Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Fri, 07 Dec 2018 13:44:20 Genetic analyses of the fusion protein genes in human parainfluenza virus types 1 and 3 among patients with acute respiratory infections in Eastern Japan from 2011 to 2015 Rika Tsutsui, 1,2 Hiroyuki Tsukagoshi, 3 Koo Nagasawa, 4 Masaki Takahashi, 5 Yuki Matsushima, 6 Akihide Ryo, 7 Makoto Kuroda, 8 Hideki Takami 2 and Hirokazu Kimura 4,7, * Abstract Purpose. To genetically explore the fusion protein gene (F) in human parainfluenza virus type 1 (HPIV1) and type 3 (HPIV3) strains, we analysed them in patients with acute respiratory infections in Eastern Japan from 2011 to 2015. Methodology. We constructed phylogenetic trees based on the HPIV and HPIV3 F gene using the maximum likelihood method and conducted P-distance and selective pressure analyses. We also predicted the linear epitopes of the protein in the prototype strains. Furthermore, we mapped the amino acid substitutions of the proteins. Results. Nineteen strains of HPIV1 and 53 strains of HPIV3 were detected among the clinical acute respiratory infection cases. The phylogenetic trees indicated that the HPIV1 and HPIV3 strains were classified into clusters II and III and cluster C, respectively. The P-distance values of the HPIV1 and HPIV3 F genes were <0.03. Two positive selection sites were inferred in the HPIV1 (aa 8 and aa 10), and one positive selection site was inferred in the HPIV3 (aa 108), but over 10 negative selection sites were inferred. Four epitopes were predicted for the HPIV1 prototype strains, while five epitopes were predicted for the HPIV3 prototype strain. A positive selection site (aa 108) or the HPIV3 F protein was involved in the predicted epitope. Additionally, we found that an amino acid substitution (R73K) in the LC76627 HPIV3 strain presumably may affect the resistance to neutralization by antibodies. Conclusion. The F gene of HPIV1 and HPIV3 was relatively well conserved in the eastern part of Japan during the investigation period. INTRODUCTION Human parainfluenza virus (HPIV) type 1 (HPIV1) and type 3 (HPIV3) belong to the genus Respirovirus and the family Paramyxoviridae. These viruses are responsible for a myriad of acute respiratory infections (ARIs), including the common cold, croup, bronchitis, bronchiolitis and pneumo- nia [1]. Previous epidemiological studies suggest that pri- mary HPIV1 and HPIV3 infections have usually occurred in over 80 % of children by the age of 5 years [2, 3]. Some infants with primary HPIV infection may develop severe clinical symptoms, including pneumonia accompanied by wheezing [4, 5]. Furthermore, HPIV infection, seasonal influenza and human respiratory syncytial virus (HRSV) infections may occur throughout life [4, 6, 7]. Although the epidemiology of HPIV is unclear, previous epidemiological research suggests that HPIV1 and HPIV3 are the dominant Received 28 July 2016; Accepted 9 January 2017 Author affiliations: 1 Aomori Prefecture Public Health and Environment Center, 1-1-1, Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan; 2 Department of Pathologic Analysis, Division of Medical Life Sciences, Hirosaki University Graduate School of Health Sciences, 66-1, Hon-cho, Hirosaki-shi, Aomori 036-8564, Japan; 3 Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan; 4 Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; 5 Research Institute for Environmental Sciences and Public Health of Iwate Prefecture, 1-11-16, Kitaiioka, Morioka-shi, Iwate 020-0857, Japan; 6 Division of Virology, Kawasaki City Institute for Public Health, 3-25-13, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210- 0821, Japan; 7 Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan; 8 Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan. *Correspondence: Hirokazu Kimura, kimhiro@nih.go.jp Keywords: HPIV1; HPIV3; F genes. Abbreviations: ARI, acute respiratory infection; FEL, fixed-effects likelihood; HN, haemagglutinin–neuraminidase; HPIV, human parainfluenza virus; HRSV, human respiratory syncytial virus; IFEL, internal fixed-effects likelihood; ML, maximum likelihood; RT-PCR, reverse transcription PCR; SLAC, single likelihood ancestor counting. Three supplementary tables are available with the online Supplementary Material. RESEARCH ARTICLE Tsutsui et al., Journal of Medical Microbiology 2017;66:160–168 DOI 10.1099/jmm.0.000431 000431 ã 2017 The Authors 160