Explanipedia

Genomic diversity and surveillance of SARS-CoV-2 in Nigeria Open

Thomas J. Y. Kono, Ezenwa James Onyemata, Natalia Blanco, Chika Onwuamah, Nnaemeka Ndodo , et al. · 2025

The findings suggest the need for a coordinated sequencing strategy and standardized protocols to improve genomic surveillance during future outbreaks of existing and novel pathogens. A network of sequencing laboratories that includes at l…

Genomic investigation reveals long-term local and regional circulation of dengue virus associated with recent outbreaks in Kenya Open

Solomon Langat, Sheila Kageha, Victor Tunje Jeza, Genay Pilarowski, Albert Nyunja , et al. · 2025

Dengue is an arbovirus disease caused by dengue virus. The virus has recently caused a global surge in cases, with Africa reporting over 250 million and 900 deaths since 2023. This study was conducted during the 2023 dengue outbreak in Mom…

Complete genome of an mpox clade 1b virus from Kenya Open

Solomon Langat, Gathii Kimita, Samson Konongoi, Abdi Roba, Millicent Ndia , et al. · 2025

We report the genome of a case of mpox detected in Kenya involving a truck driver with travel history to Uganda. Whole genome sequencing and phylogenetic analysis of the mpox virus (MPXV) showed that the genome clustered with clade Ib, whi…

Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619 Open

Nena Bollen, Samuel L. Hong, Barney Potter, Reto Lienhard, Marie-Lise Tritten , et al. · 2025

Since late 2020, the emergence of variants of concern (VOCs) of SARS-CoV-2 has been of concern to public health, researchers and policymakers. Mutations in the SARS-CoV-2 genome—for which clear evidence is available indicating a significan…

Genomic sequence analysis of the first mpox virus detected in Kenya Open

Solomon Langat, Samson Konongoi, Samoel Khamadi, Albert Nyunja, Genay Pilarowski , et al. · 2024

Mpox is a zoonotic disease caused by the Monkeypox virus (MPXV) in the family: Poxviridae, genus: Orthopoxvirus. Historically, the disease was restricted mostly to Africa with cases being reported in Central Africa (mostly caused by clade …

PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training Open

Emma Griffiths, Catarina Inês Mendes, Finlay Maguire, Jennifer L. Guthrie, Bryan A. Wee , et al. · 2024

As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achiev…

hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling Open

Catarina Inês Mendes, Emma Griffiths, Alex Manuele, Daniel Fornika, Simon H. Tausch , et al. · 2024

The detection of antimicrobial resistance (AMR) markers directly from genomic or metagenomic data is becoming a standard clinical and public health procedure. This has resulted in the development of a number of different bioinformatic AMR …

Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications Open

Ruth Timme, Ilene Karsch‐Mizrachi, Zahra Waheed, Masanori Arita, Duncan MacCannell , et al. · 2023

Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collabora…

Data science training needs in sub-Saharan Africa: Implications for biomedical research and therapeutics capacity Open

Modupe O. Coker, Olayinka Kotila, Taiwo Adigun, Temitayo Victor Lawal, Adeniyi Francis Fagbamigbe , et al. · 2023

Data use is becoming increasingly valuable worldwide and has positively improved decision-making in various sectors. Data science has revolutionized the study of epidemiology and disease control. Despite the unlimited potential of data sci…

Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications Open

Ruth Timme, Ilene Karsch‐Mizrachi, Zahra Waheed, arita nig.ac.jp, Duncan MacCannell , et al. · 2023

Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collabora…

Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications Open

Ruth Timme, Ilene Karsch‐Mizrachi, Zahra Waheed, arita nig.ac.jp, Duncan MacCannell , et al. · 2023

Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collabora…

Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria Open

Judith U. Oguzie, Brittany A. Petros, Paul E. Oluniyi, Samar Mehta, Philomena Eromon , et al. · 2023

The Prevalence of Undiagnosed Salmonella enterica Serovar Typhi in Healthy School-Aged Children in Osun State, Nigeria Open

Jessica N. Uwanibe, Adeyemi T. Kayode, Paul E. Oluniyi, Kazeem Akano, Idowu B. Olawoye , et al. · 2023

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 Ni…

Adeno-associated virus type 2 in US children with acute severe hepatitis Open

Venice Servellita, Alicia Sotomayor-González, Daryl M. Lamson, Abiodun Foresythe, Hee Jae Huh , et al. · 2023

PHA4GE Quality Control Contextual Data Tags: Standardized Annotations for Sharing Public Health Sequence Datasets with Known Quality Issues to Facilitate Testing and Training Open

Emma Griffiths, Catarina Inês Mendes, Finlay Maguire, Jennifer L. Guthrie, Leonid Chindelevitch , et al. · 2023

As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achiev…

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

Idowu B. Olawoye, Paul E. Oluniyi, Judith U. Oguzie, Jessica N. Uwanibe, Adeyemi T. Kayode , et al. · 2023

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…

Humoral and cellular immune responses to Lassa fever virus in Lassa fever survivors and their exposed contacts in Southern Nigeria Open

Chinedu Ugwu, Testimony Olumade, Ebenezer Nwakpakpa, Venatius Onyia, Elizabeth Odeh , et al. · 2022

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

Idowu B. Olawoye, Paul E. Oluniyi, Judith U. Oguzie, Jessica N. Uwanibe, Adeyemi T. Kayode , et al. · 2022

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…

Adeno-associated virus type 2 in children from the United States with acute severe hepatitis Open

Venice Servellita, Alicia Sotomayor-González, Daryl M. Lamson, Abiodun Foresythe, Hee Jae Huh , et al. · 2022

As of August 2022, cases of acute severe hepatitis of unknown etiology in children have been reported from 35 countries, including the United States. Here we used PCR testing, viral enrichment based sequencing, and agnostic metagenomic seq…

Metagenomic sequencing characterizes a wide diversity of viruses in field mosquito samples in Nigeria Open

Judith U. Oguzie, Udoka C. Nwangwu, Paul E. Oluniyi, Testimony Olumade, Uwem E. George , et al. · 2022

Molecular profiling of the artemisinin resistance Kelch 13 gene in Plasmodium falciparum from Nigeria Open

Fehintola V. Ajogbasile, Paul E. Oluniyi, Adeyemi T. Kayode, Kazeem Akano, Benjamin Adegboyega , et al. · 2022

Accurate assessment and monitoring of the Plasmodium falciparum Kelch 13 ( pfk13) gene associated with artemisinin resistance is critical to understand the emergence and spread of drug-resistant parasites in malaria-endemic regions. In thi…

PHA4GE: Improving the structure of pathogen genomics data for effective public health action Open

Allison Black, Leonid Chindelevitch, Bede Constantinides, Carla Cummins, Timothy J. Dallman , et al. · 2022

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

Emma Griffiths, Ruth Timme, Catarina Inês Mendes, Andrew J. Page, Nabil-Fareed Alikhan , et al. · 2022

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 cr…

Metagenomic Sequencing Characterizes a Wide Diversity of Viruses in Field Mosquito Samples in Nigeria Open

Judith U. Oguzie, Udoka C. Nwangwu, Paul E. Oluniyi, Testimony Olumade, Uwem E. George , et al. · 2021

Mosquito vectors are a tremendous public health threat as one in six diseases worldwide is vector-borne transmitted mainly by mosquitoes. In the last couple of years, there have been active Yellow fever virus (YFV) outbreaks in many settin…

HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria Open

Paul E. Oluniyi, Fehintola V. Ajogbasile, Shuntai Zhou, Iyanuoluwa Fred-Akintunwa, Christina S. Polyak , et al. · 2021

Objective: This study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country. Methods: We used an advanced ne…

VGEA: an RNA viral assembly toolkit Open

Paul E. Oluniyi, Fehintola V. Ajogbasile, Judith U. Oguzie, Jessica N. Uwanibe, Adeyemi T. Kayode , et al. · 2021

Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiolo…

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

Yolanda Botti-Lodovico, Parvathy Nair, Dolo Nosamiefan, Matthew Stremlau, S. F. Schaffner , et al. · 2021

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 …

Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa Open

Anise N. Happi, Olusola Ogunsanya, Judith U. Oguzie, Paul E. Oluniyi, Alhaji Olono , et al. · 2021

Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbi…

Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis Open

Fehintola V. Ajogbasile, Adeyemi T. Kayode, Paul E. Oluniyi, Kazeem Akano, Jessica N. Uwanibe , et al. · 2021

A rare case of equine Haemotropic Mycoplasma infection in Nigeria Open

Anise N. Happi, Paul E. Oluniyi · 2021

Equine haemotropic mycoplasmosis (EHM) is a condition rarely reported worldwide. A horse presented with unspecific clinical findings and non-response to treatment to the common and endemic haemoparasitic and bacterial infections, warranted…

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