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  1. Biologics Research Projects

Facilitating Influenza Virus Vaccine Production by Optimizing Vaccine Strains

Principal Investigator: Zhiping Ye, MD, PhD
Office / Division / Lab: OVRR / DVP / LPRVD

General Overview

Each year, about 38,000 people in the United States die from influenza-related infections. Influenza infections can cause a variety of serious complications, including bacterial pneumonia infections, and worsening of congestive heart failure, asthma, and other medical conditions. In addition, pandemic (worldwide epidemic) influenza outbreaks pose a global threat to public health. One of the most effective strategies for preventing seasonal and pandemic influenza infections is vaccination.

Influenza vaccines are designed to trigger immune responses against critical proteins called HA and NA, which are located on the surface of influenza viruses. However, new variants of influenza viruses carrying modified types of HA and NA appear each season. Since existing influenza vaccines would not be able to trigger effective immune responses to these new variants, new vaccines must be made to protect against an influenza outbreak caused by this virus.

The need for newer vaccines is made more urgent by the appearance of strains of influenza virus that have the potential to cause pandemics (worldwide epidemics), as in the case of H5N1 (avian influenza) and the 2009 H1N1 (swine flu) virus. Moreover, production of new vaccines for pandemic viruses is slowed by the difficulty in manufacturing these products.

The majority of vaccines used to control annual influenza epidemics in the United States are manufactured using chicken eggs that are infected with live influenza virus. These viruses are harvested, inactivated, and used to make vaccines. Most wild-type viruses (i.e., the form that appears in nature, not grown in the laboratory) that carry the right HA and NA proteins to make vaccines do not grow in large enough quantities in eggs to support vaccine production. Yet, laboratory strains that grow in large quantities don't contain the exact version of each year's influenza virus HA and NA proteins. Therefore, they are not useful for producing that season's influenza vaccine. In addition, manufacturing influenza vaccines using these pandemic strains raises additional concerns, such as the exposure of vaccine production staff to the live virus and accidental release of the virus into the environment.

To solve these problems, we modify influenza virus genes in order to produce viruses that grow in large enough quantities to make vaccines and carry the exact version of HA and NA proteins carried by that season's influenza virus. In addition, we modify the viruses so they cannot cause disease, reducing the risk to laboratory workers.

We are concentrating our work in these areas on both licensed inactivated influenza virus vaccines and new influenza vaccines that are under development and in clinical trials. This research uses state-of-the-art molecular biology techniques to, 1) improve production and safe handling during production of pandemic influenza vaccine; and 2) facilitate development of new vaccines for both seasonal and pandemic influenza virus by optimizing the production of vaccine proteins by viral genes.

Our research directly impacts the safety, effectiveness, and availability of both seasonal and pandemic influenza vaccines.

Scientific Overview

Our research program addresses several critical and unaddressed research needs of the influenza vaccine program in the U.S. We are using state-of-the-art molecular biology to: 1) ensure sufficient vaccine supply by discovering molecular mechanisms of influenza virus replication and developing techniques that enhance production of influenza vaccine; and 2) modify specific influenza virus gene(s) in order to generate attenuated live viruses that can be used to produce an attenuated internal gene donor virus for use in preparing pandemic influenza virus vaccines.

There are three types of licensed influenza vaccines in U.S.; inactivated, live attenuated and recombinant vaccines. Currently the inactivated influenza viruses are the major sources for immunization of general population against influenza virus infection in the US. Each year manufacturers and federal agencies struggle to identify influenza viruses to be used as vaccine strains, i.e., circulating viruses with appropriate antigenic characteristics and growth properties sufficient to support production of over 100 million inactivated seasonal influenza vaccine doses for use in the US.

Most wild-type viruses with appropriate antigenic characteristics do not grow to sufficiently high titer in eggs or cells to support vaccine production, and "high growth" laboratory strains do not contain the appropriate antigenic properties in surface proteins (e.g., HA, NA) of the current year's circulating wild type strains. Thus, genetic mixtures of the wild type and laboratory strains are created, termed "high growth reassortants," which contain the growth and immunogenic properties necessary for efficient preparation of commercial quantities of effective new inactivated influenza virus vaccines each year. Understanding how influenza virus proteins are control replication is crucial in generating high growth viruses by modifying virus genes.

Although multiple genes of influenza virus contribute to viral replication and attenuation/virulence properties, we started with the investigation of the roles of matrix and NA genes of influenza A virus in viral replication, attenuation and virulence in vitro and in vivo. Our laboratory has been working on the matrix (M) gene for many years and accumulating experience and knowledge on studying the function of viral proteins, especially the matrix 1 (M1) protein of influenza A virus and genetic manipulation of the matrix gene of influenza A virus.

Our research program addresses several critical research needs of the influenza vaccine program by using state- of-the-art molecular biology techniques, such as reverse genetics, to identify and analyze the functional domains of influenza virus protein(s).

Based on our work in this area, we can now modify viruses such as virulent wild-type avian influenza virus to be less pathogenic, or endow a low-yield virus with high-growth capability suitable for preparation of inactivated influenza vaccines.


Sci Rep 2017 Jul 12;7(1):5258
Different repeat annual influenza vaccinations improve the antibody response to drifted influenza strains.
Plant EP, Fredell LJ, Hatcher BA, Li X, Chiang MJ, Kosikova M, Xie H, Zoueva O, Cost AA, Ye Z, Cooper MJ

PLoS One 2017 Jun 29;12(6):e0179939
Automated interpretation of influenza hemagglutination inhibition (HAI) assays: is plate tilting necessary?
Wilson G, Ye Z, Xie H, Vahl S, Dawson E, Rowlen K

Methods Mol Biol 2017;1602:205-38
Reverse genetics of influenza B viruses.
Nogales A, Perez DR, Santos J, Finch C, Martínez-Sobrido L

Emerg Microbes Infect 2017 Apr 12;6(4):e17
Pathogenicity and transmission of a swine influenza A(H6N6) virus.
Sun H, Kaplan BS, Guan M, Zhang G, Ye J, Long LP, Blackmon S, Yang CK, Chiang MJ, Xie H, Zhao N, Cooley J, Smith DF, Liao M, Cardona C, Li L, Wang GP, Webby R, Wan XF

PLoS One 2016 Sep 22;11(9):e0163175
Sensitive detection and simultaneous discrimination of influenza A and B viruses in nasopharyngeal swabs in a single assay using next-generation sequencing-based diagnostics.
Zhao J, Liu J, Vemula SV, Lin C, Tan J, Ragupathy V, Wang X, Mbondji-Wonje C, Ye Z, Landry ML, Hewlett I

Sci Rep 2016 Jun 30;6:29110
Iron overload by superparamagnetic iron oxide nanoparticles is a high risk factor in cirrhosis by a systems toxicology assessment.
Wei Y, Zhao M, Yang F, Mao Y, Xie H, Zhou Q

Influenza Other Respir Viruses 2016 Mar;10(2):134-40
A novel approach for preparation of the antisera reagent for potency determination of inactivated H7N9 influenza vaccines.
Schmeisser F, Jing X, Joshi M, Vasudevan A, Soto J, Li X, Choudhary A, Baichoo N, Resnick J, Ye Z, McCormick W, Weir JP

Viruses 2016 Feb 2;8(2):33
Pandemic influenza A (H1N1) virus infection increases apoptosis and HIV-1 replication in HIV-1 infected Jurkat cells.
Wang X, Tan J, Biswas S, Zhao J, Devadas K, Ye Z, Hewlett I

Sci Rep 2015 Oct 16;5:15279
H3N2 mismatch of 2014-15 northern hemisphere influenza vaccines and head-to-head comparison between human and ferret antisera derived antigenic maps.
Xie H, Wan XF, Ye Z, Plant EP, Zhao Y, Xu Y, Li X, Finch C, Zhao N, Kawano T, Zoueva O, Chiang MJ, Jing X, Lin Z, Zhang A, Zhu Y

J Virol 2015 Oct 14;90(1):117-28
Comparative efficacy of monoclonal antibodies that bind to different epitopes of the 2009 pandemic H1N1 influenza virus neuraminidase.
Jiang L, Fantoni G, Couzens L, Gao J, Plant E, Ye Z, Eichelberger MC, Wan H

J Gen Virol 2015 Apr;96(Pt 4):752-5
Chimeric NA and mutant PB1 gene constellation improves growth and yield of H5N1 vaccine candidate virus.
Plant EP, Ye Z

MBio 2014 Dec 12;5(6):e02430-14
Influenza gain-of-function experiments: their role in vaccine virus recommendation and pandemic preparedness.
Schultz-Cherry S, Webby RJ, Webster RG, Kelso A, Barr IG, McCauley JW, Daniels RS, Wang D, Shu Y, Nobusawa E, Itamura S, Tashiro M, Harada Y, Watanabe S, Odagiri T, Ye Z, Grohmann G, Harvey R, Engelhardt O, Smith D, Hamilton K, Claes F, Dauphin G

PLoS One 2014 Oct 8;9(10):e109510
Crystal structures of influenza A virus matrix protein M1: variations on a theme.
Safo MK, Musayev FN, Mosier PD, Zhou Q, Xie H, Desai UR

Vaccine 2014 Aug 20;32(37):4713-25
WHO recommendations for the viruses used in the 2013-2014 Northern Hemisphere influenza vaccine: Epidemiology, antigenic and genetic characteristics of influenza A(H1N1)pdm09, A(H3N2) and B influenza viruses collected from October 2012 to January 2013.
Barr IG, Russell C, Besselaar TG, Cox NJ, Daniels RS, Donis R, Engelhardt OG, Grohmann G, Itamura S, Kelso A, McCauley J, Odagiri T, Schultz-Cherry S, Shu Y, Smith D, Tashiro M, Wang D, Webby R, Xu X, Ye Z, Zhang W, Writing Committee of the World Health Organization Consultation on Northern Hemisphere Influenza Vaccine Composition for 2013–2014

BMC Infect Dis 2014 Apr 8;14:192
Highly pathogenic avian influenza A virus (H5N1) can be transmitted in ferrets by transfusion.
Wang X, Tan J, Zhao J, Ye Z, Hewlett I

Microbes Infect 2014 Mar;16(3):178-86
Novel pandemic influenza A (H1N1) virus infection modulates apoptotic pathways that impact its replication in A549 cells.
Wang X, Tan J, Zoueva O, Zhao J, Ye Z, Hewlett I

J Proteome Res 2013 Aug 2;12(8):3707-20
Comparative Glycomics Analysis of Influenza Hemagglutinin (H5N1) Produced in Vaccine Relevant Cell Platforms.
An Y, Rininger JA, Jarvis DL, Jing X, Ye Z, Aumiller JJ, Eichelberger M, Cipollo JF

Vaccine 2013 Aug 28;31(38):4091-7
Assessment of viral replication in eggs and HA protein yield of pre-pandemic H5N1 candidate vaccine viruses.
Jing X, Soto J, Gao Y, Phy K, Ye Z

Vaccine 2013 Jul 11;31(32):3209-21
Strengthening the influenza vaccine virus selection and development process: Outcome of the 2nd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at the Centre International de Conferences (CICG) Geneva, Switzerland, 7 to 9 December 2011.
Al Busaidy S, Al-Gohary A, Ampofo WK, Bekshin Z, Cerkaoui I, Claes F, Cox NJ, Cracknell W, Cui L, Paiva TM, de Wit M, Diep LDT, Donabedian A, Donis R, Dormitzer PR, Eichelberger M, El Kholy N, Engelhardt O, Engelmann HB, Eropkin MY, Fasce R, Fontaine L, Ghadakchi HF, Ghedin E, Giovanni MY, Golding H, da Silva HC, Gysin R, Hamilton K, Hauge SH, Hay A, Huang S, Hungnes O, Ibrahim SSS, Immamura T, Inglis SC, Kadjo H, Katz J, Kawaoka Y, Kelso A, Khan MI, Kilander A, Klimov A, Kreij K, Kusmiaty D, Linde A, Liu MT, Lupulescu E, Mai LQ, Martinez VR, McCauley J, Meyer Q, Modi R, Mohammadi AA, Mokhtari-Azad T, Mol E, Music T, Nelson K, Neuhaus E, Neumeier ER, Niang MN, Odagiri T, Peiris M, Pohlmann A, Popow-Kraupp T, Trilar KP, Rabadan R, Rambaut A, Robertson JS, Rolls C, Sampurno OD, Savy V, Sawanpanyaltert P, Schmid G, Schweiger B, Shapira S, Shinde V, Shu Y, Siqueira M, Smith D, Spiro D, Stevens J, Takizawa K, Tashiro M, Taylor B, Thomas Y, Tsai T, Van der Werf S, Venter M, Waddell AL, Wan XF, Wang D, Webby R, Weir JP, Wentworth D, Wickramasinghe G, Ye ZP, Zambon M, Ziegler T

Influenza Other Respir Viruses 2013 May;7(3):480-90
Neutralizing and protective epitopes of the 2009 pandemic influenza H1N1 hemagglutinin.
Schmeisser F, Friedman R, Besho J, Lugovtsev V, Soto J, Wang W, Weiss C, Williams O, Xie H, Ye Z, Weir JP

J Virol 2013 Jan;87(1):345-53
The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal.
Xie H, Lin Z, Mosier PD, Desai UR, Gao Y

Vaccine 2012 Dec 17;31(1):207-12
Mutations to A/Puerto Rico/8/34 PB1 gene improves seasonal reassortant influenza A virus growth kinetics.
Plant EP, Liu TM, Xie H, Ye Z

Viruses 2012 Nov 9;4(11):3012-9
Rapid detection and differentiation of swine-origin influenza A virus (H1N1/2009) from other seasonal influenza A viruses.
Zhao J, Wang X, Ragupathy V, Zhang P, Tang W, Ye Z, Eichelberger M, Hewlett I

Vaccine 2012 Oct 5;30(45):6461-71
WHO recommendations for the viruses to be used in the 2012 Southern Hemisphere Influenza Vaccine: epidemiology, antigenic and genetic characteristics of influenza A(H1N1)pdm09, A(H3N2) and B influenza viruses collected from February to September 2011.
Klimov AI, Garten R, Russell C, Barr IG, Besselaar TG, Daniels R, Engelhardt OG, Grohmann G, Itamura S, Kelso A, McCauley J, Odagiri T, Smith D, Tashiro M, Xu X, Webby R, Wang D, Ye Z, Yuelong S, Zhang W, Cox N

Vaccine 2012 Jun 13;30(28):4144-52
Increased hemagglutinin content in a reassortant 2009 pandemic H1N1 influenza virus with chimeric neuraminidase containing donor A/Puerto Rico/8/34 virus transmembrane and stalk domains.
Jing XH, Phy K, Li X, Ye Z

Clin Infect Dis 2011 Dec;53(12):1179-87
Revisiting the 1976 "swine flu" vaccine clinical trials: cross-reactive hemagglutinin and neuraminidase antibodies and their role in protection against the 2009 H1N1 pandemic virus in mice.
Xie H, Li X, Gao J, Lin Z, Jing X, Plant E, Zoueva O, Eichelberger MC, Ye Z

BMC Infect Dis 2011 Dec 22;11:354
Stability and infectivity of novel pandemic influenza A (H1N1) virus in blood-derived matrices under different storage conditions.
Wang X, Zoueva O, Zhao J, Ye Z, Hewlett I

PLoS One 2011;6(12):e29553
Intranasal immunization of the combined lipooligosaccharide conjugates protects mice from the challenges with three serotypes of Moraxella catarrhalis.
Ren D, Xie H, Zhang W, Hassan F, Petralia RS, Yu S, Lim DJ, Gu XX

J Clin Microbiol 2011 Oct;49(10):3531-6
Extent of Antigenic Cross-Reactivity among Highly Pathogenic H5N1 Influenza Viruses.
Ducatez MF, Cai Z, Peiris M, Guan Y, Ye Z, Wan XF, Webby RJ

PLoS Pathog 2011 Jun;7(6):e1002081
Cross-neutralizing antibodies to pandemic 2009 H1N1 and recent seasonal H1N1 influenza A strains influenced by a mutation in hemagglutinin subunit 2.
Wang W, Anderson CM, De Feo CJ, Zhuang M, Yang H, Vassell R, Xie H, Ye Z, Scott D, Weiss CD

Vaccine 2011 Feb 17;29(9):1836-43
The development of vaccine viruses against pandemic A(H1N1) influenza.
Robertson JS, Nicolson C, Harvey R, Johnson R, Major D, Guilfoyle K, Roseby S, Newman R, Collin R, Wallis C, Engelhardt OG, Wood JM, Le J, Manojkumar R, Pokorny BA, Silverman J, Devis R, Bucher D, Verity E, Agius C, Camuglia S, Ong C, Rockman S, Curtis A, Schoofs P, Zoueva O, Xie H, Li X, Lin Z, Ye Z, Chen LM, O'Neill E, Balish A, Lipatov AS, Guo Z, Isakova I, Davis CT, Rivailler P, Gustin KM, Belser JA, Maines TR, Tumpey TM, Xu X, Katz JM, Klimov A, Cox NJ, Donis RO

PLoS One 2011 Jan 31;6(1):e16650
Immunogenicity and cross-reactivity of 2009-2010 inactivated seasonal influenza vaccine in US adults and elderly.
Xie H, Jing X, Li X, Lin Z, Plant E, Zoueva O, Yang H, Ye Z

Virology 2010 Nov 25;407(2):374-80
A mutation in the receptor binding site enhances infectivity of 2009 H1N1 influenza hemagglutinin pseudotypes without changing antigenicity.
Wang W, Castelán-Vega JA, Jiménez-Alberto A, Vassell R, Ye Z, Weiss CD

BMC Biotechnol 2010 Oct 13;10:74
Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay.
Zhao J, Tang S, Storhoff J, Marla S, Bao YP, Wang X, Wong EY, Ragupathy V, Ye Z, Hewlett IK

PLoS One 2010 Aug 12;5(8):e12099
Viremia associated with fatal outcomes in ferrets infected with avian H5N1 influenza virus.
Wang X, Zhao J, Tang S, Ye Z, Hewlett I

Appl Environ Microbiol 2010 May;76(9):2718-28
Evaluation of Mycoplasma inactivation during production of biologics: egg-based viral vaccines as a model.
David SA, Volokhov DV, Zhiping Y, Chizhikov V

J Virol Methods 2010 May;165(2):305-10
Characterization of lentiviral pseudotypes with influenza H5N1 hemagglutinin and their performance in neutralization assays.
Wang W, Xie H, Ye Z, Vassell R, Weiss CD

J Infect Dis 2009 Dec 15;200(12):1874-83
A live attenuated H1N1 M1 mutant provides broad cross-protection against influenza A viruses, including highly pathogenic A/Vietnam/1203/2004, in mice.
Xie H, Liu TM, Lu X, Wu Z, Belser JA, Katz JM, Tumpey TM, Ye Z

J Virol 2009 May;83(9):4023-9
Optimizing viral protein yield of influenza virus strain A/Vietnam/1203/2004 by modification of the neuraminidase gene.
Adamo JE, Liu T, Schmeisser F, Ye Z

J Virol Methods 2008 Nov;153(2):111-9
Establishment of retroviral pseudotypes with influenza hemagglutinins from H1, H3, and H5 subtypes for sensitive and specific detection of neutralizing antibodies.
Wang W, Butler EN, Veguilla V, Vassell R, Thomas JT, Moos M, Ye Z, Hancock K, Weiss CD

J Neurovirol 2008 Apr;14(2):136-42
Genetic contributions to influenza virus attenuation in the rat brain.
Qi L, Carbone KM, Ye Z, Liu T, Ovanesov M, Pletnikov M, Sauder C, Rubin SA

Vaccine 2007 Nov 1;25(44):7649-55
Evaluating the vaccine potential of an influenza A viral hemagglutinin and matrix double insertion DNA plasmid.
Xie H, Liu T, Chen H, Huang X, Ye Z

Virology 2007 Sep 1;365(2):315-23
Generation of the influenza B viruses with improved growth phenotype by substitution of specific amino acids of hemagglutinin.
Lugovtsev VY, Vodeiko GM, Strupczewski CM, Ye Z, Levandowski RA

Emerg Infect Dis 2007 Mar;13(3):426-35
Matrix protein 2 vaccination and protection against influenza viruses, including subtype H5N1.
Tompkins SM, Zhao ZS, Lo CY, Misplon JA, Liu T, Ye Z, Hogan RJ, Wu Z, Benton KA, Tumpey TM, Epstein SL

Retrovirology 2005 Dec 21;2:80
Targeted infection of HIV-1 Env expressing cells by HIV(CD4/CXCR4) vectors reveals a potential new rationale for HIV-1 mediated down-modulation of CD4.
Ye Z, Harmison GG, Ragheb JA, Schubert MJ Virol 2005 Feb;79(3):1918-23
Attenuating Mutations of the Matrix Gene of Influenza A/WSN/33 Virus.
Liu T, Ye Z

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