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

doi:10.3390/v16111754

Application of a Sensitive Capture Sequencing Approach to Reservoir Surveillance Detects Novel Viruses in Zambian Wild Rodents

Viruses. 2024 Nov 9;16(11):1754. doi: 10.3390/v16111754.

Authors

Lavel C Moonga^{1

2}, Jones Chipinga³, John P Collins⁴, Vishal Kapoor^{4

5}, Ngonda Saasa⁶, King S Nalubamba⁷, Bernard M Hang'ombe^{1

2}, Boniface Namangala^{1

2}, Tapiwa Lundu⁸, Xiang-Jun Lu⁴, Samuel Yingst⁴, J Kenneth Wickiser^{4

9}, Thomas Briese^{4

10}

Affiliations

¹ Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia.
² Africa Centre of Excellence in Infectious Diseases of Humans and Animals (ACEIDHA), School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia.
³ Vaughan Regional Medical Center, Selma, AL 36701, USA.
⁴ Global Alliance for Preventing Pandemics at the Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.
⁵ Department of Zoology, Rabindranath Tagore University, Bhopal 464993, India.
⁶ Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia.
⁷ Department of Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia.
⁸ Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia.
⁹ Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.
¹⁰ Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.

Abstract

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.

Keywords: One Health; adenovirus; aichivirus; chaphamaparvovirus; jeilongvirus; kobuvirus; next generation sequencing; paramyxovirus; pathogen discovery; pre-pandemic surveillance.

MeSH terms

Animals
Animals, Wild / virology
Disease Reservoirs* / virology
Genome, Viral
Phylogeny*
Rodentia* / virology
Viruses / classification
Viruses / genetics
Viruses / isolation & purification
Zambia

Grants and funding

This work was supported by the Skoll Foundation and the Moore Charitable Foundation through the Global Alliance for Preventing Pandemics (GAPP) at the Center for Infection and Immunity, Columbia University, New York, USA. Furthermore, sample collection was supported by the World Bank-funded African Centre of Excellence for Infectious Diseases of Humans and Animals (ACEIDHA) project at the University of Zambia.