Title: Whole-genome-based phylogeny of African swine fever virus

Co-author(s) :

Aslanyan Levon ; Karalyan Zaven


Aim: A genome-scale phylogenetic analysis was used to infer the evolutionary dynamics of Asfarviridae – African swine fever virus (ASFV) – and better define its genetic diversity. Materials and Methods: All complete ASFV genomes from NCBI’s resource as of March 2020 were used. The phylogenetic analysis used maximum likelihood and neighbor-joining methods. The evolutionary models detection was done with the help of the package of programs MEGA-X. Algorithms were used to build phylogenetic trees for type B DNA polymerases of ASFV (n=34) and HcDNAV (n=2), as an external group. Results: An expedient categorization of the Asfarviridae family uses five clades. Genotype 1 (except for LIV 5/40 virus isolate) as well genotype 7 are assigned to the alpha clade; genotype 2 to the beta clade; genotypes 8, 9, and 10 to the gamma clade; genotype 5 to the delta clade; and genotypes 3, 4, and 20, as well as genotype 22 and the LIV 5/40 isolate to the epsilon clade. Branch lengths on the phylogenetic tree are proportional to genetic distance along the branch. Branches at the phylogenetic tree of Asfarviridae are much shorter than branches for Baculoviridae. Shorter branches in ASFVs population suggest that Asfarviridae evolved relatively recently and remain more closely related. Conclusion: We suggest applying more robust standards using whole genomes to ensure the correct classification of ASFV and maintain phylogeny as a useful tool.


Veterinary World

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Veterinary World






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The authors are deeply grateful to the creatorof MAFFT system, Dr. Kazutaka Katoh, for his kindattention and support to our work with the MAFFTsystem. Computer experiments were conducted on16-processor 16GB GENOME SERVER, a virtual computational environment at the Institute forInformatics and Automation Problems of NationalAcademy of Sciences of Republic of Armenia.Mathematical part of this work was partially supportedby grant № 18T-1B407 of the Science Committee ofthe ESCS Ministry of Republic of Armenia.


Institute for Informatics and Automation Problems of NAS RA ; Institute of Molecular Biology of NAS RA ; Yerevan State Medical University (YSMU)




Gorbalenya, A. and Lauber, C. (2017) Phylogeny of viruses.Ref. Module Biomed. Sci., p.125-129. ; López-Otin, C., Freije, J.M., Parra, F., Mendez, E. andViñuela, E. (1990) Mapping and sequence of the gene coding for protein p72, the major capsid protein of Africanswine fever virus. Virology, 175(2): 477-484. ; Yu, M., Morrissy, C.J. and Westbury, H.A. (1996) Strongsequence conservation of African swine fever virus p 72protein provides the molecular basis for its antigenic stability. Arch. Virol., 141(9): 1795-1802. ; Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K.(2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol., 35(6): 1547-1549. ; Aslanyan, L. (2017) LCS Algorithm with Vector-markers.Revised Selected Papers, IEEE Xplore. p117-124. ; Maier, D. (1978) The complexity of some problems on subsequences and supersequences. J. ACM, 25(2): 322-336. ; Ndlovu, S., Williamson, A.L., Malesa, R., van Heerden, J.,Boshoff, C.I., Bastos, A.D.S., Heath, L. and Carulei, O.(2020) Genome sequences of three African swine feverviruses of genotypes I, III, and XXII from South Africa andZambia, isolated from ornithodoros soft ticks. Microbiol.Resour. Announc., 9(10): e01376-19. ; Bacciu, D., Deligios, M., Sanna, G., Madrau, M.P.,Sanna, M.L., Dei Giudici, S. and Oggiano, A. (2016)Genomic analysis of Sardinian 26544/OG10 isolate ofAfrican swine fever virus. Virol. Rep., 6:81-89. ; Granberg, F., Torresi, C., Oggiano, A., Malmberg, M.,Iscaro, C., De Mia, G.M. and Belák, S. (2016) Completegenome sequence of an African swine fever virus isolatefrom Sardinia, Italy. Genome Announc., 4(6): e01220-16. ; Chapman, D.A., Tcherepanov, V., Upton, C. and Dixon, L.K.(2008) Comparison of the genome sequences of non-pathogenic and pathogenic African swine fever virus isolates. J.Gen. Virol., 89(Pt 2): 397-408. ; Portugal, R., Coelho, J., Höper, D., Little, N.S., Smithson,C.,Upton, C., Martins, C., Leitão, A. and Keil, G.M. (2015)Related strains of African swine fever virus with differentvirulence: Genome comparison and analysis. J. Gen. Virol.,96(Pt 2): 408-419. ; Yanez, R.J., Rodriguez, J.M., Nogal, M.L., Yuste, L.,Enriquez, C., Rodriguez, J.F. and Vinuela, E. (1995)Analysis of the complete nucleotide sequence of Africanswine fever virus. Virology, 208(1): 249-278. ; Gilliaux, G., Garigliany, M., Licoppe, A., Paternostre, J.,Lesenfants, C., Linden, A. and Desmecht, D. (2019) Newlyemerged African swine fever virus strain Belgium/Etalle/wb/2018: Complete genomic sequence and comparativeanalysis with reference p72 genotype II strains. Transbound.Emerg. Dis., 66(6): 2566-2591. ; Wen, X., He, X., Zhang, X., Zhang, X., Liu, L., Guan, Y.,Zhang, Y. and Bu, Z. (2019) Genome sequences derivedfrom pig and dried blood pig feed samples provide important insights into the transmission of African swine fevervirus in China in 2018. Emerg. Microbes Infect., 8(1):303-306. ; Olasz, F., Mészáros, I., Marton, S., Kaján, G.L., Tamás, V.,Locsmándi, G., Magyar, T., Bálint, Á., Bányai, K. andZádori, Z.A. (2019) Simple Method for sample preparationto facilitate efficient whole-genome sequencing of Africanswine fever virus. Viruses, 11(12): E1129. ; Forth, J.H., Forth, L.F., King, J., Groza, O., Hübner, A.,Olesen, A.S., Höper, D., Dixon, L.K., Netherton, C.L.,Rasmussen, T.B., Blome, S., Pohlmann, A. and Beer, M.A.(2019) Deep-sequencing workflow for the fast and efficient generation of high-quality African swine fever viruswhole-genome sequences. Viruses, 11(9): 846. ; Kovalenko, G., Ducluzeau, A.L., Ishchenko, L., Sushko, M.,Sapachova, M., Rudova, N., Solodiankin, O., Gerilovych,A.,Dagdag, R., Redlinger, M., Bezymennyi, M., Frant, M.,Lange, C.E., Dubchak, I., Mezhenskyi, A.A., Nychyk, S.,Bortz, E. and Drown, D.M. (2019) Complete genomesequence of a virulent African swine fever virus from adomestic pig in Ukraine. Microbiol. Resour. Announc.,8(42): e00883-19. ; Gallardo, C., Soler, A., Nieto, R., Cano, C., Pelayo, V.,Sanchez, M.A., Pridotkas, G., Fernandez-Pinero, J.,Briones, V. and Arias, M. (2017) Experimental infectionof domestic pigs with African swine fever virus Lithuania2014 Genotype II field isolate. Transbound. Emerg. Dis.,64(1): 300-304. ; Farlow, J., Donduashvili, M., Kokhreidze, M.,Kotorashvili, A., Vepkhvadze, N.G., Kotaria, N. andGulbani, A. (2018) Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) fromthe country of Georgia. Virol. J., 15(1):190. ; Chapman, D.A., Darby, A.C., Da Silva, M., Upton, C.,Radford, A.D. and Dixon, L.K. (2011) Genomic analysisof highly virulent Georgia 2007/1 isolate of African SwineFever virus. Emerg. Infect. Dis., 17(4): 599-605. ; Bishop, R.P., Fleischauer, C., de Villiers, E.P., Okoth, E.A.,Arias, M., Gallardo, C. and Upton, C. (2015) Comparativeanalysis of the complete genome sequences of Kenyan.African swine fever virus isolates within p72 genotypes IXand X. Virus Genes, 50(2): 303-309. ; Masembe, C., Sreenu, V.B., Da Silva Filipe, A.,Wilkie, G.S., Ogweng, P., Mayega, F.J., Muwanika, V.B.,Biek, R., Palmarini, M. and Davison, A.J. (2018) Genomesequences of five African swine fever virus genotype IXisolates from domestic pigs in Uganda. Microbiol. Resour.Announc., 7(13): e01018-18. ; Saitou, N. and Nei, M. (1987) The neighbor-joining method:A new method for reconstructing phylogenetic trees. Mol.Biol. Evol., 4(4): 406-425. ; Nei, M. and Kumar, S. (2000) Molecular Evolution andPhylogenetics. Oxford University Press, New York. ; Felsenstein, J. (1985) Confidence limits on phylogenies: Anapproach using the bootstrap. Evolution, 39(4): 783-791. ; Gao, L. and Qi, J. (2007) Whole-genome molecular phylogeny of large dsDNA viruses using composition vectormethod. BMC Evol. Biol., 7(1):41. ; de Villiers, E.P., Gallardo, C., Arias, M., da Silva, M.,Upton, C., Martin, R. and Bishop, R.P. (2010) Phylogenomicanalysis of 11 complete African swine fever virus genomesequences. Virology, 400(1): 128-136. ; Ogata, H., Toyoda, K., Tomaru, Y., Nakayama, N., Shirai,Y.,Claverie, J.M. and Nagasaki, K. (2009) Remarkablesequence similarity between the dinoflagellate-infectingmarine girus and the terrestrial pathogen African swinefever virus. Virol. J., 6(1):178. ; Lubisi, B.A., Bastos, A.D., Dwarka, R.M. and Vosloo, W.(2005) Molecular epidemiology of African swine fever inEast Africa. Arch. Virol., 150(12): 2439-2452. ; Costard, S., Wieland, B. de Glanville, W., Jori, F.,Rowlands, R., Vosloo, W., Roger, F., Pfeiffer, D.U. andDixon, L.K. (2009) African swine fever: How can globalspread be prevented? Philos. Trans. R. Soc. Lond. B Biol. Sci., 364(1530): 2683-2696. ; Bastos, A.D., Penrith, M.L., Crucière, C., Edrich, J.L.,Hutchings, G., Roger, F., Couacy-Hymann, E. andThomson, G.R. (2003) Genotyping field strains of Africanswine fever virus by partial p72 gene characterisation. Arch.Virol., 148(4): 693-706. ; Quembo, C.J., Jori, F., Vosloo, W. and Heath, L. (2018)Genetic characterization of African swine fever virus isolates from soft ticks at the wildlife/domestic interfacein Mozambique and identification of a novel genotype.Transbound. Emerg. Dis., 65(2): 420-431. ; Malogolovkin, A., Burmakina, G., Titov, I., Sereda, A.,Gogin, A., Baryshnikova, E. and Kolbasov, D. (2015)Comparative analysis of African swine fever virus genotypes and serogroups. Emerg. Infect. Dis., 21(2): 312-315. ; King, K., Chapman, D., Argilaguet, J.M., Fishbourne, E.,Hutet, E., Cariolet, R., Hutchings, G., Oura, C.A.,Netherton, C.L., Moffat, K., Taylor, G., Le Potier, M.F.,Dixon, L.K. and Takamatsu, H.H. (2011) Protection ofEuropean domestic pigs from virulent African isolates ofAfrican swine fever virus by experimental immunisation.Vaccine, 29(28): 4593-4600. ; Muangkram, Y., Sukmak, M. and Wajjwalku, W. (2015)Phylogeographic analysis of African swine fever virusbased on the p72 gene sequence. Genet. Mol. Res., 14(2):4566-4574. ; Wang, L., Luo, Y., Zhao, Y., Gao, G.F., Bi, Y. and Qiu, H.J.(2020) Comparative genomic analysis reveals an “open”pan-genome of African swine fever virus. Transbound.Emerg. Dis., 67(4): 1553-1562. ; Hollich, V., Milchert, L., Arvestad, L. and Sonnhammer, E.L.(2005) Assessment of protein distance measures andtree-building methods for phylogenetic tree reconstruction.Mol. Biol. Evol., 22(11): 2257-2264. ; Johnson, K.P., De Kort, S., Dinwoodey, K., Mateman, A.C.,Ten Cate, C., Lessells, C.M. and Clayton, D.H. (2001) Amolecular phylogeny of the dove genera Streptopelia andColumba. Auk, 118(4): 874-887. ; Thézé, J., Lopez-Vaamonde, C., Cory, J.S. and Herniou, E.A.(2018) Biodiversity, evolution and ecological specialization of baculoviruses: A treasure trove for future appliedresearch. Viruses, 10(7): E366.


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