Commentary
More Human Avian Influenza Genetic Reassortment Failures
Recombinomics Commentary 15:20
June 2, 2008
And while none of the offspring viruses was as virulent as the original H5N1, about one in five were lethal to mice at low doses, showing they retained at least a portion of the power of their dangerous parent.
The work suggests that under the right circumstances - and no one is clear what all of those are - the two types of flu viruses could swap genes in a way that might allow the H5N1 virus to acquire the capacity to trigger a pandemic. That process is called reassortment.
"This study is just showing exactly that: There is a risk this virus can successfully reassort with a human virus," said Richard Webby, director of the World Health Organization's collaborating centre for influenza research at St. Jude Hospital in Memphis, Tenn.
"The problem is we don't know at this stage whether there's a benefit to these H5N1 viruses in doing that."
Nor can anyone say why, if the viruses swapped genes so readily in the laboratory, that hasn't seemed to have happened in the parts of the world where H5N1 has been circulating for years.
The above comments on the recent paper in PLOS demonstrates the inherent problem with human / avian reassortants involving H5N1. H5N1 has already evolved into an effective killing machine that not only can kill a wide variety of avian species, but can also kill mammals. This has been demonstrated time and again with humans, as well as mammals that eat H5N1 infected birds. Moreover, H5N1 has evolved into multiple sub-clades capable of producing confirmed fatal infections in humans. Clade 1 has produced fatal human infections in southeast Asia (Vietnam, Thailand, Cambodia). Clade 2 has been divided into three major subclades. Clade 2.1 has produced confirmed fatal infections in Indonesia. Clade 2.2 (Qinghai strain) has produced confirmed fatal infections in Turkey, Iraq, Azerbaijan, Egypt, Nigeria, Pakistan. Clade 2.3 (Fujian strain) has produced fatal infections in China, Vietnam, Laos, Cambodia. All of these fatalities have been in the past few years, demonstrating that relatively minor changes in individual genes can extend the lethality for humans to a variety of H5N1 sub-clades currently in circulation.
The property required to move H5N1 into the pandemic categoiry is not grow in mammals or virulence in mammals, it is efficient transmission between mammals. Virtually all of the clusters in the above countries include human to human transmission between family members or close contacts. However, such transmission chains have generally been limited to a few transmission cycles.
For clade 2.2, most of the clusters have been associated with receptor binding domain changes which enhance affinity for human receptors, and in several cases decrease affinity for avian receptors. However, these changes involve alterations at one or two positions. They do not involve reassortment, which swaps one or more entire genes.
Thus, the examples in the recent PLOS paper are primarily the “B list” of reassortants that are viable, but are usually not lethal in mammals. The small list of those that retain lethality have not been shown to increase transmission. Those candidates, which represent the “A list”, were published earlier in a PNAS paper. However, the “A list” also failed to match the growth or transmission efficiencies of H5N1 with eight avian gene segments, representing naturally evolving H5N1.
The failures of reassortants have led some to question whether H5N1 will develop into a pandemic strain. However, it is the successes in increased transmission efficiencies in H5N1 with receptor binding domain changes in human clusters that suggests a pandemic is only one or two nucleotide changes away.
Ironically, it is an H7N2 human / avian reassortant that has produced enhanced transmission in a ferret model, but the removal of the H7N2 sequences from Genbank shortly after the sequences were made public has created confusion on the true genetic composition of A/New York/107/2003, which was isolated from a case infected in 2002 in New York. The deposited sequences have 3 avian genes (HA, NP, NA) and 4 human genes (PB1, PA, MP, NS). The 8th gene sequence, PB2, wasn’t made public. The enhanced receptor domain binding and ferret to ferret transmission was highlighted in a recent PNAS paper. Moreover, if the submiited gene sequences are correct and the patient tested negative for H3N2, then the infection was likely transmitted human to human.
Although the published results have generated a great deal of media attention, the removal of the underlying sequences has not, and the authors of the study have not publicly commented on the sequences, which are not currently marker with a red banner stating that This record was removed at the submitter's request because the source organism cannot be confirmed.
Ironically, the CDC in Atlanta was involved in both studies, as well as a recent paper in Science on the global spread of H3N2. That paper included sequences, including one submitted by the CDC, which confirmed H3N2 HA recombination in patients in Korea in 2002. Both reassortment and recombination involve swapping of genetic information in hosts co-infected with two or more influenza viruses. While the ressortment swaps whole gene segments, recombination involves swapping portions of genes, which may lead to exchanges of single nucleotide polymorphisms, which is the type of change than can alter binding affinities for human or avian receptors.
The ressortment, or swapping of whole genes, is called genetic shift, while the changes in single nucleotide polymorphisms is called drift. One of the basic tenets of influenza genetics holds that the drift is due almost exclusively to de novo copy errors which happen during viral replication. However, the number and patterns of changes support acquisition via recombination.
Regardless of mechanism, sequence analysis demonstrates that stable small changes are far more frequent than stable reassortants, which is why an H5N1 pandemic is much more likely to involve a change in the receptor binding domain that increases affinity for human receptors, than a swapping of whole avian genes fro human genes.
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