Molecular Characterization of African Swine Fever Virus From 2019-2020 Outbreaks in Guangxi Province, Southern China

Abstract

African swine fever virus (ASFV) causes contagious hemorrhagic disease of pigs with high morbidity and mortality. To identify the molecular characteristics of ASFV strains circulating in Guangxi province, southern China, a total of 336 tissue samples collected from 336 domestic pigs that died as a result of severe hemorrhagic disease during 2019–2020 were tested for ASFV. Furthermore, 66 ASFV strains were genetically characterized by sequence analysis of the C-terminal region of B646L (p72) gene, the complete E183L (p54) gene, the variable region of EP402R (CD2v) gene, the central variable region (CVR) of B602L gene, the full MGF505-2R gene, and the tandem repeat sequence (TRS) within intergenic region (IGR) between the I73R and I329L (I73R/I329L) genes. Phylogenetic analysis revealed that the ASFV strains from Guangxi province belonged to genotypes I and II based on the B646L (p72) and E183L (p54) genes, and there were eight different tetrameric TRS variants based on the CVR of B602L gene. Phylogenetic analysis of the EP402R (CD2v) gene revealed that these ASFV strains belonged to serogroups 4 and 8. Eight of the 66 strains belonged to genotype I and serogroup 4, and showed deletion of whole MGF505-2R gene. The sequence analysis of the IGR between the I73R/I329L genes showed that IGR II and III variants were co-circulating in Guangxi province. The results indicated that ASFV strains circulating in Guangxi province during 2019–2020 outbreaks showed high genetic diversity, of which genotypes I and II, as well as serogroups 4 and 8, were simultaneously circulating in Guangxi province, and there existed wild-type and naturally gene-deleted strains in the field. This is the first detailed report on the molecular characterization of the ASFV strains circulating in southern China, and serogroup 4 in China.

Complete genome analysis of the African swine fever virus isolated from a wild boar responsible for the first viral outbreak in Korea, 2019

“…A recent study revealed that a tandem repeat sequence (TRS) located in the intergenic region between I73R and I329L can be used to determine the origin of ASFV isolates ( 18 ). Additionally, the analysis of other sequences, such as EP402R and E183L , may help improve molecular epidemiological studies of ASFV ( 19 , 20 ). To better understand and control the spread of ASF, it is necessary to analyze the genetic characteristics of ASFV strains.…”

A multi gene-approach genotyping method identifies 24 genetic clusters within the genotype II-European African swine fever viruses circulating from 2007 to 2022

“…In contrast, the ASFVs from Romania were grouped into 6 distinct groups ( 3 , 7 , 19 , 21 , 23 , 24 ). Interestingly, the 2019 epidemic wave, despite taking place in a short space of time ( 40 ), was caused by two distinct genetic groups specific only to Romania.…”

“…Even though the resolving power of this gene region in isolates from Africa ( 28 – 34 ) and the polymorphisms observed in isolates from Estonia ( 14 ), only two SNP-based CVR variants were detected in this study in wild boar viruses from Poland (CVR1-SNP2) and Lithuania (CVR1-SNP3). Recent studies describe the presence of additional CVR variants in isolates from Russia ( 35 ) and China ( 19 ) based on the presence of SNPs. However, the variants described in this study were unique and were not further identified in any of the ASFVs sequenced or available in the GenBank.…”

“…The four IGR variants were only detected in Poland, being the first description in the EU for the IGR-I and IGR-III variants. Outside the EU these variants were circulating in China, Russia Federation, South Korea and Vietnam ( 17 – 19 , 37 – 39 ). Consistent with what was described by Mazur-Panasiuk et al ( 16 ), IGR-IV was exclusively identified in northern Poland on the border with Kaliningrad Oblast, Russia.…”

“…However, despite the large number of ASFV genotype II outbreaks in the EU, only three CVR variants have been identified in Estonia, with variant 1 (Georgia 2007-type) being predominant throughout the EU ( 14 ). The analysis of additional genetic markers such as TRS present in the O174L gene ( 15 , 16 ), or in the intergenic regions (IGR) between I73R - I329L ( 8 ), has made possible to differentiate between closely related genotype II viruses ( 17 – 19 ). Similarly, sequencing of single nucleotide polymorphisms (SNPs) within the K145R gene has also been described as a useful molecular tool to track the spread of ASFV in Poland ( 16 ).…”