Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017–2019

Abstract

Background Transmission patterns and genetic diversity of dengue virus (DENV) circulating in Africa remains poorly understood. Circulation of the DENV serotype 1 (DENV1) in Angola was detected in 2013, while DENV serotype 2 (DENV2) was detected for the first time 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 samples and tested for DENV-RNA by two distinct real time RT-PCR protocols. On-site whole genome nanopore sequencing was performed for PCR+ cases. Bayesian coalescent models were used to estimate date and origin of outbreak emergence, as well as population growth rates. Results Molecular diagnosis shows that 66 out of 351 (19%) suspected cases were DENV-RNA positive across 5 provinces in Angola. DENV PCR+ cases were diagnosed more frequently in urban sites compared to rural sites. Of the DENV positive samples, 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 positive cases were also detected during the study period, including 1 co-infection 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 1.5 years 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.

Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era

“…The tree scale indicates nucleotide substitutions/site. Phylogenies are also available to view on Microreact [ 63 ]: https://microreact.org/project/bYhycuN63ZToY7348qJHbr-adenoviruscambridge .…”

“…Only residual samples were tested. Therefore, the work fell within the principles of UK Standards for Microbiology Investigations Q1 [ 63 ], which establishes that ethics approval is not required for such validation. Testing and analysis were undertaken in accordance with the UK Human Tissue Act 2004, as amended [ 64 ].…”

Demographic characteristics and risk factors related to high blood pressure among healthy blood donors from Luanda, Angola: A retrospective study

“…The large adhesion of blood donors during January 2020 is not surprising, and the possible explanation is that once in this period, Luanda province like other Angola provinces, face heavy rainfall, and due to poor sanitation, there is an increase in stagnant water and thus increases also the circulation of vectors capable of increasing cases of malaria, dengue, or other vector‐borne diseases in Luanda, as verified by other studies. 22 , 26 , 27 , 28 , 29 However, the increase in malaria and dengue cases could be one of the reasons for the increase in blood donation since many patients with malaria or dengue need blood transfusions during hospital treatment. 30 Indeed, this explanation could be supported by our results, since the risk of having high blood pressure in January 2020 was 2.5 times, compared to the other months of the same year.…”

Enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era: validation of a multiplex amplicon-MinION sequencing method

“…Here we show that PrimalScheme overlapping PCR-amplicon based sequencing [46] of HAdV-genomes on the Oxford Nanopore platform is suitable for low Ct/high virus load stool samples. Overlapping PCR amplicon-based sequencing has been successfully deployed for outbreaks of RNA viruses such as Zika and dengue (flaviviruses), Ebola (filovirus) and SARS-CoV-2 (coronavirus) [25,32,46,47]. We applied this method to sequencing a DNA virus, enteric HAdV-F41, during a period of increased case ascertainment and identification of a new virus-associated syndrome (AHUAC) in the UK [13].…”