A unified phylogenetic classification and nomenclature system for H9 Influenza viruses

Avian influenza viruses of the H9 subtype are distributed worldwide in wild and domestic birds. Although classified as low pathogenicity, strains of the H9N2 subtype have caused significant economic losses in the poultry industry and an increasing number of infections in humans. Since 1998 and as of 20 September 2024, 140 human cases have been reported. Given the inconsistent and multiple H9 lineage nomenclatures available, tracking these viruses has become a challenging task. To overcome such hindrance, the WOAH-FAO Network of Expertise on Animal Influenza (OFFLU) has brought together international experts to develop a standardised classification and naming system. This new framework is based on a comprehensive phylogenetic analysis of all the available (N=10,638) haemagglutinin sequences from H9 viruses collected worldwide. By integrating phylogenetic topology, branch support, genetic distances, epidemiologic information and shared amino acid variants, the system defines three primary lineages (Y, G and B) and 18 first-order (Y1-Y9, G1-G5; B1-B4), 16 second-order (Y2.1-Y2.2, G5.1-G5.7, B4.1-B4.7) and 2 third-order (G5.3.1 and G5.3.2) clades, capturing the genetic diversity and evolutionary dynamics of these viruses. The proposed nomenclature aligns with traditional naming conventions while enhancing clarity and facilitating comparison across studies. A tool to automate and facilitate the lineage and clade assignment of new virus sequences is available online. This unified nomenclature system underpins our understanding of the evolution and spread of H9 AIVs and counters the increasing threat of H9 viruses, thus contributing to both animal and human health security. The presentation will provide the latest data.

Alice Fusaro¹*, Juan Pu²*, Yong Zhou²*, Lu Lu³, Luca Tassoni¹, Yu Lan⁴, Tommy Tsan-Yuk Lam⁵, Zoe Song⁵, Justin Bahl⁶, Jiani Chen⁶, Celia Abolnik⁷, Ian Brown⁸, Charles Todd Davis⁹, Xiangjun Du¹⁰, Shangang Jia2, Erik A. Karlsson¹¹, Dong-Hun Lee¹², Nicola S. Lewis¹³, Hualei Liu¹⁴, Yudong Li², Yoshihiro Sakoda¹⁵, Jianzhong Shi¹⁶, David E Swayne¹⁷, Frank Y.K. Wong¹⁸, Jinfeng Zeng¹⁰, George F. Gao¹⁹, Isabella Monne¹, and Jinhua Liu² ¹Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy ²China Agricultural University, Beijing, China ³University of Edinburgh, Edinburgh, Scotland, UK ⁴Chinese Center for Disease Control and Prevention, Beijing ⁵The University of Hong Kong, Hong Kong, China ⁶University of Georgia, Athens, Georgia, USA ⁷University of Pretoria, South Africa ⁸Pirbright Institute, United Kingdom ⁹Centers for Disease Control and Prevention (CDC), Atlanta ¹⁰Sun Yat-sen University, Guangzhou, China ¹¹Institut Pasteur du Cambodge, Cambodia ¹²Konkuk University, Seoul, Korea ¹³The Francis Crick Institute, London, United Kingdom ¹⁴China Animal Health and Epidemiology Center, Qingdao, Shandong, China ¹⁵Hokkaido University, Sapporo, Hokkaido, Japan ¹⁶Harbin Veterinary Research Institute, CAAS, Harbin, China ¹⁷Birdflu Veterinarian, Watkinsville, Georgia, USA ¹⁸CSIRO Australian Center for Disease Preparedness, Geelong, Victoria, Australia ¹⁹Chinese Academy of Sciences, Beijing, China *contributed equally to this work

Notable outbreaks, field and molecular epidemiology, and surveillance in poultry