Singapore Scientists Find New Strains of Influenza A Virus in Pigs

Scientists from Duke-NUS Medical School and their collaborators announced the discovery of several previously unknown strains of swine influenza viruses that have been circulating unnoticed in Cambodian pig populations over the past 15 years, the Duke NUS Medical School in Singapore, reports in a release. 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.

The paper, published in the journal PNAS, encourages systematic surveillance to detect and warn of new strains of viruses early to prevent future pandemics.

Led by scientists Yvonne Su, Gavin Smith and Michael Zeller from the Emerging Infectious Diseases (EID) Programme, the study identified genetically diverse pools of influenza A viruses co-circulating in pigs. Pigs are a key intermediary in the emergence and potential spread of influenza viruses between animals and humans, the researchers explained in the paper, because they provide a suitable environment for the shuffling of gene segments between avian, swine and human hosts, giving rise to new viruses, the release said. International trade and movement have amplified the risks, researchers noted.

“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, marking the region as a hotspot for virus diversity and risk of new virus emergence,” Su said in the release.

Su and her colleagues from Duke-NUS collaborated with counterparts from various institutions, including the National Animal Health and Production Research Institute, Phnom Penh and London School of Hygiene & Tropical Medicine. From March 2020 to July 2022, researchers conducted swine influenza surveillance in 18 pig slaughterhouses in Cambodia. Out of the 4,089 nasal swabs collected from pigs in different districts of four provinces, 72 pigs— around 2% of the pigs—tested positive for influenza A virus.

Scientists identified "nine distinct swine influenza A virus groups," at least seven of which had not been detected for between 2 to 15 years, the release said. These include 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, researcher said.

"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 they were the first to detect this variant, their genomic analysis suggests that it had been circulating in pigs in the region since 2014, highlighting the need for better surveillance," the release said.

The scientists discovered European swine flu viruses had been sporadically introduced into South Central China and Southeast Asia in the early 2000s. Genetic evidence indicates 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, according to the study's results.  

More research is needed to understand the threat of the new viruses, including how they react with human viruses and how easily they can spread. The team is developing a platform that can identify major swine flu genetic subtypes, the release said. Screening will not be limited to swine and human subtypes, but also include avian sequences. It will be able to assess if pig and human populations have been infected with the influenza subtypes. 

“Routine and sustained surveillance is indispensable in identifying new viruses so that their transmission risk can be assessed," said Professor Patrick Tan, senior vice-dean for research at Duke-NUS. "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.”