Long term trends in the evolution of H(3) HA1 human influenza type A

Abstract

We have studied the HA1 domain of 254 human influenza A(H3N2) virus genes for clues that might help identify characteristics of hemagglutinins (HAs) of circulating strains that are predictive of that strain's epidemic potential. Our preliminary findings include the following. (i) The most parsimonious tree found requires 1,260 substitutions of which 712 are silent and 548 are replacement substitutions. (ii) The HA1 portion of the HA gene is evolving at a rate of 5.7 nucleotide substitutions/year or 5.7 x 10(-3) substitutions/site per year. (iii) The replacement substitutions are distributed randomly across the three positions of the codon when allowance is made for the number of ways each codon can change the encoded amino acid. (iv) The replacement substitutions are not distributed randomly over the branches of the tree, there being 2.2 times more changes per tip branch than for non-tip branches. This result is independent of how the virus was amplified (egg grown or kidney cell grown) prior to sequencing or if sequencing was carried out directly on the original clinical specimen by PCR. (v) These excess changes on the tip branches are probably the result of a bias in the choice of strains to sequence and the detection of deleterious mutations that had not yet been removed by negative selection. (vi) There are six hypervariable codons accumulating replacement substitutions at an average rate that is 7.2 times that of the other varied codons. (vii) The number of variable codons in the trunk branches (the winners of the competitive race against the immune system) is 47 +/- 5, significantly fewer than in the twigs (90 +/- 7), which in turn is significantly fewer variable codons than in tip branches (175 +/- 8). (viii) A minimum of one of every 12 branches has nodes at opposite ends representing viruses that reside on different continents. This is, however, no more than would be expected if one were to randomly reassign the continent of origin of the isolates. (ix) Of 99 codons with at least four mutations, 31 have ratios of non-silent to silent changes with probabilities less than 0.05 of occurring by chance, and 14 of those have probabilities <0.005. These observations strongly support positive Darwinian selection. We suggest that the small number of variable positions along the successful trunk lineage, together with knowledge of the codons that have shown positive selection, may provide clues that permit an improved prediction of which strains will cause epidemics and therefore should be used for vaccine production.

Figure 1

Overall structure of the most parsimonious trees. The thick line running from the lower left (∗ = root) to the upper right (open square) is called the trunk and represents the successful H3N2 lineage. The vertical lines indicate the range of isolates from the flu years (October 1 to September 30).

Figure 2

Rate of evolution of human influenza HA1. The y axis shows the number of replacement substitutions between the root and a tip sequence. The x axis shows the time of isolation of the virus to the month where known (206 sequences), or to the month of June if the month was not known (48 sequences). Each of the 254 sequences is represented in the graph but, if there were more than one isolate for the same month and year, their distances were averaged. A least squares fit to the data gives a slope of 3.20 replacement substitutions/year. The two tubes show an apparent increase in the rate of replacement substitutions about 1992. However, we cannot rule out the possibility that this is a consequence of a more intensive sampling of the population in the last four years.