Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity
© Liao et al.; licensee BioMed Central Ltd. 2013
Received: 14 March 2013
Accepted: 3 June 2013
Published: 11 June 2013
The World Health Organization (WHO) organizes consultations in February and September of each year, spearheaded by an advisory group of experts to analyze influenza surveillance data generated by the WHO Global Influenza Surveillance and Response System (GISRS). The purpose of these consultations is to recommend the composition on influenza virus vaccines for the northern and southern hemispheres, respectively. The latest news of influenza viruses is made available to the public and updated on the WHO website. Although WHO discloses the manner in which it has made the recommendation, usually by considering epidemiological and clinical information to analyze the antigenic and genetic characteristics of seasonal influenza viruses, most individuals do not possess an understanding of antigenic drift and when it occurs.
We have constructed a web server, named Fluctrl, and implemented a pipeline whereby HA sequence data is downloaded from the Influenza Virus Resource at NCBI along with their isolation information including isolation year and location, which are parsed and managed in MySQL database. By analyzing the frequency of each amino acid residue of the HA1 domain expressed by the viruses on annual basis, users are able to obtain evolutionary dynamics of human influenza viruses corresponding with epidemics. Users are able to upload and analyze their HA1 sequences for generating evolutionary dynamics. In addition, a distribution of amino acid residues at a particular site is represented geographically to trace the location where antigenic variants are seeded.
Fluctrl is constructed for monitoring the antigenic evolution of human influenza A viruses. This tool is intended to inform the general public how and when influenza viruses evade the human body's immunity. Furthermore, leveraging the geographic information, the original locations of emerging influenza viruses can be traced. Fluctrl is freely accessible at http://sb.nhri.org.tw/fluctrl.
Human influenza viruses are the principal viral respiratory pathogens that cause significant human morbidity and mortality. They rapid spread around the globe, resulting in influenza epidemics and outbreaks. Vaccination is the principal way to prevent influenza and to reduce the impact of epidemics. To evade the immune response, the spike-like proteins hemagglutinin (HA) and nuramenidase (NA) on the surface of the viruses continuously mutate, which result in antigenic drift; such an event warrants a vaccine update. Unfortunately, the timely and accurate identification of vaccine strains is challenging. Therefore, WHO organizes consultations to recommend the composition of influenza virus vaccines based on influenza surveillance data; the latest news is published on its website. Although WHO discloses how to make the recommendation on vaccine composition by analyzing the antigenic and genetic characteristics of seasonal influenza viruses, most individuals do not readily understand antigenic drift and when it occurs.
Amino acid substitutions of the HA were deemed to be positively selected to reduce antibody binding and therefore were supposed to be responsible for driving antigenic drift. A great body of studies have made efforts in identifying positively selected sites for understanding antigenic evolution of human influenza A viruses [1–4]. We have previously demonstrated that the evolutionary dynamics of the positively-selected surface sites could be applied for monitoring human influenza epidemics . The method we proposed is straightforward, nevertheless, it has not been utilized in any system for influenza surveillance. We therefore construct a web server named Fluctrl that implements a pipeline whereby human influenza HA viral sequences were downloaded from the NCBI database and analyzed. Users are able to freely access Fluctrl to obtain the dynamical evolutionary patterns of human influenza viruses and to trace the original locations of emerging influenza viruses.
HA protein sequences of human influenza A/H1N1, A/H1N1pdm09 and H3N2 viruses were downloaded separately from the NCBI Influenza Virus Resource . For each subtype of human influenza A virus, sequences were aligned against the reference sequences, A/Puerto Rico/8/34 (YP_163735), A/California/07/2009 (ACP41953) and A/Hong Kong/1/1968 (ACC66318), respectively, by utilizing MUSCLE . Duplicate sequences and those with length shorter than 267 amino acid residues were subsequently discarded. Strain information, including location and isolation year, were parsed from strain name. The aligned amino acid sequences along with the strain information were then stored in a MySQL database. The SQL tables are available for download in the website.
HA1 evolutionary dynamics
Sequences isolated from the same year were clustered into a single group to obtain the frequency of amino acid residues at each amino acid site. For every amino acid site, if one amino acid residue reached a frequency of ≥ 0.7 during a given year, it was assigned as a single “major amino acid residue (MAA)” corresponding to that year . Alternatively, multiple MAAs were assigned if more than one residue, whose frequency resided between 0.2 and 0.7, was discovered. The assembled MAAs throughout the isolation years examined represent an evolutionary dynamics perspective of human influenza viruses. The varied and white colors were used to label single and multiple MAAs, respectively. Therefore, an evolutionary dynamic pattern of HA1 proteins was clearly demonstrated. Fluctrl also allows users to upload and analyze HA1 sequences. An additional file describes the instructions for users [see Additional file 1].
In an attempt to visualize the evolution of influenza viruses in the context of geography and time, we firstly employed Google Geocoding API version 3 to search the latitude and longitude coordinates of the event locations, then implemented Google Map API version 3 in Fluctrl to generate a graphical distribution of the influenza viruses within a specified period.
HA1 evolutionary changes reveal positively-selected sites
In our previous studies, we have identified the refined positively-selected sites by comparing avian and human influenza viruses. In addition, we have demonstrated that the evolutionary dynamics of the positively-selected sites could be applied for monitoring human influenza epidemics . In an effort to escape antibody neutralization, HA proteins are expected to continuously mutate. Therefore, substitutes in an unexplored site are likely to occur and proliferate among the population, which warrants updating the list of the positively-selected sites. In this study, we have designed and built an interactive web server (called Fluctrl hereafter) enabling users to discover the positively-selected sites, thereby allowing them to monitor human influenza epidemics.
Simultaneous substitutions suggest an emerging epidemic and explain the recommended vaccinations
Influenza viruses continuously mutate as a method of escaping from antibody neutralization. Nevertheless, not all sites of HA1 were rendered selective advantages to persist in human populations. We hence identified the positively-selected sites as the sites that undergo substitutions and subsequently proliferate in the populations [1, 2]. With this definition, it is not surprising that substitutions in such sites correlate with antigenic drift events, because the substitutes implicate the ability of the virus to escape from the existing herd immunity. In our previous studies, we have substantiated that three simultaneous substitutes could retrospectively reflect human influenza epidemics . Since this approach is quite straightforward and easily implemented, we have analyzed the current sequence data from the NCBI Influenza Virus Resource and constructed a web server (Fluctrl) to suggest vaccine strain replacement and facilitate its selection. Although this web server mainly relies on publicly-available sequences and thus might not forecast antigenic drifts, it explains how influenza viruses evolve and why WHO recommends new vaccine formulations when a new epidemic begins to emerge. The following paragraph provides an example that explains Fluctrl’s functionality.
A northern hemisphere vaccine recommendation meeting was held by WHO in Feb. 2012 in order to make a recommended vaccine formulation containing A/California/7/2009 (H1N1)pdm09-like virus, A/Victoria/361/2011(H3N2)-like virus and B/Wisconsin/1/2010-like virus for use in the 2012–2013 influenza season. It declared that the majority of recent influenza A/H3N2 viruses were antigenically and genetically distinguishable from the vaccine virus A/Perth/16/2009 and were more closely related to A/Victoria/361/2011-like reference viruses based on influenza activity between Sep. 2009 and Jan. 2012. Accordingly, the experts suggested replacing A/Perth/16/2009 with A/Victoria/316/2011 for the new northern hemisphere season. Later, the same vaccine formulation was recommended for use in the 2013 southern hemisphere influenza season during a WHO meeting in Sep. 2012. WHO issues its recommendations and announcements publicly on its website, however, most individuals do not understand the differences between the new and former circulating viruses. In the page entitled “Evolutionary dynamics” on Fluctrl, we select “Type the specific sites” to 1–329 for the all the HA1 sites on the H3N2 virus and check the box labeled “filter with the avian conserved sites” to generate an evolutionary dynamics perspective of human influenza A/H3N2 viruses during the years between 2009 and 2012. The result exhibits the changes exhibited by human influenza A/H3N2 viruses, i.e. the substitutions of A198AS and V223IV on the HA1 domain during 2011 and 2012. The differences during this period may partly explain the genetic (or even antigenic) changes from A/Perth/16/2009-like to A/Victoria/361/2011-like viruses.
Geographic and temporal information show the original location of antigenic variants
Surveillance within E-SE Asia facilitates vaccine strain selection
The primary purpose of Fluctrl is to provide a user-friendly interface for individuals concerned about flu activity in order to understand the manner in which and the time when influenza viruses escape from human immunity. The web server is designed not only for influenza surveillance, but also for instructional value. With a greater amount of influenza sequences made publicly available (and promptly released), Fluctrl is a compelling platform for the detection and monitoring of human influenza variants and thus can be used to alert the general public to emerging epidemics.
Availability and requirements
Project name: Fluctrl
Project home page: http://sb.nhri.org.tw/fluctrl
Operation systems: Platform independent
Programming language: Java
This work was supported by National Health Research Institutes intramural funding (PH-102-PP-05) and the National Science Council, Taiwan (NSC 102-2319-B-400-001).
- Shih AC, Hsiao TC, Ho MS, Li WH: Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci USA. 2007, 104: 6283-6288. 10.1073/pnas.0701396104.PubMedPubMed CentralView ArticleGoogle Scholar
- Liao YC, Chen FC, Hsiung CA: Contrasting substitution patterns between HA proteins of avian and human influenza viruses: implication for monitoring human influenza epidemics. Vaccine. 2010, 28: 7890-7896. 10.1016/j.vaccine.2010.09.071.PubMedView ArticleGoogle Scholar
- Li W, Shi W, Qiao H, Ho SY, Luo A, Zhang Y, Zhu C: Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virol J. 2011, 8: 183-10.1186/1743-422X-8-183.PubMedPubMed CentralView ArticleGoogle Scholar
- Tusche C, Steinbruck L, McHardy AC: Detecting patches of protein sites of influenza A viruses under positive selection. Mol Biol Evol. 2012, 29: 2063-2071. 10.1093/molbev/mss095.PubMedPubMed CentralView ArticleGoogle Scholar
- Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D: The influenza virus resource at the National Center for Biotechnology Information. J Virol. 2008, 82: 596-601. 10.1128/JVI.02005-07.PubMedPubMed CentralView ArticleGoogle Scholar
- Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797. 10.1093/nar/gkh340.PubMedPubMed CentralView ArticleGoogle Scholar
- Bush RM, Fitch WM, Bender CA, Cox NJ: Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol Biol Evol. 1999, 16: 1457-1465. 10.1093/oxfordjournals.molbev.a026057.PubMedView ArticleGoogle Scholar
- Suzuki Y, Gojobori T: A method for detecting positive selection at single amino acid sites. Mol Biol Evol. 1999, 16: 1315-1328. 10.1093/oxfordjournals.molbev.a026042.PubMedView ArticleGoogle Scholar
- Plotkin JB, Dushoff J: Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. Proc Natl Acad Sci USA. 2003, 100: 7152-7157. 10.1073/pnas.1132114100.PubMedPubMed CentralView ArticleGoogle Scholar
- Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, Brilliant L: Detecting influenza epidemics using search engine query data. Nature. 2009, 457: 1012-1014. 10.1038/nature07634.PubMedView ArticleGoogle Scholar
- Yang JR, Lin CH, Chen CJ, Liu JL, Huang YP, Kuo CY, Yao CY, Hsu LC, Lo J, Ho YL, et al: A new antigenic variant of human influenza A (H3N2) virus isolated from airport and community surveillance in Taiwan in early 2009. Virus Res. 2010, 151: 33-38. 10.1016/j.virusres.2010.03.011.PubMedView ArticleGoogle Scholar
- Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, Gregory V, Gust ID, Hampson AW, Hay AJ, Hurt AC, et al: The global circulation of seasonal influenza A (H3N2) viruses. Science. 2008, 320: 340-346. 10.1126/science.1154137.PubMedView ArticleGoogle Scholar
- Du X, Dong L, Lan Y, Peng Y, Wu A, Zhang Y, Huang W, Wang D, Wang M, Guo Y, et al: Mapping of H3N2 influenza antigenic evolution in China reveals a strategy for vaccine strain recommendation. Nat Commun. 2012, 3: 709-PubMedView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.