Rapid and recent evolution of fetA phase variability among hyperinvasive MenW:cc11 disease isolates

Supplementary material for: Rapid and recent evolution of fetA phase variability among hyperinvasive MenW:cc11 disease isolates Neisseria meningitidis serogroup W (MenW) clonal complex 11 isolates are a major worldwide cause of invasive meningococcal disease. This lineage has exhibited significant plasticity with multiple evolutionary events occurring during international and national spread. Phase variation is a major mechanism for modulation of surface antigen expression including for FetA, a major immunogenic meningococcal antigen. Alterations in switching rates occur due to changes in the repeat numbers of phase-variable genes. Analysis of 1521 MenW:cc11 carriage and disease isolates detected evidence of on-going evolution within the United Kingdom. The rebound in MenW:cc11 disease in the post-COVID-19 pandemic era was associated with isolates belonging to four sub-clusters. One of these sub-clusters was associated with isolates circulating at low levels for more than 50 years while another contained novel variants. Evolution of the fetA promoter and repeat region was detected with increases in the tract length from 6C to 8C or longer becoming highly prevalent from 2015 onwards. Acquisition of phase-variable tracts of 8C or longer were correlated with other alterations in the fetA promoter and genic region. The predominant repeat number for this promoter-located repeat tract was 11C, which is associated with intermediate expression. The potential for heightened phase variation of FetA mirrors earlier evolution of increases in repeat numbers of two other surface proteins, PorA and Opa, in this lineage. On-going evolution of phase variation may be aiding maintenance of significant levels of transmission of this hypervirulent lineage and persistent associations with invasive disease despite widespread vaccine usage.本补充材料对应：高侵袭性MenW:cc11致病分离株中fetA相位变异的快速新近演化 血清群W脑膜炎奈瑟菌（Neisseria meningitidis serogroup W，简称MenW）克隆复合体11（cc11）分离株是全球侵袭性脑膜炎球菌病的主要致病原。该谱系在国际及国内传播过程中发生多起演化事件，展现出显著的遗传可塑性。相位变异是调控表面抗原表达的核心机制之一，其中包括FetA（FetA）——脑膜炎球菌的主要免疫原性抗原——的表达调控。相位可变基因的重复序列数目改变会导致相位转换速率发生变化。对1521株MenW:cc11定植与致病分离株的分析显示，英国境内该谱系仍处于持续演化过程中。新冠大流行后时期MenW:cc11致病病例的反弹与四个亚簇的分离株密切相关。其中一个亚簇的分离株已低水平传播超过50年，而另一个亚簇则包含新型变异株。研究检测到fetA启动子及重复区域的演化：2015年起，重复序列长度从6C增至8C及以上的变异株已广泛流行。携带8C及以上长度相位可变重复序列的分离株，与fetA启动子及编码区域的其他变异显著相关。该启动子区域重复序列的主要重复数目为11C，对应中等水平的基因表达。FetA相位变异潜能的提升，与该谱系另外两种表面蛋白PorA（PorA）和Opa（Opa）的重复序列数目增加的早期演化特征一致。尽管疫苗已广泛应用，相位变异的持续演化或有助于维持该高毒力谱系的高水平传播，并使其始终与侵袭性疾病保持密切关联。