Whole Genome Sequencing Shows that African Swine Fever Virus Genotype IX Is Still Circulating in Domestic Pigs in All Regions of Uganda

Okwasiimire, Rodney; Flint, Joseph F.; Kayaga, Edrine; Lakin, Steven M.; Pierce, Jacalyn H.; Barrette, Roger W.; Faburay, Bonto; Ndoboli, Dickson; Ekakoro, John E.; Wampande, Eddie M.; Havas, Karyn A.

doi:10.3390/pathogens12070912

Cited by 6 publications

(6 citation statements)

References 29 publications

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“…More studies are needed to confirm the reliability of the TK assay as an additional molecular diagnostic marker for African swine fever detection, particularly in low-resource countries where real-time PCR capabilities are limited. Acknowledged limitations of the study include the number of districts covered and the total number of samples processed may be insufficient to draw robust conclusions, especially given the geographic diversity of Uganda and virus circulation [ 35 ]. Future studies should consider the expansion of the study areas to include more districts and consider a larger sample size to draw inference for generalizability.…”

Section: Discussionmentioning

confidence: 99%

Retrospective Multi-Locus Sequence Analysis of African Swine Fever Viruses by “PACT” Confirms Co-Circulation of Multiple Outbreak Strains in Uganda

Kabuuka,

Mulindwa,

Bastos

et al. 2023

Animals

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African swine fever (ASF) is a haemorrhagic fever of swine that severely constrains pig production, globally. In Uganda, at least 388 outbreaks of ASF were documented from 2001 to 2012. We undertook a retrospective serological and molecular survey of ASF virus (ASFV) using banked samples collected from seven districts (Pallisa, Lira, Abim, Nebbi, Kabarole, Kibaale, and Mukono) of Uganda. Six assays (ELISA for antibody detection, diagnostic p72 gene PCR and genomic amplification, and sequencing of four gene regions (p72 [P], p54 [A], CVR of the 9RL-ORF [C], and TK [T]), hereinafter referred to as P-A-C-T (PACT)) were evaluated. Antibodies to ASFV were detected in the Abim district (6/25; 24.0%), and the remainder of the serum samples were negative (187/193; 96.9%). For the tissue samples, ASFV detection by assay was 8.47% for P, 6.78% for A, 8.47% for C, and 16.95% for T. The diagnostic PCR (p72 gene) detected seven positive animals from four districts, whereas the TK assay detected ten positives from all seven districts. In addition to the superior detection capability of TK, two virus variants were discernible, whereas CVR recovered three variants, and p72 and p54 sequencing each identified a single variant belonging to genotype IX. Our results indicate that dependence on serology alone underestimates ASF positivity in any infected region, that multi-locus sequence analysis provides better estimates of outbreak strain diversity, and that the TK assay is superior to the WOAH-prescribed conventional p72 diagnostic PCR, and warrants further investigation.

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Section: Discussionmentioning

confidence: 99%

Retrospective Multi-Locus Sequence Analysis of African Swine Fever Viruses by “PACT” Confirms Co-Circulation of Multiple Outbreak Strains in Uganda

Kabuuka,

Mulindwa,

Bastos

et al. 2023

Animals

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“…The whole-genome sequencing of ASFV has been widely used for virus strain characterization. Over 200 ASFV genome sequences of different origins and variable virulence have been determined and deposited in GenBank [ 7 , 18 , 19 , 20 ]. Different types of ASFV genome variation have been identified including the gain or loss of MGF members, deletion or insertion of genomic fragments, variation in the numbers of repeat units in the tandem repeat sequences, polymer tract variation and single nucleotide variation.…”

Section: Introductionmentioning

confidence: 99%

Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing

Shi,

Wang,

Liu

et al. 2024

Viruses

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African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has caused severe effects on the global pig industry. Whole-genome sequencing provides crucial information for virus strain characterization, epidemiology analysis and vaccine development. Here, we evaluated the performance of next-generation sequencing (NGS) in generating ASFV genome sequences from clinical samples. Thirty-four ASFV-positive field samples including spleen, lymph node, lung, liver and blood with a range of Ct values from 14.73 to 25.95 were sequenced. For different tissue samples collected from the same sick pigs, the proportion of ASFV reads obtained from the spleen samples was 3.69–9.86 times higher than other tissues. For the high-viral-load spleen samples (Ct < 20), a minimum of a 99.8% breadth of ≥10× coverage was revealed for all the samples. For the spleen samples with Ct ≥ 20, 6/12 samples had a minimum of a 99.8% breadth of ≥10× coverage. A high average depth of sequencing coverage was also achieved from the blood samples. According to our results, high-quality ASFV whole-genome sequences could be obtained from the spleen or blood samples with Ct < 20. The high-quality ASFV genome sequence generated in this study was further used for the high-resolution phylogenetic analysis of the ASFV genomes in the early stage of the ASF epidemic in China. Our study demonstrates that NGS may act as a useful tool for efficient ASFV genome characterization, providing valuable information for disease control.

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“…ASFV is a large, structurally complex virus, harboring a large, double-stranded DNA genome of 180–190 kilobase (kb) pairs, which encodes more than 160 genes [ 2 ]; recently, all of these genes have been predicted structurally [ 3 ] and the proteome of ASFV was determined [ 4 , 5 ]. We recently reported that there are six unique genotypes of ASFV [ 6 ], with the pandemic genotype 2 strain (previously classified as genotype II) gaining the most attention, as it is currently causing diseases in domestic and wild boar in Europe, Asia, Western Africa, and the island of Hispaniola [ 7 , 8 , 9 , 10 , 11 , 12 ]. The genotype 2 strains are highly virulent and are severely affecting pork production across the globe.…”

Section: Introductionmentioning

confidence: 99%

Deletion of the EP402R Gene from the Genome of African Swine Fever Vaccine Strain ASFV-G-∆I177L Provides the Potential Capability of Differentiating between Infected and Vaccinated Animals

Borca,

Ramirez-Medina,

Espinoza

et al. 2024

Viruses

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The African swine fever virus (ASFV) mutant ASFV-G-∆I177L is a safe and efficacious vaccine which induces protection against the challenge of its parental virus, the Georgia 2010 isolate. Although a genetic DIVA (differentiation between infected and vaccinated animals) assay has been developed for this vaccine, still there is not a serological DIVA test for differentiating between animals vaccinated with ASFV-G-∆I177L and those infected with wild-type viruses. In this report, we describe the development of the ASFV-G-∆I177L mutant having deleted the EP402R gene, which encodes for the viral protein responsible for mediating the hemadsorption of swine erythrocytes. The resulting virus, ASFV-G-∆I177L/∆EP402R, does not have a decreased ability to replicates in swine macrophages when compared with the parental ASFV-G-∆I177L. Domestic pigs intramuscularly (IM) inoculated with either 102 or 106 HAD50 of ASFV-G-∆I177L/∆EP402R remained clinically normal, when compared with a group of mock-vaccinated animals, indicating the absence of residual virulence. Interestingly, an infectious virus could not be detected in the blood samples of the ASFV-G-∆I177L/∆EP402R-inoculated animals in either group at any of the time points tested. Furthermore, while all of the mock-inoculated animals presented a quick and lethal clinical form of ASF after the intramuscular inoculation challenge with 102 HAD50 of highly virulent parental field isolate Georgia 2010 (ASFV-G), all of the ASFV-G-∆I177L/∆EP402R-inoculated animals were protected, remaining clinically normal until the end of the observational period. Most of the ASFV-G-∆I177L/∆EP402R-inoculated pigs developed strong virus-specific antibody responses against viral antigens, reaching maximum levels at 28 days post inoculation. Importantly, all of the sera collected at that time point in the ASFV-G-∆I177L/∆EP402R-inoculated pigs did not react in a direct ELISA coated with the recombinant EP402R protein. Conversely, the EP402R protein was readily recognized by the pool of sera from the animals immunized with recombinant live attenuated vaccine candidates ASFV-G-∆I177L, ASFV-G-∆MGF, or ASFV-G-∆9GL/∆UK. Therefore, ASFV-G-∆I177L/∆EP402R is a novel, safe and efficacious candidate with potential to be used as an antigenically DIVA vaccine.

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Whole Genome Sequencing Shows that African Swine Fever Virus Genotype IX Is Still Circulating in Domestic Pigs in All Regions of Uganda

Cited by 6 publications

References 29 publications

Retrospective Multi-Locus Sequence Analysis of African Swine Fever Viruses by “PACT” Confirms Co-Circulation of Multiple Outbreak Strains in Uganda

Retrospective Multi-Locus Sequence Analysis of African Swine Fever Viruses by “PACT” Confirms Co-Circulation of Multiple Outbreak Strains in Uganda

Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing

Deletion of the EP402R Gene from the Genome of African Swine Fever Vaccine Strain ASFV-G-∆I177L Provides the Potential Capability of Differentiating between Infected and Vaccinated Animals

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