{"id":7398,"date":"2026-04-02T10:59:50","date_gmt":"2026-04-02T10:59:50","guid":{"rendered":"https:\/\/www.proefschriftmaken.nl\/portfolio\/hongrui-cui\/"},"modified":"2026-04-02T10:59:58","modified_gmt":"2026-04-02T10:59:58","slug":"hongrui-cui","status":"publish","type":"us_portfolio","link":"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/hongrui-cui\/","title":{"rendered":"Hongrui Cui"},"content":{"rendered":"","protected":false},"excerpt":{"rendered":"","protected":false},"author":8,"featured_media":7401,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"us_portfolio_category":[45],"class_list":["post-7398","us_portfolio","type-us_portfolio","status-publish","has-post-thumbnail","hentry","us_portfolio_category-new-template"],"acf":{"naam_van_het_proefschift":"From transmission to evolution: low pathogenic avian influenza (LPAI) H9N2 evolving under poultry vaccination","samenvatting":"Er is geen Nederlandse samenvatting beschikbaar. De Engelse samenvatting vind je <a href=\"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/hongrui-cui\/\">hier<\/a>.","summary":"Low pathogenic avian influenza virus (LPAIV) H9N2 is one of the three avian influenza viruses (AIVs) primarily threatening poultry industry and human health, together with H5 and H7 subtype AIVs. The H9N2 AIV has become endemic in poultry in many countries all over the world. H9N2 AIVs also serve as gene donors for other subtype influenza viruses that can infect humans. In several Asian countries, such as South Korea, China, Pakistan and Iran, vaccination against H9N2 AIV was permitted to reduce economic losses in the poultry industry. However, surveillance programs initiated after the introduction of vaccination identified the persistence of H9N2 AIV in poultry (especially in chicken in South Korea and China). The aim of the research described in this PhD thesis was to quantify the transmission of LPAIV H9N2 in vaccinated chicken and to identify the characteristics and evolutionary path of the H9N2 AIV currently circulating in vaccinated poultry in China.\n\nIn Chapter 2 the transmission parameters of H9N2 AIV in vaccinated chicken were determined. Therefore, the natural infection and transmission process was mimicked in transmission experiments in chicken vaccinated with the inactivated H9N2 vaccine and challenged with the same H9N2 strain. Using a stochastic SIR model, the estimated reproduction ratio (R) of the H9N2 strain in non-vaccinated and vaccinated chicken was above one. The inactivated H9N2 vaccine was able to provide individual protection by reducing the virus shedding in high-antisera individuals, but could not stop the transmission of the H9N2 AIV in chickens vaccinated with a homologous inactivated virus vaccine.\n\nUnder the observed condition that the transmission continues in the vaccinated poultry population, Chapter 3 aimed to analyze surveillance data from local markets in southern China from 2013 till 2018 to determine how the H9N2 AIV in a partially vaccinated bird population changed over time. This surveillance consisted of 13981 samples from chickens, ducks, geese and pigeons collected at a number of local markets located in nine provinces. This survey revealed that the isolation rate of H9N2 AIV remained high in local markets, although vaccination was initiated in poultry in 1998. The H9N2 subtype was found in approximately 78% (1211 \/1549) of avian influenza-positive samples. Next, the whole genome of 126 H9N2 isolates was determined and used for phylogenetic and antigenic analyses to be able to follow the evolution of H9N2 from 2013 to 2018. The phylogenetic tree showed that current strains are rooted from the BJ94 lineage and evolved into two new subgroups (subgroup II and III) with a large genetic distance from the vaccine strain (F98), which belongs to subgroup I. Based on the antigenic distances comparing to F98 strain in HI assay, isolated strains in the two new subgroups clustered into two new antigenic clusters, respectively. The estimated mutation rate of subgroup III viruses was 6.23\u00d710^-3 substitutions\/site\/year, which was 1.5-fold faster than that of the average H9N2 HA open reading frame (3.95\u00d710^-3 substitutions\/site\/year). New antigenic properties of subgroup III viruses were identified at eleven amino acid positions in the HA protein sequence, which are examples of antigenic drift and potentially change the immunogenic properties of the H9N2 AIVs.\n\nIn Chapter 4 the continuous transmission of the H9N2 strain (the same strain as used in Chapter 2) was simulated via serial in vivo passaging in different hosts, with and without homologous vaccination, and in cell lines. The HA genes from the progeny viruses were sequenced with the Illumina MiSeq platform using Next Generation Sequencing (NGS) to determine evolutionary parameters, e.g. genetic diversity, general substitution frequency, genetic distance, and dN\/dS ratios. In the chickens\u2019 respiratory system, the average substitution frequency was approximately 2.38 \u00d7 10^-3 s\/n\/g (substitutions\/nucleotide\/infection generation), whereas in vitro it was 6.77 \u00d7 10^-4 s\/n\/g. Besides, the genetic distances of progeny viruses to parent virus were significantly lower in vivo than those in vitro. Furthermore, I identified a total of six non-synonymous mutations, which were potential mutations related to antigenic changes due to their location in the encoded HA protein. The methods and observations of the molecular evolution of the H9N2 AIV under continuous selective pressure provide references for evolutionary research on other low pathogenetic RNA viruses.\n\nIn Chapter 5 the characteristics and compatibility of novel viruses that may arise by reassortment of human and avian influenza viruses were analyzed. Reassortant viruses were generated by reverse genetics in which genes of a human H1N1 virus (A\/WSN\/1933) were replaced by genes of an avian H9N2 virus (A\/chicken\/Jiangsu\/A2O9P\/2011). Both the HA and NA (Neuraminidase) genes in combination with one of the genes involved in the viral ribonucleoprotein (RNP) complex (either PB2, PB1, PA or NP) were replaced. Reassortant viruses were able to replicate in canine MDCK and chicken DFN cells, as well as in mice. In particular, for the reassortant virus with an avian PB1 gene, an enhanced virulence for mice was measured by increased body weight loss after infection. In addition, the avian PB1 gene increased the polymerase activity of the RNP complex in luciferase reporter assays. With the NGS data of reassortant viruses passaged for five generations, a higher substitution rate for the PB1-reassortant virus in mice was estimated. The higher polymerase activity and the increased mutation frequency suggests that the avian PB1 gene drives the evolution and adaptation of novel reassortant viruses to the human host. Therefore, surveillance for infections with H9N2 viruses and the emergence of novel reassortant viruses in humans is important for pandemic preparedness.\n\nIn Chapter 6, I have integrated the discoveries and conclusions from the earlier chapters and discussed the relationships between weak herd immunity protection and the transmission of H9N2 in host populations. I further elaborated on the evolutionary changes occurring in H9N2 AIV due to: 1) selection by immunogenic pressure from vaccination and 2) reassortment with human strains (for instance, H1N1), and compared my data with previous research. Last but not least, I discussed the advantages and disadvantages of the methods used in this research. The identified molecular changes and evolutionary patterns provide a reference for vaccine development and vaccination strategies in poultry.","auteur":"Hongrui Cui","auteur_slug":"hongrui-cui","publicatiedatum":"12 november 2021","taal":"EN","url_flipbook":"https:\/\/ebook.proefschriftmaken.nl\/ebook\/hongruicui?iframe=true","url_download_pdf":"","url_epub":"","ordernummer":"FTP-202604021057","isbn":"978-94-6395-995-","doi_nummer":"","naam_universiteit":"Wageningen University","afbeeldingen":7402,"naam_student:":"","binnenwerk":"","universiteit":"Wageningen University","cover":"","afwerking":"","cover_afwerking":"","design":""},"_links":{"self":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/7398","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio"}],"about":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/types\/us_portfolio"}],"author":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/comments?post=7398"}],"version-history":[{"count":1,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/7398\/revisions"}],"predecessor-version":[{"id":7399,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/7398\/revisions\/7399"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media\/7401"}],"wp:attachment":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media?parent=7398"}],"wp:term":[{"taxonomy":"us_portfolio_category","embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio_category?post=7398"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}