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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Evaluation of population immunity against SARS-CoV-2 variants, EG.5.1, FY.4, BA.2.86, JN.1, and JN.1.4, using samples from two health demographic surveillance systems in Kenya |
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Identification Number: |
doi:10.7910/DVN/6DSHMB |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2024-06-24 |
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Version: |
1 |
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Bibliographic Citation: |
Lugano, Doreen; Kutima, Bernadette; Kimani, Makobu; Sigilai, Antipa; Gitonga, John N.; Karani, Angela; Akech, Donald; Karia,Boniface; Wairimu, Angela; Lambisia, Arnold; Omuoyo, Donwilliams; Lucinde, Ruth; Ziraba, Abdhalah K.; Newman, Joseph; Bailey, Dalan; Githinji, George; Agoti, Charles N.; Sande, Charles; Kagucia, Wangeci; Ochola-Oyier, Lynette I.; Bejon, Philip; Scott, J. Anthony G.; Agweyu, Ambrose; Warimwe, George M.; Nyagwange, James, 2024, "Replication Data for: Evaluation of population immunity against SARS-CoV-2 variants, EG.5.1, FY.4, BA.2.86, JN.1, and JN.1.4, using samples from two health demographic surveillance systems in Kenya", https://doi.org/10.7910/DVN/6DSHMB, Harvard Dataverse, V1 |
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Citation |
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Title: |
Replication Data for: Evaluation of population immunity against SARS-CoV-2 variants, EG.5.1, FY.4, BA.2.86, JN.1, and JN.1.4, using samples from two health demographic surveillance systems in Kenya |
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Identification Number: |
doi:10.7910/DVN/6DSHMB |
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Authoring Entity: |
Lugano, Doreen (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kutima, Bernadette (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kimani, Makobu (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Sigilai, Antipa (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Gitonga, John N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Karani, Angela (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Akech, Donald (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Karia,Boniface (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Wairimu, Angela (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Lambisia, Arnold (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Omuoyo, Donwilliams (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Lucinde, Ruth (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Ziraba, Abdhalah K. (African Population and Health Research Center) |
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Newman, Joseph (The Pirbright Institute, Ash Road, Woking, GU24 0NF, Surrey, United Kingdom) |
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Bailey, Dalan (The Pirbright Institute, Ash Road, Woking, GU24 0NF, Surrey, United Kingdom) |
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Githinji, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Sande, Charles (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kagucia, Wangeci (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Ochola-Oyier, Lynette I. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Bejon, Philip (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Scott, J. Anthony G. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Agweyu, Ambrose (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Warimwe, George M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Nyagwange, James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Nyagwange, James |
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Access Authority: |
The Data Governance Committee |
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Depositor: |
Lugano, Doreen |
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Date of Deposit: |
2024-06-24 |
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Holdings Information: |
https://doi.org/10.7910/DVN/6DSHMB |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, SARS-CoV-2 variants, vaccination, neutralization, population immunity |
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Abstract: |
<p>This is a replication dataset for the manuscript titled:<strong><i>Evaluation of population immunity against SARS-CoV-2 variants, EG.5.1, FY.4, BA.2.86, JN.1, and JN.1.4, using samples from two health demographic surveillance systems in Kenya</I></strong>.</p> <p>SARS-CoV-2 virus continues to mutate leading to emerging variants that escape immunity previously raised by vaccination and/or infection by earlier variants. We used genomic data to identify the most prevalent Kenyan and global variants between May 2023 and March 2024 and performed pseudoviruses neutralization assays on samples collected from two health demographic surveillance systems in Kenya (n=54), for vaccine induced immunity against circulating variants EG.5.1, FY.4 19, BA.2.86, JN.1, and JN.1.4. As a comparator, we used natural wildtype infection samples (n=20) collected in 2020 at the onset of the pandemic and confirmed to be PCR positive for SARS-CoV-2. We also assessed the effects of different doses of vaccine, age, sex, and type of vaccine on antibody-neutralizing titers.</p> |
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Kind of Data: |
Open Access |
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Notes: |
<strong>Data Access </strong>: Data will be open access under the terms of the Creative Commons CC By 4.0 License. |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Availability Status: |
Data will be open access under the terms of the Creative Commons CC By 4.0 License. |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Nyagwange, J. et al. Serum immunoglobulin G and mucosal immunoglobulin A antibodies from prepandemic samples collected in Kilifi, Kenya, neutralize SARS-CoV-2 in vitro. International Journal of Infectious Diseases 127, (2023). Lambisia, A. W. et al. Detection of a SARS-CoV-2 Beta-like variant in coastal Kenya after more than a year of disappearance. Wellcome Open Res 8, (2023). |
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Bibliographic Citation: |
Nyagwange, J. et al. Serum immunoglobulin G and mucosal immunoglobulin A antibodies from prepandemic samples collected in Kilifi, Kenya, neutralize SARS-CoV-2 in vitro. International Journal of Infectious Diseases 127, (2023). Lambisia, A. W. et al. Detection of a SARS-CoV-2 Beta-like variant in coastal Kenya after more than a year of disappearance. Wellcome Open Res 8, (2023). |
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Citation |
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Title: |
Mwanga, M. J. et al. New SARS-CoV-2 Omicron Variant with Spike Protein Mutation Y451H, Kilifi, Kenya, March-May 2023. Emerg Infect Dis 29, (2023). |
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Bibliographic Citation: |
Mwanga, M. J. et al. New SARS-CoV-2 Omicron Variant with Spike Protein Mutation Y451H, Kilifi, Kenya, March-May 2023. Emerg Infect Dis 29, (2023). |
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Citation |
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Title: |
Githinji, G. et al. The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya. medRxiv (2022). |
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Bibliographic Citation: |
Githinji, G. et al. The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya. medRxiv (2022). |
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Citation |
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Title: |
Kagucia, E. W. et al. SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February–December 2022. Influenza Other Respir Viruses 17, (2023). |
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Bibliographic Citation: |
Kagucia, E. W. et al. SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February–December 2022. Influenza Other Respir Viruses 17, (2023). |
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Citation |
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Title: |
Uyoga, S. et al. Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors. Science (1979) 371, (2021) |
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Bibliographic Citation: |
Uyoga, S. et al. Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors. Science (1979) 371, (2021) |
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Citation |
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Title: |
Kagucia, E. W. et al. SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February–December 2022. Influenza Other Respir Viruses 17, (2023) |
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Bibliographic Citation: |
Kagucia, E. W. et al. SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February–December 2022. Influenza Other Respir Viruses 17, (2023) |
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Label: |
Code.zip |
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Notes: |
application/zip |
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Label: |
Data.zip |
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Notes: |
application/zip |
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Label: |
DLugano_DATASET_Readme_14062024.txt |
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Notes: |
text/plain |