Sequence analysis Tandem repeat sequences of CVR (B602L)
The analysis of TRS of CVR (Table 4) revealed 8 TRS variants namely: Tet-10, Tet-13, Tet-18, Tet-20a, Tet-22, Tet-26, Tet-33 and Tet-41 from samples collected between April 2019 and November 2020. Six of the TRS variants were new and different from previously reported variants reported in Nigeria. The TRS variants were recovered as follows: Dawaki (1), Katsit (6) Numan (1) and Pandam (1). Katsit and Pandam share similar TRS variants (Tet-13) (Table 4), similarly Tet-13 was recovered from Katsit and Pandam LPMs.
Figure 3 : A). Katsit live pig market in Zagon Kataf LGA, Kaduna State Nigeria B). Pandam live pig market in Quan Pan LGA Plateau State, Nigeria. C: A pig with the classical presentation of African Swine Fever in a live pig market in Nigeria. D). Moribund pigs are slaughtered inside a live pig market in Nigeria.
Figure 4: Phylogenetic tree of partial p72 gene nucleotide sequences of Nigeria ASFV samples collected in live pig markets in Nigeria The tree was constructed in MEGA X using the Neighbor joining method with 1,000 bootstrap replicates. The Nigerian ASFV isolates from this study are highlighted with diamond shape (Red for 2019 and blue for 2020)
Figure 5: Phylogenetic tree of partial p54 gene nucleotide sequences of Nigeria ASFV samples collected in live pig markets in Nigeria The tree was constructed in MEGA X using the Minimum-Evolution method with 1,000 bootstrap replicates. The Nigerian ASFV isolates from this study are highlighted with diamond shape (Red for 2019 and blue for 2020)
Figure 6: Maximum Likelihood tree based on the partial amino acid sequence of CD2v protein of the EP424R gene of ASFV samples collected in live pig markets in Nigeria. The tree was constructed in MEGA X. The Nigerian ASFV isolates from this study are highlighted with diamond shape (Red for 2019 and blue for 2020). Bootstrap values greater than 75% are shown