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.