Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 May 8:8:148.
doi: 10.3389/fcimb.2018.00148. eCollection 2018.

Complete Genome Characterization of the 2017 Dengue Outbreak in Xishuangbanna, a Border City of China, Burma and Laos

Songjiao Wen  1   2   3 , Dehong Ma  4 , Yao Lin  1   2   3 , Lihua Li  4 , Shan Hong  1   2   5 , Xiaoman Li  6 , Xiaodan Wang  1   2   3 , Juemin Xi  1   2   3 , Lijuan Qiu  6 , Yue Pan  1   2   3 , Junying Chen  1   2   3 , Xiyun Shan  4 , Qiangming Sun  1   2   3
Affiliations

Complete Genome Characterization of the 2017 Dengue Outbreak in Xishuangbanna, a Border City of China, Burma and Laos

Songjiao Wen et al. Front Cell Infect Microbiol. .

Abstract

A dengue outbreak abruptly occurred at the border of China, Myanmar, and Laos in June 2017. By November 3rd 2017, 1184 infected individuals were confirmed as NS1-positivein Xishuangbanna, a city located at the border. To verify the causative agent, complete genome information was obtained through PCR and sequencing based on the viral RNAs extracted from patient samples. Phylogenetic trees were constructed by the maximum likelihood method (MEGA 6.0). Nucleotide and amino acid substitutions were analyzed by BioEdit, followed by RNA secondary structure prediction of untranslated regions (UTRs) and protein secondary structure prediction in coding sequences (CDSs). Strains YN2, YN17741, and YN176272 were isolated from local residents. Stains MY21 and MY22 were isolated from Burmese travelers. The complete genome sequences of the five isolates were 10,735 nucleotides in length. Phylogenetic analysis classified all five isolates as genotype I of DENV-1, while isolates of local residents and Burmese travelers belonged to different branches. The three locally isolates were most similar to the Dongguan strain in 2011, and the other two isolates from Burmese travelers were most similar to the Laos strain in 2008. Twenty-four amino acid substitutions were important in eight evolutionary tree branches. Comparison with DENV-1SS revealed 658 base substitutions in the local isolates, except for two mutations exclusive to YN17741, resulting in 87 synonymous mutations. Compared with the local isolates, 52 amino acid mutations occurred in the CDS of two isolates from Burmese travelers. Comparing MY21 with MY22, 17 amino acid mutations were observed, all these mutations occurred in the CDS of non-structured proteins (two in NS1, 10 in NS2, two in NS3, three in NS5). Secondary structure prediction revealed 46 changes in the potential nucleotide and protein binding sites of the CDSs in local isolates. RNA secondary structure prediction also showed base changes in the 3'UTR of local isolates, leading to two significant changes in the RNA secondary structure. To our knowledge, this study is the first complete genome analysis of isolates from the 2017 dengue outbreak that occurred at the border areas of China, Burma, and Laos.

Keywords: RNA secondary structure; complete genome; dengue outbreak; phylogenetic trees; protein secondary structure.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Phylogenetic tree data. (A) Phylogenetic tree of DENV-1 epidemic strains in Xishuangbanna, Yunnan, China, in 2017. The phylogenetic tree was constructed with the Maximum Likelihood method with 1,000 bootstrap values. • isolates from Xishuangbanna, Yunnan, China; ▴ standard strains of DENV1-4 serotypes. (B) Relationship between evolutionary tree branching and amino acid mutations in genotype I of DENV-1.
Figure 2
Figure 2
Identification of variations among genotype I of DENV-1. Variations are presented in accordance with their location in the viral genome. The various colors indicate the different variations described in Figure 1B.
Figure 3
Figure 3
Amino acid mutations between CDS of locally isolated strains and two strains isolated from Myanmar (2017).
Figure 4
Figure 4
Amino acid mutations between CDS of Dongguan strain (2011) and Yunnan strains (2017).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Alvarez D. E., De Lella Ezcurra A. L., Fucito S., Gamarnik A. V. (2005). Role of RNA structures present at the 3'UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 339, 200–212. 10.1016/j.virol.2005.06.009 - DOI - PubMed
    1. Añez G., Volkova E., Jiang Z., Heisey D. A. R., Chancey C., Fares R. C. G. (2017). Collaborative study to establish World Health Organization international reference reagents for dengue virus Types 1 to 4 RNA for use in nucleic acid testing. Transfusion 57, 1977–1987. 10.1111/trf.14130 - DOI - PubMed
    1. Bryant J. E., Vasconcelos P. F., Rijnbrand R. C., Mutebi J. P., Higgs S., Barrett A. D. (2005). Size heterogeneity in the 3' noncoding region of South American isolates of yellow fever virus. J. Virol. 79, 3807–3821. 10.1128/JVI.79.6.3807-3821.2005 - DOI - PMC - PubMed
    1. Butrapet S., Huang C. Y., Pierro D. J., Bhamarapravati N., Gubler D. J., Kinney R. M. (2000). Attenuation markers of a candidate dengue type 2 vaccine virus, strain 16681 (PDK-53), are defined by mutations in the 5' noncoding region and nonstructural proteins 1 and 3. J. Virol. 74, 3011–3019. 10.1128/JVI.74.7.3011-3019.2000 - DOI - PMC - PubMed
    1. Chen B., Liu Q. (2015). Dengue fever in China. Lancet 385, 1621–1622. 10.1016/S0140-6736(15)60793-0 - DOI - PubMed

Publication types