African Swine Fever Virus
Genomes
The African Swine Fever Virus is a double stranded DNA virus with length approximately 170-190kb encoding for around 150 proteins
see for example http://viralzone.expasy.org/viralzone/all_by_species/288.html.
Complete genomes are available for a few strains, and de Villiers et al have published an analysis of 11 complete genome sequences:
de Villier et al (2010) "Phylogenomic analysis of 11 complete African swine fever virus genome sequences" Virology 400:128-136
http://dx.doi.org/10.1016/j.virol.2010.01.019
13 Full genome sequences were downloaded from GenBank on 6 May 2014:
ASFV full genomes (genBank format)
Sequences
The P72 Major Capsid protein is frequently sequenced and used for genotyping as exemplified by the following studies.
Lubisi et al performed a sequencing study on ASFV in East Africa,
Lubisi et al (2005) "Molecular epidemiology of African swine fever in East Africa" Archives of Virology 150:2439-2452
http://link.springer.com/article/10.1007%2Fs00705-005-0602-1
A phylogenetic study was performed on P72 sequences from Southern Africa by Boshof et al (2007),
"The phylogeny revealed the presence of 14 distinct p72 genotypes of which 6 (genotypes XVII-XXII) were considered novel. Eight of these were country-specific with the remaining six having a trans-boundary distribution"
Boshof et al (2007) "Genetic characterisation of African swine fever viruses from outbreaks in southern Africa (1973-1999)" Veterniary Microbiology 121:45-55
http://dx.doi.org/10.1016/j.vetmic.2006.11.007
ASFV P72 sequences were downloaded from GenBank on 6 May 2014, and aligned manually and with MUSCLE (in MEGA 5).
The information file contains the details of the strain, date, location and host where known
| Type | Number of Sequences | Nucleotides | Fasta File | Information file | NJ Tree |
| Full length p72 | 27 | 1941 | asfv_p72_full_length.fas | See below (first 27 lines) | - |
| Partial p72 | 529 | 540 | asfv_p72_partial.fas | asfv_p72_partial_info.txt | asfv_p72_partial_tn93_nj.nwk |
| Partial p72 Subsampled | 190 | 540 | asfv_p72_partial_onePerCountryPerYear.fas | asfv_p72_partial_onePerCountryPerYear_info.txt | asfv_p72_partial_onePerCountryPerYear_tn93_nj.nwk |
