Complete genome analysis of African swine fever virus genotypes II, IX and XV from domestic pigs in Tanzania

Hakizimana, J.N.; Yona, Clara M.; Makange, Mariam; Kasisi, Ester A; Netherton, Christopher L.; Nauwynck, Hans; Misinzo, Gerald

doi:10.1038/s41598-023-32625-1

Cited by 4 publications

(5 citation statements)

References 62 publications

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“…The divergence observed amongst the genotype II ASFVs from Africa further indicates that the Madagascar/2007 outbreak might have been related to the previous 1998 outbreak on the island, rather than a new introduction related to MOZ/01/2005 and subsequently Georgia 2007/1 ASFVs. A deletion of ~550 bp was detected in the genotype II genome sequences for Madagascar (MAD/01/1998), Mauritius (MAU/01/2007) and Tanzania (TAN/01/2011), which corresponds to a previously described deletion in the 5′ region of Tanzania/Rukwa/17/1, MAL/19/Karonga, TAN/17/Mbagala, TAN/17/Kibaha and TAN/20/Mogorogo [ 21 , 22 , 23 ].…”

Section: Discussionmentioning

confidence: 72%

“…In addition to Mauritius/2007, two other genotype II ASFVs reported for the first time in Zimbabwe in 2015 [ 15 ] and South Africa in 2019, were included in this study. Recently, sequences of ASF genotype II viruses isolated in Tanzania and Malawi were published (LR813622, ON409982, ON409983, ON409979 and MW856068) [ 21 , 22 , 23 ]. Significant sequence differences were described between the African isolates and Georgia 2007, prompting this study to include a virus from Malawi and Tanzania to increase the temporal spectrum of viruses from that region.…”

Section: Discussionmentioning

confidence: 99%

“…Currently, the majority of available full genome sequences for genotype II ASF viruses are of Eurasian origin, and data for viruses of African origin are limited to five representatives from Tanzania, and Malawi, viz. Tanzania/Rukwa/17/1, TAN/17/Mbagala, TAN/17/Kibaha, TAN/20/Mogorogo, and MAL/19/Karonga, and one from Nigeria, RV502 (OP672342) [ 21 , 22 , 23 , 24 ]. These five genotype II viruses of East African origin are distinct from Georgia 2007/1, based primarily on differences in K177R gene sequence [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

“…Tanzania/Rukwa/17/1, TAN/17/Mbagala, TAN/17/Kibaha, TAN/20/Mogorogo, and MAL/19/Karonga, and one from Nigeria, RV502 (OP672342) [ 21 , 22 , 23 , 24 ]. These five genotype II viruses of East African origin are distinct from Georgia 2007/1, based primarily on differences in K177R gene sequence [ 22 , 23 ]. Differences between the virus genome sequences from Tanzania and Georgia 2007/1 arise from one large insertion/deletion (indel) and various single nucleotide polymorphisms (SNPs).…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomic Comparison of Seven African Swine Fever Genotype II Outbreak Viruses (1998–2019) Reveals the Likely African Origin of Georgia 2007/1

Mthombeni,

Bastos,

van Schalkwyk

et al. 2023

Pathogens

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Since the initial report of African swine fever (ASF) in Kenya in 1921, the disease has predominantly been confined to Africa. However, in 2007, an ASF genotype II virus of unknown provenance was introduced to Georgia. This was followed by its rampant spread to 73 countries, and the disease is now a global threat to pig production, with limited effective treatment and vaccine options. Here, we investigate the origin of Georgia 2007/1 through genome sequencing of three viruses from outbreaks that predated the genotype II introduction to the Caucasus, namely Madagascar (MAD/01/1998), Mozambique (MOZ/01/2005), and Mauritius (MAU/01/2007). In addition, genome sequences were generated for viruses from East African countries historically affected by genotype II (Malawi (MAL/04/2011) and Tanzania (TAN/01/2011)) and newly invaded southern African countries (Zimbabwe (ZIM/2015) and South Africa (RSA/08/2019). Phylogenomic analyses revealed that MOZ/01/2005, MAL/04/2011, ZIM/2015 and RSA/08/2019 share a recent common ancestor with Georgia 2007/1 and that none contain the large (~550 bp) deletion in the MGT110 4L ORF observed in the MAD/01/1998, MAU/01/2007 and TAN/01/2011 isolates. Furthermore, MOZ/01/2005 and Georgia 2007/1 only differ by a single synonymous SNP in the EP402R ORF, confirming that the closest link to Georgia 2007/1 is a virus that was circulating in Mozambique in 2005.

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Section: Discussionmentioning

confidence: 72%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Phylogenomic Comparison of Seven African Swine Fever Genotype II Outbreak Viruses (1998–2019) Reveals the Likely African Origin of Georgia 2007/1

Mthombeni,

Bastos,

van Schalkwyk

et al. 2023

Pathogens

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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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ANASFV: a workflow for ASFV whole genome sequencing, assembly, and evaluation

Li,

Han,

Shao

et al. 2024

Preprint

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African Swine Fever Virus (ASFV) poses an ongoing threat with widespread outbreaks affecting both domestic and wild pig populations globally. Effective management of ASFV outbreaks necessitates a deep understanding of its genetic diversity and evolutionary dynamics. Despite the advantages of nanopore sequencing for genome analysis, its application to ASFV genomes encounters specific challenges, such as high host DNA contamination that reduces viral genome coverage and an inherently higher error rate producing small insertions and deletions (indels).To overcome these obstacles, we developed the ANASFV (analysis of anASFV) pipeline, which enhances both laboratory and bioinformatics workflows for ASFV genome sequencing. This study introduces an amplicon sequencing approach that significantly improves genomic coverage, enabling reliable genome assembly. We also implemented reference-aided polishing techniques to correct small indels caused by nanopore sequencing errors. Additionally, we established a genome quality assessment system, akin to the Benchmarking Universal Single-Copy Orthologue (BUSCO), to evaluate the completeness and accuracy of the assembled genomes. A comprehensive phylogenetic analysis based on coding sequences (CDS) was conducted, allowing us to generate a refined phylogenetic tree that includes all known ASFV genomes. The ANASFV pipeline will facilitate ASFV full genome sequencing using the nanopore platform. It will also support robust downstream bioinformatics analyses to assess genome integrity and conduct detailed phylogenetic studies based on whole-genome data.

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Complete genome analysis of African swine fever virus genotypes II, IX and XV from domestic pigs in Tanzania

Cited by 4 publications

References 62 publications

Phylogenomic Comparison of Seven African Swine Fever Genotype II Outbreak Viruses (1998–2019) Reveals the Likely African Origin of Georgia 2007/1

Phylogenomic Comparison of Seven African Swine Fever Genotype II Outbreak Viruses (1998–2019) Reveals the Likely African Origin of Georgia 2007/1

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

ANASFV: a workflow for ASFV whole genome sequencing, assembly, and evaluation

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