Skip to main content
Premium Trial:

Request an Annual Quote

Phylogenetic Study Suggests Swine Flu Went Undetected For Months

NEW YORK (GenomeWeb News) – The influenza A H1N1 "swine flu" virus was likely capable of transmission to humans months before it was detected, according to a paper appearing in the advanced, online edition of Nature today.

Researchers from the Universities of Hong Kong, Edinburgh, Arizona, and Oxford did phylogenetic analyses of more than 800 influenza strains to estimate when — and how — the H1N1 swine flu virus originated. Consistent with previous research, their results suggest that the virus is an amalgam of several different viruses that were circulating in pig populations.

But that viral shuffling probably didn't occur recently, the team found. They suggested that the reassortment of genes found in the swine flu virus probably occurred several years ago, with the virus gaining the ability to infect humans a few months before health officials recognized the outbreak. That has the team calling for more widespread surveillance aimed of swine populations.

"Our results highlight the need for systematic surveillance of influenza in swine," senior author Andrew Rambaut, an evolutionary biologist at the University of Edinburgh, and his co-workers wrote, "and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans."

The World Health Organization's latest report, issued today, indicates that the H1N1 swine flu virus has infected tens of thousands of people in 74 countries, claiming at least 144 lives. Earlier today, WHO announced that it is declaring the swine flu outbreak a level 6 alert global pandemic — the first such designation in more than four decades, according to several news agencies.

Late last month, researchers from the US Centers for Disease Control and elsewhere conducted a genetic analysis of the H1N1 "swine flu" virus, demonstrating that it contains a previously unrecognized combination of genes from swine, avian, and human influenza. The new study supports the notion that the virus represents a combination of several strains — and offers new clues about the virus' history.

Rambaut and his colleagues created phylogenetic trees based on two H1N1 outbreak genomes, 796 human, swine, and avian influenza A strain genomes, and the genomes of 15 newly sequenced H1N1 and H1N2 swine flu strains collected in Hong Kong since the early 1990s.

Based on their subsequent Bayesian molecular clock analysis of each of viral gene, the team estimated that the outbreak virus' viral ancestors were circulating in pigs for about nine to 17 years.

When they limited their analysis to 30 H1N1 swine flu viruses isolated since the end of March, the researchers found a more recent common ancestor for the swine flu genome going back to sometime between August 2008 and January 2009.

"[T]he currently sampled [swine-origin influenza A virus] shared a common ancestor around January 2009 (no earlier than August 2008)," the authors noted. "The long, unsampled history observed for every segment suggests that the reassortment of Eurasian and North American swine lineages may not have occurred recently, and it is possible that this single reassortment lineage has been cryptically circulating rather than two distinct lineages of swine flu."

The team also noted that the outbreak strain appears to have more non-synonymous substitutions than previously surveyed strains. While that might represent an adaptation to human hosts, they cautioned that the findings could just be a consequence of the steep increase in surveillance that has accompanied the swine flu outbreak.

Given the pandemic H1N1 strain's link to swine flu viruses and the potential for viral combination and reassortment in pig populations, the researchers emphasized the need for increased influenza A surveillance in swine populations.

"[D]espite widespread surveillance in humans, the lack of systematic swine flu surveillance allowed for the undetected persistence and evolution of this potentially pandemic strain for many years," Rambaut and his co-authors concluded.

Filed under

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.