Novel swine flu strains have been found to have been circulating “unnoticed” in pigs in Cambodia (Image: Getty Images)
Several previously unknown strains of swine flu have been found to have been circulating “unnoticed” in pigs in Cambodia for years — posing a potential pandemic risk.
This is the warning of an international team of researchers, who noted that some of the novel strains appear to include viruses that have been passed to pigs by humans.
The team explained that pigs are a key intermediary in the emergence and potential spread of influenza viruses between animals and humans.
Pigs provide a suitable environment for the shuffling of gene segments between avian, swine and human hosts — allowing for the evolution of new viruses.
This risk has been heightened, experts note, by the increase in pork production over the last five decades, which has increased the movement and international trade of the animals.
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The team swabbed pigs in 18 slaughterhouses across four Cambodian provinces (Image: Zeller et al. / PNAS)
The investigation was undertaken by evolutionary biologist Professor Yvonne Su of the Duke–National University of Singapore Medical School and her colleagues.
Su said: “The long-term evolution of different lineages has led to the establishment of genetically distinct viruses that have been continuously circulating in pig populations undetected for decades.
“Our study revealed the hidden and complex genomic landscape of swine flu virus evolution in Southeast Asia.”
This region, she added, is marked “as a hotspot for virus diversity and risk of new virus emergence”.
The team found that the H1N1 subtype (depicted) was predominant and likely derived from humans (Image: Getty Images)
In their study, the team conducted surveillance for swine flu in 18 pig slaughterhouses in Cambodia between March 2020 and July 2022.
In total, they collected more than 4,000 nasal swabs from pigs located across four different provinces — of which 72 animals, or around two percent of those tested, were found to be positive for influenza A virus.
Of these viruses, Su and her colleagues identified nine different swine influenza A groups, at least seven of which have not previously been detected for between two to 15 years.
The team found multiple H3 lineages that had been passed to the pigs by humans — and appear to have been circulating undetected for around a decade.
They also report that the H1N1 subtype was predominant and likely derived from humans, dating back to the 2009 global pandemic.
In pigs from the provinces of Kandal, Phnom Penh and Takeo, the study identified two seasonal viruses that are thought to have come from Thailand.
The researchers also report isolating a new swine European H1N2 variant — originally derived from birds — with genes traced back to North America.
While the first to detect this variant, genomic analysis suggests that it has been circulating undetected in pigs in Cambodia since 2014.
Genetic evidence indicates that European swine flu viruses appear to have been sporadically introduced to China and Southeast Asia in the early 2000s.
Furthermore, South Central China appears to have been the major source of European-like swine flu virus transmissions in the region since 2010, with these strains being spread more widely across China and then into Southeast Asian countries like Cambodia.
Su and her colleagues identified nine different swine influenza A groups (Image: Zeller et al. / PNAS)
Evolutionary biologist Professor Gavin Smith is a co-author of the study and the director of the Duke–NUS Emerging Infectious Diseases program.
He said: “While swine influenza viruses typically cause mild symptoms in pigs, they pose a pandemic threat to humans.
“The human population may lack immunity or have inadequate protection against new strains of swine influenza viruses.
“Therefore, systematic surveillance is crucial in early detection and warning of new subtypes or strains.”
With their initial study complete, the researchers are now working to develop a platform that is capable of identifying all major genetic subtypes of swine flu, which they hope will aid in better assessing the spread and pandemic threat of the new viruses.
This screen, they explained, will include not only swine and human subtypes, but also several avian sequences, allowing them to identify if pig and human populations have been infected with the influenza subtypes.
Professor Patrick Tan — Duke–NUS’ Senior Vice-Dean for Research — said: “Routine and sustained surveillance is indispensable in identifying new viruses so that their transmission risk can be assessed.
“It is therefore critical that more efficient and continuous surveillance methods are integrated with automated analytical tools to rapidly provide information on changes in human and animal pathogens.
“Such a system as the team at Duke–NUS is developing would improve animal health through selection of effective vaccines, and aid in human health by monitoring viruses with the potential for transmission.”
The full findings of the study were published in the journal PNAS.
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