Molecular characterization of emerging recombinant African swine fever virus of genotype I and II in Vietnam, 2023

African swine fever virus (ASFV) recombinant strains pose new challenges for diagnosis and control. This study characterizes genotype I and II recombinant ASFV strains identified in northern Vietnam in 2023 through whole-genome sequencing and comparative genomic analysis. Seven ASFV-positive samples from six provinces were analyzed, with recombinant strains detected in Bac Giang, Phu Tho, and Vinh Phuc provinces. Isolates showed hemadsorption positivity despite having genotype I B646L, indicating their recombinant nature. Genome-wide analysis revealed 19 recombination breakpoints consistent with Chinese recombinant strains. Vietnamese isolates shared 99.86-99.98% nucleotide identity with Chinese recombinants, forming a distinct monophyletic group. Comparative analysis identified 50 SNPs and INDELs, with 39 variations found across Vietnamese strains, distinguishing them from Chinese isolates. Unique genetic markers in C962R, I329L, and MGF 505-11L genes distinguished Vietnamese recombinants from Chinese counterparts, while mutations in C122R and NP1450L differentiated all recombinants from parental genotypes. The central variable region (CVR) of the B602L gene showed diversity among Vietnamese isolates, while the I73R-I329L intergenic regions were recognized as in the IGR2 group. This study enhances understanding of recombinant ASFV evolution through homologous recombination and identifies new genetic markers for improved detection and characterization. The observed genetic diversity highlights challenges for existing diagnostic methods and vaccine development, emphasizing the need for continued surveillance and research into the functional implications of these genetic variations on ASFV pathogenicity and transmissibility.

非洲猪瘟病毒（African swine fever virus, ASFV）重组毒株给该病的诊断与防控带来了新的挑战。本研究通过全基因组测序与比较基因组学分析，对2023年在越南北部检出的基因型I和II型重组ASFV毒株进行了特征解析。研究对来自6个省份的7份ASFV阳性样本展开分析，其中在北江省、富寿省和永福省检出重组毒株。尽管分离株携带基因型I的B646L基因，但均呈现血吸附阳性，证实其重组属性。全基因组分析显示，共存在19个重组断点，与中国重组毒株的断点特征一致。越南分离株与中国重组毒株的核苷酸一致性为99.86%~99.98%，并构成一个独立的单系群。比较基因组分析共鉴定出50个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）和插入缺失变异（Insertion-Deletion, INDELs），其中越南毒株携带39个变异位点，可与中国分离株区分开来。C962R、I329L和MGF 505-11L基因中的独特遗传标记，可将越南重组毒株与中国毒株区分；而C122R和NP1450L基因的突变，则可将所有重组毒株与其亲本基因型区分。B602L基因的中央可变区（central variable region, CVR）在越南分离株中呈现多样性，而I73R-I329L基因间区被划归为IGR2组。本研究通过解析同源重组事件，加深了对重组ASFV进化机制的理解，并鉴定出可用于优化毒株检测与特征分析的新型遗传标记。本研究观察到的遗传多样性，凸显了现有诊断方法与疫苗研发面临的挑战，同时强调需持续开展监测研究，以明确这些遗传变异对ASFV致病性与传播性的功能影响。