title: Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013.
abstract: Four serotypes of dengue virus (DENV-1 to DENV-4) and their genotypes are distributed in tropical and subtropical regions. Indonesia has been recently suggested as the origin of some dengue virus genotypes. In Surabaya, the second biggest city of Indonesia, we previously reported a shift of the predominantly circulating serotype from DENV-2 to DENV-1 in November 2008, followed by a genotype shift of DENV-1 from genotype IV (GIV) to genotype I (GI) in September 2009, based on nucleotide sequences in the envelope protein coding region. Since then, GI strains had predominantly circulated until December 2010. In this report, we investigated further DENV-1 transitions in Surabaya during 2011-2013 in order to comprehend dengue dynamics during 2008-2013 in more detail. From January 2011 through December 2011, only GIV strains were isolated, indicating that a genotype shift again took place from GI to GIV. In January 2012, GI and GIV strains started co-circulating, which continued until June 2013. To further investigate this phenomenon, analysis was performed at a clade level. GI and GIV strains isolated in Surabaya formed four and three distinct clades, respectively. Concomitant with co-circulation, new clade strains appeared in both genotypes. In contrast, some previously circulating clades were not isolated during co-circulation, indicating clade shifts. Among our Surabaya isolates, nucleotide and amino acid differences in the E region were, respectively, 1.0-2.3% and 0.2-1.0% for GI isolates and 2.0-6.3% and 0.0-1.8% for GIV isolates. Several characteristic amino acid substitutions in the envelope ectodomain were observed in some clades. After July 2013, DENV-1 strains were not isolated and were replaced with DENV-2. This study showed that continuous shifts of more than one genotype resulted in their co-circulation and subsequent disappearance and suggested the relevance of clade replacement to genotype co-circulation and disappearance in Surabaya.
authors.affiliation: Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia; Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan. Electronic address: tkotaki@people.kobe-u.ac.jp.
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Kotaki
authors.affiliation: Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia; BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand; BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan(1). Electronic address: knmya@biken.osaka-u.ac.jp.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yamanaka
authors.affiliation: Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia. Electronic address: cris_tdc@yahoo.com.
authors.forename: Kris Cahyo
authors.initials: KC
authors.lastname: Mulyatno
authors.affiliation: Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia. Electronic address: sitichurrotin@yahoo.com.
authors.forename: Siti
authors.initials: S
authors.lastname: Churrotin
authors.affiliation: Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia. Electronic address: labiqah_amaliah@yahoo.com.
authors.forename: Amaliah
authors.initials: A
authors.lastname: Labiqah
authors.affiliation: Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia. Electronic address: teguhharisucipto@yahoo.co.id.
authors.forename: Teguh Hari
authors.initials: TH
authors.lastname: Sucipto
authors.affiliation: Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia. Electronic address: tu.soerya_rsab@yahoo.co.id.
authors.forename: Soegeng
authors.initials: S
authors.lastname: Soegijanto
authors.affiliation: Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan; Department of International Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan. Electronic address: mkameoka@port.kobe-u.ac.jp.
authors.forename: Masanori
authors.initials: M
authors.lastname: Kameoka
authors.affiliation: Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan; BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand; BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan(1). Electronic address: ekon@biken.osaka-u.ac.jp.
authors.forename: Eiji
authors.initials: E
authors.lastname: Konishi
mesh_terms: D003715:Dengue / Q000453:epidemiology* / Q000266:history / Q000821:virology*; D003716:Dengue Virus / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D049674:History, 21st Century; D006801:Humans; D007214:Indonesia / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral; D065288:Serogroup; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins
keywords: Clade shift; Co-circulation; Dengue virus; Genotype shift; Indonesia; Phylogeny