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Perspectives PERSPECTIVES in humans. In the 1957 H2N2-SUBTYPE pan- OPINION demic virus, both influenza surface proteins, HA and neuraminidase (NA), and one inter- nal protein, polymerase B1 (PB1), were Evidence of an absence: closely related to Eurasian wild waterfowl influenza proteins6,7.In 1968, the H3N2 pan- the genetic origins of the 1918 demic virus contained novel HA and PB1 proteins, also apparently of Eurasian wild waterfowl origin7,8.Although it is not known pandemic influenza virus exactly how these reassortant viruses were generated, pigs can be infected with both Ann H. Reid, Jeffery K. Taubenberger and Thomas G. Fanning avian and human influenza strains and this species has been suggested as a potential ‘mix- Abstract | Annual outbreaks of influenza A (HA) protein on the virus surface can greatly ing vessel’ for the generation of pandemic infection are an ongoing public health threat reduce the effectiveness of existing antibodies, viruses2,9. and novel influenza strains can periodically leaving people vulnerable to repeated influenza In 1918, the most devastating influenza emerge to which humans have little immunity, infections throughout their lives. In addition pandemic in history killed at least 40 million resulting in devastating pandemics. The 1918 to this gradual change in the influenza virus, people10,11.In addition to a death toll that is pandemic killed at least 40 million people which is known as ANTIGENIC DRIFT, influenza A several times higher than that of other worldwide and pandemics in 1957 and 1968 viruses can acquire novel surface proteins influenza pandemics, the 1918 H1N1 virus caused hundreds of thousands of deaths. against which existing antibodies are ineffec- took its greatest toll on young adults instead of The influenza A virus is capable of enormous tive2.When this kind of ANTIGENIC SHIFT occurs, the very old and very young who are usually genetic variation, both by continuous, up to one-third of the population can become most affected by influenza12–16.Recently, isola- gradual mutation and by reassortment of ill in an explosive global pandemic3,4. tion of the genetic material of the 1918 strain genome segments between viruses. Both Two characteristics of influenza A biology from formalin-fixed and frozen case material the 1957 and 1968 pandemic strains are contribute to its ability to undergo antigenic has made it possible to determine the genetic thought to have originated as reassortants in shifts. First, its RNA genome comprises eight sequence of this virus. Five of the eight which one or both human-adapted viral separate segments. Co-infection of a cell with genome segments have been sequenced17–22. surface proteins were replaced by proteins two different influenza virus strains can result Analyses of these sequences are underway to from avian influenza strains. Analyses of the in the generation of hybrid viruses that con- try to understand whether the 1918 pandemic genes of the 1918 pandemic virus, however, tain some segments from each progenitor — strain was generated by the same pattern of indicate that this strain might have had a a process known as REASSORTMENT5.Second, reassortment as the 1957 and 1968 strains. different origin. The haemagglutinin and influenza A viruses can infect many animal It is possible that the unusual characteristics nucleoprotein genome segments in particular hosts, including wild waterfowl, poultry, pigs of the 1918 pandemic were, in part, due to an are unlikely to have come directly from an and horses. Under circumstances that have unusual origin. Even if this is not the case, it is avian source that is similar to those that are not yet been fully characterized, influenza important to know whether there is another currently being sequenced. Determining strains can cross between species. The ability pathway for the generation of pandemic whether a pandemic influenza virus can to reassort and the existence of several reser- strains so that surveillance for emerging emerge by different mechanisms will affect voirs of influenza virus provide many possi- strains can be optimized. the scope and focus of surveillance and bilities for the generation of novel influenza As data have accumulated, evidence has prevention efforts. virus strains2. emerged to indicate that some of the genome Four pandemics have occurred in recent segments of the 1918 H1N1 strain might Influenza afflicts approximately 10–20% of the history — in 1890, 1918, 1957 and 1968 (REFS have a novel origin that has not been seen in population and kills an estimated 36,000 peo- 2–4).The genetic composition of the viruses strains responsible for other pandemics23. ple each year in the United States1.The annual responsible for the 1957 and 1968 pandemics The nucleoprotein (NP) gene sequence, in return of the disease is driven by the antigenic is known; these viruses seem to have been particular, seems to have been acquired variability of the influenza virus; two or three generated by reassortment between an avian directly from a source that is similar to viruses amino acid changes in the haemagglutinin influenza strain and the strain then circulating currently found in wild birds at the amino NATURE REVIEWS | MICROBIOLOGY VOLUME 2 | NOVEMBER 2004 | 909 PERSPECTIVES Table 1 | Comparison of NPs with avian consensus sequences protein in which many amino acid changes provide a selective advantage. When the Sequence* Strain nucleotide sequence of the NP from the 1918 1918 A/Duck/ A/Duck/ Bavaria/2/77 Manitoba/53 virus is compared with the NP sequence of mammalian isolates, the S/N ratios vary Overall avian consensus 173 73 71 from 2.7 (1918 compared with A/Wilson- Eurasian avian consensus 187 51 114 Smith/33) to 5.1 (1918 compared with North American avian consensus 179 137 40 A/Swine/Iowa/15/30). By contrast, when the The number of nucleotide differences between sequences are shown. *Consensus sequences were 1918 sequence is compared with 10 avian generated with the SequencherTM program, version 4.1.4, Gene Codes Corporation, using the consensus by species chosen from both the Eurasian and plurality setting. Sequences used to generate the consensus sequences are available upon request. North American avian subclades, the S/N ratio is 10.4–18.0, with an average of 13.9. acid level, but very divergent at the nucleotide from the A/Swine/Iowa/15/30 (H1N1) strain These data reinforce the results of the BLAST level, suggesting considerable evolutionary and 16 from the A/Wilson-Smith/33 (H1N1) searches — when compared with avian NP distance between the source of the 1918 NP strain (an early human virus). Conversely, the sequences, the 1918 sequence has many and the currently sequenced virus strains in 1918 NP gene differs from the A/Duck/ changes at the nucleotide level, but only a few wild birds22.In light of this conclusion, it is Bavaria/2/77 NP sequence by 193 nucleotides of these result in amino acid changes. worth re-examining the data on the other (87.1% identity), from the A/Swine/Iowa/15/30 A subset of synonymous substitutions that four sequenced 1918 genome segments, to see sequence by 67 nucleotides (95.5% identity) are known as FOUR-FOLD DEGENERATE SUBSTITU- whether a similarly unusual origin is possible. and from A/Wilson-Smith/33 by 65 nucleo- TIONS because the presence of any of the four tides (95.6% identity). The large number of bases does not lead to an amino acid replace- Nucleoprotein synonymous differences with the avian ment have been investigated. When avian PHYLOGENETIC ANALYSES of the NP segment of sequence would be expected if the NP of the sequences are compared with one another, influenza virus produce trees with two large 1918 strain had been retained from the previ- the number of nucleotide differences is usu- CLADES — a ‘mammalian’ clade with human ously circulating human strain. However, the ally 20–30%. Comparisons of the 1918 NP and classical swine subclades, and an ‘avian’ small number of amino acid differences from with avian NP sequences consistently yields clade containing equine, gull and waterfowl the avian strain indicates a recent avian origin. differences of 30–40%, indicating that the subclades. The waterfowl subclade is further Synonymous/non-synonymous (S/N) 1918 NP is different from known avian NPs. divided into North American and Eurasian ratios vary widely between different lineages This does not seem to be simply a matter of branches. The 1918 NP sequence is placed in the NP phylogenetic tree. Within the avian evolutionary time, as a region of a viral NP within the mammalian clade whether total, clade, where influenza is thought to be gene found in a strain isolated from a bird SYNONYMOUS or NON-SYNONYMOUS substitutions endemic, the average S/N ratio is 15.2. This captured in 1917 (REFS 24,25) shows identical are analysed. However, a BLAST search of the indicates that in avian strains, the NP is so patterns of four-fold degenerate differences 1918 NP protein reveals that the amino acid well adapted that most amino acid changes — 20–30% differences in comparisons with sequences to which it is most closely related are would be deleterious, and silent nucleotide modern birds and a 44% difference compared avian. It differs from the A/Duck/Bavaria/2/77 changes therefore predominate. Within the with the 1918 pandemic virus sequence. (H1N1) strain by only eight amino acids, mammalian clade, the average S/N ratio is 3.9, Given that only a limited number of wild- compared with 11 amino acid differences which indicates that NP is an actively evolving bird viruses have been sequenced, is it possi- ble that greater sampling would reveal an NP sequence that is more closely related to the 180 60 1918 NP sequences? Avian sequences vary 170 160 from each other at many synonymous sites, 150 50 but they are all similarly distant from the 140 avian consensus sequence.
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