Based on phylogenetic analyses of the gene segments, the viruses isolated and grown in MDCKs can be divided into six distinct genotypes (A, B, C, D, E, and F) (Fig. 2). The IAVs-S in genotypes A and B are prototypical EA H1N1 and H1N1/2009 pandemic, respectively. Notably, the IAVs-S in genotype C are novel triple H1N1 reassortants containing the HA and NA genes from EA H1N1, the NS gene from CS H1N1 and the rest of the gene segments are from H1N1/2009 pandemic. The genotype D IAVs-S is similar to the genotype C, except for the M gene, which is derived from EA H1N1. Genotype D IAVs-S were first reported in Tianjin, China in 201330 and caused human infection in Hunan, China in 201522, this genotype was detected continuously from 2013 to 2015 in Guangxi in our study. The three H3N2 viruses in genotypes E and F have HA and NA genes derived from swine HL H3N2 viruses. It should be noted that two viruses in genotype E are also novel triple reassortants containing five H1N1/2009 pandemic-origin internal genes and the NS gene derived from CS, similar to H1N1 viruses in genotype C. One virus in genotype F possessed six internal genes from H1N1/2009 pandemic viruses, which was soon detected after the spillovers of H1N1/2009 pandemic from human to pigs12. Our data demonstrate that there are EA H1N1 and HL H3N2 IAVs-S which have reassorted to acquire the CS H1N1 NS gene and H1N1/2009 pandemic internal genes. The similar pattern of internal gene reassortment acquired by multiple H1N1 and H3N2 IAVs-S from different times and locations in Guangxi suggest that H1N1/2009 pandemic ribonucleoprotein complex genes (PB2, PB1, PA, and NP genes) and CS H1N1 NS gene constellation is selectively advantageous and compatible with different surface genes. Importantly, IAV-S has the potential to cause epidemics in humans. The triple reassortant, A/swine/Guangxi/NNXD2023/2013(H1N1) (Sw/GX/NNXD2023/2013) in genotype D, shared 98.6–99.3% similarity at the nucleotide level with the recent human isolate A/Hunan/42443/2015 (HuN/42443/2015)22, as shown in Table 2, highlighting the potential ability of these new IAV-S reassortants to infect humans.Fig. 2Genotypes of H1N1 and H3N2 IAVs-S from Guangxi during 2013 to 2015.Origin of each gene segment is colored for representing the different lineagesTable 2Genome similarity of H1N1 novel reassortant viruses compared with the human isolated A/Hunan/42443/2015(H1N1)GenotypeName of virusGene segment (%)aHANAPB2PB1PANPMNSCA/swine/Guangxi/NN1994/201398.797.898.099.198.498.995.097.9CA/swine/Guangxi/CZ7/201498.098.097.999.097.898.792.897.7CA/swine/Guangxi/LB9/201498.097.997.999.097.898.794.897.6CA/swine/Guangxi/BS30/201498.098.097.998.997.898.694.897.7CA/swine/Guangxi /NNLX/201498.697.798.098.698.598.694.897.9DA/swine/Guangxi NNXD2023/201399.098.998.899.398.799.199.698.6DA/swine/Guangxi /QZ5/201498.698.197.999.098.598.697.398.0DA/swine/Guangxi /LZA3/201598.897.998.098.598.398.799.497.6aThe genome similarity was generated based on the open reading frame (ORF) sequences