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Advancing Pandemic Prevention through Innovation

Learn more about Sentinel's cutting edge technology, tools, and scientific advancements. Explore publications that highlight the development and validation of new diagnostics, genomic surveillance platforms, data systems, and analytical tools. This collection also features research on Sentinel's implementation across public health systems, demonstrating how scientific innovation translates into stronger disease surveillance, faster outbreak response, and lasting impact in the communities we serve.

Public Health Impact and Implementation

  • Botti-Lodovico, Y., Nair, P., Nosamiefan, D., Stremlau, M., Schaffner, S., Agignoae, S. V., Aiyepada, J. O., Ajogbasile, F. V., Akpede, G. O., Alhasan, F., Andersen, K. G., Asogun, D. A., Ayodeji, O. O., Badiane, A. S., Barnes, K., Bauer, M. R., Bell-Kareem, A., Benard, M. E., Benevolence, E. O., Blessing, O., … Happi, C. T. (2021). The origins and future of Sentinel: An early-warning system for pandemic preemption and response. Viruses, 13(8), Article 1605. https://doi.org/10.3390/v13081605

  • Petros, B. A., Paull, J. S., Tomkins-Tinch, C. H., Loftness, B. C., DeRuff, K. C., Nair, P., Gionet, G. L., Benz, A., Brock-Fisher, T., Hughes, M., Yurkovetskiy, L., Mulaudzi, S., Leenerman, E., Nyalile, T., Moreno, G. K., Specht, I., Sani, K., Adams, G., Babet, S. V., Baron, E., … Sabeti, P. C. (2022). Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework. Med, 3(12), 883-900.e13. https://doi.org/10.1016/j.medj.2022.09.003

  • Happi, C., & Nkengasong, J. (2022). Two years of COVID-19 in Africa: Lessons for the world. Nature, 601, 22-25.

  • Happi, C., et al. (2022, June 10). Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. Virological.

  • Oluniyi, P., et al. (2022). HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria. AIDS, 36, 137-146.

  • Wilkinson, E., et al. (2021). A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science.

  • Petros, B. A., et al. (2022). Early introduction and rise of the Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant in highly vaccinated university populations. Clinical Infectious Diseases, ciac413.

  • Oladele, R., et al. (2022). Emergence and genomic characterization of multidrug-resistant Candida auris in Nigeria, West Africa. Journal of Fungi, 8(8), Article 787.

  • Ajogbasile, F. V., et al. (2022). Molecular profiling of the artemisinin resistance Kelch 13 gene in Plasmodium falciparum from Nigeria. PLOS ONE, 17(2), e0264548.

  • Oguzie, J. U., et al. (2022). Metagenomic sequencing characterizes a wide diversity of viruses in field mosquito samples in Nigeria. Scientific Reports, 12, Article 7616.

  • Specht, I., Sani, K., Botti-Lodovico, Y., et al. (2022). The case for altruism in institutional diagnostic testing. Scientific Reports, 12, Article 1857.

  • Botti-Lodovico, Y., et al. (2021). The origins and future of Sentinel: An early-warning system for pandemic preemption and response. Viruses, 13(8), Article 1605. https://doi.org/10.3390/v13081605

  • George, U., George, O., Oragwa, A., et al. (2022). Detection of alpha- and betacoronaviruses in frugivorous and insectivorous bats in Nigeria. Pathogens, 11(9), Article 1017. https://doi.org/10.3390/pathogens11091017

  • George, U., George, O., Oguzie, J., et al. (2023). Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria. Virus Research, 334, Article 199174. https://doi.org/10.1016/j.virusres.2023.199174

  • Happi, A. N., Ayinla, A. O., Ogunsanya, O. A., et al. (2023). Detection of SARS-CoV-2 in terrestrial animals in southern Nigeria: Potential cases of reverse zoonosis. Viruses.

  • Oguzie, J. U., Petros, B. A., Oluniyi, P. E., et al. (2023). Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria. Nature Communications, 14, Article 4693.

  • Olawoye, I. B., Oluniyi, P. E., Oguzie, J. U., et al. (2023). Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria. Nature Communications, 14, Article 811. https://doi.org/10.1038/s41467-023-36449-5

  • Tegally, H., San, J. E., Cotten, M., et al. (2022). The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science, 378(6615), eabq5358. https://doi.org/10.1126/science.abq5358

  • Uwanibe, J. N., Olawoye, I. B., Happi, C. T., et al. (2023). Genomic characterisation of multidrug-resistant pathogenic enteric bacteria from healthy children in Osun State, Nigeria. bioRxiv. https://doi.org/10.1101/2023.07.19.549742

  • Normandin, E., Triana, S., Raju, S. S., Lan, T. C. T., Lagerborg, K., Rudy, M., et al. (2023). Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses. Cell Genomics, 3(12), Article 100440. https://doi.org/10.1016/j.xgen.2023.100440

  • Ozonoff, A., Jayavelu, N. D., Liu, S., Melamed, E., Milliren, C. E., Qi, J., et al. (2024). Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: Results from the IMPACC study. Nature Communications, 15(1), Article 216.

  • Levine, Z. C., Sene, A., Mkandawire, W., Deme, A. B., Ndiaye, T., Sy, M., et al. (2024). Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing. Nature Communications, 15(1), Article 747.

  • Happi, A. N., Ogunsanya, O. A., Ayinla, A. O., Sijuwola, A. E., Saibu, F. M., Akano, K., et al. (2024). Lassa virus in novel hosts: Insights into the epidemiology of Lassa virus infections in southern Nigeria. Emerging Microbes & Infections, 13(1), Article 2294859. https://doi.org/10.1080/22221751.2023.2294859

  • Onoja, B. A., Oguzie, J. U., George, U. E., Asoh, K. E., Ajayi, P., Omofaye, T. F., Igeleke, I. O., Eromon, P., Harouna, S., Parker, E., Adeniji, A. J., & Happi, C. T. (2024). Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria. Emerging Microbes & Infections, 13(1), Article 2307511. https://doi.org/10.1080/22221751.2024.2307511

  • Kotliar, D., Raju, S., Tabrizi, S., Odia, I., Goba, A., Momoh, M., et al. (2024). Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever. Nature Microbiology. https://doi.org/10.1038/s41564-023-01589-

  • Allan-Blitz, L. T., Sanders, G., Shah, P., Adams, G., Jarolimova, J., Ard, K., et al. (2024). Clinical performance of Cas13a-based point-of-care lateral flow assay for detecting Neisseria gonorrhoeae. medRxiv. https://doi.org/10.1101/2024.03.01.24303603

  • Adesoji, T. O., George, U. E., Sulayman, T. A., Uwanibe, J. N., Olawoye, I. B., Igbokwe, J. O., et al. (2024). Molecular characterization of non-aureus staphylococci and Mammaliicoccus from Hipposideros bats in Southwest Nigeria. Scientific Reports, 14(1), Article 6899. https://doi.org/10.1038/s41598-024-57190-z

  • Parker, E., Omah, I. F., Varilly, P., et al. (2024). Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans. medRxiv. https://doi.org/10.1101/2024.06.18.24309104

  • Kamariza, M., McMahon, K., Kim, L., Welch, N. L., Stenson, L., Allan-Blitz, L., et al. (2024). Multiplexed detection of febrile infections using CARMEN. bioRxiv. https://doi.org/10.1101/2024.07.15.24310364

  • Specht, I. O. A., Petros, B. A., Moreno, G. K., Brock-Fisher, T., Krasilnikova, L. A., Schifferli, M., et al. (2023). Inferring viral transmission pathways from within-host variation. medRxiv. https://doi.org/10.1101/2023.10.14.23297039

  • Stachler, E., Gnirke, A., McMahon, K., Gomez, M., Stenson, L., Guevara-Reyes, C., Knoll, H., Hill, T., Hill, S., Messer, K. S., Arizti-Sanz, J., Albeez, F., Curtis, E., Samani, P., Wewior, N., O'Connor, D. H., Vuyk, W., Khoury, S., Schnizlein, M. K., Rockey, N. C., … Sabeti, P. C. (2024). Establishing methods to monitor H5N1 influenza virus in dairy cattle milk. medRxiv. https://doi.org/10.1101/2024.12.04.24318491

  • Specht, I., Moreno, G. K., Brock-Fisher, T., Krasilnikova, L. A., Petros, B. A., Pekar, J. E., Schifferli, M., Fry, B., Brown, C. M., Madoff, L. C., Burns, M., Schaffner, S. F., Park, D. J., MacInnis, B. L., Ozonoff, A., Varilly, P., Mitzenmacher, M. D., & Sabeti, P. C. (2025). JUNIPER: Reconstructing transmission events from next-generation sequencing data at scale. medRxiv. https://doi.org/10.1101/2025.03.02.25323192

  • Sandi, J. D., Brock-Fisher, T. M., Kallon, T. M. P. S., Paye, M. F., Fofanah, I. U., Nosamiefan, D., Kamara, M. S., Teh, A. J., Turay, A., Wilkason, C., Baudi, I., Tomkins-Tinch, C. H., I'Anson, C., Stachler, E., Pekar, J. E., Ozonoff, A., Park, D. J., Happi, C., Sabeti, P. C., & Grant, D. S. (2026). Characterization of the first complete genome sequence of yellow fever virus (YFV) in Sierra Leone: Implications for public health. PLOS Neglected Tropical Diseases, 20(5), e0014354. https://doi.org/10.1371/journal.pntd.0014354

  • Campbell, A. K. O., Sandi, J. D., Omah, I. F., et al. (2026). Genomic epidemiology of the 2025 mpox epidemic in Sierra Leone. Nature Medicine, 32(5), 1917-1926. https://doi.org/10.1038/s41591-026-04385-8

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Technology Development

  • Arizti-Sanz, J., Bradley, A., Zhang, Y. B., Boehm, C. K., Freije, C. A., Grunberg, M. E., Kosoko-Thoroddsen, T. F., Welch, N. L., Pillai, P. P., Mantena, S., Kim, G., Uwanibe, J. N., John, O. G., Eromon, P. E., Kocher, G., Gross, R., Lee, J. S., Hensley, L. E., Happi, C. T., Johnson, J., … Myhrvold, C. (2021). Equipment-free detection of SARS-CoV-2 and variants of concern using Cas13. medRxiv. https://doi.org/10.1101/2021.11.01.21265764

  • Arizti-Sanz, J., et al. (2020, November 20). Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nature Communications.

  • Freije, C. A., & Sabeti, P. C. (2021). Detect and destroy: CRISPR-based technologies for the response against viruses. Cell Host & Microbe, 29(5), 689-703. https://doi.org/10.1016/j.chom.2021.04.003

  • Lagerborg, K., et al. (2021, March 16). DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing. bioRxiv.

  • Lagerborg, K., et al. (2022). Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows. Nature Microbiology, 7, 108-119.

  • Sabeti Laboratory. (n.d.). ADAPT: A resource of diagnostic designs for over 1,500 viruses. https://adapt.guide

  • Metsky, H. C., et al. (2022). Designing sensitive viral diagnostics with machine learning. Nature Biotechnology, 40, 108-119.

  • Welch, N., et al. (2022). Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nature Medicine, 28(5), 1083-1094.

  • Arizti-Sanz, J., Bradley, A., Zhang, Y. B., et al. (2022). Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nature Biomedical Engineering, 6(8), 932-943. https://doi.org/10.1038/s41551-022-00889-z

  • Siddiqui, S. M., Welch, N. L., Nguyen, T. G., Razmi, A., Chang, T., Senft, R., et al. (2023). Bead-based approaches to CRISPR diagnostics. medRxiv. https://doi.org/10.1101/2023.09.03.23294926

  • Metsky, H. C., Welch, N. L., Haradhvala, N. J., Rumker, L., Zhang, Y. B., Pillai, P. P., et al. (2021). Designing viral diagnostics with model-based optimization. Nature Biotechnology. (In press.)

  • Mantena, S., Pillai, P. P., Petros, B. A., Welch, N. L., Myhrvold, C., Sabeti, P. C., et al. (2023). Model-directed generation of CRISPR-Cas13a guide RNAs designs artificial sequences that improve nucleic acid detection. bioRxiv. https://doi.org/10.1101/2023.09.20.557569

  • Krasilnikova, L. A., Tomkins-Tinch, C. H., Gayton, A. C., Schaffner, S. F., Dobbins, S. T., Gladden-Young, A., Siddle, K. J., Park, D. J., & Sabeti, P. C. (2024). Polyphonia: Detecting inter-sample contamination in viral genomic sequencing data. Bioinformatics, 40(12), btae698. https://doi.org/10.1093/bioinformatics/btae698

  • Ramesh, K., Siddiqui, S., Gu, A., Mitzenmacher, M., & Sabeti, P. C. (2025). Lyra: An efficient and expressive subquadratic architecture for modeling biological sequences. arXiv. https://doi.org/10.48550/arXiv.2503.16351

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