Molecular Characterization and Viral Origin of the 2015 Dengue Outbreak in Xishuangbanna, Yunnan, China

Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome

Mosquitoes are important vector hosts for numerous viral pathogens and harbor a large number of mosquito-specific viruses as well as human-infecting viruses. Previous studies have mainly focused on the discovery of mosquito viruses, and our understanding of major ecological factors associated with virome structure in mosquitoes remains limited. We utilized metatranscriptomic sequencing to characterize the viromes of five mosquito species sampled across eight locations in Yunnan Province, China. This revealed the presence of 52 viral species, of which 19 were novel, belonging to 15 viral families/clades. Of particular note was Culex hepacivirus 1, clustering within the avian clade of hepaciviruses. Notably, both the viromic diversity and abundance of Aedes genus mosquitoes were significantly higher than those of the Culex genus, while Aedes albopictus mosquitoes harbored a higher diversity than Aedes aegypti mosquitoes. Our findings thus point to discernible differences in viromic structure between mosquito genera and even between mosquito species within the same genus. Importantly, such differences were not attributable to differences in sampling between geographical location. Our study also revealed the ubiquitous presence of the endosymbiont bacterium Wolbachia, with the genetic diversity and abundance also varying between mosquito species. In conclusion, our results suggested that the mosquito host species play an important role in shaping the virome's structure. IMPORTANCE This study revealed the huge capability of mosquitoes in harboring a rich diversity of RNA viruses, although relevant studies have characterized the intensively unparalleled diversity of RNA viruses previously. Furthermore, our findings showed discernible differences not only in viromic structure between mosquito genera and even between mosquito species within the same genus but also in the genetic diversity and abundance of Wolbachia between different mosquito populations. These findings emphasize the importance of host genetic background in shaping the virome composition of mosquitoes.

The whole-genome sequencing of prevalent DENV-1 strains during the largest dengue virus outbreak in Xishuangbanna Dai autonomous prefecture in 2019

In 2019, a serious dengue virus (DENV) infection broke out in the Xishuangbanna Dai Autonomous Prefecture, China. Therefore, we conducted a molecular epidemiological analysis in people that contracted DENV serotype 1 (DENV-1) during this year. We analyzed the molecular epidemiology of six DENV-1 epidemic strains in 2019 by full-length genome sequencing, amino acid mutation site analysis, evolutionary tree analysis, and recombination site comparison analysis. Through the analysis of amino acid mutation sites, it was found that DENV-1 strain (MW386867) was different from the other five epidemic DENV-1 strains in Xishuangbanna in 2019. MW386867 had unique mutation sites at six loci. The six epidemic DENV-1 strains in Xishuangbanna in 2019 were divided into two clusters. MW386867 was highly similar to the MG679800 (Myanmar 2017), MG679801 (Myanmar 2017), and KC172834 (Laos 2008), and the other five strains were highly similar to JQ045660 (Vietnam 2011), FJ176780 (GuangDong 2006). Genetic recombination analysis revealed that there was no recombination signal in the six epidemic DENV-1 strains in Xishuangbanna in 2019. We speculate that the DENV-1 epidemic in 2019 has a co-epidemic of local strains and cross-border strains.

Complete genome characterization of the 2018 dengue outbreak in Hunan, an inland province in central South China

In 2018, a small-scale dengue epidemic broke out in Hunan Province, an inland province in central South China, with 172 people infected. To verify the causative agent, complete genome information was obtained by PCR and sequencing based on the viral RNAs extracted from patient serum samples. Mutation and evolutionary analysis were performed by MEGA7.0 software. The online softwares "Predict protein" and "Mfold" were used to predict the secondary structure of proteins and untranslated regions, respectively. Phylogenetic analysis showed that all five isolates in this study were DENV type 2, which is most closely related to the Zhejiang strain (2017-MH110588). Compared with the DENV-2 standard strain, 773 nucleotide mutations occurred in the isolated strain, of which 666 were nonsense mutations. Of the 80 mutated amino acids, 22 occurred in the structural protein region (2 in C region, 8 in PrM/M region, 12 in E region), and 58 in the non-structural (NS) protein region (9 in NS1 region, 10 in NS2 region, 12 in NS3 region, 7 in NS4 region, 20 in NS5 region). The prM/M region had the highest AA mutation rate, while NS4B was conservative. Three amino acid mutations (E: N390^thS, and NS5: S676^thN, K800^thT) may important for the replication and virulence of the DENV. Secondary structure prediction observed 28 changes in polynucleotide binding regions and 110 changes in protein binding sites of coding sequence. 2 and 4 base substitutions resulted in 2 and 6 significant changes in the RNA secondary structure of 5' UTR and 3' UTR, respectively. Two significant positive selection sites were observed in NS5. To our knowledge, this research is the first complete genome analysis of the epidemic strain of the 2018 dengue outbreak in Hunan and will benefit further research for virus traceability and vaccine development.

Molecular characterization of structural protein genes of dengue virus serotype 1 epidemic in Yunnan, Southwest China, in 2018

A dengue virus serotype 1 (DENV-1) epidemic occurred from October to December 2018 in Xishuangbanna, Yunnan, Southwest China, neighboring Myanmar, Laos, and Vietnam. In this study, we investigated the molecular characteristics, evolution, and potential source of DENV from Xishuangbanna. The C (capsid), prM (premembrane), and E (envelope) genes of DENV isolated from 87 serum samples obtained from local patients were amplified and sequenced, and the sequences were evaluated by identification of mutations, phylogenetic and homologous recombination analysis, and secondary structure prediction. Phylogenetic analysis showed that all of the epidemic DENV strains from Xishuangbanna could be grouped in a branch with DENV-1 isolates, and were most similar to the Fujian 2005 (China, DQ193572) and Singapore 2016 (MF314188) strains. When compared with DENV-1SS (the standard strain), there were 31 non-synonymous mutations, but no obvious homologous recombination signal was found. Secondary structure prediction showed that some changes had occurred in a helical region in proteins of the MN123849 and MN123854 strains, but there were few changes in the disordered region. This study reveals the molecular characteristics of the structural genes of the Xishuangbanna epidemic strains in 2018 and provides a reference for molecular epidemiology, infection, and pathogenicity research and vaccine development.

Ethnobotanical survey and evaluation of traditional mosquito repellent plants of Dai people in Xishuangbanna, Yunnan Province, China

ETHNOPHARMACOLOGICAL RELEVANCE

Dengue is one of the most important pervasive diseases in many regions of the world, including China. There is an urgent need for new repellents, including plant derivatives, due to the resistance, toxicity, and non-degradability of synthetic insecticides. Traditional plant-based remedies may provide potential avenues for developing new strategies.

AIMS OF THE STUDY

The aims of this study were to 1) document the traditional mosquitoes repellent plants used by the Dai people of Xishuangbanna, China; 2) screen out new efficient mosquito repellent plants as candidates for further study.

MATERIALS AND METHODS

During the period August 2016 to July 2017, five field surveys were conducted in 16 villages of Xishuangbanna. A total of 81 informants (44 males and 37 females) were interviewed using semi-structured questions to collect detailed information on the plants they use to prevent mosquito bites. Ten plants with higher popularity and larger resource were collected and extracts were prepared by hydro-distillation or with petroleum ether. Extracts were tested for adult Aedes albopictus repellency using a human-bait cage. Firstly, repellency was determined as the Minimum Effective Dosage (MED) per minute at which 1% of the mosquito bite through the treated cloth. Secondly, five plant extracts with lower MEDs were tested the repellent longevity of different concentrations.

RESULTS

Eighteen plants were documented as being used in traditional remedies against mosquitoes. The methods for controlling mosquitoes were diverse: direct burning was used for most plants (16 species), followed by smearing (5 species), and placing (5 species). Laboratory analyses confirmed that ten plants did exhibit mosquito repellent activity. Of them, Artemisia indica, Nicotiana tabacum, Blumea balsamifera, Vitex trifolia, and Chromolaena odorata showed good mosquito repellency with MEDs of 0.015, 0.061, 0.090, 0.090, and 0.105 mg/cm², respectively. The protection rate provided by A. indica is also the highest among five plants. Although it provides complete protection time of only 30 min at 0.45 mg/cm² concentration, its repellency within 2 h is not significantly different from that of DEET.

CONCLUSION

Dai villagers in Xishuangbanna have a rich, diverse and scientific knowledge of plant-based mosquito repellents. Laboratory experiments screened out several plants as candidates for mosquito repellents, of which Artemisia indica was the most promising candidate plant.

Molecular and evolutionary analysis of dengue virus serotype 2 isolates from Korean travelers in 2015

In Korea, dengue infection has been frequently reported in travelers to tropical and subtropical countries. Global warming increases the probability of autochthonous dengue outbreaks in Korea. In this report, the molecular and evolutionary properties of four dengue virus (DENV) type 2 isolates from Korean overseas travelers were examined. Three of these isolates were classified as Cosmopolitan genotypes and further divided into sublineages 1 (43,253, 43,254) and 2 (43,248), while the other isolate (KBPV-VR29) was related to American genotypes. The variable amino acid motifs related to virulence and replication were identified in the structural and non-structural proteins. A negative selection mechanism was clearly verified in all of the DENV proteins. Potential recombination events were identified in the NS5 protein of the XSBN10 strain. The substitution rate (5.32 × 10⁻⁴ substitutions per site) and the time of the most recent common ancestor (TMRCA) for each evolutionary group were determined by the Bayesian skyline coalescent method. This study shows that DENV type 2 strains with distinct phylogenetic, evolutionary, and virulence characteristics have been introduced into Korea by overseas travelers and have the potential to trigger autochthonous dengue outbreaks.

The expanding pattern of Aedes aegypti in southern Yunnan, China: insights from microsatellite and mitochondrial DNA markers

BACKGROUND

Aedes aegypti, the vector of dengue fever, was first reported in Yunnan in 2002. Now, this species is found in nine counties in border areas of south-west Yunnan. Related dengue fever outbreaks have been reported since 2013. The population genetics of Ae. aegypti in these areas were studied to explain the expansion history of this species.

METHODS

Fifteen natural populations of Ae. aegypti were sampled from six counties of Yunnan, and two laboratory populations from Guangdong and Hainan were also included in this study. A total of 12 microsatellite loci and three mitochondrial genes were analysed.

RESULTS

The results indicate that Ae. aegypti populations from Yunnan show similar genetic diversity. The 17 populations could be divided into three groups: the first group included populations from Longchuan, Ruili and Gengma, which are located in the southwest of Yunnan; the second group included populations from Jinghong and Menghai, in the south of Yunnan; and the third group included populations from Mengla and the two laboratory populations from Guangdong and Hainan. Both microsatellite and mtDNA data revealed that the genetic relationships of the populations corresponded to their geographic relationships.

CONCLUSIONS

The results suggested that the expansion of Ae. aegypti from northern Myanmar and Laos to southern and southwestern Yunnan was a natural process. The effect of human activity on expansion was not obvious. Surveillance efforts should still be focused on border areas where Ae. aegypti does not occur, and a powerful control strategy should be applied to prevent outbreaks of dengue fever.

A predominant dengue virus-1 endemic strain and the vector competence of Aedes albopictus from Guangzhou City, China

INTRODUCTION

Dengue has been a serious public health burden and dengue virus-1 (DENV-1) is the predominant strain in Guangdong province, China. Differences exist in the transmission dynamics amongAedes albopictus and DENV in different geographical regions. However, little is known about the vector competence of indigenous Aedes albopictus for the predominant dengue strain in Guangdong province, China.

METHODOLOGY

In this study, the field-derivedAedes albopictus collected from Guangzhou city, Guangdong province were infected with the predominant DENV endemic strain DENV-1 GZ201401 by feeding on serially diluted artificial infectious blood or infected suckling mice. DENV-infected mosquitoes were evaluated for viral load at five-time intervals in three tissues, the head, body and legs using reverse transcription-quantitative PCR (RT-qPCR). The vertical transmission of DENV in Ades albopictus was also analysed. Suckling mice were used to assess the transmission of DENV by Aedes albopictus.

RESULTS

There was no difference in infection rates between mosquitoes infected by infected suckling mice or by artificial infectious blood. The proportion of DENV-1 positive mosquitoes increased over time after an infectious blood meal, but there was no difference in the positive rate beyond 7days after the blood meal. The positive rate of DENV-1 infected mosquitoes increased with the DENV titer in the blood meal. Most of the infections the infected mosquitoes were disseminated more than 7 days after imbibing the artificial infectious blood. The median infective doses (MID50) at 7,14,21 and 28 days after artificial infectious blood meal [7, 14, 21 and 28 days post-infection (dpi)] were 7.86 × 10⁷, 1.57 × 10⁷, 6.39 × 10⁶ and 4.96 × 10⁶ TCID₅₀ (50% tissue culture infective dose)/ml, respectively. The mosquitoes can spread DENV-1 GZ201401 to hosts as early as 3 dpi. The vertical transmission of DENV-1 was documented with a cumulative rate of 17.61%.

CONCLUSION

Our results demonstrated that Aedes albopictus mosquitoes are competent vectors for DENV-1, and are capable of maintaining autochthonous dengue outbreaks in Guangdong province, China, which may have been promoted by vertical transmission.

Co-Circulation of 4 Dengue Virus Serotypes among Travelers Entering China from Myanmar, 2017

We report 301 dengue virus infections among cross-border travelers entering Yunnan Province, China, from Myanmar during 2017. Phylogenetic analysis of 99 strains found all 4 serotypes co-circulating; genetic characteristics have also changed. This finding highlights the urgent need for monitoring dengue virus cross-border transmission as early warning of severe dengue fever.

Molecular characterization of the viral structural gene of the first dengue virus type 1 outbreak in Xishuangbanna: A border area of China, Burma and Laos

BACKGROUND

Xishuangbanna, a border area of China, Burma and Laos, had its first major DENV-1 outbreak in 2017. This study aims to explore the genetic characterization, potential source and evolution of the viruses in outbreak.

METHODS

The structural protein C/prM/E genes of viruses isolated from local residents or Burmese travelers were sequenced followed by mutation, phylogenetic, homologous recombination, molecular clock and demographic reconstruction analysis.

RESULTS

Phylogenetic analysis revealed that all of the strains were classified as three cluster of DENV-1. Cluster 1, 2 and 3 were most similar to China Guangzhou 2011, China Hubei 2014 and Laos 2008 strain, respectively. Among 236 base mutations, 31 caused nonsynonymous mutations when compared with the DENV-1SS. No homologous recombination signal was discovered. The structural protein of these strains had similar three-dimensional structure. Only site 434 showed differences among five predicted protein binding sites. Molecular clock phylogenetic and demographic reconstruction analysis showed that DENV-1 became highly diversified in 1972 followed by a slightly decreased period until 2017.

CONCLUSIONS

Dengue isolated strains show diversification between Burma and China. Amino acid substitution (I440T) may lead to weakened virulence of the epidemic strains. DENV-1 became highly diversified in 1972 followed by a slightly decreased period.

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

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.

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

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.

Mosquito-Associated Viruses in China

Mosquitoes are classified into approximately 3500 species and further grouped into 41 genera. Epidemiologically, they are considered to be among the most important disease vectors in the world and they can harbor a wide variety of viruses. Several mosquito viruses are considered to be of significant medical importance and can cause serious public health issues throughout the world. Such viruses are Japanese encephalitis virus (JEV), dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV). Others are the newly recognized mosquito viruses such as Banna virus (BAV) and Yunnan orbivirus (YNOV) with unclear medical significance. The remaining mosquito viruses are those that naturally infect mosquitoes but do not appear to infect humans or other vertebrates. With the continuous development and improvement of mosquito and mosquito-associated virus surveillance systems in China, many novel mosquito-associated viruses have been discovered in recent years. This review aims to systematically outline the history, characteristics, distribution, and/or current epidemic status of mosquito-associated viruses in China.