3.5. Phylogenetic Analysis
Phylogenetic analysis based on complete genomes clustered the CaPVs into 3 distinct species – LSDV, GTPV, and SPPV (Fig. 6). Among LSDV, two monophyletic clusters viz. cluster 1.1 and 1.2 and several novel recombinant LSDV strains have been shown as described previously (Biswas et al., 2020; Van Schalkwyk et al., 2020; 2022) Cluster 1.1 contains LSDV vaccine strains as well as vaccine-associated field strains from South Africa. All LSDV vaccines share a common ancestry with the Neethling 1959 vaccine (AF409138). Second cluster 1.2 consists of wild-type strains. The wild-type LSDV cluster comprises of subclusters of Kenyan LSDV strains and wild-type LSDV strains from other parts of Africa, the Middle East, Europe, and Asia. LSDV-WB/IND/19 clustered with Kenyan LSDV strains providing further support for the incursion of LSDV into India through illegal trade of animals, animal products, or biologicals. Kenyan strains have caused outbreaks in Kenya, but however never been reported in subsequent epidemics in Africa, the Middle East, and Europe (Tulman et al., 2001). Since 2017, recombinant LSDV strains have been detected in infected cattle in Russia (Sprygin et al., 2018; Sprygin et al., 2020; Shumilova et al., 2022); Krotova et al., 2022a), China (Ma et al., 2021), Hongkong (Flannery et al., 2021), Taiwan (Huang et al., 2022) and Vietnam (Mathijs et al., 2021; Tran et al., 2021). In phylogenetic analysis, recombinant strains formed four monophyletic groups R1, R2, R3, and R4 as described in section 3.3. These recombinant LSDV strains have demonstrated an increase in virulence as compared to other field LSDV strains and can be transmitted in vector-independent mode (Aleksandr et al., 2020; Kononov et al., 2020). Even, LSDV-Saratov/19 has been demonstrated to persist in winter in absence of vectors through direct contact or fomites (Shumilova et al., 2022). LSDV has also been reported in a giraffe in Vietnam which is closely related to recombinant Vietnamese LSDV strains (Dao et al., 2022). Evidence of genetic recombination between capripoxviruses has been established in-vitro based on RFLP (Gershon et al., 1989). The use of homologous LSDV vaccines has not been authorized in Russia but the Neethling-based Lumpyvax vaccine (KEVE-VAPI) was used in Kazakhstan near border areas of Russia where recombinant LSDV strains have been detected (Sprygin et al., 2018; Sprygin et al., 2020). It was suggested that these vaccines might be possible for the emergence of recombinant strains in adjoining regions (Sprygin et al., 2018). In addition, a commercial Lumpyvax vaccine has been demonstrated to contain Neethling-like LSDV, KSGP-like LSDV, and GTPV-like genomes have been described (Haegman et al., 2021; Vandenbussche et al., 2022). Combining closely related viruses may increase the risk of recombination either in naturally infected animals or during seed virus production (Vandenbussche et al., 2022).