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1. Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever

Author

Kotliar, Dylan, Raju, Siddharth, Tabrizi, Shervin, Odia, Ikponmwosa, Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Nair, Parvathy, Phelan, Eric, Tariyal, Ridhi, Eromon, Philomena E., Mehta, Samar, Robles-Sikisaka, Refugio, Siddle, Katherine J., Stremlau, Matt, Jalloh, Simbirie, Gire, Stephen K., Winnicki, Sarah, Chak, Bridget, Schaffner, Stephen F., Pauthner, Matthias, Karlsson, Elinor K., Chapin, Sarah R., Kennedy, Sharon G., Branco, Luis M., Kanneh, Lansana, Vitti, Joseph J., Broodie, Nisha, Gladden-Young, Adrianne, Omoniwa, Omowunmi, Jiang, Pan-Pan, Yozwiak, Nathan, Heuklom, Shannon, Moses, Lina M., Akpede, George O., Asogun, Danny A., Rubins, Kathleen, Kales, Susan, Happi, Anise N., Iruolagbe, Christopher O., Dic-Ijiewere, Mercy, Iraoyah, Kelly, Osazuwa, Omoregie O., Okonkwo, Alexander K., Kunz, Stefan, McCormick, Joseph B., Khan, S. Humarr, Honko, Anna N., Lander, Eric S., Oldstone, Michael B. A., Hensley, Lisa, Folarin, Onikepe A., Okogbenin, Sylvanus A., Günther, Stephan, Ollila, Hanna M., Tewhey, Ryan, Okokhere, Peter O., Schieffelin, John S., Andersen, Kristian G., Reilly, Steven K., Grant, Donald S., Garry, Robert F., Barnes, Kayla G., Happi, Christian T., and Sabeti, Pardis C.

Published
2024
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2. Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

Author

Oguzie, Judith U., Petros, Brittany A., Oluniyi, Paul E., Mehta, Samar B., Eromon, Philomena E., Nair, Parvathy, Adewale-Fasoro, Opeoluwa, Ifoga, Peace Damilola, Odia, Ikponmwosa, Pastusiak, Andrzej, Gbemisola, Otitoola Shobi, Aiyepada, John Oke, Uyigue, Eghosasere Anthonia, Edamhande, Akhilomen Patience, Blessing, Osiemi, Airende, Michael, Tomkins-Tinch, Christopher, Qu, James, Stenson, Liam, Schaffner, Stephen F., Oyejide, Nicholas, Ajayi, Nnenna A., Ojide, Kingsley, Ogah, Onwe, Abejegah, Chukwuyem, Adedosu, Nelson, Ayodeji, Oluwafemi, Liasu, Ahmed A., Okogbenin, Sylvanus, Okokhere, Peter O., Park, Daniel J., Folarin, Onikepe A., Komolafe, Isaac, Ihekweazu, Chikwe, Frost, Simon D. W., Jackson, Ethan K., Siddle, Katherine J., Sabeti, Pardis C., and Happi, Christian T.

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, 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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5. Acute kidney injury and mortality in pediatric Lassa fever versus question of access to dialysis

Author

Adetunji, Adewale E, Ayenale, Magdalene, Akhigbe, Irene, Akerele, Lilian O, Isibor, Efosa, Idialu, Juliet, Aideloje, Florence O, Emuebonam, Ekene, Aire, Chris, Adomeh, Donatus I, Odia, Ikponmwosa, Atafo, Rebecca O, Okonofua, Martha O, Owobu, Adaugo, Ogbaini-Emovon, Ephraim, Tobin, Ekaete A, Asogun, Danny A, Okogbenin, Sylvanus A, Sabeti, Pardis, Happi, Christian T, Günther, Stephan, Azubuike, Chukwuemeka O, Rafiu, Mojeed, Odike, Angela, Olomu, Sylvia C, Ibadin, Michael O, Okokhere, Peter O, and Akpede, George O, Prof.

Published
2021
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6. Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study

Author

Okokhere, Peter, Colubri, Andres, Azubike, Chukwuemeka, Iruolagbe, Christopher, Osazuwa, Omoregie, Tabrizi, Shervin, Chin, Elizabeth, Asad, Sara, Ediale, Ehi, Rafiu, Mojeed, Adomeh, Donatus, Odia, Ikponmwosa, Atafo, Rebecca, Aire, Chris, Okogbenin, Sylvanus, Pahlman, Meike, Becker-Ziaja, Beate, Asogun, Danny, Fradet, Terrence, Fry, Ben, Schaffner, Stephen F, Happi, Christian, Akpede, George, Günther, Stephan, and Sabeti, Pardis C

Published
2018
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7. Retrospective Cohort Study of Lassa Fever in Pregnancy, Southern Nigeria

Author

Okogbenin, Sylvanus, Okoeguale, Joseph, Akpede, George, Colubri, Andres, Barnes, Kayla G., Mehta, Samar, Eifediyi, Reuben, Okogbo, Felix, Eigbefoh, Joseph, Momoh, Mojeed, Rafiu, Mojeed, Adomeh, Donatus, Odia, Ikponmwosa, Aire, Chris, Atafo, Rebecca, Okonofua, Martha, Pahlman, Meike, Becker-Ziaja, Beate, Asogun, Danny, Okokhere, Peter, Happi, Christian, Gunther, Stephan, Sabeti, Pardis C., and Ogbaini-Emovon, Ephraim

Subjects
Infant mortality, Obstetrics, Lassa fever, Medical research, Pregnancy, Pregnant women, Death, Urination disorders, Hospital patients, Ribavirin, Teachers, Fetal death, Convulsions, Health
Abstract

Lassa fever (LF), a viral hemorrhagic fever endemic to West Africa (1-3), was first reported in 1969 from northern Nigeria (4,5). Since that time, LF has been documented in several [...]

Published
2019

8. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

Author

Metsky, Hayden C., Siddle, Katherine J., Gladden-Young, Adrianne, Qu, James, Yang, David K., Brehio, Patrick, Goldfarb, Andrew, Piantadosi, Anne, Wohl, Shirlee, Carter, Amber, Lin, Aaron E., Barnes, Kayla G., Tully, Damien C., Corleis, Bjӧrn, Hennigan, Scott, Barbosa-Lima, Giselle, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Garcia, Kimberly F., Parham, Leda A., Odia, Ikponmwosa, Eromon, Philomena, Folarin, Onikepe A., Goba, Augustine, Simon-Lorière, Etienne, Hensley, Lisa, Balmaseda, Angel, Harris, Eva, Kwon, Douglas S., Allen, Todd M., Runstadler, Jonathan A., Smole, Sandra, Bozza, Fernando A., Souza, Thiago M. L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Gehrke, Lee, Bosch, Irene, Ebel, Gregory, Grant, Donald S., Happi, Christian T., Park, Daniel J., Gnirke, Andreas, Sabeti, Pardis C., and Matranga, Christian B.

Published
2019
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9. Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

Author

Barnes, Kayla G., Lachenauer, Anna E., Nitido, Adam, Siddiqui, Sameed, Gross, Robin, Beitzel, Brett, Siddle, Katherine J., Freije, Catherine A., Dighero-Kemp, Bonnie, Mehta, Samar B., Carter, Amber, Uwanibe, Jessica, Ajogbasile, Fehintola, Olumade, Testimony, Odia, Ikponmwosa, Sandi, John Demby, Momoh, Mambu, Metsky, Hayden C., Boehm, Chloe K., Lin, Aaron E., Kemball, Molly, Park, Daniel J., Branco, Luis, Boisen, Matt, Sullivan, Brian, Amare, Mihret F., Tiamiyu, Abdulwasiu B., Parker, Zahra F., Iroezindu, Michael, Grant, Donald S., Modjarrad, Kayvon, Myhrvold, Cameron, Garry, Robert F., Palacios, Gustavo, Hensley, Lisa E., Schaffner, Stephen F., Happi, Christian T., Colubri, Andres, and Sabeti, Pardis C.

Published
2020
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10. Field evaluation of a Pan-Lassa rapid diagnostic test during the 2018 Nigerian Lassa fever outbreak

Author

Boisen, Matthew L., Uyigue, Eghosa, Aiyepada, John, Siddle, Katherine J., Oestereich, Lisa, Nelson, Diana K. S., Bush, Duane J., Rowland, Megan M., Heinrich, Megan L., Eromon, Philomena, Kayode, Adeyemi T., Odia, Ikponmwosa, Adomeh, Donatus I., Muoebonam, Ekene B., Akhilomen, Patience, Okonofua, Grace, Osiemi, Blessing, Omoregie, Omigie, Airende, Michael, Agbukor, Jacqueline, Ehikhametalor, Solomon, Aire, Chris Okafi, Duraffour, Sophie, Pahlmann, Meike, Böhm, Wiebke, Barnes, Kayla G., Mehta, Samar, Momoh, Mambu, Sandi, John Demby, Goba, Augustine, Folarin, Onikepe A., Ogbaini-Emovan, Ephraim, Asogun, Danny A., Tobin, Ekaete A., Akpede, George O., Okogbenin, Sylvanus A., Okokhere, Peter O., Grant, Donald S., Schieffelin, John S., Sabeti, Pardis C., Günther, Stephan, Happi, Christian T., Branco, Luis M., and Garry, Robert F.

Published
2020
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11. Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria

Author

Ajogbasile, Fehintola V., Oguzie, Judith U., Oluniyi, Paul E., Eromon, Philomena E., Uwanibe, Jessica N., Mehta, Samar B., Siddle, Katherine J., Odia, Ikponmwosa, Winnicki, Sarah M., Akpede, Nosa, Akpede, George, Okogbenin, Sylvanus, Ogbaini-Emovon, Ephraim, MacInnis, Bronwyn L., Folarin, Onikepe A., Modjarrad, Kayvon, Schaffner, Stephen F., Tomori, Oyewale, Ihekweazu, Chikwe, Sabeti, Pardis C., and Happi, Christian T.

Published
2020
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12. Most neutralizing human monoclonal antibodies target novel epitopes requiring both Lassa virus glycoprotein subunits

Author

James E. Robinson, Kathryn M. Hastie, Robert W. Cross, Rachael E. Yenni, Deborah H. Elliott, Julie A. Rouelle, Chandrika B. Kannadka, Ashley A. Smira, Courtney E. Garry, Benjamin T. Bradley, Haini Yu, Jeffrey G. Shaffer, Matt L. Boisen, Jessica N. Hartnett, Michelle A. Zandonatti, Megan M. Rowland, Megan L. Heinrich, Luis Martínez-Sobrido, Benson Cheng, Juan C. de la Torre, Kristian G. Andersen, Augustine Goba, Mambu Momoh, Mohamed Fullah, Michael Gbakie, Lansana Kanneh, Veronica J. Koroma, Richard Fonnie, Simbirie C. Jalloh, Brima Kargbo, Mohamed A. Vandi, Momoh Gbetuwa, Odia Ikponmwosa, Danny A. Asogun, Peter O. Okokhere, Onikepe A. Follarin, John S. Schieffelin, Kelly R. Pitts, Joan B. Geisbert, Peter C. Kulakoski, Russell B. Wilson, Christian T. Happi, Pardis C. Sabeti, Sahr M. Gevao, S. Humarr Khan, Donald S. Grant, Thomas W. Geisbert, Erica Ollmann Saphire, Luis M. Branco, and Robert F. Garry

Subjects
Science
Abstract

Lassa virus can cause haemorrhagic fever for which no specific treatment currently exists. Here the authors have cloned 113 monoclonal antibodies from the survivors of Lassa infection and show that the majority of neutralizing antibodies target a complex of GP1 and GP2 viral proteins.

Published
2016
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13. 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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14. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Author

Tegally, Houriiyah, primary, San, James E., additional, Cotten, Matthew, additional, Tegomoh, Bryan, additional, Mboowa, Gerald, additional, Martin, Darren P., additional, Baxter, Cheryl, additional, Moir, Monika, additional, Lambisia, Arnold, additional, Diallo, Amadou, additional, Amoako, Daniel G., additional, Diagne, Moussa M., additional, Sisay, Abay, additional, Zekri, Abdel-Rahman N., additional, Barakat, Abdelhamid, additional, Gueye, Abdou Salam, additional, Sangare, Abdoul K., additional, Ouedraogo, Abdoul-Salam, additional, Sow, Abdourahmane, additional, Musa, Abdualmoniem O., additional, Sesay, Abdul K., additional, Lagare, Adamou, additional, Kemi, Adedotun-Sulaiman, additional, Abar, Aden Elmi, additional, Johnson, Adeniji A., additional, Fowotade, Adeola, additional, Olubusuyi, Adewumi M., additional, Oluwapelumi, Adeyemi O., additional, Amuri, Adrienne A., additional, Juru, Agnes, additional, Ramadan, Ahmad Mabrouk, additional, Kandeil, Ahmed, additional, Mostafa, Ahmed, additional, Rebai, Ahmed, additional, Sayed, Ahmed, additional, Kazeem, Akano, additional, Balde, Aladje, additional, Christoffels, Alan, additional, Trotter, Alexander J., additional, Campbell, Allan, additional, Keita, Alpha Kabinet, additional, Kone, Amadou, additional, Bouzid, Amal, additional, Souissi, Amal, additional, Agweyu, Ambrose, additional, Gutierrez, Ana V., additional, Page, Andrew J., additional, Yadouleton, Anges, additional, Vinze, Anika, additional, Happi, Anise N., additional, Chouikha, Anissa, additional, Iranzadeh, Arash, additional, Maharaj, Arisha, additional, Batchi-Bouyou, Armel Landry, additional, Ismail, Arshad, additional, Sylverken, Augustina, additional, Goba, Augustine, additional, Femi, Ayoade, additional, Sijuwola, Ayotunde Elijah, additional, Ibrahimi, Azeddine, additional, Marycelin, Baba, additional, Salako, Babatunde Lawal, additional, Oderinde, Bamidele S., additional, Bolajoko, Bankole, additional, Dhaala, Beatrice, additional, Herring, Belinda L., additional, Tsofa, Benjamin, additional, Mvula, Bernard, additional, Njanpop-Lafourcade, Berthe-Marie, additional, Marondera, Blessing T., additional, Khaireh, Bouh Abdi, additional, Kouriba, Bourema, additional, Adu, Bright, additional, Pool, Brigitte, additional, McInnis, Bronwyn, additional, Brook, Cara, additional, Williamson, Carolyn, additional, Anscombe, Catherine, additional, Pratt, Catherine B., additional, Scheepers, Cathrine, additional, Akoua-Koffi, Chantal G., additional, Agoti, Charles N., additional, Loucoubar, Cheikh, additional, Onwuamah, Chika Kingsley, additional, Ihekweazu, Chikwe, additional, Malaka, Christian Noël, additional, Peyrefitte, Christophe, additional, Omoruyi, Chukwuma Ewean, additional, Rafaï, Clotaire Donatien, additional, Morang’a, Collins M., additional, Nokes, D. James, additional, Lule, Daniel Bugembe, additional, Bridges, Daniel J., additional, Mukadi-Bamuleka, Daniel, 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, Grant, Donald S., additional, Omuoyo, Donwilliams O., additional, Maruapula, Dorcas, additional, Wanjohi, Dorcas Waruguru, additional, Foster-Nyarko, Ebenezer, additional, Lusamaki, Eddy K., additional, Simulundu, Edgar, additional, Ong’era, Edidah M., additional, Ngabana, Edith N., additional, Abworo, Edward O., additional, Otieno, Edward, additional, Shumba, Edwin, additional, Barasa, Edwine, additional, Ahmed, El Bara, additional, Kampira, Elizabeth, additional, Fahime, Elmostafa El, additional, Lokilo, Emmanuel, additional, Mukantwari, Enatha, additional, Cyril, Erameh, additional, Philomena, Eromon, additional, Belarbi, Essia, additional, Simon-Loriere, Etienne, additional, Anoh, Etilé A., additional, Leendertz, Fabian, additional, Taweh, Fahn M., additional, Wasfi, Fares, additional, Abdelmoula, Fatma, additional, Takawira, Faustinos T., additional, Derrar, Fawzi, additional, Ajogbasile, Fehintola V, additional, Treurnicht, Florette, additional, Onikepe, Folarin, additional, Ntoumi, Francine, additional, Muyembe, Francisca M., additional, Ngiambudulu, Francisco, additional, Zongo Ragomzingba, Frank Edgard, additional, Dratibi, Fred Athanasius, additional, Iyanu, Fred-Akintunwa, additional, Mbunsu, Gabriel K., additional, Thilliez, Gaetan, additional, Kay, Gemma L., additional, Akpede, George O., additional, George, Uwem E., additional, van Zyl, Gert, additional, Awandare, Gordon A., additional, Schubert, Grit, additional, Maphalala, Gugu P., additional, Ranaivoson, Hafaliana C., additional, Lemriss, Hajar, additional, Omunakwe, Hannah E, additional, Onywera, Harris, additional, Abe, Haruka, additional, Karray, Hela, additional, Nansumba, Hellen, additional, Triki, Henda, additional, Adje Kadjo, Herve Albéric, additional, Elgahzaly, Hesham, additional, Gumbo, Hlanai, additional, mathieu, Hota, additional, Kavunga-Membo, Hugo, additional, Smeti, Ibtihel, additional, Olawoye, Idowu B., additional, Adetifa, Ifedayo, additional, Odia, Ikponmwosa, additional, Boubaker, Ilhem Boutiba-Ben, additional, Ssewanyana, Isaac, additional, Wurie, Isatta, additional, Konstantinus, Iyaloo S, additional, Afiwa Halatoko, Jacqueline Wemboo, additional, Ayei, James, additional, Sonoo, Janaki, additional, Lekana-Douki, Jean Bernard, additional, Makangara, Jean-Claude C., additional, Tamfum, Jean-Jacques M., additional, Heraud, Jean-Michel, additional, Shaffer, Jeffrey G., additional, Giandhari, Jennifer, additional, Musyoki, Jennifer, additional, Uwanibe, Jessica N., additional, Bhiman, Jinal N., additional, Yasuda, Jiro, additional, Morais, Joana, additional, Mends, Joana Q., additional, Kiconco, Jocelyn, additional, Sandi, John Demby, additional, Huddleston, John, additional, Odoom, John Kofi, additional, Morobe, John M., additional, Gyapong, John O., additional, Kayiwa, John T., additional, Okolie, Johnson C., additional, Xavier, Joicymara Santos, additional, Gyamfi, Jones, additional, Kofi Bonney, Joseph Humphrey, additional, Nyandwi, Joseph, additional, Everatt, Josie, additional, Farah, Jouali, additional, Nakaseegu, Joweria, additional, Ngoi, Joyce M., additional, Namulondo, Joyce, additional, Oguzie, Judith U., additional, Andeko, Julia C., additional, Lutwama, Julius J., additional, O’Grady, Justin, additional, Siddle, Katherine J, additional, Victoir, Kathleen, additional, Adeyemi, Kayode T., additional, Tumedi, Kefentse A., additional, Carvalho, Kevin Sanders, additional, Mohammed, Khadija Said, additional, Musonda, Kunda G., additional, Duedu, Kwabena O., additional, Belyamani, Lahcen, additional, Fki-Berrajah, Lamia, additional, Singh, Lavanya, additional, Biscornet, Leon, additional, de Oliveira Martins, Leonardo, additional, Chabuka, Lucious, additional, Olubayo, Luicer, additional, Deng, Lul Lojok, additional, Ochola-Oyier, Lynette Isabella, additional, Mine, Madisa, additional, Ramuth, Magalutcheemee, additional, Mastouri, Maha, additional, ElHefnawi, Mahmoud, additional, Mbanne, Maimouna, additional, Matsheka, Maitshwarelo I., additional, Kebabonye, Malebogo, additional, Diop, Mamadou, additional, Momoh, Mambu, additional, Lima Mendonça, Maria da Luz, additional, Venter, Marietjie, additional, Paye, Marietou F, additional, Faye, Martin, additional, Nyaga, Martin M., additional, Mareka, Mathabo, additional, Damaris, Matoke-Muhia, additional, Mburu, Maureen W., additional, Mpina, Maximillian, additional, Claujens Chastel, Mfoutou Mapanguy, additional, Owusu, Michael, additional, Wiley, Michael R., additional, Tatfeng, Mirabeau Youtchou, additional, Ayekaba, Mitoha Ondo’o, additional, Abouelhoda, Mohamed, additional, Beloufa, Mohamed Amine, additional, Seadawy, Mohamed G, additional, Khalifa, Mohamed K., additional, Dellagi, Mohammed Koussai, additional, Matobo, Mooko Marethabile, additional, Kane, Mouhamed, additional, Ouadghiri, Mouna, additional, Salou, Mounerou, additional, Mbulawa, Mphaphi B., additional, Saibu, Mudashiru Femi, additional, Mwenda, Mulenga, additional, Kaba, Muluken, additional, Phan, My V.T., additional, Abid, Nabil, additional, Touil, Nadia, additional, Rujeni, Nadine, additional, Ismael, Nalia, additional, Top, Ndeye Marieme, additional, Dia, Ndongo, additional, Mabunda, Nédio, additional, Hsiao, Nei-yuan, additional, Silochi, Nelson Boricó, additional, Saasa, Ngonda, additional, Bbosa, Nicholas, additional, Murunga, Nickson, additional, Gumede, Nicksy, additional, Wolter, Nicole, additional, Sitharam, Nikita, additional, Ndodo, Nnaemeka, additional, Ajayi, Nnennaya A., additional, Tordo, Noël, additional, Mbhele, Nokuzola, additional, Razanajatovo, Norosoa H, additional, Iguosadolo, Nosamiefan, additional, Mba, Nwando, additional, Kingsley, Ojide C., additional, Sylvanus, Okogbenin, additional, Peter, Okokhere, additional, Femi, Oladiji, additional, Testimony, Olumade, additional, Ogunsanya, Olusola Akinola, additional, Fakayode, Oluwatosin, additional, Ogah, Onwe E., additional, Faye, Ousmane, additional, Smith-Lawrence, Pamela, additional, Ondoa, Pascale, additional, Combe, Patrice, additional, Nabisubi, Patricia, additional, Semanda, Patrick, additional, Oluniyi, Paul E., additional, Arnaldo, Paulo, additional, Quashie, Peter Kojo, additional, Bejon, Philip, additional, Dussart, Philippe, additional, Bester, Phillip A., additional, Mbala, Placide K., additional, Kaleebu, Pontiano, additional, Abechi, Priscilla, additional, El-Shesheny, Rabeh, additional, Joseph, Rageema, additional, Aziz, Ramy Karam, additional, Essomba, René Ghislain, additional, Ayivor-Djanie, Reuben, additional, Njouom, Richard, additional, Phillips, Richard O., additional, Gorman, Richmond, additional, Kingsley, Robert A., additional, Audu, Rosemary, additional, Carr, Rosina A.A., additional, Kabbaj, Saâd El, additional, Gargouri, Saba, additional, Masmoudi, Saber, additional, Sankhe, Safietou, additional, Mohamed, Sahra Isse, additional, Mhalla, Salma, additional, Hosch, Salome, additional, Kassim, Samar Kamal, additional, Metha, Samar, additional, Trabelsi, Sameh, additional, Lemriss, Sanaâ, additional, Agwa, Sara Hassan, additional, Mwangi, Sarah Wambui, additional, Doumbia, Seydou, additional, Makiala-Mandanda, Sheila, additional, Aryeetey, Sherihane, additional, Ahmed, Shymaa S., additional, Ahmed, Sidi Mohamed, additional, Elhamoumi, Siham, additional, Moyo, Sikhulile, additional, Lutucuta, Silvia, additional, Gaseitsiwe, Simani, additional, Jalloh, Simbirie, additional, Andriamandimby, Soafy, additional, Oguntope, Sobajo, additional, Grayo, Solène, additional, Lekana-Douki, Sonia, additional, Prosolek, Sophie, additional, Ouangraoua, Soumeya, additional, van Wyk, Stephanie, additional, Schaffner, Stephen F., additional, Kanyerezi, Stephen, additional, Ahuka-Mundeke, Steve, additional, Rudder, Steven, additional, Pillay, Sureshnee, 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, Velavan, Thirumalaisamy P., additional, Schindler, Tobias, additional, Maponga, Tongai, additional, Bedford, Trevor, additional, Anyaneji, Ugochukwu J., additional, Chinedu, Ugwu, additional, Ramphal, Upasana, additional, Enouf, Vincent, additional, Nene, Vishvanath, additional, Gorova, Vivianne, additional, Roshdy, Wael H., additional, Karim, Wasim Abdul, additional, Ampofo, William K., additional, Preiser, Wolfgang, additional, Choga, Wonderful T., additional, Ahmed, Yahaya Ali, additional, Ramphal, Yajna, additional, Bediako, Yaw, additional, Naidoo, Yeshnee, additional, Butera, Yvan, additional, de Laurent, Zaydah R., additional, Ouma, Ahmed E.O., additional, von Gottberg, Anne, additional, Githinji, George, additional, Moeti, Matshidiso, additional, Tomori, Oyewale, additional, Sabeti, Pardis C., additional, Sall, Amadou A., additional, Oyola, Samuel O., additional, Tebeje, Yenew K., additional, Tessema, Sofonias K., additional, de Oliveira, Tulio, additional, Happi, Christian, additional, Lessells, Richard, additional, Nkengasong, John, additional, and Wilkinson, Eduan, additional

Published
2022
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15. 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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16. New variant of Hepatitis C Virus genotype 1b in a Human Immunodeficiency Virus (HIV) infected patient in Benin City, Nigeria

Author

Oladeinde, Bankole Henry, Ekejindu, Ifeoma Mercy, Omoregie, Richard, Odia, Ikponmwosa, and Aguh, Obiora Donatus

Subjects
virus diseases, Hepatitis C Virus, genotypes, nucleotides, mutation, HIV, Nigeria, digestive system diseases
Abstract

Background: Hepatitis C Virus (HCV) disease severity and treatment outcome are affected by circulating genotype. Data on genotypic prevalence of HCV among HIV infected patients in Nigeria is sparse. Against this background this study aimed at determining the genotypic prevalence of HCV among HIV infected patients in Benin City, Nigeria. Methods: A cross-sectional study was conducted among 564 HIV infected patients to determine the type and frequency of HCV genotypes among them. Four hundred and thirty-one (431) of these patients were on highly active antiretroviral therapy (HAART). Sera obtained from study participants were used to screen for antibodies to HCV using immuno-chromatographic test kits. Hepatitis C Virus nucleic acid HCV-RNA was extracted from HCV seropositive sera and the 5' untranslated region (5'UTR) of HCV amplified using specific primers, with the resulting amplicons sequenced on an ABI 350xL automated sequencer.Results: HAART did not significantly affect the sero-prevalence of HCV infection. (HAART naïve vs. HAART exposed) 1.5% vs. 0.9%; OR= 1.630, 95% CI = 0.295, 9.002, P = 0.9344). Of the six patients with HCV antibodies, only 1(16.7%) had detectable HCV-RNA in serum, and the isolate was identified as HCV genotype 1b, which did not cluster around other HCV genotype 1b isolates of Nigerian origin.Conclusions: This study reports a novel variant of HCV genotype 1b in Nigeria

Published
2021
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17. 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

18. Identification of Common CD8 + T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone

Author

Sakabe, Saori, primary, Hartnett, Jessica N., additional, Ngo, Nhi, additional, Goba, Augustine, additional, Momoh, Mambu, additional, Sandi, John Demby, additional, Kanneh, Lansana, additional, Cubitt, Beatrice, additional, Garcia, Selma D., additional, Ware, Brian C., additional, Kotliar, Dylan, additional, Robles-Sikisaka, Refugio, additional, Gangavarapu, Karthik, additional, Branco, Luis M., additional, Eromon, Philomena, additional, Odia, Ikponmwosa, additional, Ogbaini-Emovon, Ephraim, additional, Folarin, Onikepe, additional, Okogbenin, Sylvanus, additional, Okokhere, Peter O., additional, Happi, Christian, additional, Sabeti, Pardis C., additional, Andersen, Kristian G., additional, Garry, Robert F., additional, de la Torre, Juan Carlos, additional, Grant, Donald S., additional, Schieffelin, John S., additional, Oldstone, Michael B. A., additional, and Sullivan, Brian M., additional

Published
2020
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19. Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

Author

Barnes, Kayla G., primary, Lachenauer, Anna E., additional, Nitido, Adam, additional, Siddiqui, Sameed, additional, Gross, Robin, additional, Beitzel, Brett, additional, Siddle, Katherine J., additional, Freije, Catherine A., additional, Dighero-Kemp, Bonnie, additional, Mehta, Samar, additional, Carter, Amber, additional, Uwanibe, Jessica, additional, Ajogbasile, Fehintola, additional, Olumade, Testimony J., additional, Odia, Ikponmwosa, additional, Sandi, John Demby, additional, Momoh, Mambu, additional, Metsky, Hayden C., additional, Boehm, Chloe K., additional, Lin, Aaron E., additional, Kemball, Molly, additional, Park, Daniel J., additional, Grant, Donald S., additional, Happi, Christian T., additional, Branco, Luis, additional, Boisen, Matt, additional, Sullivan, Brian M., additional, Amare, Mihret, additional, Tiamiyu, Abdulwasiu, additional, Parker, Zahra, additional, Iroezindu, Michael, additional, Modjarrad, Kayvon, additional, Myhrvold, Cameron, additional, Garry, Robert F., additional, Palacios, Gustavo, additional, Hensley, Lisa E., additional, Schaffner, Stephen F., additional, Colubri, Andres, additional, and Sabeti, Pardis C., additional

Published
2020
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20. High crossreactivity of human T cell responses between Lassa virus lineages

Author

Sullivan, Brian M., primary, Sakabe, Saori, additional, Hartnett, Jessica N., additional, Ngo, Nhi, additional, Goba, Augustine, additional, Momoh, Mambu, additional, Demby Sandi, John, additional, Kanneh, Lansana, additional, Cubitt, Beatrice, additional, Garcia, Selma D., additional, Ware, Brian C., additional, Kotliar, Dylan, additional, Robles-Sikisaka, Refugio, additional, Gangavarapu, Karthik, additional, Branco, Luis, additional, Eromon, Philomena, additional, Odia, Ikponmwosa, additional, Ogbaini-Emovon, Ephraim, additional, Folarin, Onikepe, additional, Okogbenin, Sylvanus, additional, Okokhere, Peter O., additional, Happi, Christian, additional, de la Torre, Juan Carlos, additional, Sabeti, Pardis C., additional, Andersen, Kristian G., additional, Garry, Robert F., additional, Grant, Donald S., additional, Schieffelin, John S., additional, and Oldstone, Michael B. A., additional

Published
2020
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21. Most neutralizing human monoclonal antibodies target novel epitopes requiring both Lassa virus glycoprotein subunits

Author

Robert W. Cross, Matthew L. Boisen, Mambu Momoh, Megan L. Heinrich, Michelle Zandonatti, Michael Gbakie, Joan B. Geisbert, Simbirie Jalloh, Juan Carlos de la Torre, Chandrika B. Kannadka, Momoh Gbetuwa, Julie A. Rouelle, Onikepe A. Follarin, S. Humarr Khan, Ashley A. Smira, Mohamed Fullah, Benjamin T. Bradley, Richard Fonnie, Kathryn M. Hastie, Luis M. Branco, Russell B. Wilson, Veronica J. Koroma, Danny Asogun, Mohamed A. Vandi, Christian T. Happi, Megan M. Rowland, Benson Yee Hin Cheng, Robert F. Garry, Deborah H. Elliott, Augustine Goba, Pardis C. Sabeti, Kristian G. Andersen, Brima Kargbo, Jeffrey G. Shaffer, James E. Robinson, Peter C. Kulakoski, Kelly R. Pitts, Thomas W. Geisbert, Luis Martinez-Sobrido, Donald S. Grant, Erica Ollmann Saphire, Peter O Okokhere, Odia Ikponmwosa, Lansana Kanneh, Courtney E Garry, Jessica N. Hartnett, John S. Schieffelin, Rachael E. Yenni, Sahr M. Gevao, and Haini Yu

Subjects
0301 basic medicine, Models, Molecular, medicine.drug_class, viruses, Science, General Physics and Astronomy, Cross Reactions, Monoclonal antibody, medicine.disease_cause, Antibodies, Viral, General Biochemistry, Genetics and Molecular Biology, Epitope, Article, 03 medical and health sciences, Epitopes, Lassa Fever, Viral Envelope Proteins, Glycoprotein complex, Antibody Specificity, medicine, Humans, Lassa fever, Lassa virus, Antigens, Viral, Sequence Deletion, chemistry.chemical_classification, Multidisciplinary, biology, Antibodies, Monoclonal, virus diseases, General Chemistry, Arenavirus, medicine.disease, Virology, Antibodies, Neutralizing, 3. Good health, 030104 developmental biology, Epitope mapping, chemistry, biology.protein, Mutagenesis, Site-Directed, Antibody, Glycoprotein, Epitope Mapping
Abstract

Lassa fever is a severe multisystem disease that often has haemorrhagic manifestations. The epitopes of the Lassa virus (LASV) surface glycoproteins recognized by naturally infected human hosts have not been identified or characterized. Here we have cloned 113 human monoclonal antibodies (mAbs) specific for LASV glycoproteins from memory B cells of Lassa fever survivors from West Africa. One-half bind the GP2 fusion subunit, one-fourth recognize the GP1 receptor-binding subunit and the remaining fourth are specific for the assembled glycoprotein complex, requiring both GP1 and GP2 subunits for recognition. Notably, of the 16 mAbs that neutralize LASV, 13 require the assembled glycoprotein complex for binding, while the remaining 3 require GP1 only. Compared with non-neutralizing mAbs, neutralizing mAbs have higher binding affinities and greater divergence from germline progenitors. Some mAbs potently neutralize all four LASV lineages. These insights from LASV human mAb characterization will guide strategies for immunotherapeutic development and vaccine design., Lassa virus can cause haemorrhagic fever for which no specific treatment currently exists. Here the authors have cloned 113 monoclonal antibodies from the survivors of Lassa infection and show that the majority of neutralizing antibodies target a complex of GP1 and GP2 viral proteins.

Published
2016

22. Phylogeography of Lassa Virus in Nigeria

Author

Ehichioya, Deborah U., primary, Dellicour, Simon, additional, Pahlmann, Meike, additional, Rieger, Toni, additional, Oestereich, Lisa, additional, Becker-Ziaja, Beate, additional, Cadar, Daniel, additional, Ighodalo, Yemisi, additional, Olokor, Thomas, additional, Omomoh, Emmanuel, additional, Oyakhilome, Jennifer, additional, Omiunu, Racheal, additional, Agbukor, Jacqueline, additional, Ebo, Benevolence, additional, Aiyepada, John, additional, Ebhodaghe, Paulson, additional, Osiemi, Blessing, additional, Ehikhametalor, Solomon, additional, Akhilomen, Patience, additional, Airende, Michael, additional, Esumeh, Rita, additional, Muoebonam, Ekene, additional, Giwa, Rosemary, additional, Ekanem, Anieno, additional, Igenegbale, Ganiyu, additional, Odigie, George, additional, Okonofua, Grace, additional, Enigbe, Racheal, additional, Omonegho Yerumoh, Edna, additional, Pallasch, Elisa, additional, Bockholt, Sabrina, additional, Kafetzopoulou, Liana E., additional, Duraffour, Sophie, additional, Okokhere, Peter O., additional, Akpede, George O., additional, Okogbenin, Sylvanus A., additional, Odia, Ikponmwosa, additional, Aire, Chris, additional, Akpede, Nosa, additional, Tobin, Ekaete, additional, Ogbaini-Emovon, Ephraim, additional, Lemey, Philippe, additional, Adomeh, Donatus I., additional, Asogun, Danny A., additional, and Günther, Stephan, additional

Published
2019
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23. Corrigendum: Caseload and Case Fatality of Lassa Fever in Nigeria, 2001–2018: A Specialist Center's Experience and Its Implications

Author

Akpede, George O., primary, Asogun, Danny A., additional, Okogbenin, Sylvanus A., additional, Dawodu, Simeon O., additional, Momoh, Mojeed O., additional, Dongo, Andrew E., additional, Ike, Chiedozie, additional, Tobin, Ekaete, additional, Akpede, Nosa, additional, Ogbaini-Emovon, Ephraim, additional, Adewale, Adetunji E., additional, Ochei, Oboratare, additional, Onyeke, Frank, additional, Okonofua, Martha O., additional, Atafo, Rebecca O., additional, Odia, Ikponmwosa, additional, Adomeh, Donatus I., additional, Odigie, George, additional, Ogbeifun, Caroline, additional, Muoebonam, Ekene, additional, Ihekweazu, Chikwe, additional, Ramharter, Michael, additional, Colubri, Andres, additional, Sabeti, Pardis C., additional, Happi, Christian T., additional, Günther, Stephan, additional, and Agbonlahor, Dennis E., additional

Published
2019
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24. Caseload and Case Fatality of Lassa Fever in Nigeria, 2001–2018: A Specialist Center's Experience and Its Implications

Author

Akpede, George O., primary, Asogun, Danny A., additional, Okogbenin, Sylvanus A., additional, Dawodu, Simeon O., additional, Momoh, Mojeed O., additional, Dongo, Andrew E., additional, Ike, Chiedozie, additional, Tobin, Ekaete, additional, Akpede, Nosa, additional, Ogbaini-Emovon, Ephraim, additional, Adewale, Adetunji E., additional, Ochei, Oboratare, additional, Onyeke, Frank, additional, Okonofua, Martha O., additional, Atafo, Rebecca O., additional, Odia, Ikponmwosa, additional, Adomeh, Donatus I., additional, Odigie, George, additional, Ogbeifun, Caroline, additional, Muoebonam, Ekene, additional, Ihekweazu, Chikwe, additional, Ramharter, Michael, additional, Colubri, Andres, additional, Sabeti, Pardis C., additional, Happi, Christian T., additional, Günther, Stephan, additional, and Agbonlahor, Dennis E., additional

Published
2019
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25. Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria

Author

Ajogbasile, Fehintola V., primary, Oguzie, Judith U., additional, Oluniyi, Paul E., additional, Eromon, Philomena, additional, Uwanibe, Jessica, additional, Mehta, Samar B., additional, Siddle, Katherine J., additional, Odia, Ikponmwosa, additional, Winnicki, Sarah M., additional, Akpede, Nosa, additional, Akpede, George, additional, Okogbenin, Sylvanus, additional, MacInnis, Bronwyn L., additional, Folarin, Onikepe A., additional, Schaffner, Stephen F., additional, Ogbaini-Emovon, Ephraim, additional, Tomori, Oyewale, additional, Ihekweazu, Chikwe, additional, Sabeti, Pardis C., additional, and Happi, Christian T., additional

Published
2019
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26. Phylogeography of Lassa Virus in Nigeria

Author

Ehichioya, Deborah, Dellicour, Simon, Pahlmann, Meike, Rieger, Toni, Oestereich, Lisa, Becker-Ziaja, Beate, Cadar, Daniel, Ighodalo, Yemisi, Olokor, Thomas, Omomoh, Emmanuel, Oyakhilome, Jennifer, Omiunu, Racheal, Agbukor, Jacqueline, Ebo, Benevolence, Aiyepada, John, Ebhodaghe, Paulson, Osiemi, Blessing, Ehikhametalor, Solomon, Akhilomen, Patience, Airende, Michael, Esumeh, Rita, Muoebonam, Ekene, Giwa, Rosemary, Ekanem, Anieno, Igenegbale, Ganiyu, Odigie, George, Okonofua, Grace, Enigbe, Racheal, Omonegho Yerumoh, Edna, Pallasch, Elisa, Bockholt, Sabrina, Kafetzopoulou, Liana Eleni, Duraffour, Sophie, Okokhere, Peter, Akpede, George, Okogbenin, Sylvanus, Odia, Ikponmwosa, Aire, Chris, Akpede, Nosa, Tobin, Ekaete Alice, Ogbaini-Emovon, Ephraim, Lemey, Philippe, Adomeh, Donatus I., Asogun, Danny, Günther, Stephan, Ehichioya, Deborah, Dellicour, Simon, Pahlmann, Meike, Rieger, Toni, Oestereich, Lisa, Becker-Ziaja, Beate, Cadar, Daniel, Ighodalo, Yemisi, Olokor, Thomas, Omomoh, Emmanuel, Oyakhilome, Jennifer, Omiunu, Racheal, Agbukor, Jacqueline, Ebo, Benevolence, Aiyepada, John, Ebhodaghe, Paulson, Osiemi, Blessing, Ehikhametalor, Solomon, Akhilomen, Patience, Airende, Michael, Esumeh, Rita, Muoebonam, Ekene, Giwa, Rosemary, Ekanem, Anieno, Igenegbale, Ganiyu, Odigie, George, Okonofua, Grace, Enigbe, Racheal, Omonegho Yerumoh, Edna, Pallasch, Elisa, Bockholt, Sabrina, Kafetzopoulou, Liana Eleni, Duraffour, Sophie, Okokhere, Peter, Akpede, George, Okogbenin, Sylvanus, Odia, Ikponmwosa, Aire, Chris, Akpede, Nosa, Tobin, Ekaete Alice, Ogbaini-Emovon, Ephraim, Lemey, Philippe, Adomeh, Donatus I., Asogun, Danny, and Günther, Stephan

Abstract

Lassa virus is genetically diverse with several lineages circulating in West Africa. This study aimed at describing the sequence variability of Lassa virus across Nigeria and inferring its spatiotemporal evolution. We sequenced and isolated 77 Lassa virus strains from 16 Nigerian states. The final data set, including previous works, comprised metadata and sequences of 219 unique strains sampled between 1969 and 2018 in 22 states. Most of this data originated from Lassa fever patients diagnosed at Irrua Specialist Teaching Hospital, Edo State, Nigeria. The majority of sequences clustered with the main Nigerian lineages II and III, while a few sequences formed a new cluster related to Lassa virus strains from Hylomyscus pamfi .Within lineages II and III, seven and five sublineages, respectively, were distinguishable. Phylogeographic analysis suggests an origin of lineage II in the southeastern part of the country around Ebonyi State and a main vector of dispersal toward the west across the Niger River, through Anambra, Kogi, Delta, and Edo into Ondo State. The frontline of virus dispersal appears to be in Ondo. Minor vectors are directed northeast toward Taraba and Adamawa and south toward Imo and Rivers. Lineage III might have spread from northern Plateau State into Kaduna, Nasarawa, Federal Capital Territory, and Bauchi. One sublineage moved south and crossed the Benue River into Benue State. This study provides a geographic mapping of lineages and phylogenetic clusters in Nigeria at a higher resolution. In addition, we estimated the direction and time frame of virus dispersal in the country. IMPORTANCE Lassa virus is the causative agent of Lassa fever, a viral hemorrhagic fever with a case fatality rate of approximately 30% in Africa. Previous studies disclosed a geographical pattern in the distribution of Lassa virus strains and a westward movement of the virus across West Africa during evolution. Our study provides a deeper understanding of the geography, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2019

27. Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

Author

Siddle, Katherine J., primary, Eromon, Philomena, additional, Barnes, Kayla G., additional, Mehta, Samar, additional, Oguzie, Judith U., additional, Odia, Ikponmwosa, additional, Schaffner, Stephen F., additional, Winnicki, Sarah M., additional, Shah, Rickey R., additional, Qu, James, additional, Wohl, Shirlee, additional, Brehio, Patrick, additional, Iruolagbe, Christopher, additional, Aiyepada, John, additional, Uyigue, Eghosa, additional, Akhilomen, Patience, additional, Okonofua, Grace, additional, Ye, Simon, additional, Kayode, Tolulope, additional, Ajogbasile, Fehintola, additional, Uwanibe, Jessica, additional, Gaye, Amy, additional, Momoh, Mambu, additional, Chak, Bridget, additional, Kotliar, Dylan, additional, Carter, Amber, additional, Gladden-Young, Adrianne, additional, Freije, Catherine A., additional, Omoregie, Omigie, additional, Osiemi, Blessing, additional, Muoebonam, Ekene B., additional, Airende, Michael, additional, Enigbe, Rachael, additional, Ebo, Benevolence, additional, Nosamiefan, Iguosadolo, additional, Oluniyi, Paul, additional, Nekoui, Mahan, additional, Ogbaini-Emovon, Ephraim, additional, Garry, Robert F., additional, Andersen, Kristian G., additional, Park, Daniel J., additional, Yozwiak, Nathan L., additional, Akpede, George, additional, Ihekweazu, Chikwe, additional, Tomori, Oyewale, additional, Okogbenin, Sylvanus, additional, Folarin, Onikepe A., additional, Okokhere, Peter O., additional, MacInnis, Bronwyn L., additional, Sabeti, Pardis C., additional, and Happi, Christian T., additional

Published
2018
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28. Acute Lassa Virus Encephalitis with Lassa Virus in the Cerebrospinal Fluid but Absent in the Blood: A Case Report with a Positive Outcome

Author

Okokhere, Peter O., primary, Erameh, Cyril O., additional, Alikah, Francis, additional, Akhideno, Peter E., additional, Iruolagbe, Christopher O., additional, Osazuwa, Omoregie O., additional, Bankole, Idowu A., additional, Adomeh, Donatus I., additional, Odia, Ikponmwosa, additional, Aire, Chris O., additional, Oyakhilome, Jennifer, additional, Agbukor, Jacqueline, additional, Atafo, Rebecca O., additional, Asogun, Danny A., additional, Happi, Christian T., additional, Sabeti, Pardis C., additional, Günther, Stephan, additional, and Akpede, George O., additional

Published
2018
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29. Development and evaluation of antibody-capture immunoassays for detection of Lassa virus nucleoprotein-specific immunoglobulin M and G

Author

Gabriel, Martin, primary, Adomeh, Donatus I., additional, Ehimuan, Jacqueline, additional, Oyakhilome, Jennifer, additional, Omomoh, Emmanuel O., additional, Ighodalo, Yemisi, additional, Olokor, Thomas, additional, Bonney, Kofi, additional, Pahlmann, Meike, additional, Emmerich, Petra, additional, Lelke, Michaela, additional, Brunotte, Linda, additional, Ölschläger, Stephan, additional, Thomé-Bolduan, Corinna, additional, Becker-Ziaja, Beate, additional, Busch, Carola, additional, Odia, Ikponmwosa, additional, Ogbaini-Emovon, Ephraim, additional, Okokhere, Peter O., additional, Okogbenin, Sylvanus A., additional, Akpede, George O., additional, Schmitz, Herbert, additional, Asogun, Danny A., additional, and Günther, Stephan, additional

Published
2018
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33. Public awareness of Lassa fever in three rural communities of Nigeria.

Author

Oladeinde, Bankole Henry, Omoregie, Richard, and Odia, Ikponmwosa

Subjects
CHI-squared test, INFECTIOUS disease transmission, CONFIDENCE intervals, HEMORRHAGIC fever, QUESTIONNAIRES, SAMPLE size (Statistics), HEALTH literacy, DATA analysis software, ODDS ratio
Abstract

Lassa fever is endemic in west Africa. Persons at greatest risk are those living in rural areas with poor sanitary conditions and overcrowding. Against this background, this study aimed at assessing public awareness of Lassa fever among residents of three rural communities in Edo State, Nigeria. A total of 380 persons resident in rural Okada, Ogbese and Utese communities of Edo State, Nigeria were enrolled for this study. Age range of participants was between 15 and 69 years. A structured questionnaire was administered to all volunteer subjects to obtain relevant information. Irrespective of community studied, a total of 28 (7.4%) participants reported to have heard of Lassa fever. Male gender was associated with awareness of Lassa fever in all communities surveyed. The television was the most popular source of Lassa fever awareness in all communities studied. Among participants who reported to have heard of Lassa fever, vehicles of transmission of disease mentioned included mosquito bites 9 (32.1%), dog bites 7 (25%) and eating of rat-contaminated food 2 (7.1%). Sleeping under mosquito bed nets and intake of herbal concoction were the principal mode of prevention of Lassa fever reported by respondents. A total of 15 (53.4%) and 16 (57.1%) of persons aware of Lassa fever had no idea of any vehicle of transmission and mode of prevention of the disease, respectively. Grave misconceptions on mode of transmission and prevention of Lassa fever were observed in all communities surveyed. Renewed effort at enlightening residents of rural communities on causes, modes of transmission and prevention of Lassa fever is advocated. [ABSTRACT FROM PUBLISHER]

Published
2015
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34. Identification of Common CD8+ T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone.

Author

Sakabe, Saori, Hartnett, Jessica N., Nhi Ngo, Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Kanneh, Lansana, Cubitt, Beatrice, Garcia, Selma D., Ware, Brian C., Kotliar, Dylan, Robles-Sikisaka, Refugio, Gangavarapu, Karthik, Branco, Luis M., Eromon, Philomena, Odia, Ikponmwosa, Ogbaini-Emovon, Ephraim, Folarin, Onikepe, Okogbenin, Sylvanus, and Okokhere, Peter O.

Subjects
*T cells, *LASSA fever, *EPITOPES, *CELLULAR immunity, *HAPLOTYPES
Abstract

Early and robust T cell responses have been associated with survival from Lassa fever (LF), but the Lassa virus-specific memory responses have not been well characterized. Regions within the virus surface glycoprotein (GPC) and nucleoprotein (NP) are the main targets of the Lassa virus-specific T cell responses, but, to date, only a few T cell epitopes within these proteins have been identified. We identified GPC and NP regions containing T cell epitopes and HLA haplotypes from LF survivors and used predictive HLA-binding algorithms to identify putative epitopes, which were then experimentally tested using autologous survivor samples. We identified 12 CD8-positive (CD8+) T cell epitopes, including epitopes common to both Nigerian and Sierra Leonean survivors. These data should be useful for the identification of dominant Lassa virus-specific T cell responses in Lassa fever survivors and vaccinated individuals as well as for designing vaccines that elicit cell-mediated immunity. IMPORTANCE The high morbidity and mortality associated with clinical cases of Lassa fever, together with the lack of licensed vaccines and limited and partially effective interventions, make Lassa virus (LASV) an important health concern in its regions of endemicity in West Africa. Previous infection with LASV protects from disease after subsequent exposure, providing a framework for designing vaccines to elicit similar protective immunity. Multiple major lineages of LASV circulate in West Africa, and therefore, ideal vaccine candidates should elicit immunity to all lineages. We therefore sought to identify common T cell epitopes between Lassa fever survivors from Sierra Leone and Nigeria, where distinct lineages circulate. We identified three such epitopes derived from highly conserved regions within LASV proteins. In this process, we also identified nine other T cell epitopes. These data should help in the design of an effective pan-LASV vaccine. [ABSTRACT FROM AUTHOR]

Published
2020
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35. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Author

Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri AN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang'a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Muhammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O'Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, and Wilkinson E

Subjects
Africa epidemiology, Genomics, Humans, COVID-19 epidemiology, COVID-19 virology, Epidemiological Monitoring, Pandemics, SARS-CoV-2 genetics
Abstract

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Published
2022
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