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151. High crossreactivity of human T cell responses between Lassa virus lineages.

Author

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

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

Lassa virus infects hundreds of thousands of people each year across rural West Africa, resulting in a high number of cases of Lassa fever (LF), a febrile disease associated with high morbidity and significant mortality. The lack of approved treatments or interventions underscores the need for an effective vaccine. At least four viral lineages circulate in defined regions throughout West Africa with substantial interlineage nucleotide and amino acid diversity. An effective vaccine should be designed to elicit Lassa virus specific humoral and cell mediated immunity across all lineages. Most current vaccine candidates use only lineage IV antigens encoded by Lassa viruses circulating around Sierra Leone, Liberia, and Guinea but not Nigeria where lineages I-III are found. As previous infection is known to protect against disease from subsequent exposure, we sought to determine whether LF survivors from Nigeria and Sierra Leone harbor memory T cells that respond to lineage IV antigens. Our results indicate a high degree of cross-reactivity of CD8+ T cells from Nigerian LF survivors to lineage IV antigens. In addition, we identified regions within the Lassa virus glycoprotein complex and nucleoprotein that contributed to these responses while T cell epitopes were not widely conserved across our study group. These data are important for current efforts to design effective and efficient vaccine candidates that can elicit protective immunity across all Lassa virus lineages.

Published
2020
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152. Acute Lassa Virus Encephalitis with Lassa Virus in the Cerebrospinal Fluid but Absent in the Blood: A Case Report with a Positive Outcome

Author

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

Subjects
Lassa virus, Encephalitis, Ribavirin, Nigeria, Neurology. Diseases of the nervous system, RC346-429
Abstract

It is rare both to have the central nervous system (CNS) as the main focus in the acute phase of Lassa fever infection without associated bleeding, and to find Lassa virus (LAV) in the cerebrospinal fluid (CSF) but not in the serum. We report the case of a 38-year-old Nigerian woman with mainly CNS manifestation of Lassa fever. She was admitted twice within 11 days because of persistent fever. A clinical diagnosis of acute LAV encephalitis was made because of a high index of suspicion and CNS involvement confirmed by positive reverse transcriptase polymerase chain reaction (RT-PCR) for LAV in the CSF, while her blood was repeatedly negative for LAV by RT-PCR test. She recovered fully following supportive care coupled with treatment with an 18-day course of ribavirin, and suffered no long-term neurological complication or relapse. Post-treatment CSF examination by RT-PCR did not detect LAV.

Published
2018
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153. Factors contributing to anaemia after uncomplicated falciparum malaria in under five year-old Nigerian children ten years following adoption of artemisinin-based combination therapies as first-line antimalarials

Author

Akintunde Sowunmi, Bayo Fatunmbi, Kazeem Akano, Olubunmi A. Wewe, Chimere Agomo, Finomo Finomo, Joy Ebenebe, Nma Jiya, Jose Ambe, Robinson Wammanda, Godwin Ntadom, Olugbenga Mokuolu, George Emechebe, Nnenna Ezeigwe, Adejumoke I. Ayede, Elsie O. Adewoye, Grace O. Gbotosho, Onikepe A. Folarin, Christian T. Happi, Stephen Oguche, Wellington A. Oyibo, and Francis Useh

Subjects
Plasmodium falciparum malaria-associated anaemia, Artemisinin-based combination treatments, Children, Nigeria, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Artemisinin-based combination therapies (ACTs) have remained efficacious treatments of acute falciparum malaria in many endemic areas but there is little evaluation of factors contributing to the anaemia of acute falciparum malaria following long term adoption of ACTs as first-line antimalarials in African children. Methods Malarious 4% were evaluated by stepwise multiple logistic regression models. Survival analysis and kinetics of DAFH were evaluated by Kaplan-Meier estimator and non-compartment model, respectively. Results Pre-treatment, 355 of 959 children were anaemic. Duration of illness >2 days and parasitaemia ≤10,000 μL−1 were independent predictors of anaemia pre-treatment. EAA occurred in 301 of 604 children. Predictors of EAA were age ≤ 15 months, history of fever pre-treatment and enrolment haematocrit ≤35%. The probabilities of progression from normal haematocrit to EAA were similar for all treatments. MAFH >4% occurred in 446 of 694 children; its predictors were anaemia pre-treatment, enrolment parasitaemia ≤50,000 μL−1, parasitaemia one day post-treatment initiation and gametocytaemia. DAFH >4% occurred in 334 of 719 children; its predictors were history of fever pre-and fever 1 day post-treatment initiation, haematocrit ≥37%, and parasitaemia >100,000 μL−1. In 432 children, declines in DAFH deficits were monoexponential with overall estimated half-time of 2.2d (95% CI 1.9–2.6). Area under curve of deficits in DAFH versus time and estimated half-time were significantly higher in non-anaemic children indicating greater loss of haematocrit in these children. Conclusion After ten years of adoption of ACTs, anaemia is common pre-and early post-treatment, falls in haematocrit attributable to a single infection is high, and DAFH >4% is common and significantly lower in anaemic compared to non-anaemic Nigerian children. Trial registration Pan African Clinical Trial Registry (PACTR) [ PACTR201709002064150, 1 March 2017 ].

Published
2017
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158. Prime editing strategies to mediate exon skipping in DMD gene

Author

Happi Mbakam, Cedric, primary, Roustant, Jeanne, additional, Rousseau, Joel, additional, Yameogo, Pouire, additional, Lu, Yaoyao, additional, Bigot, Anne, additional, Mamchaoui, Kamel, additional, Mouly, Vincent, additional, Lamothe, Gabriel, additional, and Tremblay, Jacques P., additional

Published
2023
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159. New nomenclature for mpox (monkeypox) and monkeypox virus clades

Author

David Ulaeto, Alexander Agafonov, Jennifer Burchfield, Lisa Carter, Christian Happi, Robert Jakob, Eva Krpelanova, Krutika Kuppalli, Elliot J Lefkowitz, Matthew R Mauldin, Tulio de Oliveira, Bernard Onoja, James Otieno, Andrew Rambaut, Lorenzo Subissi, Adesola Yinka-Ogunleye, and Rosamund F Lewis

Subjects
Infectious Diseases
Published
2023

161. Antibodies from Sierra Leonean and Nigerian Lassa fever survivors cross-react with recombinant proteins representing Lassa viruses of divergent lineages

Author

Heinrich, Megan L., Boisen, Matthew L., Nelson, Diana K. S., Bush, Duane J., Cross, Robert W., Koval, Anatoliy P., Hoffmann, Andrew R., Beddingfield, Brandon J., Hastie, Kathryn M., Rowland, Megan M., Aimukanova, Irina, Koval, Sophia, Lathigra, Raju, Borisevich, Viktoriya, Momoh, Mambu, Sandi, John Demby, Goba, Augustine, Odia, lkponmwosa, Baimba, Francis, Aiyepada, John O., Ebo, Benevolence, Eromon, Philomena, Ugwu, Chinedu, Folarin, Onikepe, Olumade, Testimony, Onyechi, MacDonald N., Etafo, Johnson, Adeyemi, Rashidat, Ella, Elijah E., Aminu, Maryam, Gomerep, Simji S., Eke, Matthew Afam, Ogunsanya, Olusola, Akpede, George O., Asogun, Danny O., Okogbenin, Sylvanus A., Okokhere, Peter O., Holst, Johan, Shaffer, Jeffrey G., Schieffelin, John S., Geisbert, Thomas W., Saphire, Erica Ollmann, Happi, Christian T., Grant, Donald S., Garry, Robert F., and Branco, Luis M.

Published
2020
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162. 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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163. 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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164. 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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165. World Antimalarial Resistance Network (WARN) III: Molecular markers for drug resistant malaria

Author

Plowe, Christopher V, Roper, Cally, Barnwell, John W, Happi, Christian T, Joshi, Hema H, Mbacham, Wilfred, Meshnick, Steven R, Mugittu, Kefas, Naidoo, Inbarani, Price, Ric N, Shafer, Robert W, Sibley, Carol H, Sutherland, Colin J, Zimmerman, Peter A, and Rosenthal, Philip J

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, HIV/AIDS, Malaria, Patient Safety, Genetics, Orphan Drug, Infectious Diseases, Antimicrobial Resistance, Vector-Borne Diseases, Rare Diseases, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Infection, Good Health and Well Being, Antimalarials, Clinical Trials as Topic, Databases as Topic, Drug Resistance, Drug Therapy, Combination, Genetic Markers, Global Health, Humans, Internet, Molecular Epidemiology, Parasitic Sensitivity Tests, Sentinel Surveillance, Microbiology, Public Health and Health Services, Tropical Medicine, Medical microbiology, Public health
Abstract

Molecular markers for drug resistant malaria represent public health tools of great but mostly unrealized potential value. A key reason for the failure of molecular resistance markers to live up to their potential is that data on the their prevalence is scattered in disparate databases with no linkage to the clinical, in vitro and pharmacokinetic data that are needed to relate the genetic data to relevant phenotypes. The ongoing replacement of older monotherapies for malaria by new, more effective combination therapies presents an opportunity to create an open access database that brings together standardized data on molecular markers of drug resistant malaria from around the world. This paper presents a rationale for creating a global database of molecular markers for drug resistant malaria and for linking it to similar databases containing results from clinical trials of drug efficacy, in vitro studies of drug susceptibility, and pharmacokinetic studies of antimalarial drugs, in a World Antimalarial Resistance Network (WARN). This database will be a global resource, guiding the selection of first line drugs for treating uncomplicated malaria, for preventing malaria in travelers and for intermittent preventive treatment of malaria in pregnant women, infants and other vulnerable groups. Perhaps most important, a global database for molecular markers of drug resistant malaria will accelerate the identification and validation of markers for resistance to artemisinin-based combination therapies and, thereby, potentially prolong the useful therapeutic lives of these important new drugs.

Published
2007

166. Genomic Characterization of Alphacoronavirus from Mops Condylurus Bats, Nigeriagenomic Characterization of Alphacoronavirus from Mops Condylurus Bats, Nigeria

Author

George, Uwem, primary, George, Oluwadamilola, additional, Oguzie, Judith, additional, Osasona, Oluwadamilola, additional, Motayo, Babatunde, additional, Kamani, Joshua, additional, Eromon, Philomena, additional, Folarin, Onikepe, additional, Happi, Anise, additional, Komolafe, Isaac, additional, and Happi, Christian T., additional

Published
2023
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167. Chemistry and pharmacological aspects of Aridanin, a lead compound from Tetrapleura tetraptera (Fabaceae)

Author

Klev Gaïtan Sikam, Virginia Kien Ntabo, Gervais Mouthe Happi, Livine Zemo Meikeu, and Jean Duplex Wansi

Abstract

Aridanin, a triterpenoid N-acetylglycoside has been obtained from chemical investigations of the root of Tetrapleura tetraptera, a well-known seasoning spice from Cameroonian food. The structure of the compound has been established using its NMR data and by comparison of that data with the one reported in the literature. Further evidence has been compiled from literature and discussed on the occurrence, the extraction, isolation and analytical techniques as well as the reported biological activities of aridanin. Based on its potency and its high yield in Tetrapleura tetraptera fruits, the compound can be considered as lead compound in the development of medicine for the control of schistosomiasis and bacterial infections caused by the bacterial strainsE. coli, E. smartii and E. aeroginese. this paper sheds light on the compound aridanin which deserves more attention in the development of a new potent drug or on the formulation of Tetrapleura tetraptera for effective use by the local population.

Published
2022

168. Potential of Streptomyces in producing antiplasmodial lead compounds

Author

Gervais Mouthe Happi, Virginia Kien Ntabo, Désiré Soh, and Jean Duplex Wansi

Abstract

Streptomyces are bacteria of great importance for several decades. Numerous potent metabolites characterized as antibiotics including macrolides and polypetides have been reported from Streptomyces and developed as effective drugs for the treatment of several illnesses. Therefore, Streptomyces can be considered as an important source of bioactive compounds which might help in the eradication of malaria which remains one of the greatest threats to human life, especially in the tropical and sub-tropical regions. The reported in vitro antiplasmodial properties of chemical constituents from Streptomyces strains have led to promising results like bafilomycin A1 (9), concanamycin A (10), elaiophylin (17), cyclomarin C (23), urdamycinone E (44), geldanamycin (52) and metacycloprodigiosin (74) which individually exhibited strong antiplasmodial activity against the chloroquine-resistant strain Plasmodium falciparum K1 with IC50 values of 0.041 μg/ml, 0.2 nM, 0.22 μg/ml, 0.24 μg/ml, 0.0534 μg/ml, 0.35 μg/ml and 0.0050 μg/ml, respectively. In some cases, the tested compound was most active than the reference and without observed toxicity until the highest concentration. However, more in vivo and toxicity studies are necessary for further guidance in the process of drug development. To the best of our knowledge, no specific review has been done on the potential of Streptomyces in furnishing antiplasmodial compounds for malaria control. This paper aims to compile the literature up to 2021 on antiplasmodial compounds isolated from Streptomyces for easy and rapid access to the literature for further investigations in continuity.

Published
2022

173. Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Author

Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D'Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart L. Haagmans, Julian A. Hiscox, Umaru Jah, Jeffrey R. Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke W. Meredith, James Qu, Joshua Quick, Suzan D. Pas, My V. T. Phan, Georgios Pollakis, Chantal B. Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. G. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson 0002, Kendra West, Shannon Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia O. Blyden, Fatorma Bolay, Miles W. Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian T. Happi, Edward C. Holmes, Brima Kargbo, Sakoba Keïta, Paul Kellam, Marion Koopmans, Jens H. Kuhn, Nicholas J. Loman, N'Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo F. Palacios, Oliver G. Pybus, Pardis C. Sabeti, Amadou Sall, Ute Ströher, Isatta Wurie, Marc A. Suchard, Philippe Lemey, and Andrew Rambaut

Published
2017
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176. 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, A-RN, Gueye, AS, Sangare, AK, Ouedraogo, A-S, Sow, A, Musa, AO, Sesay, AK, Abias, AG, Elzagheid, A, Lagare, A, Kemi, A-S, 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, A, 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, B-M, 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, Rafai, 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, F, Treurnicht, F, Onikepe, F, Ntoumi, F, Muyembe, FM, Ragomzingba, FEZ, Dratibi, FA, Iyanu, F-A, 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, Mohammad, IA, Ssewanyana, I, Wurie, I, Konstantinus, IS, Halatoko, JWA, Ayei, J, Sonoo, J, Makangara, J-CC, Tamfum, J-JM, Heraud, J-M, 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, Martins, LDO, Chabuka, L, Olubayo, L, Ojok, LD, Deng, LL, Ochola-Oyier, L, Tyers, L, Mine, M, Ramuth, M, Mastouri, M, ElHefnawi, M, Mbanne, M, Matsheka, M, Kebabonye, M, Diop, M, Momoh, M, Lima Mendonca, MDL, Venter, M, Paye, MF, Faye, M, Nyaga, MM, Mareka, M, Damaris, M-M, 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, N-Y, 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, O-E, 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, Wilkinson, E, 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, A-RN, Gueye, AS, Sangare, AK, Ouedraogo, A-S, Sow, A, Musa, AO, Sesay, AK, Abias, AG, Elzagheid, A, Lagare, A, Kemi, A-S, 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, A, 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, B-M, 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, Rafai, 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, F, Treurnicht, F, Onikepe, F, Ntoumi, F, Muyembe, FM, Ragomzingba, FEZ, Dratibi, FA, Iyanu, F-A, 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, Mohammad, IA, Ssewanyana, I, Wurie, I, Konstantinus, IS, Halatoko, JWA, Ayei, J, Sonoo, J, Makangara, J-CC, Tamfum, J-JM, Heraud, J-M, 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, Martins, LDO, Chabuka, L, Olubayo, L, Ojok, LD, Deng, LL, Ochola-Oyier, L, Tyers, L, Mine, M, Ramuth, M, Mastouri, M, ElHefnawi, M, Mbanne, M, Matsheka, M, Kebabonye, M, Diop, M, Momoh, M, Lima Mendonca, MDL, Venter, M, Paye, MF, Faye, M, Nyaga, MM, Mareka, M, Damaris, M-M, 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, N-Y, 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, O-E, 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

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

177. The African Society of Human Genetics successfully launches global data science workshops

Author

Landouré, Guida, Ndiaye, Rokhaya, Dandara, Collet, Mutesa, Leon, Ramsay, Michele, El-Kamah, Ghada, Sirugo, Giorgio, Makani, Julie, Sadki, Khalid, Alimohamed, Mohamed Zahir, Nkya, Siana, Gaye, Amadou, Ramesar, Raj, Choudhury, Ananyo, Happi, Christian, Munung, Nchangwi Syntia, Kherji, Nadia, Hotchkiss, Jade, Ras, Verena, Ghansay, Anita, Musanabaganwa, Clarisse, Esoh, Kevin Kum, Adadey, Samuel Mawuli, Coughlan, Simone Christina, Nembaware, Victoria, Bennett, Declan, Chimusa, Emile R., Chikowore, Tinashe, Daodu, Richard, Bitoungui, Valentina Ngo, Williams, Scott M., Fatumo, Segun, Healy, Sandra, Seoighe, Cathal, and Wonkam, Ambroise

Published
2023
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178. Molecular Docking, Pharmacokinetics and Molecular Dynamics Simulation Studies of Some Bioactive Compounds Isolated from Entandrophragma congoënse for Antiplasmodial Activity

Author

Shina Salau, Désiré Soh, Gervais Mouthé Happi, and Sikiru Akinyeye Ahmed

Subjects
Management of Technology and Innovation
Abstract

As a follow-up to earlier reported works on the phytochemical study of some isolated bioactive compounds from the root and bark of Entandrophragma congoënse as potent anti-plasmodium drugs (Happi et. al.2005), some of the isolated compounds were tested in vitro for antiplasmodial and cytotoxicity but no insight was given into the binding affinities of these compounds, the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity), drug-likeness studies as well as molecular dynamics simulation of some of the isolates. Hence, a total of 21 compounds including 19 isolates and 2 standard drugs were computationally studied for antimalarial activity against the target receptor with Protein Data Bank code (PDB code: 5TBO), but only 4 of the isolated compounds (L1, L2, L4 and L15) showed promise potent hits against Plasmodium. The results of molecular docking, ADMET studies and molecular dynamics simulations reveal that compound L15, when isolated, can alone, or together with other qualified compounds such as L1, L2 and L4 provide a better inhibition rating compared to Chloroquine® (L21) the FDA-approved drug for the treatment of malaria.

Published
2022

179. Design, Implementation, and Coordination of Malaria Therapeutic Efficacy Studies in Nigeria in 2018

Author

Olukosi, Adeola Yetunde, primary, Musa, Adesola Zaidat, additional, Ogbulafor, Nnenna, additional, Aina, Oluwagbemiga, additional, Mokuolu, Olugbenga, additional, Oguche, Stephen, additional, Wammanda, Robinson, additional, Okafor, Henrietta, additional, Ekama, Sabdat Ozichu, additional, David, Agatha Nkiru, additional, Happi, Christian Tientcha, additional, Ozor, Lynda, additional, Babatunde, Seye, additional, Ijezie, Simon N., additional, Uhomoibhi, Perpetua E., additional, Awolola, Samson Taiwo, additional, Mohammed, Audu Bala, additional, and Salako, Babatunde Lawal, additional

Published
2023
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181. New nomenclature for mpox (monkeypox) and monkeypox virus clades

Author

Ulaeto, David, primary, Agafonov, Alexander, additional, Burchfield, Jennifer, additional, Carter, Lisa, additional, Happi, Christian, additional, Jakob, Robert, additional, Krpelanova, Eva, additional, Kuppalli, Krutika, additional, Lefkowitz, Elliot J, additional, Mauldin, Matthew R, additional, de Oliveira, Tulio, additional, Onoja, Bernard, additional, Otieno, James, additional, Rambaut, Andrew, additional, Subissi, Lorenzo, additional, Yinka-Ogunleye, Adesola, additional, and Lewis, Rosamund F, additional

Published
2023
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183. Reemergence of Human Monkeypox in Nigeria, 2017

Author

Adesola Yinka-Ogunleye, Olusola Aruna, Dimie Ogoina, Neni Aworabhi, Womi Eteng, Sikiru Badaru, Amina Mohammed, Jeremiah Agenyi, E.N. Etebu, Tamuno-Wari Numbere, Adolphe Ndoreraho, Eduard Nkunzimana, Yahyah Disu, Mahmood Dalhat, Patrick Nguku, Abdulaziz Mohammed, Muhammad Saleh, Andrea M. McCollum, Kimberly Wilkins, Ousmane Faye, Amadou Sall, Christian Happi, Nwando Mba, Olubumi Ojo, and Chikwe Ihekweazu

Subjects
Human monkeypox, disease, reemergence, Nigeria, zoonoses, viruses, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

In Nigeria, before 2017 the most recent case of human monkeypox had been reported in 1978. By mid-November 2017, a large outbreak caused by the West African clade resulted in 146 suspected cases and 42 laboratory-confirmed cases from 14 states. Although the source is unknown, multiple sources are suspected.

Published
2018
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184. Experimental study and comparative analysis of pitting fault in spur gear system

Author

Yakeu Happi, Kemajou Herbert, Tchomeni Kouejou, Bernard Xavier, Anyika Alugongo, Alfayo, Yakeu Happi, Kemajou Herbert, Tchomeni Kouejou, Bernard Xavier, and Anyika Alugongo, Alfayo

Abstract

This paper uses a dynamic six-degree-of-freedom model that considers torsional and lateral motions to predict the impact of pitting on vibration parameters in a spur gearbox for various operating speeds and torque loads. The study examines the dynamic characteristics of a gearbox with localized pitting damage on a single gear tooth using theoretical and experimental approaches. The research analyzes the forced vibrations of a single-stage spur gear system with pitting damage, which includes variations in mesh stiffness, damping, and gear error excitation, to identify symptoms of default. The equation of motion for the rotary gearbox system is established using the Lagrangian method in tandem with Short-Time Fourier Transform (STFT) and frequency-RPM map fault diagnosis. During real-time vibration monitoring, vibration signals are captured via accelerometers and processed in both the time and frequency domains using the LabVIEW data acquisition signal processing package to extract diagnostic information. The experimental findings demonstrate how vibration analysis combined with time-frequency processing can recognize machine conditions even in harsh operational conditions. Moreover, the experimental results indicate a significant similarity with the theoretical analysis and validate the effectiveness of the RPM frequency technique-based pitting detection method, which can be an asset in gear fault monitoring.

Published
2023

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

Author

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

Subjects
case fatality, caseload, center's experience, implications, Lassa fever, outbreaks, Public aspects of medicine, RA1-1270
Published
2019
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186. Detection of Antibody and Antigen for Lassa Virus Nucleoprotein in Monkeys from Southern Nigeria

Author

Bamidele Nyemike Ogunro, Babasola Oluseyi Olugasa, Adeyemi Kayode, Olayinka Olabisi Ishola, Oluseyi Noah Kolawole, Eugene Amiewanlen Odigie, and Christian Happi

Subjects
ELISA, Lassa fever virus, monkeys, sylvatic cycle, Public aspects of medicine, RA1-1270
Abstract

Lassa fever is a deadly viral haemorrhagic fever caused by Lassa Virus (LASV). Rodents, especially, Mystomys natalensis, are the known reservoirs of LASV and humans are the defined hosts. Monkeys share many illnesses with humans and experimental LASV infections in monkeys are fatal but natural LASV infection of monkeys has not been reported. Serum samples obtained between August 2015 and December 2017 from 62 monkeys belonging to six species in Southern Nigeria were tested for LASV as part of an ongoing surveillance of monkeys in the region for zoonotic pathogens. Commercially available Recombinant LASV (ReLASV) Pan-Lassa enzyme-linked immunosorbent assay (ELISA) test kits (Zalgen Labs, Germantown, MD, USA) were used to detect antibodies (IgG and IgM) and antigen specific for LASV nucleoprotein in the sera. Lassa-fever-specific IgG and IgM, and antigen specific for LASV nucleoprotein were detected in 5/62, 0/62, and 1/62 samples, respectively. The presence of LASV-specific antibodies in the sera suggests natural exposure to the virus, while the presence of LASV antigen may mean that monkeys are carriers of the virus. There is a need to broaden Lassa fever surveillance to include nonhuman primates (NHPs) for their probable role in the epidemiology of the disease. HIGHLIGHTS •Rodents are the natural reservoirs of Lassa fever virus (LASV) and humans are the defined hosts. •Experimental LASV infections in non-human primates (NHP) are fatal but natural infection of NHP with the virus have not been reported. •We detected antigen and antibody specific for LASV in free-living Monkeys from southern Nigeria which implies that monkeys in the region are naturally exposed to LASV and are probable carriers of the virus.

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

Author

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

Subjects
case fatality, caseload, center's experience, implications, Lassa fever, outbreaks, Public aspects of medicine, RA1-1270
Abstract

Background: The general lack of comprehensive data on the trends of Lassa fever (LF) outbreaks contrasts with its widespread occurrence in West Africa and is an important constraint in the design of effective control measures. We reviewed the contribution of LF to admissions and mortality among hospitalized patients from 2001 to 2018 in the bid to address this gap.Methods: Observational study of LF caseload and mortality from 2001 to 18 in terms of the contribution of confirmed LF to admissions and deaths, and case fatality (CF) among patients with confirmed LF at a specialist center in Nigeria. The diagnosis of LF was confirmed using reverse transcription polymerase chain reaction (RT-PCR) test, and medians and frequencies were compared using Kruskal-Wallis, Mann-Whitney and χ2 tests, with p-values

Published
2019
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188. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Author

Olawoye, Idowu B., primary, Oluniyi, Paul E., additional, Oguzie, Judith U., additional, Uwanibe, Jessica N., additional, Kayode, Adeyemi T., additional, Olumade, Testimony J., additional, Ajogbasile, Fehintola V., additional, Parker, Edyth, additional, Eromon, Philomena E., additional, Abechi, Priscilla, additional, Sobajo, Tope, additional, Ugwu, Chinedu, additional, Uwem, George, additional, Ayoade, Femi, additional, Akano, Kazeem, additional, Oyejide, Nicholas, additional, Fred-Akintunwa, Iyanuoluwa, additional, Adedotun-Sulaiman, Kemi, additional, Brimmo, Farida, additional, Adegboyega, Benjamin, additional, Philip, Courage, additional, Adeleke, Ayomide, additional, Chukwu, Grace C., additional, Muhammad, Ahmed I., additional, Ope-ewe, Oludayo O., additional, Otitoola, Shobi, additional, Ogunsanya, Olusola A., additional, Saibu, Mudasiru F., additional, Sijuwola, Ayotunde E., additional, Ezekiel, Grace O., additional, John, Oluwagboadurami G., additional, Akin-John, Julie O., additional, Akinlo, Oluwasemilogo O., additional, Fayemi, Olanrewaju O., additional, Ipaye, Testimony O., additional, Nwodo, Deborah C., additional, Omoniyi, Abolade E., additional, Omwanghe, Iyobosa B., additional, Terkuma, Christabel A., additional, Okolie, Johnson, additional, Ayo-Ale, Olubukola, additional, Ikponmwosa, Odia, additional, Benevolence, Ebo, additional, Naregose, Okonofua, additional, Patience, Akhilomen, additional, Blessing, Osiemi, additional, Micheal, Airende, additional, Jacqueline, Agbukor, additional, John, Aiyepada, additional, Ebhodaghe, Paulson, additional, Racheal, Omiunu, additional, Rita, Esumeh, additional, Rosemary, Giwa, additional, Solomon, Ehikhametalor, additional, Anieno, Ekanem, additional, Edna, Yerumoh, additional, Chris, Aire, additional, Donatus, Adomeh, additional, Ogbaini, Ephraim, additional, Tatfeng, Mirabeau Y., additional, Omunakwe, Hannah E., additional, Bob-Manuel, Mienye, additional, Ahmed, Rahaman, additional, Onwuamah, Chika, additional, Shaibu, Joseph, additional, Okwuraiwe, Azuka, additional, Atage, Anthony E., additional, Bock-Oruma, Andrew, additional, Daramola, Funmi, additional, Fajola, Akinwumi, additional, Ntia, Nsikak-Abasi, additional, Ekpo, Julie J., additional, Moses, Anietie, additional, Moore-Igwe, Worbianueri B., additional, Yusuf, Ibrahim F., additional, Fakayode, Enoch O., additional, Akinola, Monilade, additional, Kida, Ibrahim, additional, Oderinde, Bamidele S., additional, Wudiri, Zara, additional, Adeyemi, Olufemi O., additional, Akanbi, Olusola, additional, Ahumibe, Anthony, additional, Akinpelu, Afolabi, additional, Ayansola, Oyeronke, additional, Babatunde, Olajumoke, additional, Omoare, Adesuyi, additional, Chukwu, Chimaobi, additional, Mba, Nwando, additional, Omoruyi, Ewean C., additional, Adeniji, Johnson A., additional, Adewunmi, Moses O., additional, Olayinka, Oluseyi, additional, Olasunkanmi, Olisa, additional, Akande, Olatunji, additional, Nwafor, Ifeanyi, additional, Ekeh, Matthew, additional, Ndoma, Erim, additional, Ewah, Richard, additional, Duruihuoma, Rosemary, additional, Abu, Augustine, additional, Odeh, Elizabeth, additional, Onyia, Venatious, additional, Ojide, Kingsley C., additional, Okoro, Sylvanus, additional, Igwe, Daniel, additional, Khan, Kamran, additional, Ajayi, Anthony N., additional, Ugwu, Ebhodaghe Ngozi, additional, Ugwu, Collins N., additional, Ukwuaja, Kingsley, additional, Ogah, Emeka O., additional, Abejegah, Chukwuyem, additional, Adedosu, Nelson, additional, Ayodeji, Olufemi, additional, Isamotu, Rafiu O., additional, Gadzama, Galadima, additional, Petros, Brittany, additional, Siddle, Katherine J., additional, Schaffner, Stephen, additional, Akpede, George, additional, Erameh, Cyril Oshomah, additional, Baba, Marycelin, additional, Oladiji, Femi, additional, Audu, Rosemary, additional, Ndodo, Nnaemeka, additional, Fowotade, Adeola, additional, Okogbenin, Sylvanus, additional, Okokhere, Peter, additional, Park, Danny, additional, Mcannis, Bronwyn, additional, Adetifa, Ifedayo, additional, Ihekweazu, Chikwe, additional, Salako, Babatunde L., additional, Tomori, Oyewale, additional, Happi, Anise N., additional, Folarin, Onikepe A., additional, Andersen, Kristian G., additional, Sabeti, Pardis C., additional, and Happi, Christian T., additional

Published
2022
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190. Detection of Alpha- and Betacoronaviruses in Frugivorous and Insectivorous Bats in Nigeria

Author

George, Uwem, primary, George, Oluwadamilola, additional, Oragwa, Arthur, additional, Motayo, Babatunde, additional, Kamani, Joshua, additional, Adamu, Andrew, additional, Sowemimo, Oluyomi, additional, Adeleke, Richard, additional, Abalaka, Samson, additional, Sani, Nuhu, additional, Oguzie, Judith, additional, Eromon, Philomena, additional, Folarin, Onikepe, additional, Happi, Anise, additional, Komolafe, Isaac, additional, and Happi, Christian, additional

Published
2022
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191. Increased Prevalence of Lassa Fever Virus-Positive Rodents and Diversity of Infected Species Found during Human Lassa Fever Epidemics in Nigeria

Author

Happi, Anise N., primary, Olumade, Testimony J., additional, Ogunsanya, Olusola A., additional, Sijuwola, Ayotunde E., additional, Ogunleye, Seto C., additional, Oguzie, Judith U., additional, Nwofoke, Cecilia, additional, Ugwu, Chinedu A., additional, Okoro, Samuel J., additional, Otuh, Patricia I., additional, Ngele, Louis N., additional, Ojo, Oluwafemi O., additional, Adelabu, Ademola, additional, Adeleye, Roseline F., additional, Oyejide, Nicholas E., additional, Njaka, Clinton S., additional, Heeney, Jonathan L., additional, and Happi, Christian T., additional

Published
2022
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192. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

Author

Happi, Christian, primary, Adetifa, Ifedayo, additional, Mbala, Placide, additional, Njouom, Richard, additional, Nakoune, Emmanuel, additional, Happi, Anise, additional, Ndodo, Nnaemeka, additional, Ayansola, Oyeronke, additional, Mboowa, Gerald, additional, Bedford, Trevor, additional, Neher, Richard A., additional, Roemer, Cornelius, additional, Hodcroft, Emma, additional, Tegally, Houriiyah, additional, O’Toole, Áine, additional, Rambaut, Andrew, additional, Pybus, Oliver, additional, Kraemer, Moritz U. G., additional, Wilkinson, Eduan, additional, Isidro, Joana, additional, Borges, Vítor, additional, Pinto, Miguel, additional, Gomes, João Paulo, additional, Freitas, Lucas, additional, Resende, Paola C., additional, Lee, Raphael T. C., additional, Maurer-Stroh, Sebastian, additional, Baxter, Cheryl, additional, Lessells, Richard, additional, Ogwell, Ahmed E., additional, Kebede, Yenew, additional, Tessema, Sofonias K., additional, and de Oliveira, Tulio, additional

Published
2022
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193. An Outbreak of Ebola Virus Disease in the Lassa Fever Zone

Author

Goba, Augustine, Khan, S. Humarr, Fonnie, Mbalu, Fullah, Mohamed, Moigboi, Alex, Kovoma, Alice, Sinnah, Vandi, Yoko, Nancy, Rogers, Hawa, Safai, Siddiki, Momoh, Mambu, Koroma, Veronica, Kamara, Fatima K., Konowu, Edwin, Yillah, Mohamed, French, Issa, Mustapha, Ibraham, Kanneh, Franklyn, Foday, Momoh, McCarthy, Helena, Kallon, Tiangay, Kallon, Mustupha, Naiebu, Jenneh, Sellu, Josephine, Jalloh, Abdul A., Gbakie, Michael, Kanneh, Lansana, Massaly, James L. B., Kargbo, David, Kargbo, Brima, Vandi, Mohamed, Gbetuwa, Momoh, Gevao, Sahr M., Sandi, John D., Jalloh, Simbirie C., Grant, Donald S., Blyden, Sylvia O., Crozier, Ian, Schieffelin, John S., McLellan, Susan L., Jacob, Shevin T., Boisen, Matt L., Hartnett, Jessica N., Cross, Robert W., Branco, Luis M., Andersen, Kristian G., Yozwiak, Nathan L., Gire, Stephen K., Tariyal, Ridhi, Park, Daniel J., Haislip, Allyson M., Bishop, Christopher M., Melnik, Lilia I., Gallaher, William R., Wimley, William C., He, Jing, Shaffer, Jeffrey G., Sullivan, Brian M., Grillo, Sonia, Oman, Scott, Garry, Courtney E., Edwards, Donna R., McCormick, Stephanie J., Elliott, Deborah H., Rouelle, Julie A., Kannadka, Chandrika B., Reyna, Ashley A., Bradley, Benjamin T., Yu, Haini, Yenni, Rachael E., Hastie, Kathryn M., Geisbert, Joan B., Kulakosky, Peter C., Wilson, Russell B., Oldstone, Michael B. A., Pitts, Kelly R., Henderson, Lee A., Robinson, James E., Geisbert, Thomas W., Saphire, Erica Ollmann, Happi, Christian T., Asogun, Danny A., Sabeti, Pardis C., and Garry, Robert F.

Published
2016

194. Ebola Virus Epidemiology and Evolution in Nigeria

Author

Folarin, Onikepe A., Ehichioya, Deborah, Schaffner, Stephen F., Winnicki, Sarah M., Wohl, Shirlee, Eromon, Philomena, West, Kendra L., Gladden-Young, Adrianne, Oyejide, Nicholas E., Matranga, Christian B., Deme, Awa Bineta, James, Ayorinde, Tomkins-Tinch, Christopher, Onyewurunwa, Kenneth, Ladner, Jason T., Palacios, Gustavo, Nosamiefan, Iguosadolo, Andersen, Kristian G., Omilabu, Sunday, Park, Daniel J., Yozwiak, Nathan L., Nasidi, Abdusallam, Garry, Robert F., Tomori, Oyewale, Sabeti, Pardis C., and Happi, Christian T.

Published
2016

195. Design, Implementation, and Coordination of Malaria Therapeutic Efficacy Studies in Nigeria in 2018

Author

Adeola Yetunde Olukosi, Adesola Zaidat Musa, Nnenna Ogbulafor, Oluwagbemiga Aina, Olugbenga Mokuolu, Stephen Oguche, Robinson Wammanda, Henrietta Okafor, Sabdat Ozichu Ekama, Agatha Nkiru David, Christian Tientcha Happi, Lynda Ozor, Seye Babatunde, Simon N. Ijezie, Perpetua E. Uhomoibhi, Samson Taiwo Awolola, Audu Bala Mohammed, and Babatunde Lawal Salako

Subjects
Infectious Diseases, Virology, Parasitology
Abstract

Prior to 2018, malaria therapeutic efficacy studies (TESs) in Nigeria were implemented separately at different sites, as assigned by the National Malaria Elimination Program (NMEP). In 2018, however, the NMEP engaged the Nigerian Institute of Medical Research to coordinate the 2018 TESs in 3 of 14 sentinel sites with the objective of standardizing their conduct across all three sites: Enugu, Kano, and Plateau states in three of six geopolitical zones. Artemether–lumefantrine and artesunate–amodiaquine, the two first-line drugs for treatment of acute uncomplicated malaria in Nigeria, were tested in both Kano and Plateau states. In Enugu State, however, artemether–lumefantrine and dihydroartemisinin–piperaquine were the test drugs, with dihydroartemisinin–piperaquine being tested for potential inclusion in Nigerian treatment policy. The TES was conducted in 6-month to 8-year-old children and was funded by the Global Fund with additional support from the WHO. A multipartite core team comprised of the NMEP, the WHO, the U.S. Presidential Malaria Initiative, academia, and the Nigerian Institute of Medical Research was set up to oversee the execution of the 2018 TES. This communication reports best practices adopted to guide its coordination, and lessons learned during in the process, including applying developed standard operating procedures, powering the sample size adequately for each site to report independently, training the investigating team for fieldwork, facilitating stratification of decisions, determining efficiencies derived from monitoring and quality assessment, and optimizing logistics. The planning and coordination of the 2018 TES activities is a model of a consultative process for the sustainability of antimalarial resistance surveillance in Nigeria.

Published
2023

196. AgroLD: a Knowledge Graph for the Plant Sciences

Author

Larmande, Pierre, Pitollat, Bertrand, Tando, Ndomassi, Pomie, Yann, Happi, Bill, Guignon, Valentin, Ruiz, Manuel, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), WEB Architecture x Semantic WEB x WEB of Data (WEB3), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT) [Hanoi], Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and ANR-22-CE23-0012,DIG-AI,Decouverte des interactions genotype-phenotype à l'aide de graphe de connaissance et d'IA(2022)

Subjects
FAIR data, Knowledge Graph, Bioinformatics, Linked Data, Plant Sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract

Démonstration; International audience; Recent advances in high-throughput technologies have revolutionized the analysis in the field of the plant sciences. However, there is an urgent need to effectively integrate and assimilate complementary information to understand the biological system in its entirety. We have developed AgroLD, a knowledge graph that exploits Semantic Web technologies to integrate data of interest for the plant science community e.g., rice, wheat, arabidopsis and in this way facilitate the formulation and validation of new scientific hypotheses. AgroLD contains around 900M triples created by annotating and integrating more than 100 datasets coming from 15 data sources. Our objective is to offer a domain specific knowledge platform to answer complex biological and plant sciences questions related to the implication of genes in, for instance, plant disease resistance or adaptative responses to climate change. In this demo, we present some results which currently focused on genomics, genetics and trait associations.

Published
2023

197. 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

198. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus [perspective]

Author

Happi, Christian, Adetifa, Ifedayo, Mbala, Placide, Njouom, Richard, Nakoune, Emmanuel, Happi, Anise, Ndodo, Nnaemeka, Ayansola, Oyeronke, Mboowa, Gerald, Bedford, Trevor, Neher, Richard A, Roemer, Cornelius, Hodcroft, Emma, Tegally, Houriiyah, O'Toole, Áine, Rambaut, Andrew, Pybus, Oliver, Kraemer, Moritz U G, Wilkinson, Eduan, Isidro, Joana, Borges, Vítor, Pinto, Miguel, Gomes, João Paulo, Freitas, Lucas, Resende, Paola C, Lee, Raphael T C, Maurer-Stroh, Sebastian, Baxter, Cheryl, Lessells, Richard, Ogwell, Ahmed E, Kebede, Yenew, Tessema, Sofonias K, and de Oliveira, Tulio

Subjects
360 Social problems & social services, 610 Medicine & health
Abstract

We propose a novel, non-discriminatory classification of monkeypox virus. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomics surveillance.

Published
2022

199. Evaluation of the anti-inflammatory activity of Garcinia kola capsules on Gonarthrosis and low back pain

Author

null Happi Monthé Adelaïde Nathalie, null Djoko Ernest, and null Ngandeu Singwe Madeleine

Abstract

Garcinia kola (Clusiaceae) commonly known as "Bitter cola", is a shrub from the forests of Central and East Africa. In Cameroon it is found in Mbam and Moungo divisions. Garcinia kola seeds are widely consumed by local populations, sometimes in search of a simple pleasure, sometimes in search of its multiple pharmacological properties. The main objective of this study was to evaluate the anti-inflammatory activity and the tolerance of Garcinia kola capsules (BTK capsules *) on gonarthrosis and lumbago. A pilot study was carried out on 90 patients (68 women and 22 men). The patients were divided into 3 groups. Patients in the first group received Garcinia kola capsules at a dose of 800 mg per day while those in the second group received Diclofenac tablets at a dose of 100 mg per day and those in the third group received placebo capsules. The judgement criteria were highly sensitive C Reactiv Protein (HS-CRP), sedimentation rate (SR), visual analogue scale (VAS). The test significance threshold was set at a probability of p ˂ 0.05. The first group (Garcinia kola) showed: HS-CRP p ˂ 0.002, VAS p ˂ 0.001 and SR: p ˂ 0.003; the second group (Diclofenac): HS-CRP p = 0.001, VAS p ˂ 0.001 and SR p ˂ 0.001. For the placebo group: HS-CRP p = 0.916, VAS p = 0.002 and SR p = 0.829. These results confirm that Garcinia kola at a dose of 400 mg twice a day has anti-inflammatory properties similar to those of Diclofenac at 50 mg twice a day. Biological tests revealed that Garcinia kola (BTK *) capsules have no harmful effects on kidney function, liver function, blood sugar and blood pressure. Libido was increased in men.

Published
2022

200. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants

Author

Nicole L. Welch, Meilin Zhu, Catherine Hua, Juliane Weller, Marzieh Ezzaty Mirhashemi, Tien G. Nguyen, Sreekar Mantena, Matthew R. Bauer, Bennett M. Shaw, Cheri M. Ackerman, Sri Gowtham Thakku, Megan W. Tse, Jared Kehe, Marie-Martine Uwera, Jacqueline S. Eversley, Derek A. Bielwaski, Graham McGrath, Joseph Braidt, Jeremy Johnson, Felecia Cerrato, Gage K. Moreno, Lydia A. Krasilnikova, Brittany A. Petros, Gabrielle L. Gionet, Ewa King, Richard C. Huard, Samantha K. Jalbert, Michael L. Cleary, Nicholas A. Fitzgerald, Stacey B. Gabriel, Glen R. Gallagher, Sandra C. Smole, Lawrence C. Madoff, Catherine M. Brown, Matthew W. Keller, Malania M. Wilson, Marie K. Kirby, John R. Barnes, Daniel J. Park, Katherine J. Siddle, Christian T. Happi, Deborah T. Hung, Michael Springer, Bronwyn L. MacInnis, Jacob E. Lemieux, Eric Rosenberg, John A. Branda, Paul C. Blainey, Pardis C. Sabeti, and Cameron Myhrvold

Subjects
SARS-CoV-2, viruses, Influenza, Human, Microfluidics, COVID-19, Humans, virus diseases, General Medicine, General Biochemistry, Genetics and Molecular Biology
Abstract

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.

Published
2022

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