Data from: Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China

‘Two-way' transmission of influenza viruses between humans and swine has been frequently observed and the occurrence of the 2009 H1N1 pandemic influenza (pdm/09) demonstrated that swine-origin viruses could facilitate the genesis of a pandemic strain. Although multiple introductions to and reassortment in swine of the pdm/09 virus have been repeatedly reported in both Eurasia and the Americas, its long-term impact on the development of swine influenza viruses (SIVs) has not been systematically explored. Our comprehensive evolutionary studies on the complete genomes of 387 SIVs obtained from 2009 to 2012 in influenza surveillance in China revealed 17 reassortant genotypes with pdm/09-origin genes. Even though the entire 2009 pandemic virus and its surface genes cannot persist, its internal genes have becoming established and are now the predominant lineages in pigs in the region. The main persistent pdm/09-origin reassortant forms had at least 5 pdm/09-origin internal genes and their surface genes primarily of European avian-like (EA) or human H3N2-like SIV origin. These findings represent a marked change to the evolutionary patterns and ecosystem of SIVs in China. It is possible that the pdm/09-origin internal genes may be in the process of replacing EA- or triple reassortant-like internal genes. These alterations to the SIV gene pool need to be continually monitored to assess changes in the potential for SIVs to transmit to humans. Importance: Shortly after the emergence of the 2009 pandemic H1N1 (pdm/09) influenza virus, it was transmitted from humans to pigs and this continues to occur around the world. Many reassortants between pdm/09-origin viruses and enzootic swine influenza viruses (SIVs) have been detected. However, the long-term impact of pdm/09-origin viruses on the SIV gene pool, which could lead to the generation of influenza viruses with the potential to infect humans, has not been systematically examined. From extensive surveillance of SIVs over a 38-month period in southern China, it was found that, although neither complete pdm/09 viruses nor their surface genes could persist in pigs, their internal genes did persist. Over the survey period, these internal genes became predominant, potentially replacing those of the enzootic SIV lineages. The altered diversity of the SIV gene pool needs to be closely monitored for changes in the potential of SIVs to transmit to humans.

人与猪之间的流感病毒双向传播现象已被频繁观测到，而2009年甲型H1N1流感大流行病毒（pdm/09）的暴发表明，猪源病毒可推动大流行毒株的产生。尽管欧亚大陆与美洲地区均有多次报道称pdm/09病毒被引入猪群并发生重配，但其对猪流感病毒（SIVs）进化的长期影响尚未得到系统探究。
本研究针对2009年至2012年中国流感监测中获取的387株SIV全基因组开展全面进化分析，共鉴定出17种携带pdm/09来源基因的重配基因型。尽管完整的2009年大流行病毒及其表面基因无法在猪群中持续存在，但其内部基因已成功定植，并成为该区域猪群中的优势谱系。主要持续存在的pdm/09来源重配毒株至少携带5个pdm/09来源内部基因，其表面基因主要源自欧洲类禽（EA）或人源H3N2样SIV。上述发现标志着中国SIV的进化模式与生态系统发生显著改变，pdm/09来源内部基因或正逐步取代EA或三重重配样内部基因。针对SIV基因库的此类变化需开展持续监测，以评估其跨种传播至人类的潜在风险变化。
研究意义：2009年甲型H1N1（pdm/09）流感病毒出现后不久，便从人类传播至猪群，且这一现象在全球范围内持续发生。目前已检测到多种pdm/09来源病毒与地方流行性猪流感病毒之间的重配毒株，但pdm/09来源病毒对SIV基因库的长期影响——即可能产生具备感染人类潜力的流感病毒——尚未得到系统研究。通过对中国南方地区为期38个月的大规模SIV监测，本研究发现：尽管完整的pdm/09病毒及其表面基因无法在猪群中持续存在，但其内部基因可稳定定植；在监测周期内，此类内部基因逐渐成为优势谱系，潜在取代地方流行性SIV谱系。SIV基因库的多样性改变需被密切监测，以评估其跨种传播至人类的潜在风险变化。