Appendix 1

UNSUPPORTED SPLITS IN G&

Appendix 2

EXAMPLES OF INTRASPECIFIC DIAGNOSABILITY BASED ON GENETIC DAT

Hvilsom2013

Hvilsom201

Summary of antibody analysis by PrioCHECK FMDV NS ELISA, SPBE antibody ELISAs and VNTs.

<p>^a: one herd was sampled in each district</p><p>^b: samples with titres ≥ 80 were considered positive (all anti-NSP positive samples were tested in all SPBEs).</p><p>^c: samples with titre >45 were considered positive.</p><p>^d: sera collected during 2012 outbreaks</p><p>^e: sera collected during 2013 outbreaks</p><p>^f: the two samples positive in SAT 1-VNT had higher titres in SAT 2-VNT (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114811#pone.0114811.s001" target="_blank">S1 Table</a>)</p><p>na: not applicable because all samples were negative in the SPBE</p><p>nd: not done</p><p>Summary of antibody analysis by PrioCHECK FMDV NS ELISA, SPBE antibody ELISAs and VNTs.</p

Dataset1 and putative SNPs under selection

Dataset 1 contains the called genotypes for 60 plains zebras, 3 Grevy's zebras, 3 mountain zebras and one Quagga zebra. A total of 98,512 SNPs were called. The data is based on the RADseq technology. We used a missingness filter of 0.2 and excluded monomorphic sites.<div><br></div><div>We also include a list of SNPs inferred from pcadapt, which are putatively under selection.<br><div><br></div></div

Neighbor-joining phylogeny tree based on serotype SAT 2 FMDV VP1 coding sequences.

<p>The relationships between the Ugandan 2013 SAT 2 FMD viruses and selected East African SAT 2 viruses are shown. The five 2013 Ugandan and one 2012 Kenyan outbreak FMDV (K125/12) sequences are marked with asterisks (*), while the strain K52/84** is the SAT 2 FMD virus strain incorporated in the trivalent vaccine (O, SAT 1 and SAT 2) as used in Uganda.</p

The location of reported FMD outbreaks within Uganda in 2012–2013.

<p>The map shows the seven districts of Uganda that reported FMD outbreaks during 2012–2013. These districts were: Kiruhura, Kween and Nwoya during the 2012 outbreaks plus Isingiro, Ntungamo, Rakai and Wakiso during the 2013 outbreaks.</p

Alignment of serotype SAT 2 FMDV VP1 amino acid sequences.

<p>The VP1 amino acid sequences were inferred from one of the 2013 outbreak nucleotide sequences (marked with an asterisk (*)) and earlier SAT 2 FMDV strains. Identities with the reference vaccine strain sequence (K52/84**) are indicated by dots. Similar amino acid variation exists between the reference sequence and the Ugandan 2013 isolates and a Kenyan outbreak isolate (K125/12*) sequence (unpublished data).</p

Characterization of Foot-And-Mouth Disease Viruses (FMDVs) from Ugandan Cattle Outbreaks during 2012-2013: Evidence for Circulation of Multiple Serotypes

<div><p>To investigate the foot-and-mouth disease virus (FMDV) serotypes circulating in Uganda’s cattle population, both serological and virological analyses of samples from outbreaks that occurred during 2012–2013 were performed. Altogether, 79 sera and 60 oropharyngeal fluid (OP)/tissue/oral swab samples were collected from herds with reported FMD outbreaks in seven different Ugandan districts. Overall, 61/79 (77%) of the cattle sera were positive for antibodies against FMDV by PrioCHECK FMDV NS ELISA and solid phase blocking ELISA detected titres ≥ 80 for serotypes O, SAT 1, SAT 2 and SAT 3 in 41, 45, 30 and 45 of these 61 seropositive samples, respectively. Virus neutralisation tests detected the highest levels of neutralising antibodies (titres ≥ 45) against serotype O in the herds from Kween and Rakai districts, against SAT 1 in the herd from Nwoya district and against SAT 2 in the herds from Kiruhura, Isingiro and Ntungamo districts. The isolation of a SAT 2 FMDV from Isingiro was consistent with the detection of high levels of neutralising antibodies against SAT 2; sequencing (for the VP1 coding region) indicated that this virus belonged to lineage I within this serotype, like the currently used vaccine strain. From the Wakiso district 11 tissue/swab samples were collected; serotype A FMDV, genotype Africa (G-I), was isolated from the epithelial samples. This study shows that within a period of less than one year, FMD outbreaks in Uganda were caused by four different serotypes namely O, A, SAT 1 and SAT 2. Therefore, to enhance the control of FMD in Uganda, there is need for efficient and timely determination of outbreak virus strains/serotypes and vaccine matching. The value of incorporating serotype A antigen into the imported vaccines along with the current serotype O, SAT 1 and SAT 2 strains should be considered.</p></div

Alignment of serotype A FMDV VP1 amino acid sequences.

<p>The VP1 amino acid sequences were inferred from one of the Ugandan 2013 serotype A FMDV nucleotide sequences (marked with an asterisk (*)) and selected African serotype A FMDV strains. The dots indicate identity with the vaccine strain sequence (K5/1980**) that is the reference sequence.</p