Porcine epidemic diarrhea virus (PEDV) is a fatal epizootic swine coronavirus that presents a financial threat to the global swine industry. Since the discovery of the low-pathogenic genotype 1b (G1b) in 2014, it has been responsible for sporadic outbreaks in South Korea. In this study, we identified novel G1b variants arising from the natural recombination of a major pandemic-like G2b virus and a minor G1b virus currently circulating in the domestic field. The whole-genome sequences of two 2018–19 G1b recombinants, KNU-1808 and KNU-1909, were determined. A genomic comparison showed that these two viruses share the highest nucleotide sequence similarity with the 2017 G1b strain but share less similarity with the 2014 G1b emergent strain KNU-1406. However, the putative recombination breakpoints spanning the first 1,170 nucleotides of the spike (S) gene were almost identical among the emergent and contemporary G1b strains. Recombination detection indicated that the inter-subgroup G1b recombinant first emerged in 2017 by introducing the N-terminal domain of S from KNU-1406 into the backbone of KNU-1703, possibly leading to antigenic shift. It then evolved into KNU-1808 and KNU-1909 through genetic drift, moving toward a more G2b-like genotype. Phylogenetic analysis revealed that the 2018–2019 G1b recombinants belong to a cluster containing other G1b strains but form a new branch. This study provides an important advance warning in regard to the emergence and prevalence of new genotypes or variants that can result from genetic recombination between two different PEDV genotypes circulating in endemic areas and continuous non-lethal mutations essential for viral fitness in the host environment.

猪流行性腹泻病毒 (PEDV) 是一种致命的流行性猪冠状病毒，对全球养猪业构成财务威胁。自 2014 年发现低致病性基因型 1b (G1b) 以来，它一直是韩国零星爆发的罪魁祸首。在这项研究中，我们鉴定了新的 G1b 变体，这些变体是由目前在国内流行的主要流行性 G2b 病毒和次要 G1b 病毒的自然重组产生的。确定了两个 2018-19 G1b 重组体 KNU-1808 和 KNU-1909 的全基因组序列。基因组比较表明，这两种病毒与 2017 G1b 毒株的核苷酸序列相似性最高，但与 2014 G1b 新兴毒株 KNU-1406 的相似性较低。然而，跨越前 1 个的假定重组断点，在新兴和当代 G1b 菌株中，spike (S) 基因的 170 个核苷酸几乎相同。重组检测表明，2017年首次出现亚组间G1b重组体，将KNU-1406的S的N端结构域引入KNU-1703的主链，可能导致抗原转移。然后它通过遗传漂变进化为 KNU-1808 和 KNU-1909，朝着更像 G2b 的基因型发展。系统发育分析显示，2018-2019 G1b重组体属于包含其他G1b菌株的簇，但形成了一个新的分支。