Sun Hailiang, Liu Hanlin, Zhang Jianfeng, Qu Xiaoyun, Pang Zifeng, Xu Fengxiang, Wu Changrong, Jiang Yinglin, Shi Mang, Liu Quan, Liao Ming
College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China.
College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China.
Lancet Microbe. 2025 Apr 28:101020. doi: 10.1016/j.lanmic.2024.101020.
Pigs are recognised as crucial intermediate hosts for the emergence of influenza viruses of pandemic potential. As the largest pork-producing nation, China hosts a complex ecosystem of swine influenza viruses (SIVs). We aimed to investigate the evolutionary processes, spatiotemporal dynamics, and biological characteristics of SIVs in China.
From Jan 15, 2016, to Dec 22, 2020, we collected nasal swabs from pigs at eight abattoirs and 16 swine farms in the Guangdong, Henan, and Shandong provinces of China, as part of SIV surveillance. SIVs were detected with RT-PCR. Positive samples underwent viral isolation and genome sequencing. We analysed evolution and spatiotemporal dynamics using the whole genomes of isolated SIVs, as well as genome sequences of SIV isolates from human infections worldwide retrieved from the Global Initiative on Sharing All Influenza Data and GenBank Flu databases up to April 28, 2024. Viral sequences without a sample collection area or date were excluded from the analysis. Viral receptor-binding properties and in-vitro replication of strains isolated in this study were evaluated with a solid-phase binding assay and various cell lines, including Madin-Darby canine kidney cells, porcine alveolar macrophages, primary porcine trachea epithelial cells, human bronchial epithelioid, and human lung adenocarcinoma epithelial (A549) cells. Viral replication and transmission studies were conducted in 33 guinea pigs and 13 pigs. Additionally, we collected serum samples from pig farm workers and members of the general public recruited by the Third Affiliated Hospital of Sun Yat-sen University between Feb 28 and May 11, 2023, to detect specific antibodies against Eurasian avian-like A(H1) and human-like A(H3N2) SIVs using the haemagglutination inhibition assay.
23 (1·3%) of 1818 nasal swabs collected in abattoirs had SIVs; 22 (0·9%) of 2375 swabs from swine farms had SIVs. Further viral isolation yielded 39 strains of SIV. We identified 534 A(H1N1), 69 A(H1N2), and 92 A(H3N2) SIVs, representing 20 genotypes within the Eurasian avian-like lineage, 14 within the classical swine A(H1) lineage, and 16 within the human-like A(H3N2) lineage. The introduction of the A(H1N1)pdm/09 virus significantly influenced the internal gene pool of SIVs, enhancing genotypic diversity in China. Notably, the Eurasian avian-like A(H1), classical swine A(H1), and human-like A(H3N2) lineages showed human-mediated spread over long distances between provinces, with the Eurasian avian-like A(H1) lineage showing the most prevalent spread pathways. Eurasian avian-like A(H1) SIVs showed a preference for binding to sialic acid α-2,6 glycan receptors, predominantly found in humans, resulting in an increased production of progeny viruses in human airway epithelial cells, as well as effective transmission and infectivity among guinea pigs and pigs. Among 54 eligible serum samples collected from pig farm workers (24 from slaughterhouses and 30 from swine farms), 23 (43%) were seropositive for Eurasian avian-like A(H1) SIVs and 46 (85%) for human-like A(H3N2) SIVs. Among 100 eligible samples from members of the general public, 14 (14%) were seropositive for Eurasian avian-like A(H1) SIVs and 85 (85%) for human-like A(H3N2) SIVs.
This study elucidates the evolutionary processes and spatiotemporal patterns of SIVs, highlighting potential risks to public health. These findings are crucial for informing public health interventions that aim to prevent future SIV epidemics in China and other countries worldwide.
Scientific Innovation Strategy-Construction of High-Level Academy of Agriculture Science-Distinguished Scholar (R2020PY-JC001).
猪被认为是具有大流行潜力的流感病毒出现的关键中间宿主。作为最大的猪肉生产国，中国拥有复杂的猪流感病毒（SIV）生态系统。我们旨在研究中国SIV的进化过程、时空动态和生物学特性。
2016年1月15日至2020年12月22日，作为SIV监测的一部分，我们在中国广东省、河南省和山东省的8个屠宰场和16个养猪场采集了猪的鼻拭子。用逆转录聚合酶链反应（RT-PCR）检测SIV。对阳性样本进行病毒分离和基因组测序。我们使用分离出的SIV的全基因组，以及截至2024年4月28日从全球共享所有流感数据倡议组织（Global Initiative on Sharing All Influenza Data）和GenBank流感数据库中检索到的全球人类感染SIV分离株的基因组序列，分析进化和时空动态。分析中排除了没有样本采集地区或日期的病毒序列。用固相结合试验和包括马-达二氏犬肾细胞、猪肺泡巨噬细胞、原代猪气管上皮细胞、人支气管上皮样细胞和人肺腺癌上皮（A549）细胞在内的各种细胞系，评估本研究中分离出的毒株的病毒受体结合特性和体外复制情况。在33只豚鼠和13头猪中进行病毒复制和传播研究。此外，我们于2023年2月28日至5月11日采集了中山大学附属第三医院招募的养猪场工人和普通公众的血清样本，用血凝抑制试验检测针对欧亚禽源样A（H1）和人源样A（H3N2）SIV的特异性抗体。
在屠宰场采集的1818份鼻拭子中，23份（1.3%）检测出SIV；在养猪场采集的2375份拭子中，22份（0.9%）检测出SIV。进一步的病毒分离产生了39株SIV。我们鉴定出534株A（H1N1）、69株A（H1N2）和92株A（H3N2）SIV，分别代表欧亚禽源样谱系中的20种基因型、经典猪A（H1）谱系中的14种基因型和人源样A（H3N2）谱系中的16种基因型。A（H1N1）pdm/09病毒的引入显著影响了SIV的内部基因库，增加了中国的基因型多样性。值得注意的是，欧亚禽源样A（H1）、经典猪A（H1）和人源样A（H3N2）谱系显示出人类介导的在省份间的远距离传播，其中欧亚禽源样A（H1）谱系的传播途径最为普遍。欧亚禽源样A（H1）SIV表现出对唾液酸α-2,6聚糖受体的偏好，这种受体主要存在于人类中，导致在人气道上皮细胞中产生子代病毒的量增加，以及在豚鼠和猪之间的有效传播和感染性。在从养猪场工人中采集的54份合格血清样本（24份来自屠宰场，30份来自养猪场）中，23份（43%）对欧亚禽源样A（H1）SIV呈血清阳性，46份（85%）对人源样A（H3N2）SIV呈血清阳性。在从普通公众中采集的100份合格样本中，14份（14%）对欧亚禽源样A（H1）SIV呈血清阳性，85份（85%）对人源样A（H3N2）SIV呈血清阳性。
本研究阐明了SIV的进化过程和时空模式，突出了对公共卫生的潜在风险。这些发现对于为旨在预防中国和世界其他国家未来SIV疫情的公共卫生干预措施提供信息至关重要。
科技创新战略-建设高水平农业科学院-杰出学者（R2020PY-JC001）
