4 | DISCUSSION
During the study period (2009-2018), clinical cases in cattle were
observed year-round over a wide geographical distribution with
relatively more cases to be reported in the winter months
(December-February). So far, four FMDV serotypes have been reported in
Sudan: O, A, SAT 1 and SAT 2 (Abu Elzein, 1983), although no cases due
to the SAT 1 serotype were detected in this study or have been recorded
in Sudan since 1976 (Abu Elzein and Crowther, 1979). The low incidence
of SAT1 in Sudan is supported by serological data for SAT1-specific
antibodies in comparison to serotypes O and A (Raouf et al., 2009;
Habiela et al., 2010a). Serotype O was the most frequently detected;
findings which are also supported by recent serological data (Raouf et
al., 2016) showing higher prevalence of serotype O specific antibodies
(60.2%) compared to serotype A (30.0%) and serotype SAT 2 (12.3%).
Nucleotide distances of more than 15% (for serotypes O and A) or 20%
(for serotypes SAT 1 and SAT 2) are used to classify isolates into
different topotypes (Samuel and Knowles, 2001; Knowles and Samuel,
2003), while nucleotide differences of between 5% and 15% indicate
distinct virus lineages (Bronsvoort et al., 2004). The Sudanese
sequences reported here differed from the prototype strains of the
relevant topotypes (Knowles et al., 2016) by 7.7-12.1% (O/SUD/2/86),
13.8-16% (O/ETH/3/2004), 15.2-17.8% (O/ETH/2/2006), 12.5-15.5%
(O/ETH/1/2007), 13.4-16% (A/SUD/3/77), 7.4-9.9% (SAT2/SAU/6/2000) and
11.9-14.4% (SAT2/CAR/8/2005). These differences indicated the continued
divergence of virus lineages within each topotype.
Serological findings from 2013 (Raouf et al., 2016) demonstrate that
serotype O is present along the Nile basin up to Khartoum and in
Western, Eastern and Northern Sudan. A previous study (Habiela et al.,
2010b) highlighted that within-country circulation is an important
mechanism by which serotype O virus is maintained in Sudan. New FMDV
sequence data generated here continues to demonstrate that serotype O is
maintained in the country over successive years without any requirement
for the introduction of viruses via transboundary pathways. This point
is supported by the presence of at least two viral lineages within the
phylogenetic tree that only contain sequences from Sudan (2004-2011 and
2008-2010). The three lineages containing Sudanese and Egyptian
sequences are indicative of the northerly spread of FMDV O/EA-3 from
Sudan, which based on the dates occurred as separate independent events
during 2011-2012, 2013-2016 and 2016-2017. One of these clades also
contains a sequence from Eritrea, highlighting other potential
transboundary transmission pathways to other countries in the
neighbourhood.
Data for serotype A sequence also support the concept that FMD virus
lineages are maintained solely within Sudan. The phylogenetic tree
contains two lineages that comprise sequences only from Sudan collected
from different years (2013-2014 and 2018). In common with the serotype O
data, there was also evidence for the northerly spread of A/AFRICA/G-IV
into Egypt (during 2011-2012). Epidemiological links to FMD cases in
Ethiopia are highlighted in a second clade that contained Egyptian
sequences (from 2015-2017) and more recent sequences collected from
Sudan (from 2018), where the Ethiopian sequence (A/ETH/19/2015)
pre-dated those for the Sudanese samples. More broadly, the serotype A
(and serotype O) phylogenetic trees highlight the relationship between
recent sequences for FMD viruses collected in Ethiopia (Gizaw et al.,
2020) and contemporary data from Sudan. For both serotypes, there are
examples where Sudanese sequences have a more basal ancestral location
in the tree; for example, the relationships between O/Sudan/2012 and
O/Ethiopia/2018-19 and A/Sudan/2013-14 and A/Ethiopia/2018-19,
respectively. These results indicate that these FMD viruses have spread
from Sudan into Ethiopia; however, this interpretation of the data
should be treated cautiously in view of the likely high number of
unsampled FMD cases in both countries where the sampling density is very
low and susceptible livestock populations are high.
Serotype SAT 2 was the last FMDV serotype to be detected in Sudan in
1976 (Abu Elzein and Crowther, 1979) and 18 Sudanese isolates of
serotype SAT 2 were detected during four of the years during this study.
All of these sequences from 2010-2017 were characterised as belonging to
the SAT 2/VII/Alx-12 lineage that has spread widely in the region to
cause FMD outbreaks in countries such as Egypt, Palestine and Israel. In
common with serotypes O and A, sequences for viruses from this lineage
collected from Sudan are earlier compared to those for viruses sampled
in Ethiopia. The SAT 2/VII/Alx-12 lineage is distinct to earlier viral
clades detected in Sudan such as those that have spread previously from
East Africa into West Africa (Habiela et al., 2010b; Ularamu et al.,
2017: highlighted by presence of SAT2/SUD/1/2007 in the phylogenetic
tree).
No previous reports have described clinical FMD in Sudan in species
other than cattle (Abu Elzein, 1983; Raouf et al., 2010; Habiela et al.,
2010a). Recent serological studies suggested a relatively low
seroprevalence of non-structural protein antibodies among small
ruminants at around 14%, except in Khartoum (Habiela et al., 2009) and
Blue Nile State (Raouf, 2015; Raouf et al., 2017). This may indicate a
varied role of sheep in the epidemiology of FMD. FMD infection in wild
ruminants in Sudan has not been investigated.
In summary, FMD infection in Sudan remains regionally significant and
this study highlights the epidemiological connections between FMDV
sequences collected in Sudan and neighbouring countries such as Ethiopia
and Egypt. Due to incomplete and convenience-biased sampling, it should
be recognised that there are limitations in our understanding of the
transboundary connectivity in the region and the sequences reported here
provide only a crude snapshot survey of the underlying FMD transmission
events. Recognition of border areas as particularly risky hotspots for
the introduction of FMD viruses is of high importance in developing a
risk-based control strategy especially when resources are limited. In
this context, continued studies are warranted to improve our
understanding of FMD epidemiology in Sudan and risk-pathways in the
region.