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2019 年中国汕头登革热的基因组流行病学研究。

Genomic epidemiology of dengue in Shantou, China, 2019.

机构信息

Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China.

Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.

出版信息

Front Public Health. 2023 Jul 13;11:1035060. doi: 10.3389/fpubh.2023.1035060. eCollection 2023.

Abstract

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%, = 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.

摘要

目的

登革热在东南亚国家已经流行了几十年。很少有报告能够实时追踪登革热的动态。在这项研究中,我们生成了数百个病原体基因组,以了解登革热在一个高度流行地区的爆发的基因组流行病学。

方法

我们利用全基因组短读测序(PE150)生成登革热病毒的基因组,并调查了 2019 年在中国汕头发生的一起中规模登革热爆发的病毒传播的基因组流行病学。

结果

该爆发从 2019 年 7 月持续到 12 月。实验室确诊病例的总累计数为 944 例。没有记录到性别偏见或死亡病例。柬埔寨和新加坡是输入性登革热病例的主要来源(74.07%,=20)。共分离出 284 株登革热病毒株,包括 259 株 DENV-1、24 株 DENV-2 和 1 株 DENV-3 分离株。我们生成了 252 株 DENV 分离株的全基因组(229 株 DENV-1、22 株 DENV-2 和 1 株 DENV-3),占总病例的 26.7%。结合流行病学和系统发育分析表明存在多个独立的传入。内部传播评估和传播网络重建支持了系统发育分析的推断,BSSVS 分析中的贝叶斯因子支持度很高。在汕头的 CCH 和 LG 中检测到两个扩展的创始人和传播链。

结论

我们观察到基因组流行病学在监测 DENV 动态方面的即时效果,并强调了其在未来实时追踪其他新型病原体爆发的前景。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6061/10374217/b911d5d7f194/fpubh-11-1035060-g0001.jpg

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