Research Article: Continuous evolution of influenza A viruses of swine from 2013 to 2015 in Guangdong, China

Date Published: July 19, 2019

Publisher: Public Library of Science

Author(s): Zhenpeng Cao, Weijie Zeng, Xiangqi Hao, Junming Huang, Mengkai Cai, Pei Zhou, Guihong Zhang, Peter Gyarmati.


Southern China is considered an important source of influenza virus pandemics because of the large, diverse viral reservoirs in poultry and swine. To examine the trend in influenza A virus of swine (IAV-S), an active surveillance program has been conducted from 2013 to 2015 in Guangdong, China. The phylogenetic analyses showed that the external genes of the isolates were assigned to the Eurasian avian-like swine (EA) H1N1 and/or human-like H3N2 lineages with multiple substitutions, indicating a notable genetic shift. Moreover, the internal genes derived from different origins (PB2, PB1, PA, NP: pdm/09 (pandemic influenza virus 2009)-origin, M: pdm/09- or EA-origin, NS: North American Triple Reassortant (TR)-origin have become the dominant backbone of IAV-S in southern China. According to the origins of the eight gene segments, the isolates can be categorized into five genotypes. The results of mice experiment showed that the YJ4 (genotype 1) and DG2 (genotype 4) are the most pathogenic to mice, and the viruses are observed in kidneys and brains, indicating the systemic infection. The alterations of the IAV-S gene composition supported the continued implementation of the intensive surveillance of IAV-S and the greater attention focused on potential shifts toward transmission to humans.

Partial Text

Influenza A virus (IAV) belongs to the Orthomyxoviridae family and contains a genome composed of eight single-stranded RNA genomes. According to the antigenic properties of hemagglutinin (HA) and neuraminidase (NA), IAV can be subtyped into 16 HA and 9 NA types in aquatic birds, and 2 HA and 2 NA subtypes have been detected in bats [1, 2]. Pigs play a pivotal role in the circulation and evolution of IAVs and are regarded as “mixing vessels” for the generation of novel reassortant viruses [3]. Three main subtypes (H1H1, H1N2 and H3N2) have been detected in pigs [4]. The simple infection of pigs with influenza A virus presents mild clinical signs in the field and under experimental conditions [5]. However, influenza A virus of swine (IAV-S) can impair the host immune system in a variety of ways, subsequently suppressing the immune response to other pathogens [6].

Due to unique geographical and environmental factors, southern China is considered an important reservoir of influenza virus. In the first decade of the 21st century, Multiple lineages of IAVs-S have emerged and become established in pigs in southern China: classical swine H1N1 (CS), European avian-like H1N1 (EA) and triple-reassortant H1N2 viruses (TRIG). In 2001, the first case of infection with the EA-origin virus in pigs in Asia was reported in Hong Kong, and EA-origin viruses have since formed a stable phyletic clade in China [36]. In addition, TR-origin viruses have been regularly isolated from pigs in China since 2002 [37]. Since the pdm/09-origin virus outbreaks in humans, this virus has been repeatedly transmitted in pig herds [38–40]. Reassortant variants with pdm/09-origin gene segments and endemic genes were subsequently found in Asia [41–43]. The swine-origin H1N1 viruses were found reassorting with the H3N2 canine influenza viruses circulate endemically in Asian dogs [44]. Furthermore, the novel triple EA H1N1 and Human Like H3N2 reassortants, containing the CS H1N1 NS genes and the remaining five or four genes originating from H1N1/2009 pandemic, may have become established in pig herds in Southern China [40, 45]. Notably, the reassortant EA H1N1 viruses with EA-origin M gene, pdm/09-origin internal genes and CS-origin NS gene have been reported in human infections in Hunan, China [46].