Virus Evolution Workgroup: 1999 Workshop Abstract

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Comparison of influenza viruses from different species to determine amino acid changes important for the virus to cross species

David L. Suarez
Southeast Poultry Research Laboratory, 934 College Station Rd.
Athens, GA 30605; dsuarez@asrr.arsusda.gov

Influenza virus infects a wide variety of birds and mammals. However, the natural host and reservoir for the virus is thought to be wild waterfowl, shorebirds, and gulls. Influenza viruses are evolving slowly in its natural reservoir. When the virus has crossed species to an abnormal host, it has a greatly increased rate of evolution, which is a result of adaptation by the virus into its new host. The increased mutation and evolutionary rates has previously been documented in humans, horses, and swine by regression analysis by comparing the number of substitutions from the index case or other early point of origin against the date of isolation. Previously, influenza isolates from poultry species had been lumped together with all other avian influenza viruses when calculating mutational changes, and earlier work showed a low rate of mutational change. However, one cannot compare unrelated influenza isolates in this type of analysis and get meaningful results. When influenza isolates from the same outbreak were compared over time, the rates of mutational and evolutionary change were similar to what was observed in mammals, demonstrating that poultry are not a normal host for influenza viruses.

When the internal influenza viral genes are compared by phylogenetic analysis at the nucleotide level, the viruses will cluster into eight categories including, human, classic swine, avian-like swine, equine type 1, equine type 2, gull, avian North American, and avian Eurasian. However, at the amino acid level the distinction between the avian North American and avian Eurasian groups are lost. The greater conservation at the amino acid level allows for the determination of the consensus sequence for different genes that ideally will provide an accurate representation of the wildlife reservoir. Although it would be preferable to have only isolates from natural host species, only a few sequences are available from this source. However, you can include poultry isolates in the analysis if the viruses were sampled after a recent introduction of virus from the waterfowl source, and by including only a single isolate from outbreaks with multiple virus isolates. A consensus sequence was developed for both the North American and Eurasian influenza groups, and at the amino acid level for the internal genes the sequences were highly conserved (>99%) between the two groups. The high conservation at the amino acid level of viruses from the two groups provides additional evidence that influenza is evolving slowly in the natural host reservoir, and that the sequences can be used as reference point for comparing all poultry and mammalian influenza outbreaks. The comparison of changes among different mammalian influenza virus lineages have demonstrated multiple amino acid changes in common among different lineages. It is not known if the factors that allow influenza viruses to infect different mammalian populations are similar between species, but the use of this methodology provides some additional clues as to what changes may be important for a virus to cross species. Also, having a common starting point allows for the estimation of how recently an influenza virus had crossed species before being first detected.

Abstract - Presented at the Virus Evolution Workshop
Ardmore, OK
October 21 - 24th, 1999

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e-mail: mroossinck@noble.org

Dr. Marilyn Roossinck
Plant Biology Division
The Noble Foundation
P.O. Box 2180
Ardmore, OK 73402

phone: 580 224-6630