Whole-genome analysis of circulating influenza A virus (H3N2) strains in Shanghai, China from 2005 to 2023

Seasonal influenza A virus subtype H3N2 (A/H3N2) circulates globally and has been linked to higher hospitalization rates and summer outbreaks in temperate regions. Here, A/H3N2 circulation in Shanghai, China was systematically studied using data and materials generated by the Shanghai influenza surveillance network from 2005 to 2023. Time-series analysis of incidence and subtyping data showed that A/H3N2 co-circulated with other (sub)types and dominated in multiple seasonal influenza peaks, preferentially in summer. Whole genomes of 528 representative strains were sequenced, and spatiotemporal phylodynamic analysis using these and GISAID-archived sequences demonstrated that in the years before the COVID-19 pandemic, phylogenetically similar strains were circulating locally and elsewhere. However, clade 1a.1 (within 3C.2a.1b.2a), circulated in and only in Shanghai and domestically in 2022, while the sibling clade 2 predominated in other regions. Interestingly, clade 1a.1 was swiftly and completely replaced by clade 2, mostly 2a.3a.1, at the start of 2023. In hemagglutination inhibition and neutralization assays, sera from healthy donors collected in 2022 displayed higher or similar reactivity against 2a.3a.1 compared to 1a.1. By contrast, transcription and replication competence of 2a.3a.1 in MDCK cells was higher than 1a.1. These results indicated that instead of antigenicity differences enabling evasion of pre-existing immunity, higher replicative capability more likely contributed to 2a.3a.1 viruses achieving dominance in China. In addition to summarizing patterns of A/H3N2 local circulation in Shanghai, this work revealed an unusual episode in A/H3N2 global circulation and evolution dynamics in connection to the COVID-19 pandemic and explored possible mechanistic explanations.

季节性甲型流感病毒H3N2亚型（Seasonal influenza A virus subtype H3N2，A/H3N2）在全球范围内循环传播，且与温带地区更高的住院率及夏季暴发疫情相关。本研究依托中国上海市流感监测网络2005至2023年产生的监测数据与样本材料，对上海地区A/H3N2的流行情况开展了系统性研究。对发病率及亚型分型数据的时间序列分析显示，A/H3N2与其他（亚）型流感病毒共同循环，并在多次季节性流感流行高峰中占据主导地位，尤以夏季为甚。本研究对528株代表性毒株进行了全基因组测序，并结合上述序列及全球共享所有流感数据倡议（Global Initiative on Sharing All Influenza Data，GISAID）数据库归档的序列开展时空系统动力学分析，结果表明：在新型冠状病毒肺炎（COVID-19）大流行前的年份，系统发育相似的毒株同时在本地及其他地区流行。然而，2022年，进化分支1a.1（隶属于3C.2a.1b.2a支系）仅在上海及中国国内流行，而其姊妹进化分支2则在其他地区占据主导。值得注意的是，2023年初，进化分支1a.1迅速且完全被进化分支2（主要为2a.3a.1）取代。在血凝抑制试验与中和试验中，2022年采集的健康供者血清对2a.3a.1毒株的反应性高于或与1a.1毒株相当。与之相对，2a.3a.1毒株在犬肾细胞（Madin-Darby Canine Kidney，MDCK）中的转录与复制能力高于1a.1毒株。上述结果提示，2a.3a.1毒株得以在中国占据主导地位的关键原因并非抗原性差异导致其逃逸预存免疫，而是其更高的复制能力。本研究不仅阐明了上海地区A/H3N2的本地流行模式，还揭示了与COVID-19大流行相关的A/H3N2全球流行与进化动力学异常事件，并探讨了潜在的机制性解释。