RESULTS
A total of 8 viral isolates collected from 5 affected animals were
processed for genome sequencing. Genome assemblies having a high
percentage of genome coverage (>99%) were considered for
further analysis, which resulted in 6 genome isolates. The isolates were
assembled at an average genome coverage of 99.96% with a mean coverage
depth of 596.39X (Supplementary Data ).
A total of 177 unique variants were detected across the 6 isolates, of
which 86 were synonymous single nucleotide variants (SNVs), 58 were
nonsynonymous, 27 were indels, and 1 was a stopgain SNV while 5 variants
were found in untranslated regions (UTR). A maximum number of variants
were detected in the gene LSDVgp134 (N=7) (Supplementary Data ).
On comparison with 57 LSDV genome sequences downloaded from GenBank, we
found that 47 variants detected in the 6 sequenced isolates were novel
and were not present in any other genome sequence globally(Figure 1A) . Of the novel variants, 14 were nonsynonymous SNVs
while 27 are indels. A maximum number of variants were detected in the
gene LSDVgp134 (N=3) and LSDVgp011 (N=3) while the most number of indels
were found across 4 genes, LSDVgp026, LSDVgp067, LSDVgp134 and LSDVgp151
all of which had two indels each (Supplementary Data ). None of
the variants found in 4 genome sequences from India belonging to the
2019 outbreak of the disease deposited in GenBank was present in the 6
samples from the current outbreak
(Kumar et al., 2021).
Phylogenetic analysis showed that the 6 genome isolates from the present
outbreak form a distinct cluster on the phylogenetic tree with little
similarity to other global genomes (Supplementary Data ). The
cluster is defined by 39 unique variants which were present in all 6
isolates but not present in any other global genome. The phylogenetic
context of the samples has been summarised in Figure 1B . The
closest cluster for the 6 isolates on the phylogenetic tree comprises 12
sequences deposited from 7 Asian and European countries with collection
dates ranging from 2012 to 2022 (Figure 1C ).
Genome sequences of viruses isolated from both nasal swabs and skin
scabs were available for 2 of the 5 host animals, which allowed us to
check for intra-host variations. Analysis of the variants suggested that
one nonsynonymous variant (A30663T LSDVgp037:D286V) which was present in
the viral isolated from skin scab for 1 animal which was not present in
the nasal swab isolate of the same host sample potentially pointing to
intra-host evolution. The variant position had a good depth of coverage
(>100X) for both samples.