The evolution and genetic diversity of avian influenza A(H9N2) viruses in Cambodia, 2015 – 2016

Abstract

Low pathogenic A(H9N2) subtype avian influenza viruses (AIVs) were originally detected in Cambodian poultry in 2013, and now circulate endemically. We sequenced and characterised 64 A(H9N2) AIVs detected in Cambodian poultry (chickens and ducks) from January 2015 to May 2016. All A(H9) viruses collected in 2015 and 2016 belonged to a new BJ/94-like h9-4.2.5 sub-lineage that emerged in the region during or after 2013, and was distinct to previously detected Cambodian viruses. Overall, there was a reduction of genetic diversity of H9N2 since 2013, however two genotypes were detected in circulation, P and V, with extensive reassortment between the viruses. Phylogenetic analysis showed a close relationship between A(H9N2) AIVs detected in Cambodian and Vietnamese poultry, highlighting cross-border trade/movement of live, domestic poultry between the countries. Wild birds may also play a role in A(H9N2) transmission in the region. Some genes of the Cambodian isolates frequently clustered with zoonotic A(H7N9), A(H9N2) and A(H10N8) viruses, suggesting a common ecology. Molecular analysis showed 100% of viruses contained the hemagglutinin (HA) Q226L substitution, which favours mammalian receptor type binding. All viruses were susceptible to the neuraminidase inhibitor antivirals; however, 41% contained the matrix (M2) S31N substitution associated with resistance to adamantanes. Overall, Cambodian A(H9N2) viruses possessed factors known to increase zoonotic potential, and therefore their evolution should be continually monitored.

Co-infection of H9N2 Influenza A Virus and Escherichia coli in a BALB/c Mouse Model Aggravates Lung Injury by Synergistic Effects

“…This plays a vital role in the emergence of pandemic strains and increases risk of zoonotic transmission of AIVs from birds to humans. Several zoonotic AIVs such as H5N1, H5N6, H7N9, and H10N8 are all obtained some or all of the "internal" genes from H9N2 AIV (Sun and Liu, 2015;Suttie et al, 2019;Song and Qin, 2020).…”

Redesign and Validation of a Real-Time RT-PCR to Improve Surveillance for Avian Influenza Viruses of the H9 Subtype

“…The absence of notification obligations for H9Nx combined with insufficient surveillance for this subtype in countries with limited resources has led to an overall underestimation of its circulation [4,5]. This gap is worsened by the adverse effect of evolutionary drivers acting on viral diversification [41,65,66], which might result in diagnostic dropout for molecular-based methods. Nowadays, the resolution of such issues largely benefits from the constant increase of sequence data available that permits a timely update of diagnostic methods and improvement of laboratories responsiveness [67].…”

Current situation and control strategies of H9N2 avian influenza in South Korea

“…In Vietnam and Cambodia, Y280 H9N2 AI was reported in 2009 and 2013. Since then, the Y280 lineage of H9N2 AIV has become dominant in poultry, mainly in LBMs [ 38 39 40 ]. The Y280 lineage of H9N2 AIV of the two countries was genetically closely related to the strain in China.…”

“…The Y280 lineage of H9N2 AIV of the two countries was genetically closely related to the strain in China. These viruses may have flowed into adjacent countries locally through active poultry trading [ 19 33 40 ].…”