Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013
© 2014 Elsevier B.V. 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 reporte...
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th-mahidol.329882018-11-09T09:33:57Z Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013 Tomohiro Kotaki Atsushi Yamanaka Kris Cahyo Mulyatno Siti Churrotin Amaliah Labiqah Teguh Hari Sucipto Soegeng Soegijanto Masanori Kameoka Eiji Konishi Universitas Airlangga Kobe University School of Medicine Mahidol University Osaka University Agricultural and Biological Sciences Biochemistry, Genetics and Molecular Biology Immunology and Microbiology Medicine © 2014 Elsevier B.V. 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. 2018-11-09T01:43:57Z 2018-11-09T01:43:57Z 2014-09-09 Article Infection, Genetics and Evolution. Vol.28, (2014), 48-54 10.1016/j.meegid.2014.09.002 15677257 15671348 2-s2.0-84907466746 https://repository.li.mahidol.ac.th/handle/123456789/32988 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84907466746&origin=inward |
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Agricultural and Biological Sciences Biochemistry, Genetics and Molecular Biology Immunology and Microbiology Medicine Tomohiro Kotaki Atsushi Yamanaka Kris Cahyo Mulyatno Siti Churrotin Amaliah Labiqah Teguh Hari Sucipto Soegeng Soegijanto Masanori Kameoka Eiji Konishi Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013 |
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© 2014 Elsevier B.V. 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. |
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Universitas Airlangga |
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Universitas Airlangga Tomohiro Kotaki Atsushi Yamanaka Kris Cahyo Mulyatno Siti Churrotin Amaliah Labiqah Teguh Hari Sucipto Soegeng Soegijanto Masanori Kameoka Eiji Konishi |
format |
Article |
author |
Tomohiro Kotaki Atsushi Yamanaka Kris Cahyo Mulyatno Siti Churrotin Amaliah Labiqah Teguh Hari Sucipto Soegeng Soegijanto Masanori Kameoka Eiji Konishi |
author_sort |
Tomohiro Kotaki |
title |
Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013 |
title_short |
Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013 |
title_full |
Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013 |
title_fullStr |
Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013 |
title_full_unstemmed |
Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013 |
title_sort |
continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in surabaya, indonesia, 2008-2013 |
publishDate |
2018 |
url |
https://repository.li.mahidol.ac.th/handle/123456789/32988 |
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1763496652650315776 |