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

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.

Molecular characteristics of the VP1 region of enterovirus 71 strains in China

“…The complete VP1 sequence of EV71 strains was compared by Molecular Evolutionary Genetics Analysis (MEGA) version 6.0 [32]. In brief, a phylogenetic tree of the EV71VP1 gene was constructed by the adjacency method (neighbour-joining, N-J) with 1000 bootstrap replications.…”

FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae

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Molecular characterization of the viral structural protein genes in the first outbreak of dengue virus type 2 in Hunan Province, inland China in 2018

“…According to the data provided by the World Health Organization (WHO, the number of cases in the rst quarter of 2018 decreased by 27% compared with the same period of 2017, mainly occurring in countries such as Paraguay, Argentina, Bangladesh, Cambodia, India, Myanmar, Malaysia, Pakistan, Thailand, Yemen, and China, and mainly caused by DENV-1 and DENV-2 serotypes [7]. DF has become a serious public health problem in China, according to data provided by the Chinese Center for Disease Control (CCDC), there were 757,243 people infected in the past 42 years [8,9], largely occurring in Hainan [10], Guangdong [11,12], Zhejiang [13,14], Fujian [15], Taiwan, and Yunnan [16][17][18][19].…”