Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019
| Main Author: | |
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| Publication Date: | 2022 |
| Other Authors: | , , , , , , , , , , , , , , , , , |
| Format: | Article |
| Language: | eng |
| Source: | Repositório Institucional da UFMG |
| Download full: | https://doi.org/10.1371/journal.pntd.0010255 http://hdl.handle.net/1843/60393 https://orcid.org/0000-0003-1606-9996 https://orcid.org/0000-0002-9886-6448 https://orcid.org/0000-0002-2995-2596 https://orcid.org/0000-0001-8188-9494 https://orcid.org/0000-0003-3916-2018 https://orcid.org/0000-0003-1232-0119 https://orcid.org/0000-0002-7318-693X https://orcid.org/0000-0002-4524-4055 |
Summary: | FAPESP - Fundação de Amparo à Pesquisa do Estado de São Paulo |
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2023-10-31T21:33:12Z2023-10-31T21:33:12Z2022-05-18165e001025517https://doi.org/10.1371/journal.pntd.00102551935-2735http://hdl.handle.net/1843/60393https://orcid.org/0000-0003-1606-9996https://orcid.org/0000-0002-9886-6448https://orcid.org/0000-0002-2995-2596https://orcid.org/0000-0001-8188-9494https://orcid.org/0000-0003-3916-2018https://orcid.org/0000-0003-1232-0119https://orcid.org/0000-0002-7318-693Xhttps://orcid.org/0000-0002-4524-4055FAPESP - Fundação de Amparo à Pesquisa do Estado de São PauloBackground The transmission patterns and genetic diversity of dengue virus (DENV) circulating in Africa remain poorly understood. Circulation of the DENV serotype 1 (DENV1) in Angola was detected in 2013, while DENV serotype 2 (DENV2) was detected in 2018. Here, we report results from molecular and genomic investigations conducted at the Ministry of Health national reference laboratory (INIS) in Angola on suspected dengue cases detected between January 2017 and February 2019. Methods A total of 401 serum samples from dengue suspected cases were collected in 13 of the 18 provinces in Angola. Of those, 351 samples had complete data for demographic and epidemiological analysis, including age, gender, province, type of residence, clinical symptoms, as well as dates of onset of symptoms and sample collection. RNA was extracted from residual samples and tested for DENV-RNA using two distinct real time RT-PCR protocols. On-site whole genome nanopore sequencing was performed on RT-PCR+ samples. Bayesian coalescent models were used to estimate date and origin of outbreak emergence, as well as population growth rates. Results Molecular screening showed that 66 out of 351 (19%) suspected cases were DENV-RNA positive across 5 provinces in Angola. DENV RT-PCR+ cases were detected more frequently in urban sites compared to rural sites. Of the DENV RT-PCR+ cases most were collected within 6 days of symptom onset. 93% of infections were confirmed by serotype-specific RT-PCR as DENV2 and 1 case (1.4%) was confirmed as DENV1. Six CHIKV RT-PCR+ cases were also detected during the study period, including 1 co-infection of CHIKV with DENV1. Most cases (87%) were detected in Luanda during the rainy season between April and October. Symptoms associated with severe dengue were observed in 11 patients, including 2 with a fatal outcome. On-site nanopore genome sequencing followed by genetic analysis revealed an introduction of DENV2 Cosmopolitan genotype (also known as DENV2-II genotype) possibly from India in or around October 2015, at least 1 year before its detection in the country. Coalescent models suggest relatively moderately rapid epidemic growth rates and doubling times, and a moderate expansion of DENV2 in Angola during the studied period. Conclusion This study describes genomic, epidemiological and demographic characteristic of predominately urban transmission of DENV2 in Angola. We also find co-circulation of DENV2 with DENV1 and CHIKV and report several RT-PCR confirmed severe dengue cases in the country. Increasing dengue awareness in healthcare professional, expanding the monitorization of arboviral epidemics across the country, identifying most common mosquito breeding sites in urban settings, implementing innovative vector control interventions and dengue vaccination campaigns could help to reduce vector presence and DENV transmission in Angola. Author summary Angola has experienced dengue, yellow fever and Zika virus outbreaks between 2013–2017. To improve the detection of arbovirus outbreaks in Angola, we set up the National Arbovirus Laboratory of Surveillance Programme at the National Institute of Health Research (INIS), Ministry of Health, Angola, which officially kick-started arbovirus surveillance activities in early 2017. In this study we tested samples collected from patients with suspected dengue cases between January 2017 to February 2019. We report molecular and genomic findings on DENV2 transmission in Angola. On-site whole genome sequencing and subsequent phylogenetic analysis indicate a single introduction of the DENV2 Cosmopolitan genotype (also known as DENV2-II genotype) from Southern Asia, probably as a result of international travel, followed by moderate virus population growth. In Angola, most detections occurred in urban areas, although we detected DENV2 in 5 of the 18 provinces in Angola. This work emphasizes the importance of maintaining an active arbovirus surveillance programme throughout the country to investigate DENV transmission patterns and evaluate the risk of hyperendemicity in Angola.engUniversidade Federal de Minas GeraisUFMGBrasilICB - DEPARTAMENTO DE MICROBIOLOGIAICB - DEPARTAMENTO DE PATOLOGIAICB - INSTITUTO DE CIÊNCIAS BIOLOGICASPLOS Neglected Tropical DiseasesGenomasDengueAngolanosGenomasDengueAngolanosMolecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttps://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0010255Zoraima NetoAna Luísa Micolo CândidoFilipa VazGisel Reyes CastroJoana Paula PaixãoNicholas J. LomanPhilippe LemeyOliver G. PybusJocelyne VasconcelosJoana de MoraisPedro a. MartinezSarah C. HillDomingos JandondoJulien ThézéMarinela MirandelaRenato Santana de AguiarJoilson XavierCruz Dos Santos SebastiãoNuno Rodrigues Fariaapplication/pdfinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFMGinstname:Universidade Federal de Minas Gerais (UFMG)instacron:UFMGLICENSELicense.txtLicense.txttext/plain; charset=utf-82042https://repositorio.ufmg.br/bitstream/1843/60393/1/License.txtfa505098d172de0bc8864fc1287ffe22MD51ORIGINALMolecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019.pdfMolecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019.pdfapplication/pdf1066838https://repositorio.ufmg.br/bitstream/1843/60393/2/Molecular%20and%20genomic%20investigation%20of%20an%20urban%20outbreak%20of%20dengue%20virus%20serotype%202%20in%20Angola%2c%202017%e2%80%932019.pdf4c51d3a33954c121f3a822ba4cdf38fbMD521843/603932023-10-31 18:33:12.513oai:repositorio.ufmg.br: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Repositório de PublicaçõesPUBhttps://repositorio.ufmg.br/oaiopendoar:2023-10-31T21:33:12Repositório Institucional da UFMG - Universidade Federal de Minas Gerais (UFMG)false |
| dc.title.pt_BR.fl_str_mv |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 |
| title |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 |
| spellingShingle |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 Zoraima Neto Genomas Dengue Angolanos Genomas Dengue Angolanos |
| title_short |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 |
| title_full |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 |
| title_fullStr |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 |
| title_full_unstemmed |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 |
| title_sort |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019 |
| author |
Zoraima Neto |
| author_facet |
Zoraima Neto Ana Luísa Micolo Cândido Filipa Vaz Gisel Reyes Castro Joana Paula Paixão Nicholas J. Loman Philippe Lemey Oliver G. Pybus Jocelyne Vasconcelos Joana de Morais Pedro a. Martinez Sarah C. Hill Domingos Jandondo Julien Thézé Marinela Mirandela Renato Santana de Aguiar Joilson Xavier Cruz Dos Santos Sebastião Nuno Rodrigues Faria |
| author_role |
author |
| author2 |
Ana Luísa Micolo Cândido Filipa Vaz Gisel Reyes Castro Joana Paula Paixão Nicholas J. Loman Philippe Lemey Oliver G. Pybus Jocelyne Vasconcelos Joana de Morais Pedro a. Martinez Sarah C. Hill Domingos Jandondo Julien Thézé Marinela Mirandela Renato Santana de Aguiar Joilson Xavier Cruz Dos Santos Sebastião Nuno Rodrigues Faria |
| author2_role |
author author author author author author author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Zoraima Neto Ana Luísa Micolo Cândido Filipa Vaz Gisel Reyes Castro Joana Paula Paixão Nicholas J. Loman Philippe Lemey Oliver G. Pybus Jocelyne Vasconcelos Joana de Morais Pedro a. Martinez Sarah C. Hill Domingos Jandondo Julien Thézé Marinela Mirandela Renato Santana de Aguiar Joilson Xavier Cruz Dos Santos Sebastião Nuno Rodrigues Faria |
| dc.subject.por.fl_str_mv |
Genomas Dengue Angolanos |
| topic |
Genomas Dengue Angolanos Genomas Dengue Angolanos |
| dc.subject.other.pt_BR.fl_str_mv |
Genomas Dengue Angolanos |
| description |
FAPESP - Fundação de Amparo à Pesquisa do Estado de São Paulo |
| publishDate |
2022 |
| dc.date.issued.fl_str_mv |
2022-05-18 |
| dc.date.accessioned.fl_str_mv |
2023-10-31T21:33:12Z |
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2023-10-31T21:33:12Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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http://hdl.handle.net/1843/60393 |
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https://doi.org/10.1371/journal.pntd.0010255 |
| dc.identifier.issn.pt_BR.fl_str_mv |
1935-2735 |
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https://orcid.org/0000-0003-1606-9996 https://orcid.org/0000-0002-9886-6448 https://orcid.org/0000-0002-2995-2596 https://orcid.org/0000-0001-8188-9494 https://orcid.org/0000-0003-3916-2018 https://orcid.org/0000-0003-1232-0119 https://orcid.org/0000-0002-7318-693X https://orcid.org/0000-0002-4524-4055 |
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https://doi.org/10.1371/journal.pntd.0010255 http://hdl.handle.net/1843/60393 https://orcid.org/0000-0003-1606-9996 https://orcid.org/0000-0002-9886-6448 https://orcid.org/0000-0002-2995-2596 https://orcid.org/0000-0001-8188-9494 https://orcid.org/0000-0003-3916-2018 https://orcid.org/0000-0003-1232-0119 https://orcid.org/0000-0002-7318-693X https://orcid.org/0000-0002-4524-4055 |
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1935-2735 |
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eng |
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eng |
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PLOS Neglected Tropical Diseases |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Universidade Federal de Minas Gerais |
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UFMG |
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Brasil |
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ICB - DEPARTAMENTO DE MICROBIOLOGIA ICB - DEPARTAMENTO DE PATOLOGIA ICB - INSTITUTO DE CIÊNCIAS BIOLOGICAS |
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Universidade Federal de Minas Gerais |
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