Genetic diversity of subgenotype 2.1 isolates of classical swine fever virus

• Genetic diversity of current CSFV subgenotype 2.1 isolates in the world was revealed in this study, which were divided into 10 sub-subgenotypes (2.1a-2.1j).
• Sub-subgenotypes 2.1d-2.1j were newly classified.
• The newly classified 2.1 sub-subgenotypes were further categorized into three groups: dominant sub-subgenotype (2.1b, 2.1c, 2.1 h, 2.1i, and 2.1j), minor sub-subgenotype (2.1d and 2.1 g) and silent sub-subgenotype (2.1a, 2.1e, and 2.1f).
• Sub-subgenotype 2.1b plays a dominant role in CSF epidemics in China.

As the causative agent of classical swine fever, the economically devastating swine disease worldwide, classical swine fever virus (CSFV) is currently classified into the 11 subgenotypes, of which subgenotype 2.1 is distributed worldwide and showing more genetic diversity than other subgenotypes. Prior to this report, subgenotype 2.1 was divided into three sub-subgenotypes (2.1a–2.1c). To further analyze the genetic diversity of CSFV isolates in China, 39 CSFV isolates collected between 2004 and 2012 in two Chinese provinces Guangxi and Guangdong were sequenced and subjected to phylogenetic analysis together with reference sequences retrieved from GenBank. Phylogenetic analyses based on the 190-nt and/or 1119-nt full length E2 gene fragments showed that current CSFV subgenotype 2.1 virus isolates in the world could be divided into 10 sub-subgenotypes (2.1a–2.1j) and the 39 isolates collected in this study were grouped into 7 of them (2.1a–2.1c and 2.1g–2.1j). Among the 10 sub-subgenotypes, 2.1d–2.1j were newly identified. Sub-subgenotype 2.1d isolates were circulated only in India, however the rest 9 sub-subgenotypes were from China with some of them closely related to isolates from European and neighboring Asian countries. According to the temporal and spatial distribution of CSFV subgenotype 2.1 isolates, the newly classified 10 sub-subgenotypes were further categorized into three groups: dominant sub-subgenotype, minor sub-subgenotype and silent sub-subgenotype, and each sub-subgenotype can be found only in certain geographical areas. Taken together, this study reveals the complex genetic diversity of CSFV subgenotype 2.1 and improves our understanding about the epidemiological trends of CSFV subgenotype 2.1 in the world, particularly in China.