3.3 | Serotype O
All eighteen serotype O viruses that were genotyped during this study
fell within the O/EA-3 topotype (Figure 2). These sequences represent at
least four distinct clades; three of which occurred during the same
period (2009-2011), while a fourth cluster contained more recent
isolates from 2013, 2016 and 2017. Nucleotide identities within clusters
were mostly >95%, in contrast to sequence differences
between clusters of between 5% and 7%. The first cluster contained
isolate SUD/11/2011 which was related to other older Sudanese FMDVs
collected between 2004 and 2008, with Nigerian viruses collected between
2007 and 2014 and two Cameroon viruses collected in 2010. The second
cluster contained three isolates; SUD/1/2009, SUD/1/2010, and SUD/2/2010
related to FMDV sequences from Sudan in 2008, while a third cluster
contained five identical sequences for FMDV isolates collected in 2012,
one collected a year earlier (O/SUD/9/2011) as well as samples from
Eritrea (2011) and Egypt (2012). The final clade comprised seven
Sudanese FMDV isolates collected in 2016/17 and an earlier sample from
2013 (O/SUD/4/2013). This clade also contained Egyptian isolates that
are part of a larger temporal phylogenetic cluster representative of
O/EA-3 outbreaks reported in Egypt, Israel and Palestine.