In a recent study published in PNAS, researchers explored the evolutionary dynamics of swine influenza A virus (swIAV) populations in Asia’s southern and eastern regions.
Study: The genomic landscape of swine influenza A viruses in Southeast Asia. Image Credit: LiyaGraphics/Shutterstock.com
Background
Swine in Southeast Asia is a primary source of pandemic influenza A viruses (IAVs), causing zoonotic and reverse-zoonotic transmission. Global swine production and trade increase the chance of swine IAV transmission.
Nevertheless, the dearth of systematic surveillance infrastructure hinders identifying emerging pathogens in pigs and their potential for zoonotic spillover. Effective surveillance is required to uncover emerging viral strains, but understanding the swIAV genomic landscape stays limited.
Concerning the study
In the current longitudinal study, researchers performed IAV surveillance on 18 slaughterhouse pigs in Cambodia’s 4 provinces (Kandal, Kampong Speu, Takeo, and Phnom Penh) between March 2020 and July 2022.
A complete of 4,089 nasopharyngeal swabs from pigs were taken to point the long-unnoticed circulation and establishment of several swIAV viruses in Cambodia, including human H1N1/pdm09 and H3N2 viruses transmitted to swine by reverse zoonosis.
The team extracted swIAV ribonucleic acid (RNA) from the samples, and IAV identification was achieved using quantitative reverse-transcription polymerase chain response (RT-qPCR).
Subsequently, positive samples were submitted to next-generation sequencing (SGS), which measured amplified complementary deoxyribonucleic acid (cDNA). Pooled DNA libraries were created and sequenced.
For the evolutionary study, accessible worldwide H1N1 influenza A virus genomes (till September 8, 2022) obtained from swine and human hosts were retrieved from the worldwide Initiative on Sharing All Influenza Data (GISAID) database and the National Center for Biotechnology Information (NCBI) GenBank.
The genetic datasets were subsampled to 766 H3 and 1,008 H1 sequences. Maximum likelihood phylogenies were generated for all genetic segments of swIAV from Cambodia, including hemagglutinin (HA) and neuraminidase (NA) genes, polymerase PB (PB), and polymerase PA (PA), matrix protein (MP), non-structural protein (NS), and nucleoprotein (NP).
In total, 986, 773, 1,009, 766, 915, 923, 924, 927, 927, and 927 segments of the N1-NA, N2-NA, H1-HA, H3-HA, PA, PB1, PB2, MP, NS, and NP, respectively, were analyzed. Phylogeographic evaluation was used to analyze the geographical patterns of European avian-like (EA)-swine H1-type viral strains.
The team downloaded all H1 sequences of EA-swine viral organisms from the GISAID and NCBI databases (between 2005 and December 20, 2022), and seven.0 distinct nation-states (Southeastern Asia, Europe, northern China, eastern China, western China, northeastern China, and southern and central China) were coded.
Results
Swine IAVs were detected and characterised in slaughterhouse pigs within the southern and eastern regions of Asia, with 72 pigs (2.0%) being IAV-positive by RT-PCR. Kandal province had a better positivity rate of IAV (4.50%) than other provinces.
The study found that China’s southern and central regions were the dominant sources of swine lineages spread to other parts of China and Asia’s south and eastern areas.
The researchers also discovered nine unique swIAV viruses in Cambodia that split from their nearest progenitors between 2.0 and 15 billion years ago, indicating tremendous undiscovered genomic diversity.
A comparable era of cryptic swIAV circulation occurred for many years preceding the H1N1/2009 outbreak. The findings revealed a posh genomic landscape of swIAV in Southeast Asia, shaped by the repeated introduction and reassortment of virus lineages.
The researchers also unraveled the parental origin and gene constellations of the EA H1N2 reassortant viruses that likely emerged in late 2014, roughly seven years before their initial detection in Cambodia in 2021.
The novel EA H1N2 virus had a definite genetic constellation comprising a swine-origin EA G4-like H1-HA, an N2-HA originating from human viruses, and internal genes from the triple-reassortant internal gene (TRIG) viruses.
The swine IAV strains circulating within the southern and eastern regions of Asia acquired reassorted genetic segments from multiple geographical origins, facilitated by the intercontinental and intracontinental spread of previously segregated swIAV lineages.
Multiple instances of EA N1 coupled with CS H1 were found. The H1N1/pdm09 viral strain was found to be circulating enzootically in Cambodian swine herds. The team also identified several reverse zoonotic H3 strains amongst Cambodian pigs that were circulating unidentified for nearly ten years.
The findings emphasized the importance of early identification of novel swIAV lineages. They highlighted concerns surrounding the inter-regional spread of swIAVs as a key driver within the emergence of recent virus lineages, especially within the southern and eastern regions of Asia, where surveillance is sporadic.
The researchers found multiple instances of CS H1 coupled with EA N1 and evidence of world intermixing of previously distinct virus populations.
Conclusions
Overall, the study findings highlighted the genomic landscape of swIAVs in Southeast Asia. The outcomes showed an EA H1N2 reassortant genotype in Asia, with China being the leading source of EA swine viruses.
The study revealed nine distinct swIAV HA and NA lineages cocirculating in Cambodian pig populations, highlighting the complex evolutionary processes within the region.
As swine-rearing activities develop, pig surveillance must turn out to be more frequent and consistent to find novel viruses and assess their zoonotic risk.
By monitoring viruses with zoonotic transmission potential, more efficient and continuous surveillance approaches, reminiscent of metagenomic monitoring and automatic analytical instruments, can enhance animal health and assist in human health.
Further research is required to know the pandemic threat of EA G4-like H1N2 viruses.