First-ever genomic analysis on the African Swine Fever Virus

Kanikah Mehndiratta, MSc

African Swine Fever (ASF) is a deadly hemorrhagic condition affecting pigs worldwide with a 100% mortality rate as reported by the World Organization for Animal Health (OIE). With tremendous socio-economic losses to the pig-farming industry and the naïve swine population, especially in China, emphasis on the genotyping of the causative ASF virus is absolute for virus detection in samples. It’s relevant, more so for devising appropriate viral vaccines to target the condition. The virus roots back to East Africa in wild suids and soft tics but has been causing epidemics since 1961, in more than 50 countries in Europe, South America, and Asia. International shipment of pork products has led to the virus dissemination and movement of wild boar populations contributing to the rapid spread. 

ASF virus profile

The double-stranded DNA virus belongs to the family Asfarviridae, is 175-195 kbp long and with an oral route as the major entry portal of infection outside its natural arthropod host. Amongst the total 24 described genotypes of the ASF virus involving sequencing of the p72/B646Lgene, two of them have been detected in pig populations outside Africa. The genotype I strain first spread in Portugal pigs in 1958 while the genotype II strain is of prime concern in recent years as it is responsible for the current Eurasian pandemic. The ASF disease is characterized by initial symptoms of fever, depression, and ataxia. 

Complete genomic sequencing of the ASF virus

Countries with vast resources have invested in genomic sequencing of the specific virus variants that have been particularly reported in their domestic swine population. The evolution of the genotype II virus in Africa however, had not been prioritized until now. A research study conducted by scientists based in Kenya, Tanzania, and Scotland has isolated and sequenced the first genotype II ASF virus variant in order to tackle the current Eurasian pandemic. Data on gene analysis was available only for the p72gene and the tetrapeptide CVL at locus p602L so far. 

Research Methodology

The June 2021 article published in Nature involved complete genome sequencing of genotype II isolates from Tanzania, the Tanzania/Rukwa/2017/1. A tissue sample from a 2017 infected female pig in the Rukwa region was collected and processed, followed by isolation of peripheral blood mononuclear cells. p72 genotyping of African Swine Fever virus was done using the Sanger method by Macrogen and the Illumina short-read strategy was used for final sequencing which deduced a bp length of 183,186 and had 182 open reading frames. 

Conclusion

The genotype II sequence showed 99.960% identity with that of the polish variant MG939586 and 99.957% identity with its Chinese counterpart MK645909.1 with reported SNPs of 73 and 78 respectively. The Tanzanian variant came to be most closely related to the Georgian 2007 isolate based on a phylogeny with differences only at the level of indels. 

With the origin of the Georgian variant being unknown, the Rukwa2017/1 is now the first completely sequenced genotype II from an African country. This would help better understand the phylogeographic picture of the virus strain and to what extent it has mutated since its origin. With no vaccine or chemotherapy currently available, efforts on prevention using stricter biosecurity approaches could be the next step forward. 

Also read: The human-associated clade of S. suis.

Source:
1. Njau, E. P., Domelevo Entfellner, J. B., Machuka, E. M., Bochere, E. N., Cleaveland, S., Shirima, G. M., Kusiluka, L. J., Upton, C., Bishop, R. P., Pelle, R., & Okoth, E. A. (2021). The first genotype II African swine fever virus isolated in Africa provides insight into the current Eurasian pandemic. Scientific reports, 11(1), 13081. https://doi.org/10.1038/s41598-021-92593-2

2. Arias, M., Jurado, C., Gallardo, C., Fernández-Pinero, J., & Sánchez-Vizcaíno, J. M. (2018). Gaps in African swine fever: Analysis and priorities. Transboundary and emerging diseases, 65 Suppl 1, 235–247. https://doi.org/10.1111/tbed.12695

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About the Author- Kanikah Mehndiratta is an avid researcher in the field of Genetics with a background in Biotechnology. She is a post-graduate from the University of Glasgow in their Medical Genetics and Genomics program. Currently, based in Chandigarh as a Scientific Writer, she involves herself mainly in projects related to neurological disorders. Outside of academics, she likes to read novels, travel and is involved in volunteer work mostly.