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Phylogenetic and genome-wide mutational analysis of SARS-CoV-2 strains circulating in Nigeria: no implications for attenuated COVID-19 outcomes
Daniel B. Kolawole, Malachy I. Okeke
Osong Public Health Res Perspect. 2022;13(2):101-113.   Published online April 22, 2022
DOI: https://doi.org/10.24171/j.phrp.2021.0329
  • 1,798 View
  • 52 Download
Graphical AbstractGraphical Abstract AbstractAbstract PDF
Objectives
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The COVID-19 incidence and mortality rates are low in Nigeria compared to global trends. This research mapped the evolution of SARS-CoV-2 circulating in Nigeria and globally to determine whether the Nigerian isolates are genetically distinct from strains circulating in regions of the world with a high disease burden. Methods: Bayesian phylogenetics using BEAST 2.0, genetic similarity analyses, and genomewide mutational analyses were used to characterize the strains of SARS-CoV-2 isolated in Nigeria. Results: SARS-CoV-2 strains isolated in Nigeria showed multiple lineages and possible introductions from Europe and Asia. Phylogenetic clustering and sequence similarity analyses demonstrated that Nigerian isolates were not genetically distinct from strains isolated in other parts of the globe. Mutational analysis demonstrated that the D614G mutation in the spike protein, the P323L mutation in open reading frame 1b (and more specifically in NSP12), and the R203K/ G204R mutation pair in the nucleocapsid protein were most prevalent in the Nigerian isolates. Conclusion: The SARS-CoV-2 strains in Nigeria were neither phylogenetically nor genetically distinct from virus strains circulating in other countries of the world. Thus, differences in SARS-CoV-2 genomes are not a plausible explanation for the attenuated COVID-19 outcomes in Nigeria.
Perceptions of the COVID-19 vaccine and willingness to receive vaccination among health workers in Nigeria
Oluseyi Ademola Adejumo, Olorunfemi Akinbode Ogundele, Cynthia Roli Madubuko, Rosena Olubanke Oluwafemi, Ogochukwu Chinedum Okoye, Kenechukwu Chukwuemeka Okonkwo, Sunday Samson Owolade, Oladimeji Adedeji Junaid, Olutoyin Morenike Lawal, Adenike Christianah Enikuomehin, Maureen Iru Ntaji, Aisha Sokunbi, Aina Omodele Timothy, Olatunji Sunday Abolarin, Emmanuel Olalekan Ali, John Oghenevwirhe Ohaju-Obodo
Osong Public Health Res Perspect. 2021;12(4):236-243.   Published online July 19, 2021
DOI: https://doi.org/10.24171/j.phrp.2021.0023
  • 7,231 View
  • 402 Download
  • 21 Citations
Graphical AbstractGraphical Abstract AbstractAbstract PDF
Objectives
The study aimed to examine health workers’ perceptions of the coronavirus disease 2019 (COVID-19) vaccine in Nigeria and their willingness to receive the vaccine when it becomes available.
Methods
This multi-center cross-sectional study used non-probability convenience sampling to enroll 1,470 hospital workers aged 18 and above from 4 specialized hospitals. A structured and validated self-administered questionnaire was used for data collection. Data entry and analysis were conducted using IBM SPSS ver. 22.0.
Results
The mean age of respondents was 40±6 years. Only 53.5% of the health workers had positive perceptions of the COVID-19 vaccine, and only slightly more than half (55.5%) were willing to receive vaccination. Predictors of willingness to receive the COVID-19 vaccine included having a positive perception of the vaccine (adjusted odds ratio [AOR], 4.55; 95% confidence interval [CI], 3.50−5.69), perceiving a risk of contracting COVID-19 (AOR, 1.50; 95% CI, 1.25–3.98), having received tertiary education (AOR, 3.50; 95% CI, 1.40−6.86), and being a clinical health worker (AOR, 1.25; 95% CI, 1.01−1.68).
Conclusion
Perceptions of the COVID-19 vaccine and willingness to receive the vaccine were sub-optimal among this group. Educational interventions to improve health workers' perceptions and attitudes toward the COVID-19 vaccine are needed.

Citations

Citations to this article as recorded by  
  • ‘Why Should I Take the COVID-19 Vaccine after Recovering from the Disease?’ A Mixed-methods Study of Correlates of COVID-19 Vaccine Acceptability among Health Workers in Northern Nigeria
    Zubairu Iliyasu, Muhammad R. Garba, Auwalu U. Gajida, Taiwo G. Amole, Amina A. Umar, Hadiza M. Abdullahi, Aminatu A. Kwaku, Hamisu M. Salihu, Muktar H. Aliyu
    Pathogens and Global Health.2022; 116(4): 254.     CrossRef
  • Suspecting the Figures: What Church Leaders Think About Government’s Commitment to Combating COVID-19 in Nigeria
    Uchechukwu M. Agbo, George C. Nche
    Journal of Asian and African Studies.2022; : 002190962110696.     CrossRef
  • A Global Map of COVID-19 Vaccine Acceptance Rates per Country: An Updated Concise Narrative Review
    Malik Sallam, Mariam Al-Sanafi, Mohammed Sallam
    Journal of Multidisciplinary Healthcare.2022; Volume 15: 21.     CrossRef
  • Knowledge, Attitudes, and Perception towards COVID-19 Vaccination among the Adult Population: A Cross-Sectional Study in Turkey
    Meliha Cagla Sonmezer, Taha Koray Sahin, Enes Erul, Furkan Sacit Ceylan, Muhammed Yusuf Hamurcu, Nihal Morova, Ipek Rudvan Al, Serhat Unal
    Vaccines.2022; 10(2): 278.     CrossRef
  • Factors influencing COVID-19 vaccine uptake among adults in Nigeria
    Halimat Adedeji-Adenola, Olubusola A. Olugbake, Shakirat A. Adeosun, Ismaeel Yunusa
    PLOS ONE.2022; 17(2): e0264371.     CrossRef
  • Perception and Prevention Practices Relating to Covid 19 Infection Among Elderly in Ogun State, Nigeria
    Adenitire G., Agbede C.O.
    International Journal of Public Health and Pharmac.2022; 2(1): 29.     CrossRef
  • Predicting nursing students' intention to attend face‐to‐face classes on school reopening: A theory of planned behavior application
    Ryan Michael F. Oducado, Jerome V. Cleofas, Gil P. Soriano
    Nursing Forum.2022; 57(5): 733.     CrossRef
  • COVID-19 vaccination in Nigeria: A rapid review of vaccine acceptance rate and the associated factors
    Oluwatosin Olu-Abiodun, Olumide Abiodun, Ngozi Okafor, Nusirat Elelu
    PLOS ONE.2022; 17(5): e0267691.     CrossRef
  • COVID-19 vaccine acceptance among health care workers in Africa: A systematic review and meta-analysis
    Martin Ackah, Louise Ameyaw, Mohammed Gazali Salifu, Delali Pearl Afi Asubonteng, Cynthia Osei Yeboah, Eugene Narkotey Annor, Eunice Abena Kwartemaa Ankapong, Hosea Boakye, Muhammad Shahzad Aslam
    PLOS ONE.2022; 17(5): e0268711.     CrossRef
  • A national survey of COVID-19 vaccine acceptance in Nigeria
    Ahmad Ibrahim Al-Mustapha, Ochulor Okechukwu, Ademola Olayinka, Oyeniyi Rasheed Muhammed, Muftau Oyewo, Samuel A. Owoicho, Ahmed Tijani Abubakar, Abdulsalam Olabisi, Aliyu Jibril, Simon Ereh, Oluwatosin Enoch Fakayode, Oluwaseun Adeolu Ogundijo, Nusirat E
    Vaccine.2022; 40(33): 4726.     CrossRef
  • Access to COVID-19 vaccines and testing in Africa: the importance of COVAX - Nigeria as a case study
    Rafaella Fortini Queiroz Grenfell, Oyetunde Timothy Oyeyemi
    Pathogens and Global Health.2022; : 1.     CrossRef
  • COVID-19 vaccine hesitancy in Africa: a scoping review
    Betty B. B. Ackah, Michael Woo, Lisa Stallwood, Zahra A. Fazal, Arnold Okpani, Ugochinyere Vivian Ukah, Prince A. Adu
    Global Health Research and Policy.2022;[Epub]     CrossRef
  • COVID-19 Vaccine Acceptance and Associated Factors Among College Students in Dessie City, Northeastern Ethiopia
    Gete Berihun, Zebader Walle, Daniel Teshome, Leykun Berhanu, Mohammed Derso
    Journal of Multidisciplinary Healthcare.2022; Volume 15: 1735.     CrossRef
  • Career Aspiration Fulfillment and COVID-19 Vaccination Intention among Nigerian Youth: An Instrumental Variable Approach
    Abayomi Samuel Oyekale
    International Journal of Environmental Research an.2022; 19(16): 9813.     CrossRef
  • COVID-19 Vaccine Attitude and Its Predictors Among People Living With Chronic Health Conditions in Ibadan, Nigeria
    Lucia Yetunde Ojewale, Rotimi Felix Afolabi, Adesola Ogunniyi
    International Journal of Public Health.2022;[Epub]     CrossRef
  • Associations between COVID-19 vaccine hesitancy and the experience of violence among women and girls living with and at risk of HIV in Nigeria
    Morenike Oluwatoyin Folayan, Olujide Arije, Amaka Enemo, Aaron Sunday, Amira Muhammad, Hasiya Yunusa Nyako, Rilwan Mohammed Abdullah, Henry Okiwu, Erik Lamontagne
    African Journal of AIDS Research.2022; 21(4): 306.     CrossRef
  • Willingness to receive COVID-19 vaccine: A survey among medical radiation workers in Nigeria
    Grace Ben Inah, Samuel Archibong Efanga, Ekaete Vincent Ukpong, Christiana Ifeyinwa Obiora
    Calabar Journal of Health Sciences.2022; 6: 80.     CrossRef
  • Acceptance of COVID-19 vaccine among healthcare workers in Africa, systematic review and meta-analysis
    Zerihun Figa, Tesfaye Temesgen, Addisu Getnet Zemeskel, Moges Ganta, Asrat Alemu, Mesfin Abebe, Zemachu Ashuro
    Public Health in Practice.2022; 4: 100343.     CrossRef
  • Perception and willingness to accept COVID-19 Vaccines: A cross-sectional survey of the general population of Sokoto State, Nigeria
    Oche Mansur Oche, Habibullah Adamu, Musa Yahaya, Hudu Garba Illo, Abdulaziz Mohammad Danmadami, Adamu Ijapa, Asmau Mohammad Wali, Hamza Yusuf, Hafsat Muhammad, Abba Aji, Harapan Harapan
    PLOS ONE.2022; 17(12): e0278332.     CrossRef
  • COVID-19 vaccination acceptance among community members and health workers in Ebonyi state, Nigeria: study protocol for a concurrent-independent mixed method analyses of intention to receive, timeliness of the intention to receive, uptake and hesitancy to
    Ugwu I Omale, Osarhiemen Iyare, Richard L Ewah, Chidinma I Amuzie, Onyinyechukwu U Oka, Victor U Uduma, Azuka S Adeke, Cordis O Ikegwuonu, Olaedo O Nnachi, Okechukwu O Ukpabi, Ifeyinwa M Okeke, Glory E Nkwo, Ugochi IA Nwali
    BMJ Open.2022; 12(12): e061732.     CrossRef
  • Drivers of COVID-19 Vaccine Uptake amongst Healthcare Workers (HCWs) in Nigeria
    Sohail Agha, Adaobi Chine, Mathias Lalika, Samikshya Pandey, Aparna Seth, Alison Wiyeh, Alyssa Seng, Nandan Rao, Akhtar Badshah
    Vaccines.2021; 9(10): 1162.     CrossRef
Modeling the Spread of Ebola
Tae Sug Do, Young S. Lee
Osong Public Health Res Perspect. 2016;7(1):43-48.   Published online February 28, 2016
DOI: https://doi.org/10.1016/j.phrp.2015.12.012
  • 2,116 View
  • 17 Download
  • 13 Citations
AbstractAbstract PDF
Objectives
This study aims to create a mathematical model to better understand the spread of Ebola, the mathematical dynamics of the disease, and preventative behaviors.
Methods
An epidemiological model is created with a system of nonlinear differential equations, and the model examines the disease transmission dynamics with isolation through stability analysis. All parameters are approximated, and results are also exploited by simulations. Sensitivity analysis is used to discuss the effect of intervention strategies.
Results
The system has only one equilibrium point, which is the disease-free state (S,L,I,R,D) = (N,0,0,0,0). If traditional burials of Ebola victims are allowed, the possible end state is never stable. Provided that safe burial practices with no traditional rituals are followed, the endemic-free state is stable if the basic reproductive number, R0, is less than 1. Model behaviors correspond to empirical facts. The model simulation agrees with the data of the Nigeria outbreak in 2004: 12 recoveries, eight deaths, Ebola free in about 3 months, and an R0 value of about 2.6 initially, which signifies swift spread of the infection. The best way to reduce R0 is achieving the speedy net effect of intervention strategies. One day's delay in full compliance with building rings around the virus with isolation, close observation, and clear education may double the number of infected cases.
Conclusion
The model can predict the total number of infected cases, number of deaths, and duration of outbreaks among others. The model can be used to better understand the spread of Ebola, educate about prophylactic behaviors, and develop strategies that alter environment to achieve a disease-free state. A future work is to incorporate vaccination in the model when the vaccines are developed and the effects of vaccines are known better.

Citations

Citations to this article as recorded by  
  • Mathematical Models for Typhoid Disease Transmission: A Systematic Literature Review
    Sanubari Tansah Tresna, Subiyanto, Sudradjat Supian
    Mathematics.2022; 10(14): 2506.     CrossRef
  • Fractional COVID-19 Modeling and Analysis on Successive Optimal Control Policies
    Mohammed Subhi Hadi, Bülent Bilgehan
    Fractal and Fractional.2022; 6(10): 533.     CrossRef
  • Analysis of a Covid-19 model: Optimal control, stability and simulations
    Seda İğret Araz
    Alexandria Engineering Journal.2021; 60(1): 647.     CrossRef
  • Modeling 2018 Ebola virus disease outbreak with Cholesky decomposition
    Lagès Nadège Mouanguissa, Abdul A. Kamara, Xiangjun Wang
    Mathematical Methods in the Applied Sciences.2021; 44(7): 5739.     CrossRef
  • Mitigation strategies and compliance in the COVID-19 fight; how much compliance is enough?
    Swati Mukerjee, Clifton M. Chow, Mingfei Li, Martin Chtolongo Simuunza
    PLOS ONE.2021; 16(8): e0239352.     CrossRef
  • A Generalized Mechanistic Model for Assessing and Forecasting the Spread of the COVID-19 Pandemic
    Hamdi Friji, Raby Hamadi, Hakim Ghazzai, Hichem Besbes, Yehia Massoud
    IEEE Access.2021; 9: 13266.     CrossRef
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    Abdul A. Kamara, Xiangjun Wang, Lagès Nadège Mouanguissa
    Applied Mathematics and Computation.2020; 367: 124776.     CrossRef
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    Stéphanie M.C. Abo, Robert Smith
    Infectious Disease Modelling.2020; 5: 905.     CrossRef
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    Zhifu Xie
    Osong Public Health and Research Perspectives.2019; 10(3): 187.     CrossRef
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    Dongmei Luo, Rongjiong Zheng, Duolao Wang, Xueliang Zhang, Yi Yin, Kai Wang, Weiming Wang
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    T. Berge, A. J. Ouemba Tassé, H. M. Tenkam, J. Lubuma
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PHRP : Osong Public Health and Research Perspectives