Different host species displayed differing virus-binding receptors with preferences for either Neu5Aca2-3Gal or Neu5Aca2-6Gal epitopes [24
]. Both Neu5Aca2 -3Gal or Neu5Aca2-6Gal receptors existed in the tracheal epithelium cells in pigs, preferred by avian influenza viruses and human influenza viruses, respectively [32
] indicated that pigs could infect with swine, human, and avian viruses. Therefore, it suggested pigs could act as intermediate hosts, or mixing vessels, for the generation of genetically reassortant viruses with human pandemic potential.
Viruses sequences download from GenBank were mostly isolated in recent years. The relative strains were mainly isolated and reported in Guangdong and Shandong provinces. Most existing swine data were derived from opportunistic samples collected from diseased pigs in disparate geographical regions, not from prospective studies in defined locations [18
]. Although the sampling bias might be another reason, pigs were raised in increasing numbers continually in many provinces in mainland China, especially in Guangdong and Shandong province. Meanwhile, swine influenza virus might become prevalent in the nation. To a certain extent, it showed that swine influenza virus became prevalent in mainland China in recent years.
A first study to characterize the evolution of complete genomes of influenza A H3N2, H1N1 and H1N2 isolates from Europe from 1999 to 2006, indicated that H1N1 SIVs had been evolving and might be likely to be the prevalent strain again. And more precise knowledge about the circulating strains might be help for predicting the following season strains [34
]. A historical record of the genetic and antigenic evolution of swine influenza viruses in European, and described the transmission of European swine influenza viruses from pigs to other animal species and to humans, together with the factors that limit inter-species transmission [35
As the classification of lineages to study the influenza viral ecology, epidemiology, and evolution was of great importance, so in our study, we firstly analyzed the allover H1N1 SIVs sequences in mainland China from the GenBank and integrated the information from the publicly available sequences, identified and unified all the lineages and genotypes of H1N1 SIVs in mainland China. Recently, a study has quantified the epidemiological, genetic and antigenic dynamics of swine influenza A viruses in Hong Kong using a data set of more than 650 swine influenza A viruses isolates and more than 800 swine sera from 12 years of systematic surveillance in this region, supplemented with data stretching back 34 years. And their results showed that one reason for lineage change might be a competitive advantage of EA over CS and TRIG viruses [18
Classical H1N1 swine influenza viruses, co-circulating with H3N2 swine influenza viruses, were most prevalent for a long time. However, since the Asian avian influenza virus-like H1N1 influenza viruses had been isolated from pigs in 1993 and had circulated with classical H1N1 viruses in previous studies [36
]. In 2007–2008, European avian-like H1N1 viruses were also detected in pigs in China [39
]. Similar to the H9N2 influenza viruses [41
], the phylogenetic diversity and complexity also existed in H1N1 SIVs in mainland China. The knowledge of its diversity and complexity was still inadequate, and had not attracted much attention. Our study identified and unified all the lineages and genotypes of H1N1 subtype swine virus in mainland China, and provided the essential information supporting for further study of H1N1 subtype swine influenza viruses in Mainland China.
Influenza A viruses genetic reassortments, that might generate pandemic strains of influenza A virus, occur when two or more strains of influenza virus co-infect the same cell, especially from different host as the segmented nature of the RNA genomes [42
]. Study has shown that reassortments between EA and triple-reassortant swine viruses do occur and establish in swine as stable lineages in swine [18
]. Recombinant was a process that was a frequent generation of new reassortant but had only a few survival and persistence [44
]. Reassortment and antigenic change were linked [18
] which has been described in North America CS viruses after the events that generated the triple-reassortant swine viruses [8
]. These similar events have also been reported in human influenza [45
]. Novel lineages and genotypes of H1N1 SIVs appeared in mainland China, raising the possibility of generating novel H1N1 SIVs with the potential to infect human.
Influenza virus pandemic was considered inevitable. In the early years, studies had focused on the emergence of the next pandemic in China [46
]. China was the biggest pork producer in the world, almost all of its 50 million metric tons of production in 2010 (half of all the pork in the world) was consumed domestically. Most of the facilities of the pig farm in mainland China cannot provide sufficient temperature control, resulting in pigs susceptible to respiratory diseases, but it has not been given sufficient attention. Furthermore, increasing pig movements, and human, swine influenza viruses co-existing in swine herds made the swine influenza viruses diversity and offered more opportunities to generate reassortment viruses with the potential to infect humans.
Generally, lowly concerning to low pathogenic influenza viruses raise made these strains might have a greater opportunity to become widespread. As amino acid position 222 and 226 was in the receptor binding cavity, changes can potentially influence receptor binding of the influenza virus and host range. Three strains (AEH42763, AEH42796, ADX96236) of EA lineage possessed L at the position 226, might had a higher affinity for sialic acid α2, 6-galactose (SAα2, 6Gal) and a higher infectivity level for primary swine and human respiratory epithelial cells. The strains of other lineages possessed Q at the position 226 might had lower SAα2, 6Gal affinity and lower infectivity levels for both types of cells. A possible correlation of D222G substitution in HA subunit of 2009H viruses with severe clinical outcome was observed [50
]. So strains of 2009H, CS, ESH, and RSH lineage, which possessed D222G, should be received special attention. The clinical significance was still unclear about the other substitutions at the same position, EA strains possessed E222 K. The E627K substitution was observed to enhance virulence and viral replication in mice and other mammals [27
]. Our study suggested that H1N1 SIVs contained PB2 genes of the CS, ESH, and RSH lineage might infect human easily.
Special attention and close supervision should be got raised on the genotypes of 2009H, ESH, RSH, CS-H3N2 and 2009H-EA, which were directly related to human influenza viruses, including genes derived from human influenza virus strains. We believed that these emerging strains would certainly have a major impact on the pigs and human public health, but we could not know specifically how it affected, it required more close monitoring.
It is well known that influenza virus genomes could escape host preexisting immunity by antigenic drift or antigenic shift, resulting in influenza outbreak in animals and even humans [6
]. A recent study has revealed that the 2009H-like, TR-like, CS-like, and EA-like viruses were co-circulating in pigs in southern China with relatively, and 2009H-like viruses might have been maintained in pigs for a period of time and will likely become established in pigs [55
]. With the evolution of swine viruses and development of pork industry, in-depth and larger-scale geographic region studies on H1N1 subtype swine influenza viruses in mainland China are still required, to comprehend and monitor the variation, prevalence, transmission, potential hazard of H1N1 subtype swine influenza viruses.