Molecular epidemiology of human G2P[4] rotaviruses in Taiwan, 2004–2011 Fang-Tzy Wu a,b,1 , Krisztián Bányai c,1 , Baoming Jiang d , Ching-Yi Wu a , Hsieh-Cheng Chen a , Enik } o Fehér c , Yhu-Chering Huang e , Jen-Shiou Lin f , Fu-Chen Huang g , Chao A. Hsiung h , Jason C. Huang b,i,⇑ , Ho-Sheng Wu a,⇑ a Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan b Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming University, Taipei, Taiwan c Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary d Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA e Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan f Division of Pediatric Infectious Disease and Department of Laboratory Medicine, Changhua Christian Hospital, Changhua, Taiwan g Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan h Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan i AIDS Prevention and Research Center, National Yang-Ming University, Taipei, Taiwan article info Article history: Received 25 June 2014 Received in revised form 23 September 2014 Accepted 24 September 2014 Available online 2 October 2014 Keywords: Surveillance Genotype Phylogenetic analysis Lineage abstract In 2006, two rotavirus vaccines (Rotarix and RotaTeq) became available on the private market in Taiwan. Although vaccine coverage is currently low, molecular surveillance of rotavirus strains can provide per- tinent information for evaluation of the potential impact of vaccine introduction and infection control. During January 2008–December 2011, children aged <5 years hospitalized with acute gastroenteritis were enrolled from sentinel surveillance hospitals in three geographic areas of Taiwan. Fecal specimens collected from enrolled patients were tested for rotavirus by enzyme immunoassay and reverse trans- criptase-polymerase chain reaction. For genotyping, gene specific primer sets were used to amplify and sequence the genes encoding the neutralization antigens, VP7 and VP4. The resulting sequences were then subjected to phylogenetic analysis. In brief, a total of 4,052 fecal specimens were tested and 742 (18%) samples were positive for rotavirus. The annual range of rotavirus positive specimens varied between 16% and 20.7%. Of all specimens, genotype G1P[8] (63.3%) was the predominant strain, followed by G2P[4] (12.5%), G3P[8] (11.7%), and G9P[8] (5.1%). Uncommon strains were also detected in low per- centages. We observed that the rotavirus positivity rate steadily decreased from 21% to 16% during 2008– 2010, then slightly increased to 20% in 2011, when an increase in the number of G2P[4] cases was observed. Sequence and phylogenetic analysis was carried out to help understand any potential changes of G2P[4] rotaviruses over time. A number of G2P[4] strains collected between 2004 and 2011 were ana- lyzed in detail and our analyses showed marked genetic and antigenic variability in the VP7 and VP4 genes. The Taiwanese strains could be classified into two major G2 VP7 lineages (IV and V) and two major P[4] VP4 lineages (IV and V) and several minor sublineages within lineage IV. Lineage V within both G2 and P[4] represented newly recognized genetic variants of the respective genotypes. The distribution of individual combinations of the G2 and P[4] (sub)lineages showed some temporal variations. This study provides further evidence for the great genetic diversity among G2P[4] strains and helps understand the epidemiological trends of these strains among children in Taiwan. Ó 2014 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.meegid.2014.09.033 1567-1348/Ó 2014 Elsevier B.V. All rights reserved. ⇑ Corresponding authors. Address: No. 161, Kun-Yang Street, Taipei, Taiwan. Tel.: +886 2 27850513x821 (H. -S. Wu). Address: No. 155, Sec. 2, Linong Street, Taipei, 112 Taiwan (ROC). Tel.: +886 2 2826 7148 (J. -C. Huang). E-mail addresses: fang@cdc.gov.tw (F.-T. Wu), jchuang2@ym.edu.tw (J.C. Huang), wuhs@cdc.gov.tw (H.-S. Wu). 1 These authors have equally contributed to this work. Infection, Genetics and Evolution 28 (2014) 530–536 Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid