Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria.
Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria.
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DOI：
10.1080/22221751.2024.2307511
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发表时间：
2024-12
影响因子：
13.2
通讯作者：
中科院分区：
文献类型：
--
作者：
由于对疟疾等非特异性发热性疾病的鉴别诊断不准确、诊断检测缺乏以及临床和基因组监测不足，登革热在非洲经常被错误分类和少报。在尼日利亚，关于登革热病毒（DENV）在人类和病媒中的血清流行率和遗传多样性的报告有限。在这项研究中，我们调查了登革热在尼日利亚热带雨林地区的流行病学和遗传多样性。我们采用抗登革热IgG/IgM/NS1快速检测试剂盒和元基因组测序相结合的方法，对尼日利亚南部奥约州和埃基蒂州三家医院的515名疟疾和伤寒检测呈阴性的发热患者进行了筛查。我们发现约28%的筛查患者既往有DENV暴露，60岁以上人群患病率最高。约8%的患者显示近期或当前感染的证据，2.7%为急性感染。在对60个样本进行测序后，我们组装了20个DENV-1基因组（3个完整基因组和17个部分基因组）。我们发现所有组装的基因组都属于DENV-1基因型III。我们的系统发育分析显示了奥约州不同DENV谱系的长期隐循环的证据。由于该地区的测序数据有限，我们无法确定尼日利亚DENV的来源。然而，我们的序列与坦桑尼亚的序列和2019年有坦桑尼亚旅行史的中国人报告的序列紧密聚集。这可能反映了DENV-1在非洲更广泛的未采样双向传播，这强烈强调了基因组监测在监测非洲正在进行的DENV传播中的重要性。
Dengue is often misclassified and underreported in Africa due to inaccurate differential diagnoses of nonspecific febrile illnesses such as malaria, sparsity of diagnostic testing and poor clinical and genomic surveillance. There are limited reports on the seroprevalence and genetic diversity of dengue virus (DENV) in humans and vectors in Nigeria. In this study, we investigated the epidemiology and genetic diversity of dengue in the rainforest region of Nigeria. We screened 515 febrile patients who tested negative for malaria and typhoid fever in three hospitals in Oyo and Ekiti States in southern Nigeria with a combination of anti-dengue IgG/IgM/NS1 rapid test kits and metagenomic sequencing. We found that approximately 28% of screened patients had previous DENV exposure, with the highest prevalence in persons over sixty. Approximately 8% of the patients showed evidence of recent or current infection, and 2.7% had acute infection. Following sequencing of sixty samples, we assembled twenty DENV-1 genomes (3 complete and 17 partial). We found that all assembled genomes belonged to DENV-1 genotype III. Our phylogenetic analyses showed evidence of prolonged cryptic circulation of divergent DENV lineages in Oyo state. We were unable to resolve the source of DENV in Nigeria owing to limited sequencing data from the region. However, our sequences clustered closely with sequences in Tanzania and sequences reported in Chinese with travel history to Tanzania in 2019. This may reflect the wider unsampled bidirectional transmission of DENV-1 in Africa, which strongly emphasizes the importance of genomic surveillance in monitoring ongoing DENV transmission in Africa.
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DOI：
10.5281/zenodo.3329978
发表时间：
2019-01-01
期刊：
Acta Entomologica Serbica
影响因子：
--
作者：
Agwu, Ekenma Julia;Isaac, Clement;Igbinosa, Igho Benjamin
通讯作者：
Igbinosa, Igho Benjamin
DOI：
10.1093/bioinformatics/bty695
发表时间：
2019-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Vilsker M;Moosa Y;Nooij S;Fonseca V;Ghysens Y;Dumon K;Pauwels R;Alcantara LC;Vanden Eynden E;Vandamme AM;Deforche K;de Oliveira T
通讯作者：
de Oliveira T
森林登革热病毒 2 型在人类中的活动，尼日利亚，1966 年。
影响因子：
11.8
作者：
Vasilakis, Nikos;Tesh, Robert B.;Weaver, Scott C.
通讯作者：
Weaver, Scott C.
影响因子：
3.7
作者：
Joannides J;Dzodzomenyo M;Azerigyik F;Agbosu EE;Pratt D;Nyarko Osei JH;Pwalia R;Amlalo GK;Appawu M;Takashi H;Iwanaga S;Buchwald A;Rochford R;Boakye D;Koram K;Bonney K;Dadzie S
通讯作者：
Dadzie S
影响因子：
4.5
作者：
Bassey BE;Braka F;Onyibe R;Kolude OO;Oluwadare M;Oluwabukola A;Omotunde O;Iyanda OA;Tella AA;Olanike OS
通讯作者：
Olanike OS