Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China

Abstract

In 2015, a dengue outbreak with 1,067 reported cases occurred in Xishuangbanna, a city in China that borders Burma and Laos. To characterize the virus, the complete genome sequence was obtained and phylogenetic, mutation, substitution and recombinant analyses were performed. DENV-NS1 positive serum samples were collected from dengue fever patients, and complete genome sequences were obtained through RT-qPCR from these serum samples. Phylogenetic trees were then constructed by maximum likelihood phylogeny test (MEGA7.0), followed by analysis of nucleotide mutation and amino acid substitution. The recombination events among DENVs were also analyzed by RDP4 package. The diversity analysis of secondary structure for translated viral proteins was also performed. The complete genome sequences of four amplified viruses (YNXJ10, YNXJ12, YNXJ13, and YNXJ16) were 10,742, 10,742, 10,741, and 10,734 nucleotides in length, and phylogenetic analysis classified the viruses as cosmopolitan genotype of DENV-2. All viruses were close to DENV Singapore 2013 (KX380828.1) and the DENV China 2013 (KF479233.1). In comparison to DENV-2SS (M29095), the total numbers of base substitutions were 712 nt (YNXJ10), 809 nt (YNXJ12), 772 nt (YNXJ13), and 841 nt (YNXJ16), resulting in 109, 171, 130, and 180 amino acid substitutions in translated regions, respectively. In addition, compared with KX380828.1, there were 44, 105, 64, and 116 amino acid substitutions in translated regions, respectively. The highest mutation rate occurred in the prM region, and the lowest mutation rate occurred in the NS4B region. Most of the recombination events occurred in the prM, E and NS2B/3 regions, which corresponded with the mutation frequency of the related portion. Secondary structure prediction within the 3,391 amino acids of DENV structural proteins showed there were 7 new possible nucleotide-binding sites and 6 lost sites compared to DENV-2SS. In addition, 41 distinct amino acid changes were found in the helix regions, although the distribution of the exposed and buried regions changed only slightly. Our findings may help to understand the intrinsic geographical relatedness of DENV-2 and contributes to the understanding of viral evolution and its impact on the epidemic potential and pathogenicity of DENV.

Keywords: characterization; dengue virus; genome; phylogenetic analysis; recombinant analysis.

Figure 1

Complete genomic phylogenetic analysis of YNXJ10, YNXJ12, YNXJ13, and YNXJ16. Study sequences are labeled in the red circle. The DENV-2 standard M29095 are labeled with red diamond. Others are representative of DENV-2 from diverse geographical origins retrieved from GenBank. Phylogenetic analysis, based on the complete genomes, was conducted using the MEGA software version 7.0 (maximum likelihood phylogeny test) and gamma-distributed rates among sites with 1,000 bootstrap replicates.

Figure 2

Amino acid substitutions in YNXJ10, YNXJ12, YNXJ13, and YNXJ16 compared to the DEN2SS M29095. The first line is M29095, and the second to fifth lines are YNXJ10, YNXJ12, YNXJ13, and YNXJ16, respectively. The labeled numbers represent the amino acid position.

Figure 3

Amino acid substitutions of YNXJ10, YNXJ12, and YNXJ13 compared to the closely-related Singapore in 2013 (KX380828.1). The first line is KX380828.1, and the second to fourth lines are YNXJ10, YNXJ12, YNXJ13, respectively. The labeled numbers represent the amino acid position.

Figure 4

Recombination events in DENV-2. Schematic representation indicates the predictive recombination events among M29095, YNXJ10, YNXJ12, YNXJ13, YNXJ16, KX380828.1, KF479233, JX475906, JN851127, KX372564, KP188555, and EU687243, and analyzed by RDP package. Continuous lines indicate no recombination possibility.

Figure 5

Secondary structure prediction of the structural and non-structural proteins for DEN2SS M29095 and YNXJ10, YNXJ12, YNXJ13, and YNXJ16. The purple dots denote the RNA-binding region, the black dots denote the nucleotide-binding region, the red rhombuses denote the protein-binding region, and the yellow dots denote the DNA-binding region. Red and blue in the first line represent the strand and helix regions, respectively. Yellow and blue in the second line represent the buried and exposed regions, respectively. Purple in the third line indicates the helical transmembrane regions, and green in the fourth line represents the disordered regions. The first map is M29095, and the second, third, fourth, and fifth maps are YNXJ10, YNXJ12, YNXJ13, and YNXJ16.