Kocer Lab. on Emerging Viral Diseases


Originated from wild waterfowl, influenza A viruses are capable of infecting variety of host species including human, poultry, horses, swine, cats, dogs, sea and land mammals. Interspecies transmission risk among multiple hosts and the error-prone nature of the virus genome coupled with its segmented structure facilitate the emergence of novel subtypes and strains. Some of these novel variants show altered virulence and transmissibility that might eventually lead to emergence of novel pandemic strains. Therefore, active surveillance studies play a critical role for both public and veterinary health.

**Adopted from Koçer et al (2013) Emergence of influenza viruses and crossing the species barrier. ASM Microbiology Spectrum 1(2) doi: 10.1128/microbiolspec.OH-0010-2012




Our research is focused on the prevalence of influenza A viruses among migratory waterfowl and shorebirds, their molecular characterization and the risk assessment analysis at human-animal interface to understand ecological nature of the disease transmission between different hosts. Our recent studies showed that low pathogenic influenza A viruses (Kocer et al., 2012; Kocer et al., 2015; Zanin et al., 2016) of purely avian origin can cause disease in mammalian models. Moreover, some of these viruses were transmissible between individuals via direct contact or airborne routes of infection (Kocer et al., 2012; Kocer et al., 2015).

Global active influenza surveillance efforts have been carried out in animal and human populations annually to track down the molecular and antigenic changes in the virus genome. Comprehensive risk assessment analyses of individual isolates play a crucial role for taking precautionary actions for outbreak- and pandemic-causing strains. Turkey is located at the heart of the Mediterranean/Black Sea flyway through which billions of migratory birds travel twice a year. In that respect, our study will shed light on the diversity of low pathogenic influenza A viruses in Turkey and the data we gather will connect the dots in the big picture of influenza A evolution.

Our main goal is to perform a comprehensive risk assessment analysis for low pathogenic influenza A viruses of avian-origin in Turkey to assess their disease potential in mammals. This will help us reveal the disease ecology at human-animal interface. To achieve this goal, we aim to (1) determine the prevalence of influenza A viruses among migratory and local waterfowl and shorebirds at Gediz Delta, Izmir, (2) assess the genetic and antigenic changes in virus genomes in currently circulating viruses, and (3) assess their disease potential and transmissibility in mammalian models.

Group Members

Kocer Lab. on Emerging Viral Diseases

Research Group Leader

Zeynep KOÇER
+90 232 299 41 00 (5151)
+9 0 232 299 41 65

İlhan Mert ÖZALP Undergraduate Student  ilhan.ozalp@ibg.edu.tr

Öykü DURAK MSc Student  oyku.durak@ibg.edu.tr

Furkan ÇÖVEN PhD Student  furkan.coven@ibg.edu.tr

Duygu Elif BAYRAM Undergraduate Student  duygu.bayram@ibg.edu.tr

Emre Mert ASAR MSc Student  emremert.asar@ibg.edu.tr

Muhammet Ekin AZBAZDAR PhD Student  ekin.azbazdar@ibg.edu.tr

Feray YILMAZ Researcher  feray.yilmaz@ibg.edu.tr

0 (232) 299 _ _

Mert DİKMENOĞULLARI PhD Student  mert.dikmenogullari@ibg.edu.tr

Former Members

Yavuz MERCAN Research Assistant  yavuz.mercan@ibg.edu.tr

TANSU BIÇAKCIOĞLU PhD Student  tansu.bicakcioglu@msfr.ibg.edu.tr

Mert DİKMENOĞULLARI MSc Student  mert.dikmenogullari@ibg.edu.tr

Fatih DİNÇ Visiting Researcher  fatih.dinc@msfr.ibg.edu.tr

Fatma YAVUZ Undergraduate Student  fatma.yavuz@msfr.ibg.edu.tr

Bulut OKUMUŞOĞLU MSc Student  bulut.okumusoglu@ibg.edu.tr

Zeynep ARZUM Undergraduate Student  zeynep.arzum@ibg.edu.tr

Çağla ÖZDEMİR MSc Student  cagla.ozdemir@ibg.edu.tr

Barış KELEŞ MSc Student  baris.keles@ibg.edu.tr

Atakan DALKILIÇ MSc Student  atakan.dalkilic@msfr.ibg.edu.tr

Gaye ÇOKYÜCEL Undergraduate Student  gaye.cokyucel@msfr.ibg.edu.tr

Selected Publications

Arif E. Cetin, Zeynep A. Kocer, Seda Nur Topkaya, Ziya Ata Yazici. Handheld Plasmonic Biosensor for Virus Detection in Field-Settings. Sensors and Actuators B: Chemical. 2021 October ; 344 : 130301. doi:10.1016/j.snb.2021.130301. Download

Yavuz Mercan, Gladys Atim, Ahmed E. Kayed, M. Ekin Azbazdar, Ahmed Kandeil, Mohamed A. Ali, Adam Rubrum, Pamela McKenzie, Richard J. Webby, Bernard Erima, Fred Wabwire-Mangen, Qouilazoni A. Ukuli, Titus Tugume, Denis K. Byarugaba, Ghazi Kayali, Mariette F. Ducatez, and Zeynep A. Koçer. Molecular Characterization of Closely Related H6N2 Avian Influenza Viruses Isolated from Turkey, Egypt, and Uganda. Viruses. 2021 April ; 13 (4) : 607. doi:10.3390/v13040607. Download

Zanin M, Koçer ZA, Poulson RL, Gabbard JD, Howerth EW, Jones CA, Friedman K, Seiler J, Danner A, Kercher L, McBride R, Paulson JC, Wentworth DE, Krauss S, Tompkins SM, Stallknecht DE, Webster RG. Potential for Low-Pathogenic Avian H7 Influenza A Viruses To Replicate and Cause Disease in a Mammalian Model. Journal of virology. 2017 January ; 91 (3) . doi:10.1128/JVI.01934-16. Download

Koçer ZA, Krauss S, Zanin M, Danner A, Gulati S, Jones JC, Friedman K, Graham A, Forrest H, Seiler J, Air GM, Webster RG. Possible basis for the emergence of H1N1 viruses with pandemic potential from avian hosts.. Emerging microbes & infections. 2015 July ; 4 (7) : e40. doi:10.1038/emi.2015.40. Download

Koçer ZA, Carter R, Wu G, Zhang J, Webster RG. The Genomic Contributions of Avian H1N1 Influenza A Viruses to the Evolution of Mammalian Strains.. PloS one. 2015 July ; 10 (7) : e0133795. doi:10.1371/journal.pone.0133795. Download

Koçer ZA, Fan Y, Huether R, Obenauer J, Webby RJ, Zhang J, Webster RG, Wu G. Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses.. Scientific Reports. 2014 December ; 4 : 7455. doi:10.1038/srep07455. Download

Jones JC, Sonnberg S, Koçer ZA, Shanmuganatham K, Seiler P, Shu Y, Zhu H, Guan Y, Peiris M, Webby RJ, Webster RG. Possible role of songbirds and parakeets in transmission of influenza A(H7N9) virus to humans.. Emerging infectious diseases. 2014 March ; 20 (3) : 380-5. doi:10.3201/eid2003.131271. Download

Koçer ZA, Jones JC, Webster RG. Emergence of Influenza Viruses and Crossing the Species Barrier.. Microbiology spectrum. 2013 December ; 1 (2) . doi:10.1128/microbiolspec.OH-0010-2012. Download

SJCEIRS H9 Working Group.. Assessing the fitness of distinct clades of influenza A (H9N2) viruses.. Emerging microbes & infections. 2013 November ; 2 (11) : e75. doi:10.1038/emi.2013.75. Download

Koçer ZA, Obenauer J, Zaraket H, Zhang J, Rehg JE, Russell CJ, Webster RG. Fecal influenza in mammals: selection of novel variants.. Journal of virology. 2013 November ; 87 (21) : 11476-86. doi:10.1128/JVI.01544-13. Download

Shtarkman YM, Koçer ZA, Edgar R, Veerapaneni RS, D'Elia T, Morris PF, Rogers SO. Subglacial Lake Vostok (Antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya.. PloS one. 2013 July ; 8 (7) : e67221. doi:10.1371/journal.pone.0067221. Download

D'souza NA, Kawarasaki Y, Gantz JD, Lee RE Jr, Beall BF, Shtarkman YM, Koçer ZA, Rogers SO, Wildschutte H, Bullerjahn GS, McKay RM. Diatom assemblages promote ice formation in large lakes.. The ISME journal. 2013 August ; 7 (8) : 1632-40. doi:10.1038/ismej.2013.49. Download

Rogers SO, Shtarkman YM, Koçer ZA, Edgar R, Veerapaneni R, D'Elia T. Ecology of subglacial lake vostok (antarctica), based on metagenomic/metatranscriptomic analyses of accretion ice.. Biology. 2013 March ; 2 (2) : 629-50. doi:10.3390/biology2020629. Download

Koçer ZA, Krauss S, Stallknecht DE, Rehg JE, Webster RG. The potential of avian H1N1 influenza A viruses to replicate and cause disease in mammalian models.. PloS one. 2012 January ; 7 (7) : e41609. doi:10.1371/journal.pone.0041609. Download

ZA Kocer, AG Gozen, S Onde, Z Kaya. Indirect organogenesis from bud explants of Juniperus communis L.: Effects of genotype, gender, sampling time and growth regulator combinations. Dendrobiology. 2011 January ; 66 : 33-40. Download

Total : 15

Selected Book Chapters

One Health: People, Animals and the Environment (2014). Emergence of influenza viruses and crossing the species barrier. ASM Press (American Society for Microbiology).

Total : 1


The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of Inactive Trivalent Flu Vaccine Formulation, Ongoing

DEÜ BAP - Dokuz Eylul University Scientific Research Projects Coordination Unit - RD : Assessing the contribution of genetic variations and reassortment events that occurred in influenza viruses during 2018-2019 and 2019-2020 seasons in Aegean Region, Turkey, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Ülkemizde ve Dünyada Halk Sağlığını En Fazla Tehdit Eden HPV ve Influenza Kaynaklı Enfeksiyonlara Karşı Tanı Kitleri, İlaç Formülasyonları ve Aşı Geliştirilmesi (Turkish), Ongoing

Other National Funding Body - RD : Balb/c Farelerde Perflorooktan Sülfonik Asit ve Perflorooktanoik Asit Maruziyetinin İnterlökin17 Sinyal Yolağı ve İndüklenmiş Akciğer Hasarı Üzerine Etkilerinin İncelenmesi, Ongoing

DEÜ BAP - Dokuz Eylul University Scientific Research Projects Coordination Unit - RD : İklim Değişikliğine Uyum Kapsamında Toprak Sağlığı Araştırmaları Canlı Laboratuvarı (LivingLab), Ongoing


  • 2232 Yurda Dönüş Araştırmacı Dolaşım Programı by TUBITAK, 2018

Academic Memberships

  • Turkish Society of Microbiology, 2018
  • International Society for Influenza and Other Respiratory Diseases, 2013
  • Ecology and Evolutionary Biology Society of Turkey, 2017


Kocer Lab. on Emerging Viral Diseases

Research Group Leader

Zeynep KOÇER
+90 232 299 41 00 (5151)
+9 0 232 299 41 65