OS20 - Sequence and Phylogenetic analysis of the 2013/14 SAT2 FMD outbreak in Mpumalanga, South Africa - Danica Blight
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OS20 Online 10 December
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OS20 - Sequence and Phylogenetic analysis of the 2013/14 SAT2 FMD outbreak in Mpumalanga, South Africa - Danica Blight
- 1. 1EuFMD | Open Session special edition | #OS20se Danica Blight University of Pretoria Agricultural Research Council SEQUENCE AND PHYLOGENETIC ANALYSIS OF THE 2013/14 SAT2 FMD OUTBREAK IN MPUMALANGA, SOUTH AFRICA
- 2. 2EuFMD | Open Session special edition | #OS20se 2013/14 OUTBREAK • Bushbuckridge, Mpumalanga Province, SA • 6 August 2013 10 February 2015 STUDY & AIMS Isolates (n=10) from 2013/14 SAT2 FMD outbreak underwent NGS to generate ORF sequences Aims: • Characterize genetic variation in genome over course of outbreak • Determine genome regions with greatest change • Determine phylogenetic relationships • Determine whether selection occurred RESULTS: PHYLOGENETIC ANALYSIS Figure: Maximum-likelihood Tree depicting ORF sequences of the SAT2 FMD 2013/14 outbreak isolates and other relevant viruses from SAT2 topotypes I to X.
- 3. 3EuFMD | Open Session special edition | #OS20se RESULTS: AMINO ACID SUBSTITUTIONS AND SELECTION Most variable regions: Leader (1.17% relative to region length) • Represses innate host immune response Viral protein 1 (VP1) (0.93%) • Affects antigenicity Least variable regions: VP4, 2A, 3B & 3C (all: 0% change) • VP4, 2A & 3C: capsid stability & assembly • 2A, 3B & 3C: optimal viral replication • 3C: represses innate host immune response Table: Summary of amino acid substitutions in foot-and-mouth disease (FMD) SAT2 2013/14 outbreak isolates Shaded block shows amino acid position that underwent positive, diversifying selection; all other positions showed negative, purifying selection
- 4. 4EuFMD | Open Session special edition | #OS20se OUTCOMES Genetic Variation Greatest variation: Leader & VP1 • Represses innate host immune response & affects antigenicity Least variation: VP4, 2A, 3B & 3C • Capsid stability & assembly, viral replication efficiency & represses innate host immune response Phylogenetic Relationships • 2013/14 outbreak isolates cluster in Topotype I • Isolates collected from same location clustered together • Suggests two independent transmission pathways: Location A B & C, & Location A D & E • Direct/indirect transmission at dip tank or within same herd Selection 23 variable amino acid sites • Positive (diversifying) selection at 1 amino acid site • Negative (purifying) selection at 22 amino acid sites Identified variable sites that may affect vaccination efficacy • Further investigation needed to determine if variable sites are of importance Implications • SAT2 FMDV undergoes genetic variation during outbreak • Important to regularly update & change SAT2 FMDV vaccines to include viruses with suitable antigenic properties
- 5. eufmdvirtual.com 8, 10, 15, 17 December 2020 EuFMD / Open Session