Application of a Sensitive Capture Sequencing Approach to Reservoir Surveillance Detects Novel Viruses in Zambian Wild Rodents
Lavel C. Moonga,
Jones Chipinga,
John P. Collins,
Vishal Kapoor,
Ngonda Saasa,
King S. Nalubamba,
Bernard M. Hang’ombe,
Boniface Namangala,
Tapiwa Lundu,
Xiang-Jun Lu,
Samuel Yingst,
J. Kenneth Wickiser,
Thomas Briese
Affiliations
Lavel C. Moonga
Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
Jones Chipinga
Vaughan Regional Medical Center, Selma, AL 36701, USA
John P. Collins
Global Alliance for Preventing Pandemics at the Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
Vishal Kapoor
Global Alliance for Preventing Pandemics at the Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
Ngonda Saasa
Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
King S. Nalubamba
Department of Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
Bernard M. Hang’ombe
Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
Boniface Namangala
Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
Tapiwa Lundu
Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
Xiang-Jun Lu
Global Alliance for Preventing Pandemics at the Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
Samuel Yingst
Global Alliance for Preventing Pandemics at the Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
J. Kenneth Wickiser
Global Alliance for Preventing Pandemics at the Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
Thomas Briese
Global Alliance for Preventing Pandemics at the Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
We utilized a pan-viral capture sequencing assay, VirCapSeq-VERT, to assess viral diversity in rodents from the Eastern Province of Zambia as a model for pre-pandemic viral reservoir surveillance. We report rodent adeno-, parvo-, paramyxo-, and picornaviruses that represent novel species or isolates, including murine adenovirus 4, two additional species in the genus Chaphamaparvovirus, two paramyxoviruses distantly related to unclassified viruses in the genus Jeilongvirus, and the first Aichivirus A sequence identified from rodents in Africa. Our results emphasize the importance of rodents as a reservoir for potential zoonotic viruses.
