Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019.
Background 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...
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ftdoajarticles:oai:doaj.org/article:0739aa998cbc430e882593d9b7ab403e 2023-05-15T15:17:57+02:00 Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019. Zoraima Neto Pedro A Martinez Sarah C Hill Domingos Jandondo Julien Thézé Marinela Mirandela Renato Santana Aguiar Joilson Xavier Cruz Dos Santos Sebastião Ana Luísa Micolo Cândido Filipa Vaz Gisel Reyes Castro Joana Paula Paixão Nicholas J Loman Philippe Lemey Oliver G Pybus Jocelyne Vasconcelos Nuno Rodrigues Faria Joana de Morais 2022-05-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0010255 https://doaj.org/article/0739aa998cbc430e882593d9b7ab403e EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0010255 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0010255 https://doaj.org/article/0739aa998cbc430e882593d9b7ab403e PLoS Neglected Tropical Diseases, Vol 16, Iss 5, p e0010255 (2022) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2022 ftdoajarticles https://doi.org/10.1371/journal.pntd.0010255 2023-02-19T01:27:19Z Background 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 ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 16 5 e0010255 |
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Directory of Open Access Journals: DOAJ Articles |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Zoraima Neto Pedro A Martinez Sarah C Hill Domingos Jandondo Julien Thézé Marinela Mirandela Renato Santana Aguiar Joilson Xavier Cruz Dos Santos Sebastião Ana Luísa Micolo Cândido Filipa Vaz Gisel Reyes Castro Joana Paula Paixão Nicholas J Loman Philippe Lemey Oliver G Pybus Jocelyne Vasconcelos Nuno Rodrigues Faria Joana de Morais Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
Background 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 ... |
format |
Article in Journal/Newspaper |
author |
Zoraima Neto Pedro A Martinez Sarah C Hill Domingos Jandondo Julien Thézé Marinela Mirandela Renato Santana Aguiar Joilson Xavier Cruz Dos Santos Sebastião Ana Luísa Micolo Cândido Filipa Vaz Gisel Reyes Castro Joana Paula Paixão Nicholas J Loman Philippe Lemey Oliver G Pybus Jocelyne Vasconcelos Nuno Rodrigues Faria Joana de Morais |
author_facet |
Zoraima Neto Pedro A Martinez Sarah C Hill Domingos Jandondo Julien Thézé Marinela Mirandela Renato Santana Aguiar Joilson Xavier Cruz Dos Santos Sebastião Ana Luísa Micolo Cândido Filipa Vaz Gisel Reyes Castro Joana Paula Paixão Nicholas J Loman Philippe Lemey Oliver G Pybus Jocelyne Vasconcelos Nuno Rodrigues Faria Joana de Morais |
author_sort |
Zoraima Neto |
title |
Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019. |
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. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2022 |
url |
https://doi.org/10.1371/journal.pntd.0010255 https://doaj.org/article/0739aa998cbc430e882593d9b7ab403e |
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Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 16, Iss 5, p e0010255 (2022) |
op_relation |
https://doi.org/10.1371/journal.pntd.0010255 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0010255 https://doaj.org/article/0739aa998cbc430e882593d9b7ab403e |
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https://doi.org/10.1371/journal.pntd.0010255 |
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PLOS Neglected Tropical Diseases |
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