Foot-and-mouth disease (FMD) continues to be a major burden for livestock owners in endemic countries and a continuous threat to FMD-free countries. The epidemiology and control of FMD in Africa is complicated by the presence of five clinically indistinguishable serotypes. Of these the Southern African Territories (SAT) type 3 has received limited attention, likely due to its restricted distribution and it being less frequently detected. We investigated the intratypic genetic variation of the complete P1 capsid-coding region of 22 SAT3 viruses and confirmed the geographical distribution of five of the six SAT3 topotypes. The antigenic cross-reactivity of 12 SAT3 viruses against reference antisera was assessed by performing virus neutralization assays and calculating the r₁-values, which is a ratio of the heterologous neutralizing titer to the homologous neutralizing titer. Interestingly, cross-reactivity between the SAT3 reference antisera and many SAT3 viruses was notably high (r₁-values >0.3). Moreover, some of the SAT3 viruses reacted more strongly to the reference sera compared to the homologous virus (r₁-values >1). An increase in the avidity of the reference antisera to the heterologous viruses could explain some of the higher neutralization titers observed. Subsequently, we used the antigenic variability data and corresponding genetic and structural data to predict naturally occurring amino acid positions that correlate with antigenic changes. We identified four unique residues within the VP1, VP2, and VP3 proteins, associated with a change in cross-reactivity, with two sites that change simultaneously. The analysis of antigenic variation in the context of sequence differences is critical for both surveillance-informed selection of effective vaccines and the rational design of vaccine antigens tailored for specific geographic localities, using reverse genetics.

口蹄疫仍然是流行国家牲畜所有者的主要负担，并且对无口蹄疫的国家构成持续威胁。由于存在五种临床上无法区分的血清型，非洲口蹄疫的流行病学和控制变得复杂。在这些南部非洲领土（SAT）中，类型3受到的关注有限，这可能是由于其分布受限制且被发现的频率较低。我们调查了22个SAT3病毒的完整P1衣壳编码区的基因型内遗传变异，并确认了六个SAT3拓扑类型中的五个的地理分布。通过执行病毒中和测定并计算r ₁来评估12种SAT3病毒对参考抗血清的抗原交叉反应性。-值是异源中和效价与同源中和效价之比。有趣的是，SAT3参考抗血清与许多SAT3病毒之间的交叉反应性非常高（r _1值> 0.3）。此外，与同源病毒相比，某些SAT3病毒对参考血清的反应更强（r ₁-values> 1）。参比抗血清对异源病毒的亲和力增加可以解释一些观察到的较高中和效价。随后，我们使用抗原变异性数据以及相应的遗传和结构数据来预测与抗原变化相关的天然氨基酸位置。我们在VP1，VP2和VP3蛋白中鉴定出四个独特的残基，这些残基与交叉反应性的变化相关，并且两个位点同时变化。在序列差异的背景下进行抗原变异的分析对于使用监测信息进行有效疫苗的选择以及使用反向遗传学针对特定地理区域量身定制的疫苗抗原的合理设计都至关重要。