob-Manuel, Mienye, Ahmed, Rahaman A., Onwuamah, Chika K., Shaibu, Joseph O., Okwuraiwe, Azuka, Ataga, Anthony E., Bock-Oruma, Andrew, Daramola, Funmi, Yusuf, Ibrahim F., Fajola, Akinwumi, Ntia, Nsikak-Abasi, Ekpo, Julie J., Moses, Anietie E., Moore-Igwe, Beatrice W., Fakayode, Oluwatosin E., Akinola, Monilade, Kida, Ibrahim M., Oderinde, Bamidele S., Wudiri, Zara W., Adeyemi, Oluwapelumi O., Akanbi, Olusola A., Ahumibe, Anthony, Akinpelu, Afolabi, Ayansola, Oyeronke, Babatunde, Olajumoke, Omoare, Adesuyi A., Chukwu, Chimaobi, Mba, Nwando G., Omoruyi, Ewean C., Olisa, Olasunkanmi, Akande, Olatunji K., Nwafor, Ifeanyi E., Ekeh, Matthew A., Ndoma, Erim, Ewah, Richard L., Duruihuoma, Rosemary O., Abu, Augustine, Odeh, Elizabeth, Onyia, Venatius, Ojide, Chiedozie K., Okoro, Sylvanus, Igwe, Daniel, Ogah, Emeka O., Khan, Kamran, Ajayi, Nnennaya A., Ugwu, Collins N., Ukwaja, Kingsley N., Ugwu, Ngozi I., Abejegah, Chukwuyem, Adedosu, Nelson, Ayodeji, Olufemi, Liasu, Ahmed A., Isamotu, Rafiu O., Gadzama, Galadima, Petros, Brittany A., Siddle, Katherine J., Schaffner, Stephen F., Akpede, George, Erameh, Cyril Oshomah, Baba, Marycelin M., Oladiji, Femi, Audu, Rosemary, Ndodo, Nnaemeka, Fowotade, Adeola, Okogbenin, Sylvanus, Okokhere, Peter O., Park, Danny J., Mcannis, Bronwyn L., Adetifa, Ifedayo M., Ihekweazu, Chikwe, Salako, Babatunde L., Tomori, Oyewale, Happi, Anise N., Folarin, Onikepe A., Andersen, Kristian G., Sabeti, Pardis C., and Happi, Christian T.

Published
2023
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6. Genomic Epidemiology of Mycobacterium abscessus on the Island of Montréal Is Not Suggestive of Health Care-Associated Person-to-Person Transmission.

Author

Olawoye, Idowu B, Waglechner, Nicholas, McIntosh, Fiona, Akochy, Pierre-Marie, Cloutier, Nancy, Lapierre, Simon Grandjean, Tannir, Bouchra, Greenaway, Christina, Matouk, Elias, Poirier, Louise, Levesque, Roger C, Boyle, Brian, Quach, Caroline, Soualhine, Hafid, Batt, Jane, Behr, Marcel A, Lee, Robyn S, and Guthrie, Jennifer L

Subjects
*HEALTH facilities, *EPIDEMIOLOGY, *WHOLE genome sequencing, *PAN-genome, *GENOMICS
Abstract

Background Mycobacterium abscessus complex (MABC), an opportunistic nontuberculous mycobacteria, can lead to poor clinical outcomes in pulmonary infections. Conflicting data exist on person-to-person transmission of MABC within and across health care facilities. To investigate further, a comprehensive retrospective study across 5 health care institutions on the Island of Montréal was undertaken. Methods We analyzed the genomes of 221 MABC isolates obtained from 115 individuals (2010–2018) to identify possible links. Genetic similarity, defined as ≤25 single-nucleotide polymorphisms (SNPs), was investigated through a blinded epidemiological inquiry. Results Bioinformatics analyses identified 28 sequence types, including globally observed dominant circulating clones (DCCs). Further analysis revealed 210 isolate pairs within the SNP threshold. Among these pairs, there was 1 possible laboratory contamination where isolates from different patients processed in the same laboratory differed by only 2 SNPs. There were 37 isolate pairs from patients who had provided specimens from the same hospital; however, epidemiological analysis found no evidence of health care-associated person-to-person transmission between these patients. Additionally, pangenome analysis showed higher discriminatory power than core genome analysis for examining genomic similarity. Conclusions Genomics alone is insufficient to establish MABC transmission, particularly considering the genetic similarity and wide distribution of DCCs, although pangenome analysis has the potential to add further insight. Our findings indicate that MABC infections in Montréal are unlikely attributable to health care-associated person-to-person transmission. [ABSTRACT FROM AUTHOR]

Published
2025
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7. Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

Author

Jessica N. Uwanibe, Idowu B. Olawoye, Christian T. Happi, and Onikepe A. Folarin

Subjects
whole genome sequencing, multidrug resistance, AMR genes, plasmid, virulence, enterobacteriaceae, Biology (General), QH301-705.5
Abstract

Antimicrobial resistance (AMR) is responsible for the spread and persistence of bacterial infections. Surveillance of AMR in healthy individuals is usually not considered, though these individuals serve as reservoirs for continuous disease transmission. Therefore, it is essential to conduct epidemiological surveillance of AMR in healthy individuals to fully understand the dynamics of AMR transmission in Nigeria. Thirteen multidrug-resistant Citrobacter spp., Enterobacter spp., Klebsiella pneumoniae, and Escherichia coli isolated from stool samples of healthy children were subjected to whole genome sequencing (WGS) using Illumina and Oxford nanopore sequencing platforms. A bioinformatics analysis revealed antimicrobial resistance genes such as the pmrB_Y358N gene responsible for colistin resistance detected in E. coli ST219, virulence genes such as senB, and ybtP&Q, and plasmids in the isolates sequenced. All isolates harbored more than three plasmid replicons of either the Col and/or Inc type. Plasmid reconstruction revealed an integrated tetA gene, a toxin production caa gene in two E. coli isolates, and a cusC gene in K. quasivariicola ST3879, which induces neonatal meningitis. The global spread of AMR pathogenic enteric bacteria is of concern, and surveillance should be extended to healthy individuals, especially children. WGS for epidemiological surveillance will improve the detection of AMR pathogens for management and control.

Published
2024
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8. Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa

Author

Idowu B. Olawoye, Jessica N. Uwanibe, Chioma N. Kunle-Ope, Olabisi F. Davies-Bolorunduro, Temitope A. Abiodun, Rosemary A. Audu, Babatunde L. Salako, and Christian T. Happi

Subjects
Medicine, Science
Abstract

Abstract Multi-drug (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) continues to be a global public health problem especially in high TB burden countries like Nigeria. Many of these cases are undetected and go on to infect high risk individuals. Clinical samples from positive rifampicin resistant Xpert®MTB/Rif assay were subjected to direct whole genome sequencing and bioinformatics analysis to identify the full antibiotics resistance and lineage profile. We report two (2) XDR TB samples also belonging to the East-Asian/Beijing family of lineage 2 Mycobacterium tuberculosis complex from clinical samples in Nigeria. Our findings further reveal the presence of mutations that confer resistance to first-line drugs (rifampicin, isoniazid, ethambutol and pyrazanimide), second-line injectables (capreomycin, streptomycin, kanamycin and/or amikacin) and at least one of the fluoroquinolones (ofloxacin, moxifloxacin, levofloxacin and/or ciprofloxacin) in both samples. The genomic sequence data from this study not only provide the first evidence of XDR TB in Nigeria and West Africa, but also emphasize the importance of WGS in accurately detecting MDR and XDR TB, to ensure adequate and proper management treatment regimens for affected individuals. This will greatly aid in preventing the spread of drug resistance TB in high burden countries.

Published
2021
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10. The Prevalence of Undiagnosed Salmonella enterica Serovar Typhi in Healthy School-Aged Children in Osun State, Nigeria

Author

Jessica N. Uwanibe, Tolulope A. Kayode, Paul E. Oluniyi, Kazeem Akano, Idowu B. Olawoye, Chinedu A. Ugwu, Christian T. Happi, and Onikepe A. Folarin

Subjects
Salmonella Typhi, typhoid fever, ELISA, lipopolysaccharide, asymptomatic, next-generation sequencing, Medicine
Abstract

Typhoid fever remains a significant public health concern due to cases of mis-/overdiagnosis. Asymptomatic carriers play a role in the transmission and persistence of typhoid fever, especially among children, where limited data exist in Nigeria and other endemic countries. We aim to elucidate the burden of typhoid fever among healthy school-aged children using the best surveillance tool(s). In a semi-urban/urban state (Osun), 120 healthy school-aged children under 15 years were enrolled. Whole blood and fecal samples were obtained from consenting children. ELISA targeting the antigen lipopolysaccharide (LPS) and anti-LPS antibodies of Salmonella Typhi, culture, polymerase chain reaction (PCR), and next-generation sequencing (NGS) were used to analyze the samples. At least one of the immunological markers was detected in 65.8% of children, with 40.8%, 37.5%, and 39% of children testing positive for IgM, IgG, and antigen, respectively. Culture, PCR, and NGS assays did not detect the presence of Salmonella Typhi in the isolates. This study demonstrates a high seroprevalence of Salmonella Typhi in these healthy children but no carriage, indicating the inability to sustain transmission. We also demonstrate that using a single technique is insufficient for typhoid fever surveillance in healthy children living in endemic areas.

Published
2023
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13. Emergence and Genomic Characterization of Multidrug Resistant Candida auris in Nigeria, West Africa

Author

Rita Oladele, Jessica N. Uwanibe, Idowu B. Olawoye, Abdul-Wahab O. Ettu, Jacques F. Meis, and Christian T. Happi

Subjects
Candida auris, multidrug resistance, azoles, sequencing, fungaemia, Biology (General), QH301-705.5
Abstract

Candida auris is an emerging multidrug-resistant fungal pathogen that has become a worldwide public health threat due to the limitations of treatment options, difficulty in diagnosis, and its potential for clonal transmission. Four ICU patients from three different healthcare facilities in Southern Nigeria presented features suggestive of severe sepsis and the blood cultures yielded the growth of Candida spp., which was identified using VITEK 2 as C. auris. Further confirmation was performed using whole genome sequencing (WGS). From the genomic analysis, two had mutations that conferred resistance to the antifungal azole group and other non-synonymous mutations in hotspot genes, such as ERG2, ERG11, and FKS1. From the phylogenetic analysis, cases 2 and 4 had a confirmed mutation (ERG11:Y132F) that conferred drug resistance to azoles clustered with clade 1, whilst cases 1 and 3 clustered with clade 4. Three of the patients died, and the fourth was most likely a case of colonization since he received no antifungals and was discharged home. These first cases of C. auris reported from Nigeria were most likely introduced from different sources. It is of public health importance as it highlights diagnostic gaps in our setting and the need for active disease surveillance in the region.

Published
2022
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14. The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake

Author

Idowu B. Olawoye, Simon D.W. Frost, and Christian T. Happi

Subjects
Bacteria genomics, Bioinformatics, Pipeline, Workflow, Medicine, Biology (General), QH301-705.5
Abstract

Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pipeline called BAGEP for monomorphic bacteria that performs quality control on FASTQ paired end files, scan reads for contaminants using a taxonomic classifier, maps reads to a reference genome of choice for variant detection, detects antimicrobial resistant (AMR) genes, constructs a phylogenetic tree from core genome alignments and provide interactive short nucleotide polymorphism (SNP) visualization across core genomes in the data set. The objective of our research was to create an easy-to-use pipeline from existing bioinformatics tools that can be deployed on a personal computer. The pipeline was built on the Snakemake framework and utilizes existing tools for each processing step: fastp for quality trimming, snippy for variant calling, Centrifuge for taxonomic classification, Abricate for AMR gene detection, snippy-core for generating whole and core genome alignments, IQ-TREE for phylogenetic tree construction and vcfR for an interactive heatmap visualization which shows SNPs at specific locations across the genomes. BAGEP was successfully tested and validated with Mycobacterium tuberculosis (n = 20) and Salmonella enterica serovar Typhi (n = 20) genomes which are about 4.4 million and 4.8 million base pairs, respectively. Running these test data on a 8 GB RAM, 2.5 GHz quad core laptop took 122 and 61 minutes on respective data sets to complete the analysis. BAGEP is a fast, calls accurate SNPs and an easy to run pipeline that can be executed on a mid-range laptop; it is freely available on: https://github.com/idolawoye/BAGEP.

Published
2020
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16. The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response

Author

Yolanda Botti-Lodovico, Parvathy Nair, Dolo Nosamiefan, Matthew Stremlau, Stephen Schaffner, Sebastian V. Agignoae, John Oke Aiyepada, Fehintola V. Ajogbasile, George O. Akpede, Foday Alhasan, Kristian G. Andersen, Danny A. Asogun, Oladele Oluwafemi Ayodeji, Aida S. Badiane, Kayla Barnes, Matthew R. Bauer, Antoinette Bell-Kareem, Muoebonam Ekene Benard, Ebo Ohomoime Benevolence, Osiemi Blessing, Chloe K. Boehm, Matthew L. Boisen, Nell G. Bond, Luis M. Branco, Michael J. Butts, Amber Carter, Andres Colubri, Awa B. Deme, Katherine C. DeRuff, Younousse Diédhiou, Akhilomen Patience Edamhande, Siham Elhamoumi, Emily J. Engel, Philomena Eromon, Mosoka Fallah, Onikepe A. Folarin, Ben Fry, Robert Garry, Amy Gaye, Michael Gbakie, Sahr M. Gevao, Gabrielle Gionet, Adrianne Gladden-Young, Augustine Goba, Jules Francois Gomis, Anise N. Happi, Mary Houghton, Chikwe Ihekwuazu, Christopher Ojemiega Iruolagbe, Jonathan Jackson, Simbirie Jalloh, Jeremy Johnson, Lansana Kanneh, Adeyemi Kayode, Molly Kemball, Ojide Chiedozie Kingsley, Veronica Koroma, Dylan Kotliar, Samar Mehta, Hayden C. Metsky, Airende Michael, Marzieh Ezzaty Mirhashemi, Kayvon Modjarrad, Mambu Momoh, Cameron A. Myhrvold, Okonofua Grace Naregose, Tolla Ndiaye, Mouhamadou Ndiaye, Aliou Ndiaye, Erica Normandin, Ikponmwosa Odia, Judith Uche Oguzie, Sylvanus A. Okogbenin, Peter O. Okokhere, Johnson Okolie, Idowu B. Olawoye, Testimony J. Olumade, Paul E. Oluniyi, Omigie Omoregie, Daniel J. Park, Mariétou Faye Paye, Brittany Petros, Anthony A. Philippakis, Abechi Priscilla, Alan Ricks, Anne Rimoin, John Demby Sandi, John S. Schieffelin, Monica Schreiber, Mame Cheikh Seck, Sameed Siddiqui, Katherine Siddle, Allison R. Smither, Mouhamad Sy, Ngayo Sy, Christopher H. Tomkins-Tinch, Oyewale Tomori, Chinedu Ugwu, Jessica N. Uwanibe, Eghosasere Anthonia Uyigue, Dada Ireti Victoria, Anika Vinzé, Megan E. Vodzak, Nicole Welch, Haja Isatta Wurie, Daba Zoumarou, Donald S. Grant, Daouda Ndiaye, Bronwyn MacInnis, Pardis C. Sabeti, and Christian Happi

Subjects
pandemic preemption, pandemic response, diagnostic tools, bioinformatics, genomic surveillance, infectious disease, Microbiology, QR1-502
Abstract

While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE—detected in the Yoruba population of Nigeria—conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the “emerging” nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz’s critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts.

Published
2021
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17. Immunological insights into COVID-19 in Southern Nigeria.

Author

Ugwu, Chinedu A., Alao, Oluwasina, John, Oluwagboadurami G., Akinnawo, Blossom, Ajayi, Israel, Odebode, Ooreofe, Bejide, Ifeoluwa, Campbell, Allan, Campbell, Julian, Adole, Jolly A., Olawoye, Idowu B., Akano, Kazeem, Okolie, Johnson, Eromon, Philomena, Olaitan, Peter, Olagunoye, Ajibola, Adebayo, Ibukun, Adebayo, Victor, Babalola, Elizabeth, and Abioye, Omowumi

Subjects
COVID-19, COVID-19 pandemic, ANTIBODY formation, INTERFERON gamma, SARS-CoV-2 Omicron variant
Abstract

Introduction: One of the unexpected outcomes of the COVID-19 pandemic was the relatively low levels of morbidity and mortality in Africa compared to the rest of the world. Nigeria, Africa's most populous nation, accounted for less than 0.01% of the global COVID-19 fatalities. The factors responsible for Nigeria's relatively low loss of life due to COVID-19 are unknown. Also, the correlates of protective immunity to SARS-CoV-2 and the impact of pre-existing immunity on the outcome of the COVID-19 pandemic in Africa are yet to be elucidated. Here, we evaluated the natural and vaccine-induced immune responses from vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria throughout the three waves of the COVID-19 pandemic in Nigeria. We also examined the pre-existing immune responses to SARS-CoV-2 from samples collected prior to the COVID-19 pandemic. Methods: We used spike RBD and N-IgG antibody ELISA to measure binding antibody responses, SARS-CoV-2 pseudotype assay protocol expressing the spike protein of different variants (D614G, Delta, Beta, Omicron BA1) to measure neutralizing antibody responses and nucleoprotein (N) and spike (S1, S2) direct ex vivo interferon gamma (IFNγ) T cell ELISpot to measure T cell responses. Result: Our study demonstrated a similar magnitude of both binding (N-IgG (74% and 62%), S-RBD IgG (70% and 53%) and neutralizing (D614G (49% and 29%), Delta (56% and 47%), Beta (48% and 24%), Omicron BA1 (41% and 21%)) antibody responses from symptomatic and asymptomatic survivors in Nigeria. A similar magnitude was also seen among vaccinated participants. Interestingly, we revealed the presence of preexisting binding antibodies (N-IgG (60%) and S-RBD IgG (44%)) but no neutralizing antibodies from samples collected prior to the pandemic. Discussion: These findings revealed that both vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria make similar magnitude of both binding and cross-reactive neutralizing antibody responses. It supported the presence of preexisting binding antibody responses among some Nigerians prior to the COVID-19 pandemic. Lastly, hybrid immunity and heterologous vaccine boosting induced the strongest binding and broadly neutralizing antibody responses compared to vaccine or infection-acquired immunity alone. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Effects of watershed delineation on the prediction of water quality parameters in Gaa Akanbi area, Ilorin

Author

Adeogun, A. G., Ganiyu, H. O., Adetoro, A. E., and Idowu, B. S.

Subjects
Geographical Information System (GIS), hydrological modelling, water quality parameters, Soil and Water Assessment Tool (SWAT)
Abstract

Watershed delineation is a required step when conducting any spatially distributed hydrological modelling. The prediction of water quality parameters in a basin entails delineation of watershed into different number of sub-basins. Thus, this research evaluated effects of watershed delineation on the prediction of water quality parameters in Gaa Akanbi area of Ilorin, Kwara state, Nigeria. The objectives are to model and predict water quality parameters in the watershed; delineate the selected watershed in various numbers of sub-basins and study the effects of watershed delineation in the prediction of water quality parameters of the basin. For proper implementation of this study, Geographical Information System (GIS) software, physically based watershed model - Soil and Water Assessment Tool (SWAT) and other data processing software were used. Since the model is physically based, the surface properties (i.e. Digital Elevation Model (DEM), stream network, digital soil map, digital land use and land cover map, climatic and hydrological data) served as input in the model. The model was daily for a period of 30 years (i.e. January 1991 to December, 2020). The results showed that the watershed was successfully delineated to 3,7,11,21,32,53 sub-basins. Also, it was noted that the predicted values of water quality parameters (Nitrate, organic phosphorus and sediment concentration) are directly proportional to increase in the number of sub-basins delineated in the watershed.

Published
2023

20. Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa

Author

Temitope A. Abiodun, Idowu B. Olawoye, Babatunde L. Salako, Chioma Kunle-Ope, Rosemary A. Audu, Olabisi F. Davies-Bolorunduro, Jessica N. Uwanibe, and Christian T. Happi

Subjects
Adult, DNA, Bacterial, Male, Tuberculosis, Capreomycin, Extensively Drug-Resistant Tuberculosis, Science, Antitubercular Agents, Nigeria, HIV Infections, Microbial Sensitivity Tests, Drug resistance, Article, Genomic analysis, Young Adult, Antibiotic resistance, medicine, Humans, Phylogeny, Ethambutol, Public health, Multidisciplinary, Whole Genome Sequencing, biology, Extensively drug-resistant tuberculosis, Genomics, Mycobacterium tuberculosis, Middle Aged, biology.organism_classification, medicine.disease, bacterial infections and mycoses, Virology, Computational biology and bioinformatics, Mycobacterium tuberculosis complex, Medicine, Female, Rifampin, Rifampicin, Fluoroquinolones, medicine.drug
Abstract

Multi-drug (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) continues to be a global public health problem especially in high TB burden countries like Nigeria. Many of these cases are undetected and go on to infect high risk individuals. Clinical samples from positive rifampicin resistant Xpert®MTB/Rif assay were subjected to direct whole genome sequencing and bioinformatics analysis to identify the full antibiotics resistance and lineage profile. We report two (2) XDR TB samples also belonging to the East-Asian/Beijing family of lineage 2 Mycobacterium tuberculosis complex (MTBC) from clinical samples in Nigeria. Our findings further reveal the presence of resistance genes to first-line drugs (rifampicin, isoniazid, ethambutol and pyrazanimide), second-line injectables (capreomycin, streptomycin, kanamycin and/or amikacin) and at least one of the fluoroquinolones (ofloxacin, moxifloxacin, levofloxacin and/or ciprofloxacin) in both samples. The genomic sequence data from this study not only provide the first evidence of XDR TB in Nigeria and West Africa, but also emphasize the importance of WGS in accurately detecting MDR and XDR TB, to ensure adequate and proper management treatment regimens for affected individuals. This will greatly aid in preventing the spread of drug resistance TB in high burden countries.

Published
2021

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

Author

Idowu B. Olawoye, Paul E. Oluniyi, Judith U. Oguzie, Jessica N. Uwanibe, Adeyemi T. Kayode, Testimony J. Olumade, Fehintola V. Ajogbasile, Edyth Parker, Philomena E. Eromon, Priscilla Abechi, Tope Sobajo, Chinedu Ugwu, George Uwem, Femi Ayoade, Kazeem Akano, Nicholas Oyejide, Iyanuoluwa Fred-Akintunwa, Kemi Adedotun-Sulaiman, Farida Brimmo, Benjamin Adegboyega, Courage Philip, Ayomide Adeleke, Grace C. Chukwu, Ahmed I. Muhammad, Oludayo O. Ope-ewe, Shobi Otitoola, Olusola A. Ogunsanya, Mudasiru F. Saibu, Ayotunde E. Sijuwola, Grace O. Ezekiel, Oluwagboadurami G. John, Julie O. Akin-John, Oluwasemilogo O. Akinlo, Olanrewaju O. Fayemi, Testimony O. Ipaye, Deborah C. Nwodo, Abolade E. Omoniyi, Iyobosa B. Omwanghe, Christabel A. Terkuma, Johnson Okolie, Olubukola Ayo-Ale, Odia Ikponmwosa, Ebo Benevolence, Okonofua Naregose, Akhilomen Patience, Osiemi Blessing, Airende Micheal, Agbukor Jacqueline, Aiyepada John, Paulson Ebhodaghe, Omiunu Racheal, Esumeh Rita, Giwa Rosemary, Ehikhametalor Solomon, Ekanem Anieno, Yerumoh Edna, Aire Chris, Adomeh Donatus, Ephraim Ogbaini, Mirabeau Y. Tatfeng, Hannah E. Omunakwe, Mienye Bob-Manuel, Rahaman Ahmed, Chika Onwuamah, Joseph Shaibu, Azuka Okwuraiwe, Anthony E. Atage, Andrew Bock-Oruma, Funmi Daramola, Akinwumi Fajola, Nsikak-Abasi Ntia, Julie J. Ekpo, Anietie Moses, Worbianueri B. Moore-Igwe, Ibrahim F. Yusuf, Enoch O. Fakayode, Monilade Akinola, Ibrahim Kida, Bamidele S. Oderinde, Zara Wudiri, Olufemi O. Adeyemi, Olusola Akanbi, Anthony Ahumibe, Afolabi Akinpelu, Oyeronke Ayansola, Olajumoke Babatunde, Adesuyi Omoare, Chimaobi Chukwu, Nwando Mba, Ewean C. Omoruyi, Johnson A. Adeniji, Moses O. Adewunmi, Oluseyi Olayinka, Olisa Olasunkanmi, Olatunji Akande, Ifeanyi Nwafor, Matthew Ekeh, Erim Ndoma, Richard Ewah, Rosemary Duruihuoma, Augustine Abu, Elizabeth Odeh, Venatious Onyia, Kingsley C. Ojide, Sylvanus Okoro, Daniel Igwe, Kamran Khan, Anthony N. Ajayi, Ebhodaghe Ngozi Ugwu, Collins N. Ugwu, Kingsley Ukwuaja, Emeka O. Ogah, Chukwuyem Abejegah, Nelson Adedosu, Olufemi Ayodeji, Rafiu O. Isamotu, Galadima Gadzama, Brittany Petros, Katherine J. Siddle, Stephen Schaffner, George Akpede, Cyril Oshomah Erameh, Marycelin Baba, Femi Oladiji, Rosemary Audu, Nnaemeka Ndodo, Adeola Fowotade, Sylvanus Okogbenin, Peter Okokhere, Danny Park, Bronwyn Mcannis, Ifedayo Adetifa, Chikwe Ihekweazu, Babatunde L. Salako, Oyewale Tomori, Anise N. Happi, Onikepe A. Folarin, Kristian G. Andersen, Pardis C. Sabeti, and Christian T. Happi

Abstract

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 B.1.1.318 and B.1.525 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 emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Our results show how regional connectivity in downsampled regions like Africa can often influence virus transmissions between neighbouring countries. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission in the region, generating actionable information for public health decision makers in the region.

Published
2022
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22. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Author

Olawoye, Idowu B., primary, Oluniyi, Paul E., additional, Oguzie, Judith U., additional, Uwanibe, Jessica N., additional, Kayode, Adeyemi T., additional, Olumade, Testimony J., additional, Ajogbasile, Fehintola V., additional, Parker, Edyth, additional, Eromon, Philomena E., additional, Abechi, Priscilla, additional, Sobajo, Tope, additional, Ugwu, Chinedu, additional, Uwem, George, additional, Ayoade, Femi, additional, Akano, Kazeem, additional, Oyejide, Nicholas, additional, Fred-Akintunwa, Iyanuoluwa, additional, Adedotun-Sulaiman, Kemi, additional, Brimmo, Farida, additional, Adegboyega, Benjamin, additional, Philip, Courage, additional, Adeleke, Ayomide, additional, Chukwu, Grace C., additional, Muhammad, Ahmed I., additional, Ope-ewe, Oludayo O., additional, Otitoola, Shobi, additional, Ogunsanya, Olusola A., additional, Saibu, Mudasiru F., additional, Sijuwola, Ayotunde E., additional, Ezekiel, Grace O., additional, John, Oluwagboadurami G., additional, Akin-John, Julie O., additional, Akinlo, Oluwasemilogo O., additional, Fayemi, Olanrewaju O., additional, Ipaye, Testimony O., additional, Nwodo, Deborah C., additional, Omoniyi, Abolade E., additional, Omwanghe, Iyobosa B., additional, Terkuma, Christabel A., additional, Okolie, Johnson, additional, Ayo-Ale, Olubukola, additional, Ikponmwosa, Odia, additional, Benevolence, Ebo, additional, Naregose, Okonofua, additional, Patience, Akhilomen, additional, Blessing, Osiemi, additional, Micheal, Airende, additional, Jacqueline, Agbukor, additional, John, Aiyepada, additional, Ebhodaghe, Paulson, additional, Racheal, Omiunu, additional, Rita, Esumeh, additional, Rosemary, Giwa, additional, Solomon, Ehikhametalor, additional, Anieno, Ekanem, additional, Edna, Yerumoh, additional, Chris, Aire, additional, Donatus, Adomeh, additional, Ogbaini, Ephraim, additional, Tatfeng, Mirabeau Y., additional, Omunakwe, Hannah E., additional, Bob-Manuel, Mienye, additional, Ahmed, Rahaman, additional, Onwuamah, Chika, additional, Shaibu, Joseph, additional, Okwuraiwe, Azuka, additional, Atage, Anthony E., additional, Bock-Oruma, Andrew, additional, Daramola, Funmi, additional, Fajola, Akinwumi, additional, Ntia, Nsikak-Abasi, additional, Ekpo, Julie J., additional, Moses, Anietie, additional, Moore-Igwe, Worbianueri B., additional, Yusuf, Ibrahim F., additional, Fakayode, Enoch O., additional, Akinola, Monilade, additional, Kida, Ibrahim, additional, Oderinde, Bamidele S., additional, Wudiri, Zara, additional, Adeyemi, Olufemi O., additional, Akanbi, Olusola, additional, Ahumibe, Anthony, additional, Akinpelu, Afolabi, additional, Ayansola, Oyeronke, additional, Babatunde, Olajumoke, additional, Omoare, Adesuyi, additional, Chukwu, Chimaobi, additional, Mba, Nwando, additional, Omoruyi, Ewean C., additional, Adeniji, Johnson A., additional, Adewunmi, Moses O., additional, Olayinka, Oluseyi, additional, Olasunkanmi, Olisa, additional, Akande, Olatunji, additional, Nwafor, Ifeanyi, additional, Ekeh, Matthew, additional, Ndoma, Erim, additional, Ewah, Richard, additional, Duruihuoma, Rosemary, additional, Abu, Augustine, additional, Odeh, Elizabeth, additional, Onyia, Venatious, additional, Ojide, Kingsley C., additional, Okoro, Sylvanus, additional, Igwe, Daniel, additional, Khan, Kamran, additional, Ajayi, Anthony N., additional, Ugwu, Ebhodaghe Ngozi, additional, Ugwu, Collins N., additional, Ukwuaja, Kingsley, additional, Ogah, Emeka O., additional, Abejegah, Chukwuyem, additional, Adedosu, Nelson, additional, Ayodeji, Olufemi, additional, Isamotu, Rafiu O., additional, Gadzama, Galadima, additional, Petros, Brittany, additional, Siddle, Katherine J., additional, Schaffner, Stephen, additional, Akpede, George, additional, Erameh, Cyril Oshomah, additional, Baba, Marycelin, additional, Oladiji, Femi, additional, Audu, Rosemary, additional, Ndodo, Nnaemeka, additional, Fowotade, Adeola, additional, Okogbenin, Sylvanus, additional, Okokhere, Peter, additional, Park, Danny, additional, Mcannis, Bronwyn, additional, Adetifa, Ifedayo, additional, Ihekweazu, Chikwe, additional, Salako, Babatunde L., additional, Tomori, Oyewale, additional, Happi, Anise N., additional, Folarin, Onikepe A., additional, Andersen, Kristian G., additional, Sabeti, Pardis C., additional, and Happi, Christian T., additional

Published
2022
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24. Emergence and Genomic Characterization of Multidrug resistant Candida auris in West Africa

Author

Rita Oladele, Jessica N. Uwanibe, Idowu B. Olawoye, Abdul-Wahab O. Ettu, and Christian T. Happi

Abstract

Candida auris is an emerging multidrug-resistant fungal pathogen that has become a worldwide public health threat due to limitations of treatment options, difficulty in diagnosis, and its potential for clonal transmission. Antifungal suceptibility tests and next generation sequencing were carried out on cultured isolates. Bioinformatics analysis was done using variant calling methods and genome-wide short nucleotide polymorphism (SNP) based phylogeny. Here, we report the first four cases of C. auris infection and colonization reported in West Africa. A total of four isolates from four reported cases of candidemia were analyzed. Three patients had fungaemia, which led to fatal invasive infection and the last patient was a likely case of colonization. Of the four patients, two had mutations which conferred resistance to the antifungal azole group and other non-synonymous mutations in hotspot genes such as ERG2, ERG11 and FKS1. Isolates from these patients clustered to clades I and IV, which indicates more than one introduction of C.auris into Nigeria. The first report of C. auris in Nigeria and West Africa is of public health importance as this report will aid identification, surveillance and intervention of resistant drug resistant candidiasis in the region.

Published
2022
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26. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Author

Tegally, Houriiyah, primary, San, James E., additional, Cotten, Matthew, additional, Tegomoh, Bryan, additional, Mboowa, Gerald, additional, Martin, Darren P., additional, Baxter, Cheryl, additional, Moir, Monika, additional, Lambisia, Arnold, additional, Diallo, Amadou, additional, Amoako, Daniel G., additional, Diagne, Moussa M., additional, Sisay, Abay, additional, Zekri, Abdel-Rahman N., additional, Barakat, Abdelhamid, additional, Gueye, Abdou Salam, additional, Sangare, Abdoul K., additional, Ouedraogo, Abdoul-Salam, additional, Sow, Abdourahmane, additional, Musa, Abdualmoniem O., additional, Sesay, Abdul K., additional, Lagare, Adamou, additional, Kemi, Adedotun-Sulaiman, additional, Abar, Aden Elmi, additional, Johnson, Adeniji A., additional, Fowotade, Adeola, additional, Olubusuyi, Adewumi M., additional, Oluwapelumi, Adeyemi O., additional, Amuri, Adrienne A., additional, Juru, Agnes, additional, Ramadan, Ahmad Mabrouk, additional, Kandeil, Ahmed, additional, Mostafa, Ahmed, additional, Rebai, Ahmed, additional, Sayed, Ahmed, additional, Kazeem, Akano, additional, Balde, Aladje, additional, Christoffels, Alan, additional, Trotter, Alexander J., additional, Campbell, Allan, additional, Keita, Alpha Kabinet, additional, Kone, Amadou, additional, Bouzid, Amal, additional, Souissi, Amal, additional, Agweyu, Ambrose, additional, Gutierrez, Ana V., additional, Page, Andrew J., additional, Yadouleton, Anges, additional, Vinze, Anika, additional, Happi, Anise N., additional, Chouikha, Anissa, additional, Iranzadeh, Arash, additional, Maharaj, Arisha, additional, Batchi-Bouyou, Armel Landry, additional, Ismail, Arshad, additional, Sylverken, Augustina, additional, Goba, Augustine, additional, Femi, Ayoade, additional, Sijuwola, Ayotunde Elijah, additional, Ibrahimi, Azeddine, additional, Marycelin, Baba, additional, Salako, Babatunde Lawal, additional, Oderinde, Bamidele S., additional, Bolajoko, Bankole, additional, Dhaala, Beatrice, additional, Herring, Belinda L., additional, Tsofa, Benjamin, additional, Mvula, Bernard, additional, Njanpop-Lafourcade, Berthe-Marie, additional, Marondera, Blessing T., additional, Khaireh, Bouh Abdi, additional, Kouriba, Bourema, additional, Adu, Bright, additional, Pool, Brigitte, additional, McInnis, Bronwyn, additional, Brook, Cara, additional, Williamson, Carolyn, additional, Anscombe, Catherine, additional, Pratt, Catherine B., additional, Scheepers, Cathrine, additional, Akoua-Koffi, Chantal G., additional, Agoti, Charles N., additional, Loucoubar, Cheikh, additional, Onwuamah, Chika Kingsley, additional, Ihekweazu, Chikwe, additional, Malaka, Christian Noël, additional, Peyrefitte, Christophe, additional, Omoruyi, Chukwuma Ewean, additional, Rafaï, Clotaire Donatien, additional, Morang’a, Collins M., additional, Nokes, D. James, additional, Lule, Daniel Bugembe, additional, Bridges, Daniel J., additional, Mukadi-Bamuleka, Daniel, additional, Park, Danny, additional, Baker, David, additional, Doolabh, Deelan, additional, Ssemwanga, Deogratius, additional, Tshiabuila, Derek, additional, Bassirou, Diarra, additional, Amuzu, Dominic S.Y., additional, Goedhals, Dominique, additional, Grant, Donald S., additional, Omuoyo, Donwilliams O., additional, Maruapula, Dorcas, additional, Wanjohi, Dorcas Waruguru, additional, Foster-Nyarko, Ebenezer, additional, Lusamaki, Eddy K., additional, Simulundu, Edgar, additional, Ong’era, Edidah M., additional, Ngabana, Edith N., additional, Abworo, Edward O., additional, Otieno, Edward, additional, Shumba, Edwin, additional, Barasa, Edwine, additional, Ahmed, El Bara, additional, Kampira, Elizabeth, additional, Fahime, Elmostafa El, additional, Lokilo, Emmanuel, additional, Mukantwari, Enatha, additional, Cyril, Erameh, additional, Philomena, Eromon, additional, Belarbi, Essia, additional, Simon-Loriere, Etienne, additional, Anoh, Etilé A., additional, Leendertz, Fabian, additional, Taweh, Fahn M., additional, Wasfi, Fares, additional, Abdelmoula, Fatma, additional, Takawira, Faustinos T., additional, Derrar, Fawzi, additional, Ajogbasile, Fehintola V, additional, Treurnicht, Florette, additional, Onikepe, Folarin, additional, Ntoumi, Francine, additional, Muyembe, Francisca M., additional, Ngiambudulu, Francisco, additional, Zongo Ragomzingba, Frank Edgard, additional, Dratibi, Fred Athanasius, additional, Iyanu, Fred-Akintunwa, additional, Mbunsu, Gabriel K., additional, Thilliez, Gaetan, additional, Kay, Gemma L., additional, Akpede, George O., additional, George, Uwem E., additional, van Zyl, Gert, additional, Awandare, Gordon A., additional, Schubert, Grit, additional, Maphalala, Gugu P., additional, Ranaivoson, Hafaliana C., additional, Lemriss, Hajar, additional, Omunakwe, Hannah E, additional, Onywera, Harris, additional, Abe, Haruka, additional, Karray, Hela, additional, Nansumba, Hellen, additional, Triki, Henda, additional, Adje Kadjo, Herve Albéric, additional, Elgahzaly, Hesham, additional, Gumbo, Hlanai, additional, mathieu, Hota, additional, Kavunga-Membo, Hugo, additional, Smeti, Ibtihel, additional, Olawoye, Idowu B., additional, Adetifa, Ifedayo, additional, Odia, Ikponmwosa, additional, Boubaker, Ilhem Boutiba-Ben, additional, Ssewanyana, Isaac, additional, Wurie, Isatta, additional, Konstantinus, Iyaloo S, additional, Afiwa Halatoko, Jacqueline Wemboo, additional, Ayei, James, additional, Sonoo, Janaki, additional, Lekana-Douki, Jean Bernard, additional, Makangara, Jean-Claude C., additional, Tamfum, Jean-Jacques M., additional, Heraud, Jean-Michel, additional, Shaffer, Jeffrey G., additional, Giandhari, Jennifer, additional, Musyoki, Jennifer, additional, Uwanibe, Jessica N., additional, Bhiman, Jinal N., additional, Yasuda, Jiro, additional, Morais, Joana, additional, Mends, Joana Q., additional, Kiconco, Jocelyn, additional, Sandi, John Demby, additional, Huddleston, John, additional, Odoom, John Kofi, additional, Morobe, John M., additional, Gyapong, John O., additional, Kayiwa, John T., additional, Okolie, Johnson C., additional, Xavier, Joicymara Santos, additional, Gyamfi, Jones, additional, Kofi Bonney, Joseph Humphrey, additional, Nyandwi, Joseph, additional, Everatt, Josie, additional, Farah, Jouali, additional, Nakaseegu, Joweria, additional, Ngoi, Joyce M., additional, Namulondo, Joyce, additional, Oguzie, Judith U., additional, Andeko, Julia C., additional, Lutwama, Julius J., additional, O’Grady, Justin, additional, Siddle, Katherine J, additional, Victoir, Kathleen, additional, Adeyemi, Kayode T., additional, Tumedi, Kefentse A., additional, Carvalho, Kevin Sanders, additional, Mohammed, Khadija Said, additional, Musonda, Kunda G., additional, Duedu, Kwabena O., additional, Belyamani, Lahcen, additional, Fki-Berrajah, Lamia, additional, Singh, Lavanya, additional, Biscornet, Leon, additional, de Oliveira Martins, Leonardo, additional, Chabuka, Lucious, additional, Olubayo, Luicer, additional, Deng, Lul Lojok, additional, Ochola-Oyier, Lynette Isabella, additional, Mine, Madisa, additional, Ramuth, Magalutcheemee, additional, Mastouri, Maha, additional, ElHefnawi, Mahmoud, additional, Mbanne, Maimouna, additional, Matsheka, Maitshwarelo I., additional, Kebabonye, Malebogo, additional, Diop, Mamadou, additional, Momoh, Mambu, additional, Lima Mendonça, Maria da Luz, additional, Venter, Marietjie, additional, Paye, Marietou F, additional, Faye, Martin, additional, Nyaga, Martin M., additional, Mareka, Mathabo, additional, Damaris, Matoke-Muhia, additional, Mburu, Maureen W., additional, Mpina, Maximillian, additional, Claujens Chastel, Mfoutou Mapanguy, additional, Owusu, Michael, additional, Wiley, Michael R., additional, Tatfeng, Mirabeau Youtchou, additional, Ayekaba, Mitoha Ondo’o, additional, Abouelhoda, Mohamed, additional, Beloufa, Mohamed Amine, additional, Seadawy, Mohamed G, additional, Khalifa, Mohamed K., additional, Dellagi, Mohammed Koussai, additional, Matobo, Mooko Marethabile, additional, Kane, Mouhamed, additional, Ouadghiri, Mouna, additional, Salou, Mounerou, additional, Mbulawa, Mphaphi B., additional, Saibu, Mudashiru Femi, additional, Mwenda, Mulenga, additional, Kaba, Muluken, additional, Phan, My V.T., additional, Abid, Nabil, additional, Touil, Nadia, additional, Rujeni, Nadine, additional, Ismael, Nalia, additional, Top, Ndeye Marieme, additional, Dia, Ndongo, additional, Mabunda, Nédio, additional, Hsiao, Nei-yuan, additional, Silochi, Nelson Boricó, additional, Saasa, Ngonda, additional, Bbosa, Nicholas, additional, Murunga, Nickson, additional, Gumede, Nicksy, additional, Wolter, Nicole, additional, Sitharam, Nikita, additional, Ndodo, Nnaemeka, additional, Ajayi, Nnennaya A., additional, Tordo, Noël, additional, Mbhele, Nokuzola, additional, Razanajatovo, Norosoa H, additional, Iguosadolo, Nosamiefan, additional, Mba, Nwando, additional, Kingsley, Ojide C., additional, Sylvanus, Okogbenin, additional, Peter, Okokhere, additional, Femi, Oladiji, additional, Testimony, Olumade, additional, Ogunsanya, Olusola Akinola, additional, Fakayode, Oluwatosin, additional, Ogah, Onwe E., additional, Faye, Ousmane, additional, Smith-Lawrence, Pamela, additional, Ondoa, Pascale, additional, Combe, Patrice, additional, Nabisubi, Patricia, additional, Semanda, Patrick, additional, Oluniyi, Paul E., additional, Arnaldo, Paulo, additional, Quashie, Peter Kojo, additional, Bejon, Philip, additional, Dussart, Philippe, additional, Bester, Phillip A., additional, Mbala, Placide K., additional, Kaleebu, Pontiano, additional, Abechi, Priscilla, additional, El-Shesheny, Rabeh, additional, Joseph, Rageema, additional, Aziz, Ramy Karam, additional, Essomba, René Ghislain, additional, Ayivor-Djanie, Reuben, additional, Njouom, Richard, additional, Phillips, Richard O., additional, Gorman, Richmond, additional, Kingsley, Robert A., additional, Audu, Rosemary, additional, Carr, Rosina A.A., additional, Kabbaj, Saâd El, additional, Gargouri, Saba, additional, Masmoudi, Saber, additional, Sankhe, Safietou, additional, Mohamed, Sahra Isse, additional, Mhalla, Salma, additional, Hosch, Salome, additional, Kassim, Samar Kamal, additional, Metha, Samar, additional, Trabelsi, Sameh, additional, Lemriss, Sanaâ, additional, Agwa, Sara Hassan, additional, Mwangi, Sarah Wambui, additional, Doumbia, Seydou, additional, Makiala-Mandanda, Sheila, additional, Aryeetey, Sherihane, additional, Ahmed, Shymaa S., additional, Ahmed, Sidi Mohamed, additional, Elhamoumi, Siham, additional, Moyo, Sikhulile, additional, Lutucuta, Silvia, additional, Gaseitsiwe, Simani, additional, Jalloh, Simbirie, additional, Andriamandimby, Soafy, additional, Oguntope, Sobajo, additional, Grayo, Solène, additional, Lekana-Douki, Sonia, additional, Prosolek, Sophie, additional, Ouangraoua, Soumeya, additional, van Wyk, Stephanie, additional, Schaffner, Stephen F., additional, Kanyerezi, Stephen, additional, Ahuka-Mundeke, Steve, additional, Rudder, Steven, additional, Pillay, Sureshnee, additional, Nabadda, Susan, additional, Behillil, Sylvie, additional, Budiaki, Sylvie L., additional, van der Werf, Sylvie, additional, Mashe, Tapfumanei, additional, Aanniz, Tarik, additional, Mohale, Thabo, additional, Le-Viet, Thanh, additional, Velavan, Thirumalaisamy P., additional, Schindler, Tobias, additional, Maponga, Tongai, additional, Bedford, Trevor, additional, Anyaneji, Ugochukwu J., additional, Chinedu, Ugwu, additional, Ramphal, Upasana, additional, Enouf, Vincent, additional, Nene, Vishvanath, additional, Gorova, Vivianne, additional, Roshdy, Wael H., additional, Karim, Wasim Abdul, additional, Ampofo, William K., additional, Preiser, Wolfgang, additional, Choga, Wonderful T., additional, Ahmed, Yahaya Ali, additional, Ramphal, Yajna, additional, Bediako, Yaw, additional, Naidoo, Yeshnee, additional, Butera, Yvan, additional, de Laurent, Zaydah R., additional, Ouma, Ahmed E.O., additional, von Gottberg, Anne, additional, Githinji, George, additional, Moeti, Matshidiso, additional, Tomori, Oyewale, additional, Sabeti, Pardis C., additional, Sall, Amadou A., additional, Oyola, Samuel O., additional, Tebeje, Yenew K., additional, Tessema, Sofonias K., additional, de Oliveira, Tulio, additional, Happi, Christian, additional, Lessells, Richard, additional, Nkengasong, John, additional, and Wilkinson, Eduan, additional

Published
2022
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27. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

Author

Emma J Griffiths, Ruth E Timme, Catarina Inês Mendes, Andrew J Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B Olawoye, Paul E Oluniyi, Dominique Anderson, Alan Christoffels, Anders Gonçalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R Connor, Samuel M Nicholls, Adam A Witney, Gregory H Tyson, Simon H Tausch, Amogelang R Raphenya, Brian Alcock, David M Aanensen, Emma Hodcroft, William W L Hsiao, Ana Tereza R Vasconcelos, and Duncan R MacCannell

Subjects
Metadata, SARS-CoV-2, COVID-19, Humans, Reproducibility of Results, Health Informatics, Genomics, Public Health, Computer Science Applications
Abstract

Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. Results As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Conclusions Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.

Published
2022

28. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

Author

Griffiths, Emma J, primary, Timme, Ruth E, additional, Mendes, Catarina Inês, additional, Page, Andrew J, additional, Alikhan, Nabil-Fareed, additional, Fornika, Dan, additional, Maguire, Finlay, additional, Campos, Josefina, additional, Park, Daniel, additional, Olawoye, Idowu B, additional, Oluniyi, Paul E, additional, Anderson, Dominique, additional, Christoffels, Alan, additional, da Silva, Anders Gonçalves, additional, Cameron, Rhiannon, additional, Dooley, Damion, additional, Katz, Lee S, additional, Black, Allison, additional, Karsch-Mizrachi, Ilene, additional, Barrett, Tanya, additional, Johnston, Anjanette, additional, Connor, Thomas R, additional, Nicholls, Samuel M, additional, Witney, Adam A, additional, Tyson, Gregory H, additional, Tausch, Simon H, additional, Raphenya, Amogelang R, additional, Alcock, Brian, additional, Aanensen, David M, additional, Hodcroft, Emma, additional, Hsiao, William W L, additional, Vasconcelos, Ana Tereza R, additional, and MacCannell, Duncan R, additional

Published
2022
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30. The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response

Author

Botti-Lodovico, Yolanda, primary, Nair, Parvathy, additional, Nosamiefan, Dolo, additional, Stremlau, Matthew, additional, Schaffner, Stephen, additional, Agignoae, Sebastian V., additional, Aiyepada, John Oke, additional, Ajogbasile, Fehintola V., additional, Akpede, George O., additional, Alhasan, Foday, additional, Andersen, Kristian G., additional, Asogun, Danny A., additional, Ayodeji, Oladele Oluwafemi, additional, Badiane, Aida S., additional, Barnes, Kayla, additional, Bauer, Matthew R., additional, Bell-Kareem, Antoinette, additional, Benard, Muoebonam Ekene, additional, Benevolence, Ebo Ohomoime, additional, Blessing, Osiemi, additional, Boehm, Chloe K., additional, Boisen, Matthew L., additional, Bond, Nell G., additional, Branco, Luis M., additional, Butts, Michael J., additional, Carter, Amber, additional, Colubri, Andres, additional, Deme, Awa B., additional, DeRuff, Katherine C., additional, Diédhiou, Younousse, additional, Edamhande, Akhilomen Patience, additional, Elhamoumi, Siham, additional, Engel, Emily J., additional, Eromon, Philomena, additional, Fallah, Mosoka, additional, Folarin, Onikepe A., additional, Fry, Ben, additional, Garry, Robert, additional, Gaye, Amy, additional, Gbakie, Michael, additional, Gevao, Sahr M., additional, Gionet, Gabrielle, additional, Gladden-Young, Adrianne, additional, Goba, Augustine, additional, Gomis, Jules Francois, additional, Happi, Anise N., additional, Houghton, Mary, additional, Ihekwuazu, Chikwe, additional, Iruolagbe, Christopher Ojemiega, additional, Jackson, Jonathan, additional, Jalloh, Simbirie, additional, Johnson, Jeremy, additional, Kanneh, Lansana, additional, Kayode, Adeyemi, additional, Kemball, Molly, additional, Kingsley, Ojide Chiedozie, additional, Koroma, Veronica, additional, Kotliar, Dylan, additional, Mehta, Samar, additional, Metsky, Hayden C., additional, Michael, Airende, additional, Mirhashemi, Marzieh Ezzaty, additional, Modjarrad, Kayvon, additional, Momoh, Mambu, additional, Myhrvold, Cameron A., additional, Naregose, Okonofua Grace, additional, Ndiaye, Tolla, additional, Ndiaye, Mouhamadou, additional, Ndiaye, Aliou, additional, Normandin, Erica, additional, Odia, Ikponmwosa, additional, Oguzie, Judith Uche, additional, Okogbenin, Sylvanus A., additional, Okokhere, Peter O., additional, Okolie, Johnson, additional, Olawoye, Idowu B., additional, Olumade, Testimony J., additional, Oluniyi, Paul E., additional, Omoregie, Omigie, additional, Park, Daniel J., additional, Paye, Mariétou Faye, additional, Petros, Brittany, additional, Philippakis, Anthony A., additional, Priscilla, Abechi, additional, Ricks, Alan, additional, Rimoin, Anne, additional, Sandi, John Demby, additional, Schieffelin, John S., additional, Schreiber, Monica, additional, Seck, Mame Cheikh, additional, Siddiqui, Sameed, additional, Siddle, Katherine, additional, Smither, Allison R., additional, Sy, Mouhamad, additional, Sy, Ngayo, additional, Tomkins-Tinch, Christopher H., additional, Tomori, Oyewale, additional, Ugwu, Chinedu, additional, Uwanibe, Jessica N., additional, Uyigue, Eghosasere Anthonia, additional, Victoria, Dada Ireti, additional, Vinzé, Anika, additional, Vodzak, Megan E., additional, Welch, Nicole, additional, Wurie, Haja Isatta, additional, Zoumarou, Daba, additional, Grant, Donald S., additional, Ndiaye, Daouda, additional, MacInnis, Bronwyn, additional, Sabeti, Pardis C., additional, and Happi, Christian, additional

Published
2021
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32. A simple multi-stable chaotic jerk system with two saddle-foci equilibrium points: analysis, synchronization via active backstepping control and electronic circuit design

Author

Sambas, A, Vaidyanathan, S, Moroz, I, Idowu, B, Mohamed, MA, Mamat, M, and Sanjaya, WSM

Abstract

This paper announces a new three-dimensional chaotic jerk system with two saddle-focus equilibrium points and gives a dynamic analysis of the properties of the jerk system such as Lyapunov exponents, phase portraits, Kaplan-Yorke dimension and equilibrium points. By modifying the Genesio-Tesi jerk dynamics (1992), a new jerk system is derived in this research study. The new jerk model is equipped with multistability and dissipative chaos with two saddle-foci equilibrium points. By invoking backstepping technique, new results for synchronizing chaos between the proposed jerk models are successfully yielded. MultiSim software is used to implement a circuit model for the new jerk dynamics. A good qualitative agreement has been shown between the MATLAB simulations of the theoretical chaotic jerk model and the MultiSIM results.

Published
2020
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33. The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology

Author

Anders Gonçalves da Silva, Emma Griffiths, Ana Tereza Ribeiro de Vasconcelos, Adam A. Witney, Allison Black, Emma B. Hodcroft, Amogelang R. Raphenya, Paul E. Oluniyi, Simon H. Tausch, Finlay Maguire, Thomas R. Connor, Gregory H. Tyson, Samuel M. Nicholls, Ruth Timme, Andrew J. Page, Josefina Campos, Catarina I. Mendes, Duncan MacCannell, Nabil-Fareed Alikhan, Idowu B. Olawoye, Daniel Fornika, Lee S. Katz, Brian Alcock, David M. Aanensen, Alan Christoffels, and William W. L. Hsiao

Subjects
Metadata, medicine.medical_specialty, Contextual design, Geography, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Epidemiology, medicine, other, Genomics, Computational biology
Abstract

The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed an extension to the INSDC pathogen package, providing a SARS-CoV-2 contextual data specification based on harmonisable, publicly available, community standards. The specification is implementable via a collection template, as well as an array of protocols and tools to support the harmonisation and submission of sequence data and contextual information to public repositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19.

Published
2020

34. Gauging the laboratory responses to coronavirus disease (COVID‐19) in Africa

Author

Olakitan Wahab Ogunbanjo, Festus Ayotunde Odeyemi, Jamiu Bello Folorunso, Thompson Akinbolaji, Idowu B. Olawoye, and Ibrahim Ayoade Adekunle

Subjects
2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Public Administration, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 05 social sciences, Academic Papers, Disease, medicine.disease_cause, Geography, Environmental health, 0502 economics and business, Political Science and International Relations, parasitic diseases, medicine, Academic Paper, High incidence, 050207 economics, 050203 business & management, Coronavirus
Abstract

The rampaging effect of coronavirus disease (COVID-19) in Africa is huge and have impacted almost every area of life. Across African states, there exist variations in the laboratory measures adopted, and these heterogeneous approaches, in turn, determines the successes or otherwise recorded. In this study, we assessed the various forms of laboratory responses to the containment, risk analyses, structures and features of COVID-19 in high incidence African countries (Nigeria, South Africa, Egypt, Ghana, Algeria, Morocco, etc.) to aid better and efficient laboratory responses to the highly infectious diseases.

Published
2020

35. The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response

Author

Harvard University--MIT Division of Health Sciences and Technology, Botti-Lodovico, Yolanda, Nair, Parvathy, Nosamiefan, Dolo, Stremlau, Matthew, Schaffner, Stephen, Agignoae, Sebastian V., Aiyepada, John Oke, Ajogbasile, Fehintola V., Akpede, George O., Alhasan, Foday, Andersen, Kristian G., Asogun, Danny A., Ayodeji, Oladele Oluwafemi, Badiane, Aida S., Barnes, Kayla, Bauer, Matthew R., Bell-Kareem, Antoinette, Benard, Muoebonam Ekene, Benevolence, Ebo Ohomoime, Blessing, Osiemi, Boehm, Chloe K., Boisen, Matthew L., Bond, Nell G., Branco, Luis M., Butts, Michael J., Carter, Amber, Colubri, Andres, Deme, Awa B., DeRuff, Katherine C., Diédhiou, Younousse, Edamhande, Akhilomen Patience, Elhamoumi, Siham, Engel, Emily J., Eromon, Philomena, Fallah, Mosoka, Folarin, Onikepe A., Fry, Ben, Garry, Robert, Gaye, Amy, Gbakie, Michael, Gevao, Sahr M., Gionet, Gabrielle, Gladden-Young, Adrianne, Goba, Augustine, Gomis, Jules Francois, Happi, Anise N., Houghton, Mary, Ihekwuazu, Chikwe, Iruolagbe, Christopher Ojemiega, Jackson, Jonathan, Jalloh, Simbirie, Johnson, Jeremy, Kanneh, Lansana, Kayode, Adeyemi, Kemball, Molly, Kingsley, Ojide Chiedozie, Koroma, Veronica, Kotliar, Dylan, Mehta, Samar, Metsky, Hayden C., Michael, Airende, Mirhashemi, Marzieh Ezzaty, Modjarrad, Kayvon, Momoh, Mambu, Myhrvold, Cameron A., Naregose, Okonofua Grace, Ndiaye, Tolla, Ndiaye, Mouhamadou, Ndiaye, Aliou, Normandin, Erica, Odia, Ikponmwosa, Oguzie, Judith Uche, Okogbenin, Sylvanus A., Okokhere, Peter O., Okolie, Johnson, Olawoye, Idowu B., Olumade, Testimony J., Oluniyi, Paul E., Omoregie, Omigie, Park, Daniel J., Paye, Mariétou Faye, Petros, Brittany A., Philippakis, Anthony A., Priscilla, Abechi, Ricks, Alan, Rimoin, Anne, Sandi, John Demby, Schieffelin, John S., Schreiber, Monica, Seck, Mame Cheikh, Siddiqui, Sameed, Siddle, Katherine, Smither, Allison R., Sy, Mouhamad, Sy, Ngayo, Tomkins-Tinch, Christopher H., Tomori, Oyewale, Ugwu, Chinedu, Uwanibe, Jessica N., Uyigue, Eghosasere Anthonia, Victoria, Dada Ireti, Vinzé, Anika, Vodzak, Megan E., Welch, Nicole, Wurie, Haja Isatta, Zoumarou, Daba, Grant, Donald S., Ndiaye, Daouda, MacInnis, Bronwyn, Sabeti, Pardis C., Happi, Christian, Harvard University--MIT Division of Health Sciences and Technology, Botti-Lodovico, Yolanda, Nair, Parvathy, Nosamiefan, Dolo, Stremlau, Matthew, Schaffner, Stephen, Agignoae, Sebastian V., Aiyepada, John Oke, Ajogbasile, Fehintola V., Akpede, George O., Alhasan, Foday, Andersen, Kristian G., Asogun, Danny A., Ayodeji, Oladele Oluwafemi, Badiane, Aida S., Barnes, Kayla, Bauer, Matthew R., Bell-Kareem, Antoinette, Benard, Muoebonam Ekene, Benevolence, Ebo Ohomoime, Blessing, Osiemi, Boehm, Chloe K., Boisen, Matthew L., Bond, Nell G., Branco, Luis M., Butts, Michael J., Carter, Amber, Colubri, Andres, Deme, Awa B., DeRuff, Katherine C., Diédhiou, Younousse, Edamhande, Akhilomen Patience, Elhamoumi, Siham, Engel, Emily J., Eromon, Philomena, Fallah, Mosoka, Folarin, Onikepe A., Fry, Ben, Garry, Robert, Gaye, Amy, Gbakie, Michael, Gevao, Sahr M., Gionet, Gabrielle, Gladden-Young, Adrianne, Goba, Augustine, Gomis, Jules Francois, Happi, Anise N., Houghton, Mary, Ihekwuazu, Chikwe, Iruolagbe, Christopher Ojemiega, Jackson, Jonathan, Jalloh, Simbirie, Johnson, Jeremy, Kanneh, Lansana, Kayode, Adeyemi, Kemball, Molly, Kingsley, Ojide Chiedozie, Koroma, Veronica, Kotliar, Dylan, Mehta, Samar, Metsky, Hayden C., Michael, Airende, Mirhashemi, Marzieh Ezzaty, Modjarrad, Kayvon, Momoh, Mambu, Myhrvold, Cameron A., Naregose, Okonofua Grace, Ndiaye, Tolla, Ndiaye, Mouhamadou, Ndiaye, Aliou, Normandin, Erica, Odia, Ikponmwosa, Oguzie, Judith Uche, Okogbenin, Sylvanus A., Okokhere, Peter O., Okolie, Johnson, Olawoye, Idowu B., Olumade, Testimony J., Oluniyi, Paul E., Omoregie, Omigie, Park, Daniel J., Paye, Mariétou Faye, Petros, Brittany A., Philippakis, Anthony A., Priscilla, Abechi, Ricks, Alan, Rimoin, Anne, Sandi, John Demby, Schieffelin, John S., Schreiber, Monica, Seck, Mame Cheikh, Siddiqui, Sameed, Siddle, Katherine, Smither, Allison R., Sy, Mouhamad, Sy, Ngayo, Tomkins-Tinch, Christopher H., Tomori, Oyewale, Ugwu, Chinedu, Uwanibe, Jessica N., Uyigue, Eghosasere Anthonia, Victoria, Dada Ireti, Vinzé, Anika, Vodzak, Megan E., Welch, Nicole, Wurie, Haja Isatta, Zoumarou, Daba, Grant, Donald S., Ndiaye, Daouda, MacInnis, Bronwyn, Sabeti, Pardis C., and Happi, Christian

Abstract

While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE—detected in the Yoruba population of Nigeria—conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the “emerging” nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz’s critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts.

Published
2021

39. The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology

Author

Griffiths, Emma J., primary, Timme, Ruth E., additional, Page, Andrew J., additional, Alikhan, Nabil-Fareed, additional, Fornika, Dan, additional, Maguire, Finlay, additional, Mendes, Catarina Inês, additional, Tausch, Simon H., additional, Black, Allison, additional, Connor, Thomas R., additional, Tyson, Gregory H., additional, Aanensen, David M., additional, Alcock, Brian, additional, Campos, Josefina, additional, Christoffels, Alan, additional, Gonçalves da Silva, Anders, additional, Hodcroft, Emma, additional, Hsiao, William W.L., additional, Katz, Lee S., additional, Nicholls, Samuel M., additional, Oluniyi, Paul E., additional, Olawoye, Idowu B., additional, Raphenya, Amogelang R., additional, Vasconcelos, Ana Tereza R., additional, Witney, Adam A., additional, and MacCannell, Duncan R., additional

Published
2020
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40. Pan-genome analysis of Mycobacterium africanum: insights to dynamics and evolution

Author

Simon D. W. Frost, Idowu B. Olawoye, and Christian T. Happi

Subjects
0303 health sciences, biology, 030306 microbiology, Multiple copy, Strain (biology), Lineage (evolution), Pan-genome, biology.organism_classification, Genome, 03 medical and health sciences, Mycobacterium tuberculosis complex, Evolutionary biology, Gene, Mycobacterium africanum, 030304 developmental biology
Abstract

Background: Mycobacterium tuberculosis complex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.We tested the hypothesis that M. africanum West African 2 (lineage 6) might have emigrated out of West Africa but was outcompeted by more virulent modern strains of M. tuberculosis (MTB).Whole genome sequences of M. tuberculosis from Nigeria (n=21), South Africa (n=24) and M. africanum West African 2 from Mali (n=22) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. Results: The outcome of this analysis shows that Lineages 2, 4 and 6 all have a close pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.Conclusions: The findings in this study provides a perspective to one of the hypotheses that M. africanum West African 2 might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.

Published
2020
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41. Gauging the laboratory responses to coronavirus disease (Covid-19) in Africa

Author

Odeyemi, Festus A., Adekunle, Ibrahim A., Ogunbanjo, Olakitan W., Folorunso, Jamiu B., Akinbolaji, Thompson, and Olawoye, Idowu B.

Subjects
PCR, Sample Pooling, Laboratory responses, parasitic diseases, Africa, ddc:330, COVID-19
Abstract

The rampaging effect of coronavirus disease (COVID-19) in Africa is huge and have impacted almost every area of life. Across African states, there exist variations in the laboratory measures adopted, and these heterogeneous approaches, in turn, determines the successes or otherwise recorded. In this study, we assessed the various forms of laboratory responses to the containment, risk analyses, structures and features of COVID-19 in high incidence African countries (Nigeria, South Africa, Egypt, Ghana, Algeria, Morocco, etc.) to aid better and efficient laboratory responses to the highly infectious diseases.

Published
2020

48. Shortened versus standard post-partum maintenance therapy of magnesium sulphate in severe pre-eclampsia: a randomised control trial

Author

Chibuzor P. Oriji, Idowu B. Orisabinone, Uche Onwudiegwu, Olakunle I. Makinde, and Adebanjo B. Adeyemi

Subjects
medicine.medical_specialty, Eclampsia, Maintenance therapy, chemistry, Obstetrics, Magnesium, business.industry, fungi, medicine, chemistry.chemical_element, medicine.disease, business, Post partum
Abstract

Background: Pre-eclampsia is a pregnancy-associated multi-organ disorder caused by altered trophoblastic invasion and endothelial cell dysfunction. It is associated with significant maternal and perinatal morbidity and mortality, especially in developing countries. Magnesium sulphate (MgSO4) is effective in the management of severe pre-eclampsia/eclampsia. Objective of this study was to compare the effectiveness of a shortened course of MgSO4 to the Pritchard regimen in patients with severe pre-eclampsiaMethods: This study was carried out at the obstetrics and gynecology department of the Obafemi Awolowo University Teaching Hospital, Ile-Ife. It was a randomised control study of 116 patients, 58 in each group. Group A received the standard Pritchard regimen: a loading dose of MgSO4 4g slow IV bolus plus 10 g IM (5 g in each buttock), followed by maintenance dose of 5g MgSO4 IM 4-hourly into alternate buttocks until 24 hours after delivery. Group B received same loading dose, but the maintenance dose was limited to three doses of 5g MgSO4 IM four hours apart after delivery. In both regimens, 2g MgSO4 was given IV for breakthrough fit. Data were analyzed using SPSS version 20.Results: This study revealed that twelve-hour postpartum MgSO4 was as effective as the Pritchard regime with no statistically difference in occurrence of seizures (X2 = 0.341, df = 1, p = 0.514). The average total dose of magnesium sulphate used was lower in the study Group B.Conclusions: Twelve-hour postpartum MgSO4 is as effective as the standard 24-hour Pritchard regime.

Published
2020
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49. The use of NAAT- PCR to determine asymptomatic chlamydia and gonorrhoea infections in infertile patients undergoing hysterosalpingogram at the federal medical centre, Yenagoa, South-South Nigeria

Author

Dennis O. Allagoa, Idowu B. Orisabinone, Kelvin E. Kiridi, Olakunle I. Makinde, James Omietimi, Chibuzor P. Oriji, and Chidiebere Njoku

Subjects
medicine.medical_specialty, Chlamydia, Obstetrics, business.industry, medicine, medicine.symptom, medicine.disease, business, Asymptomatic, female genital diseases and pregnancy complications
Abstract

Background: The roles of Chlamydia trachomatis and Neisseria gonorrhoeae in the aetiology of infertility due to tubal occlusion have been established by various studies. These organisms may lead to pelvic infection by ascending into the upper genital tract through any instrumentation like hysterosalpingography. The objectives were to determine the prevalence of asymptomatic chlamydial and gonorrhoeal infections of the genital tract among women being investigated for infertility referred for hysterosalpingography; the relationship of these infections with tubal pathologies; and if routine endo-cervical screening and prophylactic antibiotics be recommended for these patients.Methods: This was a descriptive cross-sectional study. The study population consisted of consecutive 220 infertile women that met the inclusion criteria for this study. Consent was obtained. Endo-cervical swab was taken for NAAT-PCR for Chlamydia trachomatis and Neisseria gonorrhoeae. Hysterosalpingography was carried out. Data was analyzed using SPSS (version 22).Results: Amongst the 220 women, 9 (4.1%) had asymptomatic chlamydia infection. None had gonorrhoea infection and 211 (95.9%) had none of these two organisms. Forty-eight (21.9%) of the 220 women had bilateral tubal blockage and 9 (18.8%) out of these 48 women had asymptomatic infection with Chlamydia trachomatis.Conclusions: There is a statistically significant association between tubal blockage and chlamydia infection (p = 0.00) [RR 4.31 (3.37-5.50)]. There was no evidence to recommend routine screening/antibiotics considering the low prevalence of microbes and the absence of post-HSG pelvic infection. Results from a multicenter randomized controlled trial will be more representative.

Published
2020
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