Understanding Influenza Virus

By Dr Richard Webby - Division of Virology, St. Jude Children’s Research Hospital, Memphis. This paper, presented at the 2002 ISU Swine Conference, summarizes understanding of the current influenza viruses circulating in the swine populations of the world with particular emphasis on the situation in North America.
calendar icon 30 January 2004
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Swine Influenza Histology

Influenza is an acute respiratory disease affecting a variety of mammalian species including swine, humans, and horses. The major reservoir of influenza virus, however, is the aquatic birds of the world. Although fortuitously an infrequent event, it is from these aquatic birds that viruses sporadically transmit to other avian and mammalian species. The presence of this vast reservoir of influenza viruses in the aquatic birds of the world precludes this viral disease from eradication. Thus, the quest for control of influenza in animal and human health sectors lies heavily in the area of prophylactic treatment with vaccines.

Despite our ability to produce vaccines of proven efficacy, the influenza virus has developed avenues of counter assault that make vaccination a challenging and constantly changing task. In addition to its vast reservoirs, the influenza virus has alternative mechanisms to promote constant evolution and evasion of the hosts' immune response. The ability of influenza to undergo genetic changes drives the continual emergence of antigenically and genetically novel viruses. It is the aim of this report to summarize our understanding of the current influenza viruses circulating in the swine populations of the world with particular emphasis on current situations in North America.

Antigenic variation

The ability of the influenza virus to continually evolve resides in the fundamental properties of the virus particle itself. Through the genetic processes termed antigenic drift and antigenic shift, the virus has the ability to constantly sidestep the immune response and sporadically cause pandemic disease of noteworthy proportions.

Antigenic drift, which is driven by the infidelity of the virally encoded polymerase, results in point mutations in the viral hemagglutinin (HA) and neuraminidase (NA) glycoproteins. The HA molecule is the major viral antigenic determinant, and the selection applied by the host immune system constantly selects for drift variants that can no longer be neutralized by circulating antibodies. In this way, influenza emerges seasonally as an endemic disease and can reemerge in populations that have considerable immunity from previous exposures.

Less frequent, but potentially of far greater concern, is the process of antigenic shift. The influenza A genome is composed of eight single-stranded negative-sense RNA molecules. Infection of a single cell by two different influenza viruses can result in the production of progeny viruses containing a mixture of RNA segments from the parental viruses. Such reassortment has the potential to completely change the antigenic nature of the circulating virus and, as such, allow unimpeded spread through a host population.

Pigs as intermediate hosts

It has been postulated that swine play a central role in the ecology of influenza. In addition to being a natural host for a limited number of viral subtypes (see below) there is convincing evidence that pigs can act as an intermediate host for human disease. The limiting factor in the emergence of pandemic influenza in humans is the inability of many viruses from aquatic birds to replicate effectively in the respiratory tract of primates.1,19 Likewise, human viruses inoculated using natural routes of infection replicate poorly in waterfowl12 In contrast pigs seem to be readily infected by human viruses3,7 and most, if not all, avian HA subtypes are capable of replicating to some extent in swine.16 This trait has led to the hypotheses that pigs act as the mixing vessel for human, swine, and avian viruses with the resulting potential for reassortment and generation of novel viruses. Current theories on the source of the 1957 and 1968 human influenza pandemics are that the causative viruses were derived through reassortment in pig populations.

The molecular features responsible for the permissive nature of swine as a host of influenza reside in the nature of the viral receptors. Avian and human influenza viruses bind to different sialic acid moieties on the surface of target cells. The preference for the different receptors directly reflects the relative abundance of these receptors in the host. Avian cells contain primarily the receptors recognized by avian viruses and human cells contain primarily those recognized by human viruses. In comparison, the cells lining the respiratory tract of swine contain both types of receptor allowing attachment of both avian and human viruses.13

In addition to the potential pigs have as the mixing vessel for mammalian and swine viruses, there have also been numerous reports of human infection with swine viruses. Although some of these infections have been fatal23,25 the infections have all been self limiting and there has been little or no human-to-human spread.

Current strains of influenza in swine

Since the first influenza virus was isolated from a swine in 1930, only two HA (H1 and H2) and two NA (N1 and N2) subtypes have formed stable lineages in swine populations. Reports appear sporadically that describe other subtypes infecting swine, such as H1N7,5 H4N6,14 and H9N2,24 but these events have so far remained isolated cases and none have become established in swine populations. Endemic influenza in swine is restricted to three subtype combinations: H1N1, H3N2, and H1N2. Although only three established viral subtype combinations are found, the different geographical populations are reservoirs for a much larger number of distinct viral lineages.

Classical-swine H1N1, which is phylogenetically related to the virus responsible for the 1918 human Spanish flu pandemic, circulates predominantly in North America and Asia.20 In Europe, H1N1 viruses also circulate, but this lineage is derived from a wholly avian-like virus that was first detected in the pig population in 1979.22 This virus superceded the classical-swine viruses circulating at the time and is the current H1N1 throughout Europe. In addition a distinct lineage of avian H1N1 virus has been reported in China, although it is uncertain to what degree, if at all, it has spread.10

H3N2 viruses were first detected in swine in 1970, shortly after the emergence of similar viruses in humans.17 Since this time, human-like H3N2 viruses have been isolated from swine throughout Europe, Asia, and the Americas and analogously to the situation in humans these viruses continue to cocirculate with H1N1 viruses in most parts of the world. For reasons unknown, H3N2 viruses did not emerge in the United States swine population until late 1998. The gene segments of these viruses, which have since become established, are of mixed origin and contain human virus (HA, NA, PB1), swine virus (NP, M, NS), and avian virus (PA and PB2) genes.30

Reassortant H1N2 viruses of different lineages have been identified in various swine populations and are becoming more prominent. A reassortant H1N2 virus containing avian-like swine and human genes has become a significant problem in the United Kingdom, and this virus seems to have now spread to continental Europe.4,27 Reassortant H1N2 viruses derived from classical H1N1 and various H3N2 viruses also have been isolated in France, Japan, and the United States.9,15,26

Recent evolution of swine influenza viruses

Historical dogma has us believe that swine viruses do not evolve as quickly as human viruses. In addition, it seems that viruses can be maintained for prolonged periods in swine without any marked change in antigenic structure.2,21 Many consider this reduced drift rate to be due to the continual availability of immunologically naive animals in swine populations. The lack of immunologic pressure means that changes in the swine HA tend to be evenly distributed throughout the HA molecule, whereas changes in human virus HA genes frequently occur at or around antigenic sites.3 Although the reduced antigenic drift in swine may historically be true, recent events in both Europe and North America demonstrate that the swine populations of the world are becoming reservoirs for a very genetically diverse pool of viruses.

Recent influenza activity in European swine populations includes reassortment between H1N2 and H1N1 and/or H3N2 viruses, the isolation of antigenically distinct H1N1 viruses, and the isolation of contemporary human-like H3N2 viruses.18 Sequence analysis of HA genes has shown that antigenic drift does occur in both European H1N1 and H3N2 viruses of swine6,8 raising concerns from some investigators that vaccines in swine may need to be continually updated as in human populations. Heinen and colleagues11 have shown, however, that vaccination with A/Port Chalmers/1/73 (H3N2) was sufficient to stop the development of fever and transmission upon challenge with a recent field strain.

The vaccine was not able, however, to completely stop viral shedding from the challenged animal. Similar studies with the European H1N1 viruses have revealed similar results in that heterologous virus vaccination can protect from clinical disease and reduce viral load although not viral replication.28

Similar levels of viral reassortment have been recently identified in the U.S. swine population. Prior to the emergence of H3N2 viruses in 1998, swine influenza in the United States was caused exclusively by H1N1 viruses. By the end of 1999, H3N2 viruses had spread throughout the United States. Of particular concern was the identification of three antigenically distinct virus groups, each having a different HA gene obtained from contemporary human H3 viruses.29 Shortly after the identification of the H3N2 viruses the first generation of H1N1/H3N2 reassortments were identified.15 These reassortant viruses were H1N2 viruses containing seven H3N2 genes and the HA from a classical H1N1 virus. H1N2 viruses have continued to spread and phylogenetic analysis suggests that multiple independent reassortment events have resulted in their genesis. A further reassortment event between the H3N2 and H1N1 viruses has resulted in the emergence of yet another variant of virus. These viruses contain the HA and NA of the classical swine virus but all other genes from the H3N2 viruses. Our ongoing research suggests that these may be becoming one of the dominant viral genotypes in the U.S. swine population. It is also interesting to note that a virus of this genotype has been isolated from a human with a nonfatal respiratory disease.

The current swine and human commercial vaccines are both killed vaccines in which protection is afforded by the development of neutralizing antibodies primarily to the HA molecule. In such circumstances the amount of juggling of the other gene segments is of no consequence. Unfortunately, at least in the case of the North American situation, the reassortment of viral gene segments has been followed by a concomitant change in the HA molecule. The recent H1 molecules seem to be gathering mutations at an increased rate. The amount of sequence divergence between certain 2001 isolates is as much as the difference between classical H1N1 viruses isolated in the 1960s and those isolated in the early 1990s. Studies similar to those described above in Europe are needed to assess the cross protection potential of the current vaccines against all antigenic variants.

Taken together, these data show the huge impact that the introduction of a single new virus into a swine population can have on the diversity of viral genotypes. The U.S. swine population has thus gone from a reservoir containing a single virus to one where H1N2, two antigenically distinct H3N2, and two distinct genotypes of H1N1 co-circulate (Figure 1). Which of these viral lineages will eventually predominate will only become apparent if surveillance is intensified and centralized.


Influenza activity in recent years in the human population has been relatively mild in terms of disease and viral evolution. The last major human drift variant was the 1997 A/Sydney/1/97-like H3N2 viruses. In contrast, the last few years has seen major activity in influenza viruses in global swine populations, particularly in the United States. The resulting increase in genetic diversity of swine influenza viruses is of concern for both human and animal health. The likelihood is that both H1 and H3 viruses will continue to evolve and cocirculate in swine populations and that the key to managing this situation is surveillance. The challenge for the swine industry is to develop a surveillance system that incorporates genetic and antigenic characteristics of circulating viruses. Such a system will be indispensable for ensuring the efficacy of vaccines and for the early detection of novel and potentially devastating viruses.


The work described in this report is part of an ongoing collaboration between the laboratories of Dr Robert Webster at St Jude Children’s Research Hospital, Dr’s Kurt Rossow and Sagar Goyal from the University of Minnesota, St Paul, and Dr Gene Erickson at the Rollins Animal Disease Diagnostic Laboratory, NC. This project has been supported by the National Institutes of Health and the American Lebanese and Syrian Associated Charities.


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Source: Iowa State University, 2002 Swine Conference
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