A pig farm. Credit: Kallerna
Key points:
- Examining 4,089 nasal swabs from pigs in 19 slaughterhouses, scientists identified nine distinct swine influenza A virus groups.
- At least seven viruses had not been detected for between 2 to 15 years.
- The authors say their study highlights the need for better, routine and sustained surveillance to prevent future pandemics.
Scientists from Duke-NUS Medical School and their collaborators have uncovered several previously unknown strains of swine flu viruses that have been circulating unnoticed in Cambodian pig populations over the past 15 years. The strains include viruses that have been passed by humans to pigs, as well as some with genes originating from as far as North America.
Given what transpired during the COVID-19 pandemic, the study authors say their paper makes the case for systematic surveillance to detect and warn of new strains of viruses early to prevent future pandemics.
For the study, published in PNAS, researchers collected 4,089 nasal swabs from pigs in 18 pig slaughterhouses in Cambodia from Narch 2020 to July 2022. Among these, 72 pigs—or around 2%—tested positive for influenza A virus.
The scientists identified nine distinct swine influenza A virus groups, at least seven of which had not been detected for between 2 to 15 years. Among these are multiple H3 lineages that had been passed by humans to pigs, circulating undetected for about 10 years; as well as the H1N1 subtype, which was predominant and likely derived from human origins dating back to the 2009 pandemic.
Two seasonal viruses were detected in pigs from Kandal, Phnom Penh, and Takeo provinces, and likely originated from Thailand. The team also isolated a new swine European H1N2 variant—that originally came from birds—with North American genes in Cambodia. While the authors were the first to detect this variant, their genomic analysis suggests that it had been circulating in pigs in the region since 2014.
The researchers also found that European swine flu viruses had been sporadically introduced into South Central China and Southeast Asia in the early 2000s. Genetic evidence indicated South Central China has served as the major source of European-like swine flu virus transmission in the region since around 2010, with the viruses subsequently spreading more widely across China and Southeast Asian countries, such as Cambodia.
While further studies are needed to understand if any of the detected viruses could become a pandemic threat, the study highlights the need for better, routine and sustained surveillance. To that end, the team is currently developing a platform that can identify major swine flu genetic subtypes. The screening will not include swine and human subtypes, as well as avian sequences. With the set up, they will be able to assess if pig and human populations have been infected with the influenza subtypes.