Scientists from Duke-NUS Medical School and elsewhere have identified several novel strains of swine flu viruses circulating in Cambodian pigs that pose a potential pandemic risk. The new strains include viruses that have jumped from humans to pigs and some strains with genes that originate from North America. The findings point to a need for stronger surveillance methods to identify new viruses and assess their transmission risks before they become a major threat. 

Full details of the study and findings are published in the Proceedings of the National Academy of Sciences.  The team was led by scientists in Duke-NUS’ Emerging Infectious Diseases (EID) program with collaborators at the National Animal Health and Production Research Institute in Phnom Penh, the London School of Hygiene & Tropical Medicine, and elsewhere.

Over several months in 2022, the team gathered over 4,000 nasal swabs from pigs in 18 slaughterhouses located in four Cambodian provinces. About 2% of the tested population, or 72 pigs, tested positive for influenza A viral strains, according to the paper. In the positive cases, the scientists identified nine distinct influenza A virus groups. Some of the strains had multiple H3 lineages that passed from humans to pigs and have been circulating undetected in pigs for about 10 years. This included an H1N1 subtype that is linked to the 2009 swine flu pandemic. 

The team also detected two seasonal viruses in pigs from three provinces, Kandal, Phnom Penh, and Takeo, that likely originated from Thailand. And they isolated a new European H1N2 variant in pigs—originally from birds—that has North American genes. Genomic analysis of this strain suggests that it has been circulating in Cambodian pigs since 2014 although this is the first time that it has been identified. 

Furthermore, the scientists connected European swine flu viruses to South Central China and Southeast Asia. They found that South Central China has been the major source of European-like swine flu virus transmission in the region since 2010. From there, the strains spread across China and into other Southeast Asian countries like Cambodia.  

“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,” said Yvonne Su, PhD, an associate professor at Duke-NUS and a senior and corresponding author of the study. “Our study revealed the hidden and complex genomic landscape of swine flu virus evolution in Southeast Asia, marking the region as a hotspot for virus diversity and risk of new virus emergence.”

More studies are needed to assess the pandemic threat of these new viruses including how easily they might spread and interact with other human viruses. The Duke-NUS team and their collaborators are currently working on a platform that can identify major swine flu genetic subtypes including avian sequences and monitor their transmission potential. The platform will also be able to assess if pig and human populations have been infected with the influenza subtypes. 

“While swine influenza viruses typically cause mild symptoms in pigs, they pose a pandemic threat to humans, as the human population may lack immunity or have inadequate protection against new strains of swine influenza viruses,” said Gavin Smith, PhD, director of the EID program and one of the study’s authors. “Therefore, systematic surveillance is crucial in early detection and warning of new subtypes or strains.”

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