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. 2011;6(11):e27322.
doi: 10.1371/journal.pone.0027322. Epub 2011 Nov 7.

Displacement of the predominant dengue virus from type 2 to type 1 with a subsequent genotype shift from IV to I in Surabaya, Indonesia 2008-2010

Atsushi Yamanaka  1 , Kris C Mulyatno, Helen Susilowati, Eryk Hendrianto, Amor P Ginting, Dian D Sary, Fedik A Rantam, Soegeng Soegijanto, Eiji Konishi
Affiliations

Displacement of the predominant dengue virus from type 2 to type 1 with a subsequent genotype shift from IV to I in Surabaya, Indonesia 2008-2010

Atsushi Yamanaka et al. PLoS One. 2011.

Abstract

Indonesia has annually experienced approximately 100,000 reported cases of dengue fever (DF) and dengue hemorrhagic fever (DHF) in recent years. However, epidemiological surveys of dengue viruses (DENVs) have been limited in this country. In Surabaya, the second largest city, a single report indicated that dengue virus type 2 (DENV2) was the predominant circulating virus in 2003-2005. We conducted three surveys in Surabaya during: (i) April 2007, (ii) June 2008 to April 2009, and (iii) September 2009 to December 2010. A total of 231 isolates were obtained from dengue patients and examined by PCR typing. We found that the predominant DENV shifted from type 2 to type 1 between October and November 2008. Another survey using wild-caught mosquitoes in April 2009 confirmed that dengue type 1 virus (DENV1) was the predominant type in Surabaya. Phylogenetic analyses of the nucleotide sequences of the complete envelope gene of DENV1 indicated that all 22 selected isolates in the second survey belonged to genotype IV and all 17 selected isolates in the third survey belonged to genotype I, indicating a genotype shift between April and September 2009. Furthermore, in December 2010, isolates were grouped into a new clade of DENV1 genotype I, suggesting clade shift between September and December 2010. According to statistics reported by the Surabaya Health Office, the proportion of DHF cases among the total number of dengue cases increased about three times after the type shift in 2008. In addition, the subsequent genotype shift in 2009 was associated with the increased number of total dengue cases. This indicates the need for continuous surveillance of circulating viruses to predict the risk of DHF and DF.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. The monthly number of dengue isolates.
The number of isolates is indicated monthly for each dengue virus (DENV) type between June 2008 and December 2010. Solid red bar, number of DENV1 genotype IV isolates; hatched red bar, number of DENV1 genotype I isolates; blue bar, DENV2 isolates; green bar, DENV4 isolates. In this study period, DENV3 was not isolated.
Figure 2
Figure 2. Phylogenetic tree based on the E gene sequence of DENV1 strains constructed using the neighbor-joining method.
The GenBank accession number is described in parentheses, followed by the country and year in which the strains were isolated (in quotations). ‘NA’ indicates that the information was not available. The representative Surabaya isolates are indicated in red, purple, blue or green letters. For strains isolated from other areas available in the GenBank database, only selected strains which had been used in previous reports are shown , , . Strains that showed the highest BLAST score against the Surabaya isolates are enclosed individually with red, blue or green squares. Major bootstrap values are shown at nodes, and the scale bar represents 0.01 nucleotide changes per site. Asterisks indicate isolates D1/SBY19/09, D1/SBY6.1Mos/09, D1/SBY82/10 and D1/SBY87/10, which represent the 15, 2, 11 and 2 Surabaya isolates, respectively, with an identical nucleotide sequence in the E region.
Figure 3
Figure 3. Maximum clade credibility (MCC) tree of the E coding region of DENV1.
The representative Surabaya isolates are indicated in red, purple, blue or green letters, and strains with the highest BLAST score are enclosed individually with red, blue or green squares. Horizontal branches are drawn to a scale of the estimated year of divergence with tip times reflecting sampling date (year). The arrow on the horizontal line indicates the year of the first outbreak in Indonesia. The coalescent times of some key nodes, as well as their 95% HPD values, are shown. Posterior probability values of ≥0.9 are shown above nodes. The tree is automatically rooted under the assumption of a molecular clock. The Surabaya isolates are indicated in boldface and underlined. Strains that showed the highest BLAST score against the Surabaya isolates are underlined. Squares with blue and red backgrounds indicate the preliminarily designated Indonesia and China groups, respectively.
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