3.3. Comparison with other LSDV, GTPV, and SPPV genomes
In comparison with other LSDV genomes, the intraspecies nucleotide identity of LSDV genomes was 98.13%-100%. The LSDV-WB/IND/19 strain was found to be most closely related to the Kenyan LSDV-NI2490 strain with an nt identity of 99.86% whereas, 99.79% and 99.5% nt identities were seen with LSDV-KSGO 240 and LSDV-Kenya/58 strains, respectively. Earlier reports based on EEV glycoprotein (LSD_126), RPO30, and GPCR (LSD_011) genes showed high similarity to Kenyan LSDV strains (Sudhakar et al., 2022). Identical to Indian strains, LSDV strains from Bangladesh (Badhy et al., 2021), Nepal (Koirala et al., 2022), and Myanmar (Maw et al., 2022), showed a high resemblance to Kenyan LSDV strains based on EEV glycoprotein, RPO30, and GPCR genes indicating the common source of infection through illegal trade of biologicals, animal products or animals. LSDV strains from Vietnam, Thailand, China, and Russia are not related to Kenyan strains but instead are recombinant strains.
With the wild-type, vaccine, and recombinant LSDV strains, LSDV-WB/IND/19 shared 99.44%-99.86%, 98.13%-98.25%, and 98.59%-99.08% nt identities, respectively. Wild-type LSDV strains had 99.44%-99.86% nt identity among each other, whereas 98.18%-98.5% and 98.64%-99.17% nt identities were observed with vaccine and recombinant LSDV strains, respectively. LSDV vaccine strains showed 99.72%-100% nt identity among each other as compared to 98.97%-99.53% nt identity with recombinant LSDV strains. Recombinant LSDV strains shared 98.96%-100% nt identity among each other. With GTPV and SPPV strains, 95.72%-96.74% identities were observed. Due to high nucleotide identity and serological cross-reactivity within theCapripoxvirus genus, heterologous GTPV vaccines have been used in cattle with equal protection against LSDV (Gari et al., 2015; Zhugunissov et al., 2020; Tuppurainen et al., 2022).
With intraspecies nucleotide similarity of 98.13%-100% amongst LSDV strains over the length of their genomes, several insertions, deletions, and substitutions were observed in the comparison of InDel/SNP patterns (Fig. 1) which indicates a high genetic variation among different LSDV strains globally. The wild-type LSDV cluster comprises subclusters of Kenyan LSDV strains, and wild-type LSDV strains from Africa, the Middle East, Europe, and Asia. Vaccine LSDV strains form another cluster. Recombinant strains could be divided into 4 groups, R1 to R4 as described previously with slight differences (Van Schalkwyk et al., 2022; Krotova et al., 2022b; Vandenbussche et al., 2022). Group R1 consists of LSDV-Russia/Saratov/17 and LSDV-Russia/Saratov/19. LSDV-Russia/Tyumen/2019 and LSDV-Udmurtiya/19 form groups R2 and R3, respectively. LSDV strains from China, Vietnam, Hongkong, and Thailand, as well as LSDV-Russia/Tomsk/2020 and LSDV-Russia/Khabarovsk/2020 strains, form group R4. Most LSDV strains from Russia and a larger part of Asia appear to be vaccine-like recombinant strains with signatures from Neethling and KSGP-based vaccines (Vandenbussche et al., 2022).