The genes coding for the surface glycoproteins of influenza A viruses contain a small conserved and a large variable region

Perspectives on influenza evolution and the role of research

Influenza is a highly contagious respiratory pathogen that continues to evolve and threaten both veterinary and human public health. Influenza A viruses are continually undergoing molecular changes through mutations, reassortment, and, in rare instances, recombination. While they generally cause benign enteric infection in their natural reservoir of wild aquatic birds, they can cause catastrophic and potentially lethal disease outbreaks in humans, domestic poultry, and pigs when they cross the host species barrier. The continuing circulation of highly pathogenic (HP) H5N1 influenza viruses in domestic poultry in parts of Eurasia and the emergence and global spread of pandemic H1N1 2009 are current examples of influenza evolution. The spread of both HP H5N1 and pandemic H1N1 to multiple hosts emphasizes the potential for continued evolution. In this review, we discuss the current understanding of influenza A virus structure and strategies of variation, with a specific focus on the HP H5N1 and pandemic H1N1 influenza viruses. Additionally, we attempt to identify the gaps in our knowledge of H5N1 and pandemic H1N1 influenza viruses. These gaps include (i) an understanding of the molecular determinants of influenza virus and the host that permit efficient transmissibility and pandemic potential, (ii) the urgent need for prospective surveillance in apparently healthy swine, (iii) the molecular determinants of high pathogenicity in poultry, pigs, and people, (iv) the genetic basis of host susceptibility, (v) antigenic variability, (vi) the use of vaccine to control influenza, (vii) the role of wild birds as the reservoir of highly pathogenic avian influenza, (viii) the problems with vaccines, (ix) seasonality, (x) co-infections, and (xi) anti-influenza drug resistance. Our failure to eradicate HP H5N1 globally and to explain why H5N1 does not transmit efficiently in humans while an H1N1 pandemic virus of swine origin spread globally in months are key examples that emphasize the critical need to bridge these knowledge gaps. Future directions in influenza research that will help us resolve each of the above-mentioned knowledge gaps include complete genomic and proteomic analysis of both the virus and the host with the prospect of designing new control strategies and the development of genetically resistant hosts.

A group of V3 sequences from human immunodeficiency virus type 1 subtype E non-syncytium-inducing, CCR5-using variants are resistant to positive selection pressure

In a human immunodeficiency virus type 1 (HIV-1)-infected individual, immune-pressure-mediated positive selection operates to maintain the antigenic polymorphism on the gp120 third variable (V3) loop. Recently, we suggested on the basis of sequencing C2/V3 segments from an HIV-1 subtype E-infected family that a V3 sequence lineage group of the non-syncytium-inducing (NSI) variants (group 1) was relatively resistant to positive selection pressure (35). To better understand the relationship between the intensity of positive selection pressure and cell tropism of the virus, we determined the linkage between each V3 genotype and its function of directing coreceptor preference and MT2 cell tropism. The biological characterization of a panel of V3 recombinant viruses showed that all of the group 1 V3 sequences could confer an NSI/CCR5-using (NSI/R5) phenotype on HIV-1(LAI), whereas the group 2 V3 sequence, which was more positively charged than the group 1 sequence, dictated mainly a syncytium-inducing, CXCR4-using (SI/X4) phenotype. Phylogenetic analysis of C2/V3 sequences encoding group 1 or 2 V3 suggested that the variants carrying group 1 V3 are the ancestors of the intrafamilial infection and persisted in the family, while the variants carrying group 2 V3 evolved convergently from the group 1 V3 variants during disease progression in the individuals. Finally, a statistical test showed that the V3 sequence that could dictate an NSI/R5 phenotype had a synonymous substitution rate significantly higher than the nonsynonymous substitution rate. These data suggest that V3 sequences of the subtype E NSI/R5 variants are more resistant to positive selection pressure than those of the SI/X4 variants.

Molecular aspects of the epidemiology of virus disease

With regard to molecular epidemiology, influenza A viruses belong to the best-studied virus systems. At least two large reservoirs of influenza A viruses have been built up in nature, one in humans and another one in water fowls. The latter one is very heterogenous, consisting of viruses belonging to 13 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes in almost all possible combinations. The segmented structure of the influenza virus genome allows the creation of new influenza strains by reassortment. By replacement of the HA gene of human strains new pandemic viruses can be generated (antigenic shift). The particular structure of the HA enables the human influenza A-viruses to create variants which can escape the immune response of the host (antigenic drift). The nucleoprotein is responsible for keeping those two large reservoirs apart. Mixing of genes of viruses from these two reservoirs seems to happen predominantly by double infection of pigs, which apparently are tolerant for infection by either human or avian influenza viruses. The molecular mechanisms described for influenza viruses can be explained by the particular structure of their genome and their components and cannot be generalized. Each virus has developed its own strategy to multiply and to spread.

Correlation of influenza A virus nucleoprotein genes with host species

The RNAs coding for the nucleoproteins of a panel of influenza isolates from human and nonhuman hosts were compared by RNA-RNA hybridization to determine the extent of genetic diversity of this protein and to determine if related nucleoproteins (NP) are consistently found in viruses from certain hosts. Five nucleoprotein groups were defined. Group 1 contains nearly all of the avian influenza viruses, group 2 includes only certain viruses isolated from gulls, group 3 includes all recent equine influenza strains, group 4 contains only equine/Prague/1/56, and group 5 contains all human and swine influenza isolates. The maintenance of specific nucleoproteins in viruses from certain species suggests that these proteins have evolved functionally significant differences that favor their replication in a specific host.

Hemagglutinin-specific enzyme-linked immunosorbent assay for antibodies to influenza A and B viruses

An enzyme-linked immunosorbent assay (ELISA) was developed to detect antibodies present in human serum or nasal washes directed against influenza A or B hemagglutinin glycoproteins. The assay was modified to measure the immunoglobulin isotype specificity of the anti-hemagglutinin response in serum and nasal secretions. In the postinfection sera anti-hemagglutinin of the immunoglobulin G isotype was predominant, whereas in nasal secretions the antibody was predominantly immunoglobulin A. The antibody response detected by the ELISA manifested hemagglutinin subgroup specificity. In addition, there was a good correlation between the ELISA antibody titer and the hemagglutination-inhibition or neutralizing antibody titer. The ELISA was more sensitive than the hemagglutination-inhibition assay, and the range of antibody titers measurable by ELISA in human serum was from less than 1:20 for children who had never experienced influenza infection to 1:400,000 for adults convalescing from a secondary infection. With more sensitive tests to detect antibody to the influenza hemagglutinin it should be possible to determine the relative contribution of local and systemic immunity to resistance to influenza virus infection.

Genetic relatedness of the neuramindase of influenza A strains Nav2, Nav3, and Nav6

By molecular hybridization and by neuraminidase inhibition tests it is shown that all influenza A strains tested carrying an Nav3 or Nav2 neuraminidase (NA) are genetically highly related in their NA genes and cross-react serologically with specific antineuraminidase sera. The Nav6 strains exhibit a very low RNase protection after hybridization and do not cross-react serologically with Nav2 or Nav3 strains. Thus, the Nav2 and Nav3 strains comprise one group which is distinct from that of Nav6 strains.