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

Abstract

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.

Keywords: African swine fever virus; diagnostic markers; genetic markers; genotype I and II; homologous recombination; recombinant strains.

Figure 1.

Genomic comparison of recombinant African Swine Fever Virus (ASFV) strains. (A) Schematic representation of genomic differences between Vietnamese and Chinese recombinant ASFV strains. The genome is divided into fragments (F1-F20) based on recombination breakpoints. Red fragments indicate regions derived from genotype I, while blue fragments are from genotype II. Red boxes highlight unique mutations in Vietnamese strains. (B) Multiple sequence alignment of C122R and NP1450L gene regions across various ASFV strains. Red dots represent Vietnamese recombinant ASFV strains, while blue dots indicate Chinese ones. The alignment shows the G151A variant in C122R and the G3048A variant in NP1450L, which are consistently observed in all recombinant ASFV isolates, distinguishing them from genotype I and II parental strains.