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).