Primer Design for Sequencing DENV-4 to be used in Molecular Epidemiology of Dengue Viruses in Jakarta

• Main Authors: Nadia Tita Indriasti, Beti Ernawati Dewi
• Format: Article
• Language: English
• Published: Universitas Indonesia 2014-08-01
• Series: Journal Kedokteran Indonesia
• Online Access: http://journal.ui.ac.id/index.php/eJKI/article/view/4010
• ISSN: 2338-1426; 2338-6037

<div><strong><em>Abstract</em></strong></div><div><em>This study is aimed to recognize the characteristic of dengue patients in Jakarta, to identify the genotype of dengue virus serotype 4 (DENV-4) in Jakarta and to design primer for DENV-4. This cross-sectional study involved 100 patients with positive result of NS-1 examination. This research was conducted at the Department of Microbiology, Faculty of Medicine, Universitas Indonesia. The specimen were collected from March until December 2010, while the virus sequencing was perfomed between January and October 2011. The patients were categorized based on RT-PCR confirmation results, gender, age and domicile. The identification of serotipe of dengue viruses is determined by RT-PCR examination. The genotipe of DENV-4 is determined by sequencing of whole genome of DENV-4 by using Genetyx software. The primer design for DENV-4 was carried out by using Primer Designer program. The highest prevalence of DF was found among patients of 14-20 years old (41,4%) and those who lived in East Jakarta. The ratio of DF between male and female is not significantly different. &nbsp;The predominant serotype circulating in Jakarta was DENV 2. The genotype of serotype 4 circulating in Jakarta in 2010-2011 was type II. Primer design for dengue serotype 4 had a size of 406-692 base pairs, no hairpin developed, dimer formation was within two and Tm difference ranged from 0 to 8C.</em></div><div><em><strong>Keywords:</strong> DHF, serotype 4, genotype, primer</em></div><div><br /></div><div><strong>Abstrak</strong></div><div>Penelitian ini bertujuan untuk mengidentifikasi karakteristik pasien demam berdarah dengue di Jakarta dan mengidentifikasi genotipe virus dengue serotype 4 (DENV 4) di Jakarta serta membuat desain primer DENV-4. Penelitian dilakukan secara potong lintang pada 100 pasien dengan hasil pemeriksaan NS-1 positif. Penelitian dilakukan di Departemen Mikrobiologi, Faculty of Medicine, Universitas Indonesia. Pengambilan data dilakukan pada bulan Maret-December 2010, virus sequencing dilakukan pada bulan Januari-Oktober 2011. Sampel dibagi berdasarkan hasil konfirmasi RT-PCR, jenis kelamin, usia dan tempat tinggal. Identifikasi virus dengue dan penentuan serotipe menggunakan RT-PCR. Penentuan genotipe DENV-4 dilakukan dengan melakukan sekuensing whole genome DENV-4 menggunakan software Genetyx. Pembuatan primer DENV-4</div><div>dilakukan dengan program Primer Designer. Prevalensi demam berdarah dengue tertinggi terdapat pada usia 14-20 tahun (41,4%) dan pada pasien yang bertempat tinggal di Jakarta Timur. Ratio penderita perempuan dan laki-laki tidak menunjukkan perbedaan bermakna. Genotipe DENV-4 yang bersirkulasi di Jakarta adalah tipe II. Desain primer DENV-4 memiliki ukuran 406-692 pasang basa, tidak ada hairpin, formasi dimer dengan dua dan Tm yang berbeda yang berkisar antara 0-8 C.</div><div><strong>Kata Kunci: </strong>DBD, serotipe 4, genotipe, primer</div>