US hosted wide mix of flu strains in 2006-07

Sep 4, 2008 (CIDRAP News) – Researchers who conducted genetic analyses of hundreds of influenza viruses collected during the 2006-07 flu season found that many different variants circulated in the US at the same time, suggesting that the way each year's epidemic spreads is more complicated than previously suspected.

The scientists, led by Martha I. Nelson of Pennsylvania State University as first author, found that several different clades, or lineages, of influenza A subtypes H1N1 and H3N2 circulated at the same time and even in the same localities, according to the report in PLoS Pathogens.

"Overall, the co-circulation of multiple viral clades during the 2006-2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus," the report states. It says the findings indicate that several viral strains were introduced separately into the country.

Among other things, the authors found that clades of the same subtype (H1N1 or H3N2) exchanged genetic material through reassortment in a number of instances. In one case, this gave rise to an H3N2 variant that was sensitive to the antiviral drugs amantadine and rimantadine, unlike most H3N2 strains in recent years.

Isolates gathered in 21 states
The researchers analyzed viruses collected as part of a larger surveillance effort by Surveillance Data Inc., involving 56 physicians from 21 states. The physicians took samples from patients at least 1 year old who had fever and upper respiratory symptoms. A rapid test was used to identify influenza A or B, and positive samples were sent to a reference laboratory for subtyping. Genetic sequencing was handled by the J. Craig Venter Institute in Rockville, Md.

The 2006-07 flu season, unlike most other recent seasons, was dominated by H1N1 viruses. This was reflected in the distribution of viruses analyzed by the authors: 284 H1N1 and 69 H3N2 isolates.

They identified eight different clades of H1N1 viruses, designated A through H. Clade A was dominant, accounting for 175 of the 284 isolates, or 62%, and was found in 24 of 30 localities.

By comparing the US H1N1 viruses with 48 "background" H1N1 isolates collected in both hemispheres between 2001 and 2006, the authors determined that clades A, B, C, D, and E were descendants of New Caledonia–like viruses that circulated from 2002 through 2005. Clade F was found to be a reassortant that combined gene segments from New Caledonia–like and Solomon Islands–like strains. The researchers also found that only one of their H1N1 isolates contained the "S31N" mutation in the M2 protein that signals resistance to adamantane drugs.

In analyzing the 69 H3N2 viruses, the authors determined that 60 (87%) fell into one clade, designated "a." All the clade a isolates had the S31N mutation conferring adamantine resistance. Five other isolates were grouped in a second clade, called "b," which lacked the resistance mutation, a finding the authors call surprising. The other four isolates all represented distinct strains.

The researchers determined that most of the genome of clade b isolates was "more closely related to the adamantane-resistant clade a than to older adamantane-sensitive clades." This suggested that, instead of evolving directly form older adamantane-sensitive viruses, clade b re-acquired sensitivity by incorporating two genome segments from those viruses through reassortment.

Different clades circulated together
As for geographic distribution of the viruses, the authors found more than one clade of H1N1 in every locality where more than one viral sample was obtained. Six different H1N1 clades were found in Houston, the most heavily sampled area, and three H1N1 clades circulated in Los Angeles, Denver, and New York City, as well as in smaller cities such as Tullahoma, Tenn., and Aberdeen, Miss. Similarly, the two H3N2 clades were geographically widespread.

Over the course of the season, a total of eight clades of H1N1 and H3N2 circulated in Houston, seven in New York City, six in Los Angeles, and five each in Denver, Cincinnati, and Hopkinsville, Ky. In some cases, several clades of both subtypes circulated in the same localities at the same time. For example, at least two clades of each subtype circulated late in the season in Chicago, Houston, and Los Angeles.

Amid all the circulating strains, the authors detected no clear signal of the pathway the viruses traced across the country.

"Rather than a single viral lineage spreading across the US, multiple lineages of both A/H3N2 and A/H1N1 influenza virus were separately introduced and co-circulated, allowing for reassortment within subtypes and greatly complicating patterns of spatial-temporal spread," the report states. "Given the extent of genetic diversity observed during this season, obtaining a strong signal for the spatial-temporal pattern of spread of multiple different lineages clearly would entail a large increase in sampling."

While concluding that influenza viruses are introduced multiple times during each season, the authors say they can't exclude the possibility that one co-infected person introduced more than one viral clade into the country in the 2006-07 season. In addition, they write that the evolutionary dynamics of the season may have been unusually complex, particularly since it was not dominated by H3N2 viruses, which tend to spread faster than H1N1 strains. "Repeating this sampling effort during an A/H3N2-dominated influenza season could yield a stronger spatial pattern," they state.

They also observe that too few influenza genetic sequences were available from the rest of the world to permit any conclusions about the geographic origins of the viruses introduced into the United States.

Nelson MI, Edelman L, Spiro DJ, et al. Molecular epidemiology of A/H3N2 and AH1N1 influenza viruses during a single epidemic season in the United States. PLoS Pathog 2008;4(8) [Full text]

See also:

Jan 14, 2006, CIDRAP News story "CDC: Resistance makes 2 older flu drugs ineffective"

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