Genetic Profiles of Ten African Swine Fever Virus Strains from Outbreaks in Select Provinces of Luzon, Visayas, and Mindanao, Philippines, Between 2021 and 2023

Figures

• 

  Figure 1. A map of select provinces in the Philippines as sources of ASF-positive samples from 2021 to 2023. Representative samples were obtained from Luzon, Visayas, and Mindanao, Philippines. Map data © 2024 Google.

• 

  Figure 2. Maximum likelihood consensus tree of select ASFV genomes and the genomes of the Philippine strains inferred using the ultrafast bootstrap implemented in the IQ-TREE software v. 2.3.1 (substitution model: GTR + F + I + R4) with the U18466.2 BA71V genome as the outgroup. The scale bar shows numbers of substitutions per site and bootstrap resampling (1000 iterations) support values are shown at the nodes. ASFV VP72 genotype II genomes are highlighted in blue. Support values lower than 70% are not shown.

• 

  Figure 3. Maximum likelihood tree based on the full-length ASFV p72 (B646L) sequence alignment of the recently sequenced nine strains from the Philippines and select publicly available representative ASFV isolates from other genotypes with midpoint roots. Philippine strains are highlighted in blue and the corresponding p72 genotype is indicated. Different genotypes are labeled, respectively. Phylogeny was inferred using the TVM + V + I model in IQTREE following 1000 ultrafast bootstrap iterations. Bootstrap values greater than 70 are indicated at appropriate nodes and the scale bar indicates nucleotide substitutions per site.

• 

  Figure 4. Maximum likelihood tree of full-length ASFV CD2v (EP402R) protein sequence alignment of the Philippine strains (highlighted in blue) and representative ASFV strains and corresponding serogroup (SG) is indicated. Phylogeny was inferred using HKY + F + G4 model in IQTREE following 1000 ultrafast bootstrap iterations. Bootstrap values greater than 70 are indicated at appropriate nodes and the scale bar indicates nucleotide substitutions per site.

• 

  Figure 5. Amino acid sequence alignment of the tetrameric tandem repeat sequences (TRSs) of the central variable region (CVR) of the B602L gene of the Philippine strains showing a ‘BNDBNDBNAA’ pattern with 10 repeating patterns. Letters in the CVR sequence represent the TRSs in ASFV strains: A = CAST, CVST, CTST, and CASI; B = CADT, CADI, CTDT, CAGT, and CVDT; N = NVDT, NVGT, and NVDI; D = CASM. Color scheme used was Unipro UGENE Software default for protein alignment.

• 

  Figure 6. Nucleotide sequence alignment of the intergenic region (IGR) between the I73R and I329L genes. The Philippine strains belonged to IGR II, with one insertion of 10 nucleotides (GGAATATATA) compared to Georgia 2007/1 (GenBank accession no. FR682468.2). Color scheme used was Unipro UGENE Software default for nucleotide sequence alignment.

• 

  Figure 7. Analysis of IGRA179L-A137R of the 10 ASFV strains from select provinces in the Philippines from outbreaks between 2021 and 2023. Positions 143 and 144 from the start of the IGR of strains from Negros Occidental (PP737712-PP737715) and from Mindoro Oriental (PP737716) had C-to-T substitution. The reference strain (Georgia 2007/1, GenBank Acc. No.: NC_044959) is highlighted. Color scheme used was Unipro UGENE Software default for nucleotide sequence alignment.

• 

  Figure 8. Genome alignment of the Bataan 2022 strain (PP737708) and Georgia 2007/1 (NC_044959.2), showing the genes affected by a 1.9 kb deletion corresponding to the 17,000th and 18,939th positions of the reference Georgia 2007/1 genome. The MGF 360-4L, ASFV G ACD 00300, and MGF 360-6L genes of the Bataan 2022 strain were affected.