Molecular Characterization and Phylogenetic Analysis of the 2019 Dengue Outbreak in Wenzhou, China

Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis

Since its first academic record in 1978, dengue epidemics have occurred in all provinces of China, except Xizang. The epidemiological and molecular features of the whole genome of dengue virus (DENV) have not yet been completely elucidated, interfering with prevention and control strategies for dengue fever in China. Here, we obtained 553 complete genomes of the four serotypes of DENV (DENV1-4) isolated in China from the GenBank database to analyze the phylogeny, recombination, genomic variants, and selection pressure and to estimate the substitution rates of DENV genomes. Phylogenetic analyses indicated that DENV sequences from China did not cluster together and were genetically closer to those from Southeast Asian countries in the maximum likelihood trees, indicating that DENV was not endemic in China. Thirty intra-serotype recombinant sequences were identified for DENV1-4, with the highest frequency in DENV4. Selection pressure analyses revealed that 13 codons under positive selection were located in the C, NS1, NS2A, NS3, and NS5 proteins. For DENV1 to DENV3, the substitution rates evaluated in this study were 9.23 × 10-4, 7.59 × 10-4, and 7.06 × 10-4 substitutions per site per year, respectively. These findings improve our understanding of the evolution of DENV in China.

Dynamics and Efficacy: A Comprehensive Evaluation of the Advanced Dengue Fever Surveillance and Early Warning System in Ningbo City, 2023

Objective

To conduct a comprehensive evaluation of the Dengue Fever Surveillance and Early Warning System deployed in Ningbo City during 2023, focusing on its capacity for timely identification and reporting of dengue fever cases, particularly imported cases from endemic regions.

Methods

A detailed data of patient clinical features and blood profile trends was collected from clinical records and surveillance reports, focusing on the rapid diagnostic processes and surveillance rigor. This study assessed the effectiveness of the system in identifying and reporting dengue cases and identified the limitations of the existing framework through a basic statistical approach.

Results

The system demonstrated timely identification and reporting of dengue fever cases, with a particular emphasis on imported cases. However, several limitations were identified, including the need for more precise monitoring criteria and improved coordination with medical entities.

Conclusion

The study underscores the critical role of public health bodies in managing disease outbreaks and advocates for enhanced methodologies to refine epidemic control efforts. The findings contribute to the advancement of early warning mechanisms and the improvement of proactive infectious disease monitoring in metropolitan environments, providing valuable insights for fortifying the Dengue Fever Surveillance and Early Warning System in Ningbo City.

Genomic characterization of dengue virus serotype 2 during dengue outbreak and endemics in Hangzhou, Zhejiang (2017-2019)

Introduction

Dengue fever (DF) is a mosquito-borne viral disease caused by the dengue virus (DENV). In recent years, Hangzhou has undergone a DF epidemic, particularly in 2017, with an outbreak of 1,128 patients. The study aimed to investigate the genetic diversity and molecular evolution among the DF clinical isolates during and after the outbreak to aid in mapping its spread.

Methods

To understand the genetic diversity, 74 DENV-2 strains were isolated from DF epidemic cases between 2017 and 2019. Combining whole genome sequencing (WGS) technology, additional phylogenetic, haplotype, amino acid (AA) substitution, and recombination analyses were performed.

Results

The results revealed that strains from 2017 were closely related to those from Singapore, Malaysia, and Thailand, indicating an imported international transmission. Local strains from 2018 were clustered with those recovered from 2019 and were closely associated with Guangzhou isolates, suggesting a within-country transmission after the significant outbreak in 2017. Compared to DENV-2 virus P14337 (Thailand/0168/1979), a total of 20 AA substitutions were detected. Notably, V431I, T2881I, and K3291T mutations only occurred in indigenous cases from 2017, and A1402T, V1457I, Q2777E, R3189K, and Q3310R mutations were exclusively found in imported cases from 2018 to 2019. The recombination analysis indicated that a total of 14 recombination events were observed.

Conclusion

This study may improve our understanding of DENV transmission in Hangzhou and provide further insight into DENV-2 transmission and the local vaccine choice.

Genomic epidemiology of dengue in Shantou, China, 2019

Objectives

Dengue has been endemic in Southeast Asian countries for decades. There are few reports tracing the dynamics of dengue in real time. In this study, we generated hundreds of pathogen genomes to understand the genomic epidemiology of an outbreak in a hyper-endemic area of dengue.

Methods

We leveraged whole-genome short-read sequencing (PE150) to generate genomes of the dengue virus and investigated the genomic epidemiology of a dengue virus transmission in a mesoscale outbreak in Shantou, China, in 2019.

Results

The outbreak was sustained from July to December 2019. The total accumulated number of laboratory-confirmed cases was 944. No gender bias or fatalities were recorded. Cambodia and Singapore were the main sources of imported dengue cases (74.07%, n = 20). A total of 284 dengue virus strains were isolated, including 259 DENV-1, 24 DENV-2, and 1 DENV-3 isolates. We generated the entire genome of 252 DENV isolates (229 DENV-1, 22 DENV-2, and 1 DENV-3), which represented 26.7% of the total cases. Combined epidemiological and phylogenetic analyses indicated multiple independent introductions. The internal transmission evaluations and transmission network reconstruction supported the inference of phylodynamic analysis, with high Bayes factor support in BSSVS analysis. Two expansion founders and transmission chains were detected in CCH and LG of Shantou.

Conclusions

We observed the instant effects of genomic epidemiology in monitoring the dynamics of DENV and highlighted its prospects for real-time tracing of outbreaks of other novel agents in the future.