Whole Genome Sequencing Shows that African Swine Fever Virus Genotype IX Is Still Circulating in Domestic Pigs in All Regions of Uganda
Rodney Okwasiimire,
Joseph F. Flint,
Edrine B. Kayaga,
Steven Lakin,
Jim Pierce,
Roger W. Barrette,
Bonto Faburay,
Dickson Ndoboli,
John E. Ekakoro,
Eddie M. Wampande,
Karyn A. Havas
Affiliations
Rodney Okwasiimire
Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda
Joseph F. Flint
Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
Edrine B. Kayaga
Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda
Steven Lakin
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Services, United States Department of Agriculture, Greenport, NY 11957, USA
Jim Pierce
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Services, United States Department of Agriculture, Greenport, NY 11957, USA
Roger W. Barrette
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Services, United States Department of Agriculture, Greenport, NY 11957, USA
Bonto Faburay
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Services, United States Department of Agriculture, Greenport, NY 11957, USA
Dickson Ndoboli
Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda
John E. Ekakoro
Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
Eddie M. Wampande
Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda
Karyn A. Havas
Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
Blood samples were collected from pigs at six abattoirs in the Kampala, Uganda metropolitan area from May 2021 through June 2022, and tested for African swine fever virus. Thirty-one samples with cycle threshold values Ornithodoros moubata exposure underwent whole genome sequencing. The p72 gene was used to genotype the isolates, and all were found to be genotype IX; whole genome sequences to previous genotype IX isolates confirmed their similarity. Six of the isolates had enough coverage to evaluate single nucleotide polymorphisms (SNPs). Five of the isolates differed from historic regional isolates, but had similar SNPs to one another, and the sixth isolate also differed from historic regional isolates, but also differed from the other five isolates, even though they are all genotype IX. Whole genome sequencing data provide additional detail on viral evolution that can be useful for molecular epidemiology, and understanding the impact of changes in genes to disease phenotypes, and may be needed for vaccine targeting should a commercial vaccine become available. More sequencing of African swine fever virus isolates is needed in Uganda to understand how and when the virus is changing.
