A recurring theme in this blog has been the remarkable spread and growing diversity of (first) HPAI H5N1, followed later by a bevy of related H5Nx viruses (H5N2, H5N3, H5N5, H5N6, H5N8, etc.), all of which have diverged into a dizzying number of lineages, clades, subclades, and genotypes around the globe.
Driven, at least in part, by the use of poorly matched poultry vaccines (see EID Journal: Subclinical HPAI In Vaccinated Poultry – China & Virology Journal: Evolution of H5N1 Clade 2.2.1 In Egypt) along with H5's superior ability to reassort with other avian viruses (most notoriously, H9N2), H5N1's family tree continues to expand.
A paper published today by Nature's Scientific Reports takes an extremely detailed look at H5N1's evolution - both in China, and around the world - since it emerged just over 20 years ago.
This research deals primarily with H5N1's evolution between 2004 and 2013 (prior to the emergence of H5N8 & H5N6).
Due to its length and rather technical nature, and since I've only had time to skim the report, I've just reproduced the abstract and some excerpts from the introduction. Follow the link below to read and appreciate the full, open-access, report.
Continual Antigenic Diversification in China Leads to Global Antigenic Complexity of Avian Influenza H5N1 Viruses
Yousong Peng , Xiaodan Li , Hongbo Zhou , Aiping Wu , Libo Dong , Ye Zhang, Rongbao Gao, Hong Bo, Lei Yang, Dayan Wang , Xian Lin, Meilin Jin, Yuelong Shu & Taijiao Jiang
Scientific Reports 7, Article number: 43566 (2017)
Published online: 06 March 2017
The highly pathogenic avian influenza (HPAI) H5N1 virus poses a significant potential threat to human society due to its wide spread and rapid evolution. In this study, we present a comprehensive antigenic map for HPAI H5N1 viruses including 218 newly sequenced isolates from diverse regions of mainland China, by computationally separating almost all HPAI H5N1 viruses into 15 major antigenic clusters (ACs) based on their hemagglutinin sequences.
Phylogenetic analysis showed that 12 of these 15 ACs originated in China in a divergent pattern. Further analysis of the dissemination of HPAI H5N1 virus in China identified that the virus’s geographic expansion was co-incident with a significant divergence in antigenicity. Moreover, this antigenic diversification leads to global antigenic complexity, as typified by the recent HPAI H5N1 spread, showing extensive co-circulation and local persistence. This analysis has highlighted the challenge in H5N1 prevention and control that requires different planning strategies even inside China.
The highly pathogenic avian influenza (HPAI) H5N1 virus has become of global concern since the isolation and identification of the strain A/Goose/Guangdong/1/1996 (GsGD) in Guangdong province of China in 19961,2,3. Since then, the GsGD lineage of HPAI H5N1 virus has spread into many countries and regions in Asia, Europe, Africa and North America, causing epizootic and panzootic infections in birds of many species, killing tens of millions of birds and spurring the culling of hundreds of millions of poultry to halt its spread1,3. Moreover, as of 21 November 2016, sporadic infections of the HPAI H5N1 virus have been responsible for 452 known fatalities among 856 confirmed human infections4.
Given the wide spread of the virus among animals of many species and a relatively high fatality rate in humans following zoonotic infection, the concern of a host jump that would allow human-to-human spread has led to global efforts to prepare for a potential devastating threat5,6.
However, due to its propagation in multiple hosts, diverse H5N1 viral populations exist that comprise of genetic variants, shaped by collected mutations and frequent re-assortments of genes from different strains7,8,9,10,11. This diversity is higher than that observed for seasonal influenza viruses like human H1N1 and H3N212,13. Given this diversity, H5N1 antigenic variants can rapidly evolve to escape host immune surveillance. Moreover, the dissemination of the virus is complicated. Previous studies have shown that the global persistence of the HPAI H5N1 virus results from the interplay between a high capacity to persist in domestic poultry in localized areas, combined with sporadic long-distance introduction events involving migratory birds1,14,15. This makes the battle against the HPAI H5N1 virus quite a challenge.
Because vaccination is currently the most effective way to prevent and control infections by influenza viruses, several variants of the HPAI H5N1 virus have been recommended as vaccine strains for protection of poultry3,16, and it has been proposed that such vaccines should be stockpiled to be prepared for future outbreaks3,17. However, due to the rapid evolution of the virus and its unknown evolutionary patterns, in many cases vaccines for poultry are not well matched to the strains in circulation, and such vaccines could actually drive the evolution of the virus18,19,20,21. Therefore, understanding the evolution of HPAI H5N1, especially the evolution of its antigenicity in a temporal-spatial manner, is critical for efficient prevention and control of the virus. Despite multiple global efforts, the antigenic evolution of HPAI H5N1 is not adequately understood22,23.
(Continue . . . )