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Genome Sequence of African Swine Fever Virus BA71, the Virulent Parental Strain of the Nonpathogenic and Tissue-Culture Adapted BA71V.

Rodríguez JM, Moreno LT, Alejo A, Lacasta A, Rodríguez F, Salas ML - PLoS ONE (2015)

Bottom Line: They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes.We discuss the possible contribution of these changes to virulence.Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network.

View Article: PubMed Central - PubMed

Affiliation: Centro Nacional de Microbiología, Instituto Nacional de Salud Carlos III, Majadahonda, Madrid, Spain.

ABSTRACT
The strain BA71V has played a key role in African swine fever virus (ASFV) research. It was the first genome sequenced, and remains the only genome completely determined. A large part of the studies on the function of ASFV genes, viral transcription, replication, DNA repair and morphogenesis, has been performed using this model. This avirulent strain was obtained by adaptation to grow in Vero cells of the highly virulent BA71 strain. We report here the analysis of the genome sequence of BA71 in comparison with that of BA71V. They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes. We discuss the possible contribution of these changes to virulence. Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network.

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Related in: MedlinePlus

5’- and 3’- ends of the ASFV BA71 and BA71V genomes.The figure shows dot plot comparisons of the 5’- (A) and 3’-end (B) variable regions. For each of the four large deletions observed between the genomes, the deleted region is indicated by a light blue box in the corresponding axis and the position where the deletion occurred is indicated by an arrow in the opposite axis. ORFs are indicated by arrows, and the different groups of ORFs are identified by colors: MGF 360, violet; MGF 110, yellow; MGF 300, green; MGF 505, red; MGF 100, rose; p22 family, gray, other ORFs, black.
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pone.0142889.g002: 5’- and 3’- ends of the ASFV BA71 and BA71V genomes.The figure shows dot plot comparisons of the 5’- (A) and 3’-end (B) variable regions. For each of the four large deletions observed between the genomes, the deleted region is indicated by a light blue box in the corresponding axis and the position where the deletion occurred is indicated by an arrow in the opposite axis. ORFs are indicated by arrows, and the different groups of ORFs are identified by colors: MGF 360, violet; MGF 110, yellow; MGF 300, green; MGF 505, red; MGF 100, rose; p22 family, gray, other ORFs, black.

Mentions: BA71 and BA71V genomes are collinear and largely identical. The identity is interrupted 69 times by 37 point mutations and 32 insertions or deletions. Eighty of the 170 kbp of the sequence of BA71V genome were obtained as a collage of small sequencing projects with very different techniques, including chemical sequencing [1]. Given the high quality of the BA71 sequence and the extent of the identity between both genomes, we thought possible that some of these differences were due to errors in the sequence of the BA71V genome. To answer this question, we verified the sequence of BA71V in the positions where it differs from BA71 in the plasmid library used for the determination of the original BA71V sequence [42]. The errors detected are summarized in S1 Table. The corrections introduced in the sequence of BA71V do not alter the total number of nucleotides but modify some genome features. The sequence of the left TIR, and the ORFs KP360L, KP362L, J268L, J104L, J182L, C122R and DP311R are altered. The sequence of the encoded protein is modified for KP360L, J268L and DP311R. In the corrected genome, the sequence of ORFs J104L and J182L is fused into a larger ORF, J328L. This ORF is a member of the MGF 300, orthologous to MGF300-4L, and is present with a similar size in all the viral genomes sequenced to date. The correction at position 67449 changes the size of the involved ORF (C122R) to 105 amino acids, the size of the orthologous protein in other ASFV genomes. According to the naming conventions for the BA71V strain the ORF is now labeled as C105R. The correction of the error at position 13543/13544 results in the increment to 64 amino acids of a previously considered minor (non-annotated) ORF. Orthologues to this ORF, J64R, are present in the genomes of the European isolates (E75, Lisbon60, OURT88/3, NH/P68, annotated as X64R), and in some African isolates (Pretoriuskop/96/4 and Benin97/1, although not annotated). Interestingly, although this ORF does not show any detectable similarity to proteins in the databases, it is remarkably similar to the ASFV ORF X69R (S1 Fig). After the corrections introduced in the sequence of the BA71V genome, the alignment between the BA71 and BA71V genomes is interrupted 52 times by 30 point mutations and 22 deletions or insertions. These differences can be grouped in four classes according to its nature: (i) Large deletions in the variable regions of the genome (1354–8238 nts, Fig 2, Table 2), likely originated by misalignment during replication or by recombination between the highly similar sequences of the multigene families; (ii) Small deletions or duplications (10–408 nts, Table 3) produced by variations in the number of tandem repeats by slipped-strand mispairing during replication [55]; (iii) Variations of one or two nucleotides in polynucleotide tracks (Table 4) produced by polymerase slippage during replication and (iv) Point mutations (Table 5), produced during genome replication or repair. We will refer to the different changes by its ordinal number from 5’ to 3’ of the genome, which is indicated in the first column of Tables 2–5.


Genome Sequence of African Swine Fever Virus BA71, the Virulent Parental Strain of the Nonpathogenic and Tissue-Culture Adapted BA71V.

Rodríguez JM, Moreno LT, Alejo A, Lacasta A, Rodríguez F, Salas ML - PLoS ONE (2015)

5’- and 3’- ends of the ASFV BA71 and BA71V genomes.The figure shows dot plot comparisons of the 5’- (A) and 3’-end (B) variable regions. For each of the four large deletions observed between the genomes, the deleted region is indicated by a light blue box in the corresponding axis and the position where the deletion occurred is indicated by an arrow in the opposite axis. ORFs are indicated by arrows, and the different groups of ORFs are identified by colors: MGF 360, violet; MGF 110, yellow; MGF 300, green; MGF 505, red; MGF 100, rose; p22 family, gray, other ORFs, black.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4664411&req=5

pone.0142889.g002: 5’- and 3’- ends of the ASFV BA71 and BA71V genomes.The figure shows dot plot comparisons of the 5’- (A) and 3’-end (B) variable regions. For each of the four large deletions observed between the genomes, the deleted region is indicated by a light blue box in the corresponding axis and the position where the deletion occurred is indicated by an arrow in the opposite axis. ORFs are indicated by arrows, and the different groups of ORFs are identified by colors: MGF 360, violet; MGF 110, yellow; MGF 300, green; MGF 505, red; MGF 100, rose; p22 family, gray, other ORFs, black.
Mentions: BA71 and BA71V genomes are collinear and largely identical. The identity is interrupted 69 times by 37 point mutations and 32 insertions or deletions. Eighty of the 170 kbp of the sequence of BA71V genome were obtained as a collage of small sequencing projects with very different techniques, including chemical sequencing [1]. Given the high quality of the BA71 sequence and the extent of the identity between both genomes, we thought possible that some of these differences were due to errors in the sequence of the BA71V genome. To answer this question, we verified the sequence of BA71V in the positions where it differs from BA71 in the plasmid library used for the determination of the original BA71V sequence [42]. The errors detected are summarized in S1 Table. The corrections introduced in the sequence of BA71V do not alter the total number of nucleotides but modify some genome features. The sequence of the left TIR, and the ORFs KP360L, KP362L, J268L, J104L, J182L, C122R and DP311R are altered. The sequence of the encoded protein is modified for KP360L, J268L and DP311R. In the corrected genome, the sequence of ORFs J104L and J182L is fused into a larger ORF, J328L. This ORF is a member of the MGF 300, orthologous to MGF300-4L, and is present with a similar size in all the viral genomes sequenced to date. The correction at position 67449 changes the size of the involved ORF (C122R) to 105 amino acids, the size of the orthologous protein in other ASFV genomes. According to the naming conventions for the BA71V strain the ORF is now labeled as C105R. The correction of the error at position 13543/13544 results in the increment to 64 amino acids of a previously considered minor (non-annotated) ORF. Orthologues to this ORF, J64R, are present in the genomes of the European isolates (E75, Lisbon60, OURT88/3, NH/P68, annotated as X64R), and in some African isolates (Pretoriuskop/96/4 and Benin97/1, although not annotated). Interestingly, although this ORF does not show any detectable similarity to proteins in the databases, it is remarkably similar to the ASFV ORF X69R (S1 Fig). After the corrections introduced in the sequence of the BA71V genome, the alignment between the BA71 and BA71V genomes is interrupted 52 times by 30 point mutations and 22 deletions or insertions. These differences can be grouped in four classes according to its nature: (i) Large deletions in the variable regions of the genome (1354–8238 nts, Fig 2, Table 2), likely originated by misalignment during replication or by recombination between the highly similar sequences of the multigene families; (ii) Small deletions or duplications (10–408 nts, Table 3) produced by variations in the number of tandem repeats by slipped-strand mispairing during replication [55]; (iii) Variations of one or two nucleotides in polynucleotide tracks (Table 4) produced by polymerase slippage during replication and (iv) Point mutations (Table 5), produced during genome replication or repair. We will refer to the different changes by its ordinal number from 5’ to 3’ of the genome, which is indicated in the first column of Tables 2–5.

Bottom Line: They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes.We discuss the possible contribution of these changes to virulence.Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network.

View Article: PubMed Central - PubMed

Affiliation: Centro Nacional de Microbiología, Instituto Nacional de Salud Carlos III, Majadahonda, Madrid, Spain.

ABSTRACT
The strain BA71V has played a key role in African swine fever virus (ASFV) research. It was the first genome sequenced, and remains the only genome completely determined. A large part of the studies on the function of ASFV genes, viral transcription, replication, DNA repair and morphogenesis, has been performed using this model. This avirulent strain was obtained by adaptation to grow in Vero cells of the highly virulent BA71 strain. We report here the analysis of the genome sequence of BA71 in comparison with that of BA71V. They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes. We discuss the possible contribution of these changes to virulence. Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network.

Show MeSH
Related in: MedlinePlus