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

Subjects
Science
Abstract

Data on geographically restricted SARS-CoV-2 variants is lacking in some regions. In this nationwide effort including 18 public health labs, the authors used genomic epidemiology and travel data to understand the origin and spread of 2 variants of interest that predominated during the second wave of the pandemic in Nigeria.

Published
2023
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3. The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response.

Author

Botti-Lodovico, Yolanda, Nair, Parvathy, Nosamiefan, Dolo, Stremlau, Matthew, Schaffner, Stephen, Agignoae, Sebastian, Aiyepada, John, Ajogbasile, Fehintola, Akpede, George, Alhasan, Foday, Andersen, Kristian, Asogun, Danny, Ayodeji, Oladele, Badiane, Aida, Barnes, Kayla, Bauer, Matthew, Bell-Kareem, Antoinette, Benard, Muoebonam, Benevolence, Ebo, Blessing, Osiemi, Boehm, Chloe, Boisen, Matthew, Bond, Nell, Branco, Luis, Butts, Michael, Carter, Amber, Colubri, Andres, Deme, Awa, DeRuff, Katherine, Diédhiou, Younousse, Edamhande, Akhilomen, Elhamoumi, Siham, Engel, Emily, Eromon, Philomena, Fallah, Mosoka, Folarin, Onikepe, Fry, Ben, Garry, Robert, Gaye, Amy, Gbakie, Michael, Gevao, Sahr, Gionet, Gabrielle, Gladden-Young, Adrianne, Goba, Augustine, Gomis, Jules, Happi, Anise, Houghton, Mary, Ihekwuazu, Chikwe, Iruolagbe, Christopher, Jackson, Jonathan, Jalloh, Simbirie, Johnson, Jeremy, Kanneh, Lansana, Kayode, Adeyemi, Kemball, Molly, Kingsley, Ojide, Koroma, Veronica, Kotliar, Dylan, Mehta, Samar, Metsky, Hayden, Michael, Airende, Mirhashemi, Marzieh, Modjarrad, Kayvon, Momoh, Mambu, Myhrvold, Cameron, Naregose, Okonofua, Ndiaye, Tolla, Ndiaye, Mouhamadou, Ndiaye, Aliou, Normandin, Erica, Odia, Ikponmwosa, Oguzie, Judith, Okogbenin, Sylvanus, Okokhere, Peter, Okolie, Johnson, Olawoye, Idowu, Olumade, Testimony, Oluniyi, Paul, Omoregie, Omigie, Park, Daniel, Paye, Mariétou, Petros, Brittany, Philippakis, Anthony, Priscilla, Abechi, Ricks, Alan, Rimoin, Anne, Sandi, John, Schieffelin, John, Schreiber, Monica, Seck, Mame, Siddiqui, Sameed, Siddle, Katherine, Smither, Allison, Sy, Mouhamad, Sy, Ngayo, Tomkins-Tinch, Christopher, Tomori, Oyewale, Ugwu, Chinedu, Uwanibe, Jessica, and Uyigue, Eghosasere

Subjects
Ebola, LARGE, Lassa fever, Lassa virus, bioinformatics, diagnostic tools, genomic surveillance, infectious disease, pandemic preemption, pandemic response, Africa, Western, Disaster Planning, Humans, Lassa Fever, Lassa virus, N-Acetylglucosaminyltransferases, Nigeria, Pandemics, Polymorphism, Genetic, Receptors, Virus
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 Kunzs 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

4. 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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5. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Author

Wilkinson, Eduan, primary, Giovanetti, Marta, additional, Tegally, Houriiyah, additional, San, James E., additional, Lessells, Richard, additional, Cuadros, Diego, additional, Martin, Darren P., additional, Rasmussen, David A., additional, Zekri, Abdel-Rahman N., additional, Sangare, Abdoul K., additional, Ouedraogo, Abdoul-Salam, additional, Sesay, Abdul K., additional, Priscilla, Abechi, additional, Kemi, Adedotun-Sulaiman, additional, Olubusuyi, Adewunmi M., additional, Oluwapelumi, Adeyemi O. O., additional, Hammami, Adnène, additional, Amuri, Adrienne A., additional, Sayed, Ahmad, additional, Ouma, Ahmed E. O., additional, Elargoubi, Aida, additional, Ajayi, Nnennaya A., additional, Victoria, Ajogbasile F., additional, Kazeem, Akano, additional, George, Akpede, additional, Trotter, Alexander J., additional, Yahaya, Ali A., additional, Keita, Alpha K., additional, Diallo, Amadou, additional, Kone, Amadou, additional, Souissi, Amal, additional, Chtourou, Amel, additional, Gutierrez, Ana V., additional, Page, Andrew J., additional, Vinze, Anika, additional, Iranzadeh, Arash, additional, Lambisia, Arnold, additional, Ismail, Arshad, additional, Rosemary, Audu, additional, Sylverken, Augustina, additional, Femi, Ayoade, additional, Ibrahimi, Azeddine, additional, Marycelin, Baba, additional, Oderinde, Bamidele S., additional, Bolajoko, Bankole, additional, Dhaala, Beatrice, additional, Herring, Belinda L., additional, Njanpop-Lafourcade, Berthe-Marie, additional, Kleinhans, Bronwyn, additional, McInnis, Bronwyn, additional, Tegomoh, Bryan, additional, Brook, Cara, additional, Pratt, Catherine B., additional, Scheepers, Cathrine, additional, Akoua-Koffi, Chantal G., additional, Agoti, Charles N., additional, Peyrefitte, Christophe, additional, Daubenberger, Claudia, additional, Morang’a, Collins M., additional, Nokes, D. James, additional, Amoako, Daniel G., additional, Bugembe, Daniel L., 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, Omuoyo, Donwilliams O., additional, Maruapula, Dorcas, additional, Foster-Nyarko, Ebenezer, additional, Lusamaki, Eddy K., additional, Simulundu, Edgar, additional, Ong’era, Edidah M., additional, Ngabana, Edith N., additional, Shumba, Edwin, additional, El Fahime, Elmostafa, additional, Lokilo, Emmanuel, additional, Mukantwari, Enatha, additional, Philomena, Eromon, additional, Belarbi, Essia, additional, Simon-Loriere, Etienne, additional, Anoh, Etilé A., additional, Leendertz, Fabian, additional, Ajili, Faida, additional, Enoch, Fakayode O., additional, Wasfi, Fares, additional, Abdelmoula, Fatma, additional, Mosha, Fausta S., additional, Takawira, Faustinos T., additional, Derrar, Fawzi, additional, Bouzid, Feriel, additional, Onikepe, Folarin, additional, Adeola, Fowotade, additional, Muyembe, Francisca M., additional, Tanser, Frank, additional, Dratibi, Fred A., additional, Mbunsu, Gabriel K., additional, Thilliez, Gaetan, additional, Kay, Gemma L., additional, Githinji, George, additional, van Zyl, Gert, additional, Awandare, Gordon A., additional, Schubert, Grit, additional, Maphalala, Gugu P., additional, Ranaivoson, Hafaliana C., additional, Lemriss, Hajar, additional, Anise, Happi, additional, Abe, Haruka, additional, Karray, Hela H., additional, Nansumba, Hellen, additional, Elgahzaly, Hesham A., additional, Gumbo, Hlanai, additional, Smeti, Ibtihel, additional, Ayed, Ikhlas B., additional, Odia, Ikponmwosa, additional, Ben Boubaker, Ilhem Boutiba, additional, Gaaloul, Imed, additional, Gazy, Inbal, additional, Mudau, Innocent, additional, Ssewanyana, Isaac, additional, Konstantinus, Iyaloo, additional, Lekana-Douk, Jean B., additional, Makangara, Jean-Claude C., additional, Tamfum, Jean-Jacques M., additional, Heraud, Jean-Michel, additional, Shaffer, Jeffrey G., additional, Giandhari, Jennifer, additional, Li, Jingjing, additional, Yasuda, Jiro, additional, Mends, Joana Q., additional, Kiconco, Jocelyn, additional, Morobe, John M., additional, Gyapong, John O., additional, Okolie, Johnson C., additional, Kayiwa, John T., additional, Edwards, Johnathan A., additional, Gyamfi, Jones, additional, Farah, Jouali, additional, Nakaseegu, Joweria, additional, Ngoi, Joyce M., additional, Namulondo, Joyce, additional, Andeko, Julia C., additional, Lutwama, Julius J., additional, O’Grady, Justin, additional, Siddle, Katherine, additional, Adeyemi, Kayode T., additional, Tumedi, Kefentse A., additional, Said, Khadija M., additional, Hae-Young, Kim, additional, Duedu, Kwabena O., additional, Belyamani, Lahcen, additional, Fki-Berrajah, Lamia, additional, Singh, Lavanya, additional, Martins, Leonardo de O., additional, Tyers, Lynn, additional, Ramuth, Magalutcheemee, additional, Mastouri, Maha, additional, Aouni, Mahjoub, additional, el Hefnawi, Mahmoud, additional, Matsheka, Maitshwarelo I., additional, Kebabonye, Malebogo, additional, Diop, Mamadou, additional, Turki, Manel, additional, Paye, Marietou, additional, Nyaga, Martin M., additional, Mareka, Mathabo, additional, Damaris, Matoke-Muhia, additional, Mburu, Maureen W., additional, Mpina, Maximillian, additional, Nwando, Mba, additional, Owusu, Michael, additional, Wiley, Michael R., additional, Youtchou, Mirabeau T., additional, Ayekaba, Mitoha O., additional, Abouelhoda, Mohamed, additional, Seadawy, Mohamed G., additional, Khalifa, Mohamed K., additional, Sekhele, Mooko, additional, Ouadghiri, Mouna, additional, Diagne, Moussa M., additional, Mwenda, Mulenga, additional, Allam, Mushal, additional, Phan, My V. T., additional, Abid, Nabil, additional, Touil, Nadia, additional, Rujeni, Nadine, additional, Kharrat, Najla, additional, Ismael, Nalia, additional, Dia, Ndongo, additional, Mabunda, Nedio, additional, Hsiao, Nei-yuan, additional, Silochi, Nelson B., additional, Nsenga, Ngoy, additional, Gumede, Nicksy, additional, Mulder, Nicola, additional, Ndodo, Nnaemeka, additional, Razanajatovo, Norosoa H, additional, Iguosadolo, Nosamiefan, additional, Judith, Oguzie, additional, Kingsley, Ojide C., additional, Sylvanus, Okogbenin, additional, Peter, Okokhere, additional, Femi, Oladiji, additional, Idowu, Olawoye, additional, Testimony, Olumade, additional, Chukwuma, Omoruyi E., additional, Ogah, Onwe E., additional, Onwuamah, Chika K., additional, Cyril, Oshomah, additional, Faye, Ousmane, additional, Tomori, Oyewale, additional, Ondoa, Pascale, additional, Combe, Patrice, additional, Semanda, Patrick, additional, Oluniyi, Paul E., additional, Arnaldo, Paulo, additional, Quashie, Peter K., additional, Dussart, Philippe, additional, Bester, Phillip A., additional, Mbala, Placide K., additional, Ayivor-Djanie, Reuben, additional, Njouom, Richard, additional, Phillips, Richard O., additional, Gorman, Richmond, additional, Kingsley, Robert A., additional, Carr, Rosina A. A., additional, El Kabbaj, Saâd, additional, Gargouri, Saba, additional, Masmoudi, Saber, additional, Sankhe, Safietou, additional, Lawal, Salako B., additional, Kassim, Samar, additional, Trabelsi, Sameh, additional, Metha, Samar, additional, Kammoun, Sami, additional, Lemriss, Sanaâ, additional, Agwa, Sara H. A., additional, Calvignac-Spencer, Sébastien, additional, Schaffner, Stephen F., additional, Doumbia, Seydou, additional, Mandanda, Sheila M., additional, Aryeetey, Sherihane, additional, Ahmed, Shymaa S., additional, Elhamoumi, Siham, additional, Andriamandimby, Soafy, additional, Tope, Sobajo, additional, Lekana-Douki, Sonia, additional, Prosolek, Sophie, additional, Ouangraoua, Soumeya, additional, Mundeke, Steve A., additional, Rudder, Steven, additional, Panji, Sumir, additional, Pillay, Sureshnee, additional, Engelbrecht, Susan, 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, Schindler, Tobias, additional, Anyaneji, Ugochukwu J., additional, Chinedu, Ugwu, additional, Ramphal, Upasana, additional, Jessica, Uwanibe, additional, George, Uwem, additional, Fonseca, Vagner, additional, Enouf, Vincent, additional, Gorova, Vivianne, additional, Roshdy, Wael H., additional, Ampofo, William K., additional, Preiser, Wolfgang, additional, Choga, Wonderful T., additional, Bediako, Yaw, additional, Naidoo, Yeshnee, additional, Butera, Yvan, additional, de Laurent, Zaydah R., additional, Sall, Amadou A., additional, Rebai, Ahmed, additional, von Gottberg, Anne, additional, Kouriba, Bourema, additional, Williamson, Carolyn, additional, Bridges, Daniel J., additional, Chikwe, Ihekweazu, additional, Bhiman, Jinal N., additional, Mine, Madisa, additional, Cotten, Matthew, additional, Moyo, Sikhulile, additional, Gaseitsiwe, Simani, additional, Saasa, Ngonda, additional, Sabeti, Pardis C., additional, Kaleebu, Pontiano, additional, Tebeje, Yenew K., additional, Tessema, Sofonias K., additional, Happi, Christian, additional, Nkengasong, John, additional, and de Oliveira, Tulio, additional

Published
2021
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7. 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

8. Transcriptomic dysregulations associated with SARS-CoV-2 infection in human nasopharyngeal and peripheral blood mononuclear cells

Author

L I Uzairue, Priscilla Abechi, Abisogun Mujib Olamilekan, Stephen Kanyerezi, Sarah H. Carl, Olayemi David Rotimi, Oluwapelumi John Adejinmi, Tiffany Ezinne George, Jabale Rahmat, Monsurat Ademidun Ibironke, Oyewumi Akinpelu, Karan Kumar, Akadiri Olalekan, Khatendra Reang, Maruf Ahmed Bhuiyan, Winfred Nyoroka Gatua, Ifeoluwa Adewunmi, Olajide Emmanuel, Caroline Vilas Boas de Melo, Mahmood Usman, Gracious Mwandira, Dina Aly Mahmoud Aly Abo-Elenein, Ridwanullah Abiodun Abubakar, and Abdulazeez Giwa

Subjects
Transcriptome, Immunoglobulin mediated immune response, Immune system, Innate immune system, Downregulation and upregulation, Interferon, Gene expression, Immunology, medicine, Biology, Peripheral blood mononuclear cell, medicine.drug
Abstract

IntroductionOver 24 million people have been infected globally with the novel coronavirus, SARS-CoV-2, with more than 820,000 succumbing to the resulting COVID-19 disease as of the end of August 2020. The molecular mechanisms underlying the pathogenesis of the disease are not completely elucidated. Thus, we aim to understand host response to SARS-CoV-2 infection by comparing samples collected from two distinct compartments (infection site and blood), obtained from COVID-19 subjects and healthy controls.MethodsWe used two publicly available gene expression datasets generated via RNA sequencing in two different samples; nasopharyngeal swabs and peripheral blood mononuclear cells (PBMCs). We performed a differential gene expression analysis between COVID-19 subjects and healthy controls in the two datasets and then functionally profiled their differentially expressed genes (DEGs). The genes involved in innate immunity were also determined.ResultsWe found a clear difference in the host response to SARS-CoV-2 infection between the two sample groups. In COVID-19 subjects, the nasopharyngeal sample group indicated upregulation of genes involved in cytokine activity and interferon signalling pathway, as well as downregulation of genes involved in oxidative phosphorylation and viral transcription. Host response in COVID-19 subjects for the PBMC group, involved upregulation of genes involved in the complement system and immunoglobulin mediated immune response. CXCL13, GABRE, IFITM3 were upregulated and HSPA1B was downregulated in COVID-19 subjects in both sample groups.ConclusionOur results indicate the host response to SARS-CoV-2 is compartmentalized and suggests potential biomarkers of response to SARS-CoV-2 infection.HighlightsTranscriptomic profiling from publicly available RNA-seq count data revealed a site-specific immune response in COVID-19.Host response was found cellular-mediated in nasopharyngeal samples and humoral-mediated in PBMCs samples.CXCL13, GABRE and IFITM3 commonly upregulated and HSPA1B downregulated in both sample groups highlights the potential of these molecules as markers of response to SARS-CoV-2 infection.

Published
2020
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