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.
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).
Infect Genet Evol. 2014 Dec;28:48-54. doi: 10.1016/j.meegid.2014.09.002. Epub 2014 Sep 9.
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.
登革病毒有四个血清型（DENV-1 至 DENV-4）和它们的基因型分布在热带和亚热带地区。印度尼西亚最近被认为是一些登革病毒基因型的起源地。在印度尼西亚第二大城市泗水，我们之前报道了 2008 年 11 月主要流行血清型从 DENV-2 转变为 DENV-1，随后 2009 年 9 月 DENV-1 的基因型从基因型 IV（GIV）转变为基因型 I（GI），这是基于包膜蛋白编码区的核苷酸序列。此后，GI 株一直占主导地位，直到 2010 年 12 月。在本报告中，我们进一步调查了 2011 年至 2013 年期间泗水的 DENV-1 转变情况，以便更详细地了解 2008 年至 2013 年期间的登革热动态。从 2011 年 1 月至 2011 年 12 月，仅分离到 GIV 株，表明 GI 到 GIV 的基因型再次发生转变。2012 年 1 月，GI 和 GIV 株开始共同循环，一直持续到 2013 年 6 月。为了进一步研究这一现象，我们在进化枝水平上进行了分析。在泗水分离到的 GI 和 GIV 株分别形成了四个和三个不同的进化枝。随着共同循环，两种基因型中都出现了新的进化枝株。相反，在共同循环期间没有分离到一些以前循环的进化枝，表明进化枝发生了转变。在我们的泗水分离株中，E 区核苷酸和氨基酸差异分别为 GI 分离株的 1.0-2.3%和 0.2-1.0%，GIV 分离株的 2.0-6.3%和 0.0-1.8%。在一些进化枝中观察到包膜外区的几个特征性氨基酸取代。2013 年 7 月后，未分离到 DENV-1 株，被 DENV-2 取代。本研究表明，一个以上基因型的连续转变导致了它们的共同循环和随后的消失，并提示进化枝取代与基因型的共同循环和消失有关。
