Predicting the potential for zoonotic transmission and host associations for novel viruses

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Predicting the potential for zoonotic transmission and host associations for novel viruses

Authors:
P. S. Pandit^1*, S.J. Anthony^2**, T. Goldstein^1**, K. J. Olival³, M. M. Doyle¹, N. R. Gardner¹, B. Bird¹, W. Smith¹, D. Wolking¹, K. Gilardi¹, C. Monagin¹, T. Kelly¹, M. Uhart¹, J. H. Epstein³, C. Machalaba³, M. K. Rostal³, P. Dawson³, E. Hagan³, A. Sullivan³, H. Li³, A. A. Chmura³, A. Latinne³, C. Lange⁴, T. O’Rourke⁴, S. Olson⁵, L. Keatts¹, P. Mendoza⁵, A. Perez⁵, C. Dejuste de Paula⁵, D. Zimmerman⁶, M. Valitutto⁶, M. LeBreton⁷, D. McIver⁸, A. Islam³, V. Duong⁹, M. Mouiche⁷, Z. Shi¹⁰, P. Mulembakani¹¹, C. Kumakamba¹², M. Ali¹³, N. Kebede¹⁴, U. Tamoufe¹⁵, S. Bel-Nono¹⁶, A. Camara¹⁷, J. Pamungkas^{18, 19}, K. Coulibaly²⁰, E. Abu-Basha²¹, J. Kamau²², S. Silithammavong⁸, J. Desmond³, T. Hughes^3,23, E. Shiilegdamba²⁴, O. Aung⁶, D. Karmacharya²⁵, J. Nziza²⁶, D. Ndiaye²⁷, A. Gbakima²⁸, Z. Sijali²⁹, S. Wacharapluesadee³⁰, E. Alandia Robles³¹,B. Ssebide²⁶, G. Suzán³², L. F. Aguirre³³, M. R. Solorio³⁴, T. N. Dhole³⁵, P. L. Hitchens³⁶, D. O. Joly³⁷, K. Saylors⁴, A. Fine⁶, S. Murray⁷, W. Karesh³, P. Daszak³, J. A. K. Mazet¹, PREDICT Consortium, & C. K. Johnson^1*
*Corresponding author: P.S. Pandit, pspandit@ucdavis.edu and C. K. Johnson, ckjohnson@ucdavis.edu

Affiliations:

¹One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, 95616, USA.
²Center for Infection and Immunity, Columbia University, New York, NY, 10032, USA.
³EcoHealth Alliance, 520 Eighth Avenue, New York, NY, 10018, USA.
⁴Labyrinth Global Health, Inc., 546 15th Ave NE, St Petersburg, FL 33704, USA.
⁵Wildlife Conservation Society, Bronx, NY, 10460, USA.
⁶Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
⁷Mosaic/Global Viral Cameroon, Yaoundé, Cameroon
⁸Metabiota Inc, Nanaimo, Canada
⁹Institut Pasteur du Cambodge, 5 Monivong Blvd, PO Box 983, Phnom Penh, 12201, Cambodia.
¹⁰CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
¹¹Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.
¹²Metabiota Inc., Kinshasa, Democratic Republic of the Congo
¹³Egypt National Research Centre, 12311 Dokki, Giza, Egypt
¹⁴Addis Ababa University, Aklilu Lemma Institute of Pathobiology, P.O.Box 1176, Addis Ababa, Ethiopia
¹⁵Metabiota Inc. Cameroon.
¹⁶Military Veterinarian (Rtd.), P.O. Box CT2585, Accra, Ghana.
¹⁷Centre de Recherche en Virologie (VRV) Projet Fievres Hemoraquiques en Guinée; BP:5680 Nongo/Contéya-Commune de Ratoma, Guinea.
¹⁸Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia.
¹⁹Faculty of Veterinary Medicine, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia.
²⁰Department Environment and Health, Institut Pasteur de Côte d’Ivoire, PO BOX 490 Abidjan 01, Ivory Coast.
²¹Department of Basic Medical Veterinary Sciences, College of Veterinary Medicine, Jordan University of Science and Technology, Jordan.
²²Molecular Biology Laboratory, Institute of Primate Research, Nairobi, Kenya, Department of Biochemistry, University of Nairobi, Nairobi, Kenya.
²³Conservation Medicine, Selangor, Malaysia.
²⁴Wildlife Conservation Society (WCS) - Vietnam Program, 1302, 57 Lang Ha, Hanoi, Vietnam
²⁵Center for Molecular Dynamics Nepal (CMDN), Thapathali -11, Kathmandu, Nepal.
²⁶Regional Headquarters, Mountain Gorilla Veterinary Project, Musanze, Rwanda.
²⁷Université Cheikh Anta Diop, BP 5005, Dakar, Sénégal.
²⁸Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone.
²⁹Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.
³⁰Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
³¹Wildlife Conservation Society (WCS) – Bolivia Program, c. Gabino Villanueva 340, La Paz, Bolivia.
³²Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México City, 04510, Mexico.
³³Centro de Biodiversidad y Genética, Universidad Mayor de San Simón, Cochabamba, Bolivia.
³⁴Laboratório de Epidemiologia e Geoprocessamento (EpiGeo), Instituto de Medicina Veterinária (IMV) Universidade Federal do Pará (UFPA), BR-316 Km 31, Castanhal, PA 69746-360, Brazil.
³⁵Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Uttar Pradesh, India.
³⁶Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, VIC 3030, Australia
³⁷Nyati Health Consulting, 2175 Dodds Road, Nanaimo V9X0A4, Canada.

*Correspondence to: pspandit@ucdavis.edu, ckjohnson@ucdavis.edu
**Contributed equally to the manuscript

Abstract:

Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as host for 513 newly discovered viruses detected by large scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.