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3. Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages

Author

Courcelle, Maxime, primary, Salami, Habib, additional, Tounkara, Kadidia, additional, Lo, Modou Moustapha, additional, Ba, Aminata, additional, Diop, Mariame, additional, Niang, Mamadou, additional, Sidibe, Cheick Abou Kounta, additional, Sery, Amadou, additional, Dakouo, Marthin, additional, Kaba, Lanceï, additional, Sidime, Youssouf, additional, Keyra, Mohamed, additional, Diallo, Alpha Oumar Sily, additional, El Mamy, Ahmed Bezeid, additional, El Arbi, Ahmed Salem, additional, Barry, Yahya, additional, Isselmou, Ekaterina, additional, Habiboullah, Habiboullah, additional, Doumbia, Baba, additional, Gueya, Mohamed Baba, additional, Awuni, Joseph, additional, Odoom, Theophilus, additional, Ababio, Patrick Tetteh, additional, TawiahYingar, Daniel Nana Yaw, additional, Coste, Caroline, additional, Guendouz, Samia, additional, Kwiatek, Olivier, additional, Libeau, Geneviève, additional, and Bataille, Arnaud, additional

Published
2024
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4. A Phylogeographic Analysis of Porcine Parvovirus 1 in Africa

Author

Franzo, Giovanni, primary, Zerbo, Habibata Lamouni, additional, Ouoba, Bruno Lalidia, additional, Dji-Tombo, Adama Drabo, additional, Kindo, Marietou Guitti, additional, Sawadogo, Rasablaga, additional, Chang’a, Jelly, additional, Bitanyi, Stella, additional, Kamigwe, Aloyce, additional, Mayenga, Charles, additional, Lo, Modou Moustapha, additional, Ndiaye, Mbengué, additional, Ba, Aminata, additional, Diop, Gaye Laye, additional, Anahory, Iolanda Vieira, additional, Mapaco, Lourenço P., additional, Achá, Sara J., additional, Kouakou, Valere Kouame, additional, Couacy-Hymann, Emmanuel, additional, Gacheru, Stephen G., additional, Lichoti, Jacqueline K., additional, Kasivalu, Justus K., additional, Njagi, Obadiah N., additional, Settypalli, Tirumala B. K., additional, Cattoli, Giovanni, additional, Lamien, Charles E., additional, Molini, Umberto, additional, and Dundon, William G., additional

Published
2023
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5. Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

Author

Saylors, Karen, Wolking, David J., Hagan, Emily, Martinez, Stephanie, Francisco, Leilani, Euren, Jason, Olson, Sarah H., Miller, Maureen, Fine, Amanda E., Thanh, Nga Nguyen Thi, Tran Minh, Phuc, Kalengkongan, Jusuf D., Kusumaningrum, Tina, Latinne, Alice, Pamungkas, Joko, Safari, Dodi, Saputro, Suryo, Bamba, Djeneba, Coulibaly, Kalpy Julien, Dosso, Mireille, Laudisoit, Anne, N'guettia Jean, Kouassi Manzan, Dutta, Shusmita, Islam, Ariful, Shano, Shahanaj, Mwanzalila, Mwokozi I., Trupin, Ian P., Gbakima, Aiah, Bangura, James, Yondah, Sylvester T., Karmacharya, Dibesh, Shrestha, Rima D., Kamta, Marcelle Annie Matsida, Mouiche, Mohamed Moctar Mouliom, Ndolo, Hilarion Moukala, Niama, Fabien Roch, Onikrotin, Dionne, Daszak, Peter, Johnson, Christine K., Mazet, Jonna A. K., Abaneh, Ola, Ababneh, Mustafa, Rafia, Jum, Sukor, Abd, Abdullah, Mohd Lufti, Abedin, Josefina, Abu-Basha, Ehab, Ali, Mohamed, Beal Akoundze, Junior, Akpaki, Joel, Al Hanandeh, Sief Addeen, Al Omari, Bilal, Al Shakil, Abdullah, Al-Zghoul, Mohammed, Albart, Stephenie Ann, Alshammari, Abdullah, Amarneh, Basil H., Ampofo, William, Andrew, Victoria, Ahn, Dao Le, Ankhanbaatar, Ulaankhuu, Anthony, Simon, Antonjaya, Ungke, Araya, Kidan, Arku, Jallah, Arshat, Norsharina, Asigbee, Theodore, Aung, Ohnmar, Awuni, Joseph, Ayukebong, James, Azian, Mohammed, Aziz, Nor Adilah, Ba, Aminata, Bassan, Ganzorig, Bagato, Ola, Bamba, Aboubacar, Bamba, Djenba, Barkhasbaatar, Ariunbaatar, Barrera, June, Basaraba, Cale, Bel-nono, Samuel, Belaganahalli, Manjunatha, Belay, Desalgen, Belkharia, Jaber, Binol, Ridzki M. F., Bird, Brian, Bista, Manisha, Biswas, Pitu, Blake, Matthew, Boatemaa, Linda, Bonason, Margret, Brandful, James, Brown, Joseph, Brownstein, John, Camara, Mamadi, Camara, Salif, Chai, Daniel, Chakraborty, Debapriyo, Chale, Hannah, Chaudhary, Ashok, Chea, Sokha, Chmura, Aleksei, Goossens, Benoit, Chow, Andrew, Churchill, Carolina, Commey, Abraham, Couacy-Hymann, Emmanuel, Coulibaly, Julien Kalpy, Cranfield, Michael, Damanik, Wirda, Damdinjav, Batchullum, Danial, Norhidayah, Dasak, Peter, David, Runie, Dawson, Patrick, Dembele, Arjouma, Deme, Awa, Desmond, James, Dewantari, Arghianditya Kresno, Dhanota, Jaseet, Dhole, Tapan, Diep, Nguyen Thi, Dionkounda, Artistide, Diop, Gaye Laye, Dodd, Kimberly, Dogby, Otilia, Dorjnyam, Tumendemberel, Dosso, Mireielle, Doumbouya, Kalil, Doumbouya, Mohamed Idriss, Doyle, Megan, Dramou, Simone, Drazenovich, Tracy, Duc Ahn, Dang, Duc Luu, Bach, Duendkae, Prateep, Duoc, Vu Trong, Duong, Tran Nhu, Duong, Veasna, Dursman, Huda, Dussart, Phillipe, Ee, Tan Jun, Ekiri, Abel, El Rifay, Amira S., El Shesheny, Rabel, El Taween, Ahmed N., Emmanuel, Zena Babu, Epstein, Jonathan H., Evans, Tierra Smiley, Fahmawi, Alaa, Fahn, Simeon, Feferholtz, Yasha, Ferdous, Jinnat, Fine, Amanda, Flora, Meerjady, Fransisco, Leilani, Fui Fui, Lem, Gabourie, Taylor, Gani, Millawati, Garbo, Michael, Gardner, Nicole, Gbamele, Marie, Ge, Xingyi, Gee, Lee Heng, Genovese, Brooke, Gibson, Alexandra, Gilardi, Kirsten, Gilbert, Martin, Gillis, Amethyst, Ginsos, Andrew, Godji Gnabro, Privat, Goldstein, Tracey, Gomaa, Moktar, Gomis, Jules, Gonzalez, Kevin, Grange, Zoe, Greig, Denise, Grodus, Michael, Gueu, Kpon Kakeuma Romeo, Gutierrez, Leticia, Haba, Dan Marcelin, Hamid, Suraya, Harris, Daniel K., Hashim, Abdul Kadir Abu, Hassan, Moushumi, Hassan, Quazar Nizamuddin, He, Qun, Hemachudha, Thiravat, Henry, Helen, Herbert, Ronald, Hijazeen, Zaidoun, Hilarion, Moukala Ndolo, Hill, Rebecca, Hoa, Nguyen Thi, Horwood, Paul, Hossain, Md. Enayet, Hossain, Saddam, Htun, Moh Moh, Hu, Ben, Hughes, Tom, Hul, Vibol, Van, Vo, Hussein, Fatima, Indola, Ghislain Dzeret, Iskandriati, Diah, Islam, Md. Tarikul, Islam, Shariful, Isnaim Ismail, Mohd, Ismail, Zuhair Bani, Iyanya, Jacques, Jaimin, Joel Judson, Jambai, Amara, Japning, Jeffrine Rovie Ryan, Japrin, Alexter, Jean Louis, Frantz, Joe, Titus, Johnson, Erica, Joly, Damien, Joshi, Jyotsna, Kalengkongan, Jusuf, Kalivogui, Douokoro, Kamara-Chieyoe, Nenneh, Kamau, Joseph, Kambale Syaluha, Eddy, Kandeil, Ahmed, Kane, Yogouba, Karesh, William, Kargo, Kandeh, Kasenda, Novie, Kayali, Ghazi, Kayed, Ahmed S., Kazwala, Rudovick, Ke, Changwen, Keates, Lucy, Kebede, Nigatu, Khamphaphongphane, Bouaphanh, Kheong, Chong Chee, Kilonzo, Christopher, Koffa, Ma-Sue, Kollie, Amos G., Kondiano, Marcel Sidik, Koropo, Michel, Kouamé Kouakou, Valere, Kouassi Koffi, Eugene, Kourouma, Mariam, Koutate, Abdoulaye Ousmane, Kowel, Citra Liv, Krou, Hermann Assemien, Kumakamba, Charles, Kutkat, Omnia, Lamah, François, Lan, Nguyen Thi, Lane, Jennifer, Lange, Christian, Larmouth, Emmanuel, Le Doux, Joseph Diffo, Leasure, Elizabeth, Leasure, Katherine, LeBreton, Mat, Lee, Jimmy, Lee, Helen, Lee, Mei Ho, Leno, Amara, Li, Hongying, Liang, Eliza, Liang, Neal, Lim, Dorothy, Lipkin, W. Ian, Liu, Jun, Lo, Modou Moustafa, Lojivis, Leonoris, Long, Nguyen Van, Lucas, Ashley, Lukusa, Jean Paul, Lungay, Victor, Lushima, Shongo, Lutwama, Julius, Ma, Wenjun, Machalaba, Catherine, Maganga, Grace, Magesa, Walter Simon, Mahmoud, Sara H., Makuwa, Maria, Makweta, Asha, Mamun, Abdullah Al, Manandhar, Prajwol, Maneeorn, Patarapol, Mann, Harjeet, Maomy, Bhele, Maptue, Victorine, Mathew, Alice, Mavoungou, Yanne Vanessa, Maw, Min Thein, Mazet, Jonna, Mbala, Placide, Mbuba, Emmanuel, Mbunwe, Eric, McIver, David, Mendelsohn, Emma, Miegakanda, Valchy Bel-Bebi, Minh, Phan Quang, Mkali, Happy, Moatasim, Yassmin, Mombouli, Jean Vivien, Monagin, Corina, Montecino-Latorre, Diego, Mossoun Mossoun, Arsene, Mostafa, Ahmed, Mouiche, Moctar, Mpassi, Romain Bagamboula, Msigwa, Alphonce, Mudakikwa, Antoine, Mugok, Laura Benedict, Mulembakani, Prime, Murray, Suzan, Musa, Fakhrul Hatta, Musabimana, Pacifique, Mutura, Samson, Mwamlima, Tunu, Mwanzanilla, Mwokozi, Myaing, Tin Tin, Myat, Theingi Win, Myo Chit, Aung, N’faly, Magassouba, N’Guettia, Manzan Jean, N’télo, Anatole, Nakimera, Sylivia, Nam, Vu Sinh, Napit, Rajindra, Nathan, Senthilvel K. S. S., Navarrete-Macias, Isamara, Ndebe, Kortu M., Ndiaye, Amadou, Ndiaye, Daouda, Negash, Yohannes, Nga, Nguyen Thi Thanh, Ngay, Ipos, Ngoc, Pham Thi Bich, Niama, Fabien, Nina, Rock Aimé, Niyonzima, Schadrack, Nkom, Felix, Nkoua, Cynthia, Noordin, Noorliza, Noviana, Rachmitasari, Nwobegahay, Julius, Nziza, Julius, O’Rourke, Daniel, O’Rourke, Tammie, Obodai, Evangeline, Okello Okwir, Ricky, Olival, Kevin, Olson, Sarah, Olva, Onkirotin Dionne, Ontiveros, Victoria, Opook, Fernandes, Panchadcharam, Chandrawathani, Pandit, Pranav, Parra, Henri-Joseph, Phuc, Tran Minh, Phuong, Nguyen Thanh, Poultolnor, Jackson Y., Pradhan, Saman, Preston, Eunah Cho, Pruvot, Mathieu, Purevtseren, Dulam, Puri, Dhiraj, Quang, Le Tin Vinh, Rachmitasari, Novie, Rahman, Kaisar, Rahman, Mizanur, Rahman, Mohammed Ziaur, Rahman, Mustafizur, Ramirez, Diana, Randhawa, Nistara, Raut, Samita, Rosario, Joseph, Ross, Albert, Ross, Noam, Rostal, Melinda, Roualdes, Pamela, Rubin, Eddy, Rumi, Aftab Uddin, Rundi, Christina, Sackie, Melkor, Sajali, Zikankuba, Samuels, Sandra G, Sango, Mathias, Saptu, Ammar Rafidah, Saraka, Daniel N’guessan, Sartee, Alvis A., Sayandouno, Sia Alida, Seck, Mame Cheikh, Sedor, Victoria, Sharma, Ajay Narayan, Sharminie, Velsri, Shehata, Mahmoud M., Sheikh, Gafur, Shi, Zhengli, Shiilegdamba, Enkhtuvshin, Shrestha, Bishwo, Shrestha, Rima, Sidibey, Mohammed, Silithammavong, Soubanh, Simon, Daniel, Sion, Emilly, Sipangkui, Symphorosa, Sitam, Frankie Thomas, Smith, Brett, Smith, Bridgette, Smith, Woutrina, Sodnom, Batsikhan, Ssebide, Benard, Suleiman, Maria, Sullivan, Ava, Sungif, Nur Amirah, Suu-Ire, Richard, Sy, Mouhamed, Takuo, Jean Michel, Talafha, Hani, Tamoufe, Ubald, Tetteh, Emmanuel, Than Toe, Aung, Thanda, Lanash, Thanh Long, Ngo, Thein, Wai Zin, Theppangna, Watthana, Thinh, Nguyen Duc, Thuy, Hoang Bich, Thuy, Nguyen Thu, Togami, Eri, Tolno, Moise Bendoua, Tolovou, Kevin, Topani, Rahmat, Tremeau-Bravard, Alexandre, Trupin, Ian, Tumushime, Jean Claude, Tun, Kyaw Yan Naing, Turay, Joseph, Uddin, Helal, Uhart, Marcela, Ureda, Nicole, Valitutto, Marc, Verasahib, Khebir, Vodzak, Megan, Wacharapluesadee, Supaporn, Wahad, Mohammad Yuery Wazlan Abdul, Watson, Brooke, Wells, Heather, White, Allison, Willoughby, Anna, Wiyatno, Ageng, Wolking, David, Yang, Xinglou, Yao, Lim Ming, Yombouno, Sayon, Young, Cristin, Zambrana-Torrelio, Carlos, Zeid, Zahidah Izzati, Zghoul, Ghadeer, Zhang, Libiao, Zhang, Yunzhi, Zhu, Guangjian, Zimmerman, Dawn, Zoumarou, Daba, Aguirre, Alonso, Aguirre, Luis, Akongo, Mark-Joel, Alandia Robles, Erika, Ambu, Laurentius, Ayala Aguilar, Glenda, Barcena, Luis, Barradas, Rosario, Basir, Misliah Mohamad, Bogich, Tiffany, Bounga, Gerard, Buchy, Philippe, Bunn, David, Byaruba, Denis, Cameron, Ken, Carroll, Dennis, Cavero, Nancy, Cespedes, Manuel, Che, Xiaoyu, Chiu, Charles, Chor, Kimashalen, Clements, Andrew, Dary Acevedo, Luz, de Almeida Campos, Angelica, De La Puente, Micaela, de Lamballerie, Xavier, de Paula, Catia, Delwart, Eric, Diffo Le Doux, Joseph, Doyle-Capitman, Catherine, Durigon, Edison, Fair, Joseph, Ferrer-Paris, José R., Formenty, Pierre, Galarza, Isabel, Garcia, Joel, Grard, Gilda, Greatorex, Zoe, Harris, Laurie, Hitchens, Peta, Ho, Mei, Hosseini, Parviez, In, Samath, Iñíguez, Volga, Jain, Komal, Jamaluddin, Abd. Aziz, Johnson, Christine, Jones, Kate, Joyner, Priscilla, Kaba, Serge, Kambale, Eddy, Kataregga, Abdulhameed, Kelly, Terra, Khammavong, Kongsy, Kilpatrick, A. Marm, Laimun, Samsir, Lee, Mei-Ho, LeRoy, Eric, Levinson, Jordan, Levy, Marc, Limachi, Rolando, Loh, Elizabeth, Lowenstine, Linda J., Luis Mollericona, José, Maganga, Ruth, Malakalinga, Joseph, Manhas, Melissa, Marra, Pete, Mbabazi, Rachael, Medellín, Rodrigo, Mendoza, Patricia, Miller, Sireeda, Miranda, Flavia, Mitchell, Megan, Mohamed, Ramlan, Mollard, Debbie, Morse, Stephen, Mouellet, Wivine, Moya, Isabel, Murillo, Yovanna, Murray, Kris, Muyembe Tamfum, Jean-Jacques, Nassar, Fernando, Nathan, Sen, Nsengimana, Olivier, Ogg Keatts, Lucy, Ojeda-Flore, Rafael, Okwir Okello, Ricky, Ondzie, Alain, Paweska, Janusz, Pereira, Alisa, Pereira, Victoria, Perez, Alberto, Perez, Jocelyn, Phon, Simorn, Reed, Patricia, Rejmanek, Dan, Rico, Oscar, Rivera, Rosario, Romero, Monica, Roy, Celina, Saepuloh, Uus, Schneider, Brad, Schwind, Jessica, Singhalath, Sinpakhome, Smith, Kristine, Suárez, Fabiola, Suzan, Gerardo, Thanh Nga, Nguyen Thi, Thomas, Kate, Ticona, Herminio, VanWormer, Elizabeth, Villar, Sandra, Weisman, Wendy, Westfall, Michael, Whittier, Chris, Wicker, Leanne, Wolfe, Nathan, Yang, Angela, Zariquiey, Carlos, Zhang, Shu-Yi, Zorine Nkouants, Baudelaire, Zainuddin, Zainal, Chrisman, Cara, Pabst, August, Shek, Amalhin, and Trostle, Murray

Subjects
0301 basic medicine, Behavioral risk, medicine.medical_specialty, Behavioural sciences, Disease, Community integration, Basic Behavioral and Social Science, 03 medical and health sciences, 0302 clinical medicine, Clinical Research, 2.3 Psychological, Behavioral and Social Science, Agency (sociology), medicine, 2.2 Factors relating to the physical environment, GE1-350, Aetiology, One health, Social science research, business.industry, Prevention, Research, Public health, PREDICT Consortium, Public relations, Focus group, Environmental sciences, Good Health and Well Being, 030104 developmental biology, One Health, Multi-disciplinary surveillance, social and economic factors, Public aspects of medicine, RA1-1270, Infection, Psychology, International development, business, 030217 neurology & neurosurgery
Abstract

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security. Supplementary Information The online version contains supplementary material available at 10.1186/s42522-021-00036-9.

Published
2021

6. Persistence of the historical lineage I of West Africa against the ongoing spread of the Asian lineage of peste des petits ruminants virus

Author

Tounkara, Kalidia, Kwiatek, Olivier, Sidibé, Cheick Abou Kounta, Sery, Amadou, Dakouo, Martin, Salami, Habib, Lo, Modou Moustapha, Ba, Aminata, Diop, Mariame, Niang, Mamadou, Libeau, Geneviève, Bataille, Arnaud, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Central Vétérinaire [Bamako, Mali], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), The research was funded a grant from the European Commission Animal Health and Welfare European Research Area Network for the IUEPPR Project 'Improved Understanding of Epidemiology of PPR', in the framework of ANIHWA 2013, and by a grant (SI2.756606) from the European Commission Directorate General for Health and Food Safety awarded to the European Union Reference Laboratory for peste des petits ruminants (EURL-PPR)., and European Project: 291815,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ANIHWA(2012)

Subjects
disease control, [SDV]Life Sciences [q-bio], Nigeria, L73 - Maladies des animaux, phylogeny, molecular epidemiology, Virus peste petits ruminants, Peste-des-petits-ruminants virus, Peste des petits ruminants, Lignée, Peste-des-Petits-Ruminants, parasitic diseases, small ruminant, Animals, Transmission des maladies, Goat Diseases, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Goats, Contrôle de maladies, fungi, Migration animale, Maladie transfrontière, Épidémiologie, Africa, Western, transboundary, Morbillivirus, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, L20 - Écologie animale
Abstract

International audience; Peste des petits ruminants (PPR) is a highly contagious disease of small ruminants. The causal agent, PPR virus (PPRV), is classified into four genetically distinct lineages. Lineage IV, originally from Asia, has shown a unique capacity to spread across Asia, the Middle East and Africa. Recent studies have reported its presence in two West African countries: Nigeria and Niger. Animals are frequently exchanged between Mali and Niger, which could allow the virus to enter and progress in Mali and to other West African countries. Here, PPRV samples were collected from sick goats between 2014 and 2017 in both Mali and in Senegal, on the border with Mali. Partial PPRV nucleoprotein gene was sequenced to identify the genetic lineage of the strains. Our results showed that lineage IV was present in south-eastern Mali in 2017. This is currently the furthest West the lineage has been detected in West Africa. Surprisingly, we identified the persistence at least until 2014 of the supposedly extinct lineage I in two regions of Mali, Segou and Sikasso. Most PPRV sequences obtained in this study belonged to lineage II, which is dominant in West Africa. Phylogenetic analyses showed a close relationship between sequences obtained at the border between Senegal and Mali, supporting the hypothesis of an important movement of the virus between the two countries. Understanding the movement of animals between these countries, where the livestock trade is not fully controlled, is very important in the design of efficient control strategies to combat this devastating disease.

Published
2021

7. Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa

Author

Bataille, Arnaud, Salami, Habib, Seck, Ismaïla, Lo, Modou Moustapha, Ba, Aminata, Diop, Mariame, Sall, Baba, Faye, Coumba, Lo, Mbargou, Kaba, Lanceï, Sidime, Youssouf, Keyra, Mohamed, Diallo, Alpha Oumar Sily, Niang, Mamadou, Sidibé, Cheick Abou Kounta, Sery, Amadou, Dakouo, Martin, El Mamy, Ahmed Bezeid, El Arbi, Ahmed Salem, Barry, Yahya, Isselmou, Ekaterina, Habiboullah, Habiboullah, Lella, Abdellahi Salem, Doumbia, Baba, Baba Gueya, Mohamed, Coste, Caroline, Squarzoni Diaw, Cécile, Kwiatek, Olivier, Libeau, Geneviève, Apolloni, Andrea, Bataille, Arnaud, Salami, Habib, Seck, Ismaïla, Lo, Modou Moustapha, Ba, Aminata, Diop, Mariame, Sall, Baba, Faye, Coumba, Lo, Mbargou, Kaba, Lanceï, Sidime, Youssouf, Keyra, Mohamed, Diallo, Alpha Oumar Sily, Niang, Mamadou, Sidibé, Cheick Abou Kounta, Sery, Amadou, Dakouo, Martin, El Mamy, Ahmed Bezeid, El Arbi, Ahmed Salem, Barry, Yahya, Isselmou, Ekaterina, Habiboullah, Habiboullah, Lella, Abdellahi Salem, Doumbia, Baba, Baba Gueya, Mohamed, Coste, Caroline, Squarzoni Diaw, Cécile, Kwiatek, Olivier, Libeau, Geneviève, and Apolloni, Andrea

Abstract

Peste des petits ruminants (PPR) is a deadly viral disease that mainly affects small domestic ruminants. This disease threaten global food security and rural economy but its control is complicated notably because of extensive, poorly monitored animal movements in infected regions. Here we combined the largest PPR virus genetic and animal mobility network data ever collected in a single region to improve our understanding of PPR endemic transmission dynamics in West African countries. Phylogenetic analyses identified the presence of multiple PPRV genetic clades that may be considered as part of different transmission networks evolving in parallel in West Africa. A strong correlation was found between virus genetic distance and network-related distances. Viruses sampled within the same mobility communities are significantly more likely to belong to the same genetic clade. These results provide evidence for the importance of animal mobility in PPR transmission in the region. Some nodes of the network were associated with PPRV sequences belonging to different clades, representing potential “hotspots” for PPR circulation. Our results suggest that combining genetic and mobility network data could help identifying sites that are key for virus entrance and spread in specific areas. Such information could enhance our capacity to develop locally adapted control and surveillance strategies, using among other risk factors, information on animal mobility.

Published
2021

8. Assessing the Risk of Occurrence of Bluetongue in Senegal

Author

Gahn, Marie, Niakh, Fallou, Ciss, Mamadou, Seck, Ismaila, Lo, Modou, Fall, Assane, Biteye, Biram, Fall, Moussa, Ndiaye, Mbengué, Ba, Aminata, Seck, Momar, Sall, Baba, Lo, Mbargou, Faye, Coumba, Squarzoni-Diaw, Cécile, Ka, Alioune, Amevoin, Yves, Apolloni, Andrea, Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École Nationale de la Statistique et de l'Administration Économique (ENSAE Paris), Food and Agriculture Organization of the United Nations, Global Emergency Centre for Transboundary Animal Diseases (ECTAD), Direction des Services Vétérinaires de Dakar, This research was funded by European Project H2020 Pale-Blu (project no. 727393-2), European Project: 727393,PALE Blu, Ministère de l’Élevage et des Productions Animales [Dakar], and European Project: 727393,H2020,H2020-EU.3.2.1.1.,PALE-Blu(2017)

Subjects
[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, risk map, lcsh:Biology (General), vector abundance model, basic reproduction number, compartmental model, lcsh:QH301-705.5, Article
Abstract

Bluetongue is a non-contagious viral disease affecting small ruminants and cattle that can cause severe economic losses in the livestock sector. The virus is transmitted by certain species of the genus Culicoides and consequently, understanding their distribution is essential to enable the identification of high-risk transmission areas. In this work we use bioclimatic and environmental variables to predict vector abundance, and estimate spatial variations in the basic reproductive ratio &nbsp, R0. The resulting estimates were combined with livestock mobility and serological data to assess the risk of Bluetongue outbreaks in Senegal. The results show an increasing abundance of C. imicola, C. oxystoma, C. enderleini, and C. miombo from north to south. R0 &lt, 1 for most areas of Senegal, whilst southern (Casamance) and southeastern (Kedougou and part of Tambacounda) agro-pastoral areas have the highest risk of outbreak (R0 = 2.7 and 2.9, respectively). The next higher risk areas are in the Senegal River Valley (R0 = 1.07), and the Atlantic coast zones. Seroprevalence rates, shown by cELISA, weren&rsquo, t positively correlated with outbreak probability. Future works should include follow-up studies of competent vector abundancies and serological surveys based on the results of the risk analysis conducted here to optimize the national epidemiological surveillance system.

Published
2020

9. Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa

Author

Bataille, Arnaud, primary, Salami, Habib, additional, Seck, Ismaila, additional, Lo, Modou Moustapha, additional, Ba, Aminata, additional, Diop, Mariame, additional, Sall, Baba, additional, Faye, Coumba, additional, Lo, Mbargou, additional, Kaba, Lanceï, additional, Sidime, Youssouf, additional, Keyra, Mohamed, additional, Diallo, Alpha Oumar Sily, additional, Niang, Mamadou, additional, Sidibe, Cheick Abou Kounta, additional, Sery, Amadou, additional, Dakouo, Martin, additional, El Mamy, Ahmed Bezeid, additional, El Arbi, Ahmed Salem, additional, Barry, Yahya, additional, Isselmou, Ekaterina, additional, Habiboullah, Habiboullah, additional, Lella, Abdellahi Salem, additional, Doumbia, Baba, additional, Gueya, Mohamed Baba, additional, Coste, Caroline, additional, Squarzoni Diaw, Cécile, additional, Kwiatek, Olivier, additional, Libeau, Geneviève, additional, and Apolloni, Andrea, additional

Published
2021
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10. Rift Valley fever in northern Senegal: A modelling approach to analyse the processes underlying virus circulation recurrence

Author

Durand, Benoit, Fall, Assane Gueye, Biteye, Biram, Chevalier, Véronique, Durand Id, Benoit, Lo Modou, Moustapha, Tran, Annelise, Ba, Aminata, Sow, Fafa, Belkhiria, Jaber, Gueye Fall, Assane, Biteye Id, Biram, Grosbois, Vladimir, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Environnements et Sociétés (Cirad-ES), School of Veterinary Medicine [UC Davis], University of California [Davis] (UC Davis), University of California-University of California, and This study was supported by Vmerge project (Emerging viral vector-borne diseases) and by the Ile-de-France Region as part of the DIM-1Health project.

Subjects
Male, RNA viruses, Rift Valley Fever, [SDV]Life Sciences [q-bio], RC955-962, Population Dynamics, Prevalence, Marine and Aquatic Sciences, Disease Vectors, L73 - Maladies des animaux, Mosquitoes, Geographical Locations, Aedes vexans, Recurrence, Seroepidemiologic Studies, Aedes, Arctic medicine. Tropical medicine, Bunyaviruses, MESH: Rift Valley Fever, Dynamique des populations, Rift Valley fever, Socioeconomics, Disease outbreaks, Pathology and laboratory medicine, Mammals, education.field_of_study, biology, U10 - Informatique, mathématiques et statistiques, Fièvre de la Vallée du Rift, Eukaryota, Ruminants, MESH: Aedes, Medical microbiology, Senegal, Insects, Geography, Infectious Diseases, Serology, Vertebrates, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Public aspects of medicine, RA1-1270, Pathogens, L72 - Organismes nuisibles des animaux, Research Article, Wet season, Arthropoda, Population, Vector Borne Diseases, Virus de la fièvre de la vallée du Rift, Microbiology, Bovines, medicine, Disease Transmission, Infectious, Seroprevalence, Humans, Animals, education, Ponds, Transmission des maladies, Medicine and health sciences, Models, Statistical, Population Biology, Organisms, Viral pathogens, Biology and Life Sciences, Bodies of Water, biology.organism_classification, medicine.disease, Rift Valley fever virus, Invertebrates, Microbial pathogens, Insect Vectors, Species Interactions, Culicidae, Modélisation, Amniotes, People and Places, Africa, Herd, Earth Sciences, Cattle, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract

Rift Valley fever (RVF) is endemic in northern Senegal, a Sahelian area characterized by a temporary pond network that drive both RVF mosquito population dynamics and nomadic herd movements. To investigate the mechanisms that explain RVF recurrent circulation, we modelled a realistic epidemiological system at the pond level integrating vector population dynamics, resident and nomadic ruminant herd population dynamics, and nomadic herd movements recorded in Younoufere area. To calibrate the model, serological surveys were performed in 2015–2016 on both resident and nomadic domestic herds in the same area. Mosquito population dynamics were obtained from a published model trained in the same region. Model comparison techniques were used to compare five different scenarios of virus introduction by nomadic herds associated or not with vertical transmission in Aedes vexans. Our serological results confirmed a long lasting RVF endemicity in resident herds (IgG seroprevalence rate of 15.3%, n = 222), and provided the first estimation of RVF IgG seroprevalence in nomadic herds in West Africa (12.4%, n = 660). Multivariate analysis of serological data suggested an amplification of the transmission cycle during the rainy season with a peak of circulation at the end of that season. The best scenario of virus introduction combined yearly introductions of RVFV from 2008 to 2015 (the study period) by nomadic herds, with a proportion of viraemic individuals predicted to be larger in animals arriving during the 2nd half of the rainy season (3.4%). This result is coherent with the IgM prevalence rate (4%) found in nomadic herds sampled during the 2nd half of the rainy season. Although the existence of a vertical transmission mechanism in Aedes cannot be ruled out, our model demonstrates that nomadic movements are sufficient to account for this endemic circulation in northern Senegal., Author summary Rift Valley fever (RVF) is one of the most important vector borne disease in Africa, seriously affecting the health of domestic ruminants and humans and leading to severe economic consequences. This disease is endemic in northern Senegal, a Sahelian area characterized by a temporary pond network that drive both RVF mosquito population dynamics and nomadic herd movements. Two non-exclusive mechanisms may support this endemicity: recurrent introductions of the virus by nomadic animals, and vertical transmission of the virus (i.e. from infected female mosquito to eggs) in local Aedes populations. The authors followed resident and nomadic domestic herds for 1 year. They used the data thus obtained to model a realistic epidemiological system at the pond level integrating vector population dynamics, resident and nomadic ruminant herd population dynamics. They found that the best scenario explaining RVF remanence combined yearly introductions of RVFV by nomadic herds, with a viraemic proportion predicted to be larger in animals arriving during the 2nd half of the rainy season, which is consistent with an amplification of virus circulation in the area during the rainy season. Although the existence of a vertical transmission mechanism in Aedes cannot be ruled out, their results demonstrates that nomadic movements are sufficient to account for this endemic circulation in northern Senegal.

Published
2020

11. Assessing the risk of occurrence of bluetongue in Senegal

Author

Ba Gahn, Marie Cicille, Niakh, Fallou, Ciss, Mamadou, Seck, Ismaïla, Lo, Modou Moustapha, Fall, Assane Gueye, Biteye, Biram, Fall, Moussa, Ndiaye, Mbengué, Ba, Aminata, Seck, Momar Talla, Sall, Baba, Lo, Mbargou, Faye, Coumba, Squarzoni Diaw, Cécile, Ka, Alioune, Amevoin, Yves, Apolloni, Andrea, Ba Gahn, Marie Cicille, Niakh, Fallou, Ciss, Mamadou, Seck, Ismaïla, Lo, Modou Moustapha, Fall, Assane Gueye, Biteye, Biram, Fall, Moussa, Ndiaye, Mbengué, Ba, Aminata, Seck, Momar Talla, Sall, Baba, Lo, Mbargou, Faye, Coumba, Squarzoni Diaw, Cécile, Ka, Alioune, Amevoin, Yves, and Apolloni, Andrea

Abstract

Bluetongue is a non-contagious viral disease affecting small ruminants and cattle that can cause severe economic losses in the livestock sector. The virus is transmitted by certain species of the genus Culicoides and consequently, understanding their distribution is essential to enable the identification of high-risk transmission areas. In this work we use bioclimatic and environmental variables to predict vector abundance, and estimate spatial variations in the basic reproductive ratio

Published
2020

12. Genetic Evidence for Transboundary Circulation of Peste Des Petits Ruminants Across West Africa

Author

Tounkara, Kadidia, Kwiatek, Olivier, Niang, Mamadou, Sidibé, Cheick Abou Kounta, Sery, Amadou, Dakouo, Martin, Salami, Habib, Lo, Modou Moustapha, Ba, Aminata, Diop, Mariame, El Mamy, Ahmed Bezeid, El Arbi, Ahmed Salem, Barry, Yahya, Isselmou, Ekaterina, Habiboullah, Habiboullah, Lella, Abdellahi Salem, Doumbia, Baba, Baba Gueya, Mohamed, Savadogo, Joseph, Ouattara, Lassina, Minougou, Germaine, Libeau, Geneviève, Bataille, Arnaud, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Central Vétérinaire [Bamako, Mali], Institut Sénégalais de Recherches Agricoles (ISRA), Centre National d’Elevage et de Recherches Vétérinaires (CNERV), Ministère des Ressources Animales (MRA), CIRAD, European Commission Animal Health and Welfare European Research Area Network, and project Vaccine Standards and Pilot Approach to PPR Control in Africa (VSPA) - Bill & Melinda Gates Foundation

Subjects
Phylogénie, L73 - Maladies des animaux, phylogeny, eradication, small ruminant, Surveillance épidémiologique, Original Research, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, Éradication des maladies, Correction, Maladie transfrontière, peste des petits ruminants, morbillivirus, Paramyxoviridae, virus spread, Veterinary Science, Virose
Abstract

International audience; Peste des Petits Ruminants (PPR) is a viral disease affecting predominantly small ruminants. Due to its transboundary nature, regional coordination of control strategies will be key to the success of the on-going PPR eradication campaign. Here, we aimed at exploring the extent of transboundary movement of PPR in West Africa using phylogenetic analyses based on partial viral gene sequences. We collected samples and obtained partial nucleoprotein gene sequence from PPR-infected small ruminants across countries within West and Central Africa. This new sequence data was combined with publically available data from the region to perform phylogenetic analyses. A total of fifty-five sequences were obtained in a region still poorly sampled. Phylogenetic analyses showed that the majority of virus sequences obtained in this study were placed within genetic clusters regrouping samples from multiple West African and Central African countries. Some of these clusters contained samples from countries sharing borders. In other cases, clusters grouped samples from very distant countries. Our results suggest extensive and recurrent transboundary movements of PPR within West Africa, supporting the need for a regional coordinated strategy for PPR surveillance and control in the region. Simple phylogenetic analyses based on readily available data can provide information on PPR transboundary dynamics and, therefore, could contribute to improve control strategies. On-going and future projects dedicated to PPR should include extensive genetic characterization and phylogenetic analyses of circulating viral strains in their effort to support the campaign for global eradication of the disease.

Published
2019

13. Corrigendum: Genetic Evidence for Transboundary Circulation of Peste Des Petits Ruminants Across West Africa

Author

Tounkara, Kadidia, primary, Kwiatek, Olivier, additional, Niang, Mamadou, additional, Abou Kounta Sidibe, Cheik, additional, Sery, Amadou, additional, Dakouo, Martin, additional, Salami, Habib, additional, Lo, Modou Moustapha, additional, Ba, Aminata, additional, Diop, Mariame, additional, El Mamy, Ahmed Bezeid, additional, Salem El Arbi, Ahmed, additional, Barry, Yahya, additional, Isselmou, Ekaterina, additional, Habiboullah, Habiboullah, additional, Lella, Abdellahi Salem, additional, Doumbia, Baba, additional, Gueya, Mohamed Baba, additional, Savadogo, Joseph, additional, Ouattara, Lassina, additional, Minougou, Germaine, additional, Libeau, Geneviève, additional, and Bataille, Arnaud, additional

Published
2019
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14. Persistence of the historical lineage I of West Africa against the ongoing spread of the Asian lineage of peste des petits ruminants virus.

Author

Tounkara K, Kwiatek O, Sidibe CAK, Sery A, Dakouo M, Salami H, Lo MM, Ba A, Diop M, Niang M, Libeau G, and Bataille A

Subjects
Africa, Western epidemiology, Animals, Goats, Nigeria, Phylogeny, Goat Diseases epidemiology, Peste-des-Petits-Ruminants epidemiology, Peste-des-petits-ruminants virus genetics
Abstract

Peste des petits ruminants (PPR) is a highly contagious disease of small ruminants. The causal agent, PPR virus (PPRV), is classified into four genetically distinct lineages. Lineage IV, originally from Asia, has shown a unique capacity to spread across Asia, the Middle East and Africa. Recent studies have reported its presence in two West African countries: Nigeria and Niger. Animals are frequently exchanged between Mali and Niger, which could allow the virus to enter and progress in Mali and to other West African countries. Here, PPRV samples were collected from sick goats between 2014 and 2017 in both Mali and in Senegal, on the border with Mali. Partial PPRV nucleoprotein gene was sequenced to identify the genetic lineage of the strains. Our results showed that lineage IV was present in south-eastern Mali in 2017. This is currently the furthest West the lineage has been detected in West Africa. Surprisingly, we identified the persistence at least until 2014 of the supposedly extinct lineage I in two regions of Mali, Segou and Sikasso. Most PPRV sequences obtained in this study belonged to lineage II, which is dominant in West Africa. Phylogenetic analyses showed a close relationship between sequences obtained at the border between Senegal and Mali, supporting the hypothesis of an important movement of the virus between the two countries. Understanding the movement of animals between these countries, where the livestock trade is not fully controlled, is very important in the design of efficient control strategies to combat this devastating disease., (© 2021 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

Published
2021
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15. Rift Valley fever in northern Senegal: A modelling approach to analyse the processes underlying virus circulation recurrence.

Author

Durand B, Lo Modou M, Tran A, Ba A, Sow F, Belkhiria J, Fall AG, Biteye B, Grosbois V, and Chevalier V

Subjects
Animals, Disease Transmission, Infectious, Female, Humans, Male, Recurrence, Rift Valley Fever transmission, Senegal epidemiology, Seroepidemiologic Studies, Vector Borne Diseases transmission, Aedes growth & development, Disease Outbreaks, Models, Statistical, Rift Valley Fever epidemiology, Vector Borne Diseases epidemiology, Vector Borne Diseases veterinary
Abstract

Rift Valley fever (RVF) is endemic in northern Senegal, a Sahelian area characterized by a temporary pond network that drive both RVF mosquito population dynamics and nomadic herd movements. To investigate the mechanisms that explain RVF recurrent circulation, we modelled a realistic epidemiological system at the pond level integrating vector population dynamics, resident and nomadic ruminant herd population dynamics, and nomadic herd movements recorded in Younoufere area. To calibrate the model, serological surveys were performed in 2015-2016 on both resident and nomadic domestic herds in the same area. Mosquito population dynamics were obtained from a published model trained in the same region. Model comparison techniques were used to compare five different scenarios of virus introduction by nomadic herds associated or not with vertical transmission in Aedes vexans. Our serological results confirmed a long lasting RVF endemicity in resident herds (IgG seroprevalence rate of 15.3%, n = 222), and provided the first estimation of RVF IgG seroprevalence in nomadic herds in West Africa (12.4%, n = 660). Multivariate analysis of serological data suggested an amplification of the transmission cycle during the rainy season with a peak of circulation at the end of that season. The best scenario of virus introduction combined yearly introductions of RVFV from 2008 to 2015 (the study period) by nomadic herds, with a proportion of viraemic individuals predicted to be larger in animals arriving during the 2nd half of the rainy season (3.4%). This result is coherent with the IgM prevalence rate (4%) found in nomadic herds sampled during the 2nd half of the rainy season. Although the existence of a vertical transmission mechanism in Aedes cannot be ruled out, our model demonstrates that nomadic movements are sufficient to account for this endemic circulation in northern Senegal., Competing Interests: The authors have declared that no competing interests exist.

Published
2020
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