Results and Discussion
All partial B646L and EP402R sequences of the ASFV
isolates were identical to those of the original Korean isolate,
Korea/19S804/wb/2019 (GenBank accession nos. MN817977 and MN817978).
These sequences were categorised into the genotype II (Fig. 2A) and
serogroup 8 (Fig. 2B) groups, respectively. Most IGR fragments also
showed 100% sequence identity to the corresponding region of the
Korea/19S804/wb/2019 isolate (GenBank accession no. MN817979), except
for those of two isolates collected in Paju (Korea/19S3965/wb/2019 on
December 3 and Korea/19S5464/wb/2019 on December 30). The IGR fragment
contained an STR (5′-GGAATATATA-3′), with a repeat time varying in or
among ASFV populations (Goller et al., 2015; Nix et al., 2006). The
10-bp STR was inserted three times in the corresponding regions of the
major Korean ASFV isolates from the wild boar (IGR variant II), similar
to those in the Russia/Volgograd/wb/2014 (GenBank accession no.
KP137637), Belgium/Etalle/wb/2018 (GenBank accession no. MH998359.1),
and China/2018/Domestic pig (GenBank accession no. MH 735144) strains.
The genome of another Korean isolate from a domestic pig
(Korea/2019/Domestic pig, GenBank accession no. MN603969 [Kim H. J. et
al., 2020]) also belonged to the variant II group. On the other hand,
the nucleotide stretch was repeated two and four times in the genomes of
the Korea/19S3965/wb/2019 (IGR variant I) and Korea/19S5464/wb/2019 (IGR
variant III) isolates, respectively (Table 2).
Because the genomes of DNA viruses, including ASFV, show relatively low
evolutionary divergence, few informative molecular markers have been
detected within the genic regions of the viral genomes, as observed for
the by B646L and EP402R sequences in this study. However,
the lengths of genomic STR are readily expanded or contracted during DNA
replication largely by slipped strand mispairing (slippage mechanism).
If the affected STR is in an intergenic noncoding region, the allelic
variant can be fixed in the population because of the low levels of
purifying selection (Gemayel et al., 2010). ASFV strains with variant
IGR genotypes have been discovered in Russia (Goller et al., 2015) and
China (Ge et al., 2019; Li et al., 2019). However, unlike the IGR
variants in these countries, those identified in this study were
sympatrically distributed with the pre-existing type in a small county
(Fig. 1B). The time intervals for their emergence were also very short
(approximately two and three months after the first outbreak in wild
boars). Taken together, these facts may suggest that the Korean IGR
variants I and III were sporadically generated rather than being
independently transported from other countries through replication error
in the pre-existing IGR variant II population.
In this study, we identified ASFV variants with different genotypes
collected during the comprehensive survey of wild boars in small
counties of South Korea surrounding the original ASF outbreak point.
Considering the short emergence periods of less than three months and
sympatric distributions within a narrow geographical region, these
variant strains are likely to have spontaneously emerged in the local
viral population through a molecular mechanism(s) such as replication
slippage.
The probable transmission routes of ASF can be predicted by analysing
the spatiotemporal distributions of ASFV with distinct IGR genotypes
(Goller et al., 2015). Therefore, the polymorphic STR was suggested as
an informative marker to discriminate closely related ASFV strains (Ge
et al., 2019). Currently, we have no evidence supporting clonal
expansion of these variants in the relevant region, which may be because
of their recent emergence. Surveillance of wild boars will be continued
until the viral disease is eliminated. If simultaneous propagation of
these IGR variants is observed in the near future, our data will provide
a highly informative genetic marker for molecular epidemiological
approaches to trace both local and global transmission of ASFV.