Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jun 21;15(7):1408.
doi: 10.3390/v15071408.

Genomic Surveillance of Recent Dengue Outbreaks in Colombo, Sri Lanka

Sachith Maduranga  1   2 , Braulio Mark Valencia  2 , Chathurani Sigera  3 , Thiruni Adikari  1 , Praveen Weeratunga  3 , Deepika Fernando  3 , Senaka Rajapakse  3 , Andrew R Lloyd  2 , Rowena A Bull  1   2 , Chaturaka Rodrigo  1   2
Affiliations

Genomic Surveillance of Recent Dengue Outbreaks in Colombo, Sri Lanka

Sachith Maduranga et al. Viruses. .

Abstract

All four serotypes of the dengue virus (DENV1-4) cause a phenotypically similar illness, but serial infections from different serotypes increase the risk of severe disease. Thus, genomic surveillance of circulating viruses is important to detect serotype switches that precede community outbreaks of disproportionate magnitude. A phylogenetic analysis was conducted on near full length DENV genomes sequenced from serum collected from a prospective cohort study from the Colombo district, Sri Lanka during a 28-month period using Oxford nanopore technology, and the consensus sequences were analyzed using maximum likelihood and Bayesian evolutionary analysis. From 523 patients, 328 DENV sequences were successfully generated (DENV1: 43, DENV2: 219, DENV3:66). Most circulating sequences originated from a common ancestor that was estimated to have existed from around 2010 for DENV2 and around 2015/2016 for DENV1 and DENV3. Four distinct outbreaks coinciding with monsoon rain seasons were identified during the observation period mostly driven by DENV2 cosmopolitan genotype, except for a large outbreak in 2019 contributed by DENV3 genotype I. This serotype switch did not result in a more clinically severe illness. Phylogeographic analyses showed that all outbreaks started within Colombo city and then spread to the rest of the district. In 2019, DENV3 genotype I, previously, rarely reported in Sri Lanka, is likely to have contributed to a disease outbreak. However, this did not result in more severe disease in those infected, probably due to pre-existing DENV3 immunity in the community. Targeted vector control within Colombo city before anticipated seasonal outbreaks may help to limit the geographic spread of outbreaks.

Keywords: Sri Lanka; dengue; epidemiology; genotype; phylogenetics; phylogeography; serotype.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Panel (a)—Colombo district within Sri Lanka, Panel (b)—Colombo city (shaded dark red) within the Colombo district, Panel (c)—Postcodes 00100—01500 of Colombo city.
Figure 2
Figure 2
Flowchart showing sequence selection for each component of analysis. General phylogenies were made with 328 sequences meeting quality control requirements. Outbreak and phylogeography analyses were performed with sequences isolated from people resident within the Colombo district (n = 228).
Figure 3
Figure 3
Maximum Clade Credibility tree generated from Bayesian evolutionary analysis (BEAST) with nodes collapsed to show only those with posterior probability >0.5. DENV1—red, DENV2—green, DENV3—blue. The timeline is in calendar years.
Figure 4
Figure 4
Monthly dengue case numbers reported (Source: Epidemiology Unit, Ministry of Health, Sri Lanka) from September 2017 to January 2020 (red) superimposed on the 10-year (2010–2020) mean of the same parameter (blue). The temporal outbreak bins are shaded in yellow, green, pale blue and purple, respectively.
Figure 5
Figure 5
Maximum Clade Credibility (MCC) trees generated from (A) Cluster Q (DENV2 cosmopolitan sequences from April 2018 to September 2018), (B) Cluster R (DENV2 cosmopolitan sequences from April 2019 to January 2020), (C) Cluster S (DENV2 cosmopolitan sequences from April 2019 to January 2020), and (D) Cluster T (DENV3 genotype I sequences from April 2018 to September 2018). The branches are collapsed to show nodes with a posterior probability >0.5. The timeline at the bottom of each tree shows the time of existence of each extant sequence and their ancestors. The tips (circles) show postcodes of extant sequences, and nodes (squares) show imputed postcodes of ancestral sequences. Postcodes starting with 0 are within Colombo city and those starting with 1 are outside the city. The root of the whole tree indicates the most likely postcode of the most recent common ancestor.
Figure 5
Figure 5
Maximum Clade Credibility (MCC) trees generated from (A) Cluster Q (DENV2 cosmopolitan sequences from April 2018 to September 2018), (B) Cluster R (DENV2 cosmopolitan sequences from April 2019 to January 2020), (C) Cluster S (DENV2 cosmopolitan sequences from April 2019 to January 2020), and (D) Cluster T (DENV3 genotype I sequences from April 2018 to September 2018). The branches are collapsed to show nodes with a posterior probability >0.5. The timeline at the bottom of each tree shows the time of existence of each extant sequence and their ancestors. The tips (circles) show postcodes of extant sequences, and nodes (squares) show imputed postcodes of ancestral sequences. Postcodes starting with 0 are within Colombo city and those starting with 1 are outside the city. The root of the whole tree indicates the most likely postcode of the most recent common ancestor.
Figure 5
Figure 5
Maximum Clade Credibility (MCC) trees generated from (A) Cluster Q (DENV2 cosmopolitan sequences from April 2018 to September 2018), (B) Cluster R (DENV2 cosmopolitan sequences from April 2019 to January 2020), (C) Cluster S (DENV2 cosmopolitan sequences from April 2019 to January 2020), and (D) Cluster T (DENV3 genotype I sequences from April 2018 to September 2018). The branches are collapsed to show nodes with a posterior probability >0.5. The timeline at the bottom of each tree shows the time of existence of each extant sequence and their ancestors. The tips (circles) show postcodes of extant sequences, and nodes (squares) show imputed postcodes of ancestral sequences. Postcodes starting with 0 are within Colombo city and those starting with 1 are outside the city. The root of the whole tree indicates the most likely postcode of the most recent common ancestor.
Figure 5
Figure 5
Maximum Clade Credibility (MCC) trees generated from (A) Cluster Q (DENV2 cosmopolitan sequences from April 2018 to September 2018), (B) Cluster R (DENV2 cosmopolitan sequences from April 2019 to January 2020), (C) Cluster S (DENV2 cosmopolitan sequences from April 2019 to January 2020), and (D) Cluster T (DENV3 genotype I sequences from April 2018 to September 2018). The branches are collapsed to show nodes with a posterior probability >0.5. The timeline at the bottom of each tree shows the time of existence of each extant sequence and their ancestors. The tips (circles) show postcodes of extant sequences, and nodes (squares) show imputed postcodes of ancestral sequences. Postcodes starting with 0 are within Colombo city and those starting with 1 are outside the city. The root of the whole tree indicates the most likely postcode of the most recent common ancestor.
See this image and copyright information in PMC

References

    1. Horstick O., Tozan Y., Wilder-Smith A. Reviewing Dengue: Still a Neglected Tropical Disease? PLoS Negl. Trop. Dis. 2015;9:e0003632. doi: 10.1371/journal.pntd.0003632. - DOI - PMC - PubMed
    1. Bhatt S., Gething P.W., Brady O.J., Messina J.P., Farlow A.W., Moyes C.L., Drake J.M., Brownstein J.S., Hoen A.G., Sankoh O., et al. The global distribution and burden of dengue. Nature. 2013;496:504–507. doi: 10.1038/nature12060. - DOI - PMC - PubMed
    1. Brady O.J., Gething P.W., Bhatt S., Messina J.P., Brownstein J.S., Hoen A.G., Moyes C.L., Farlow A.W., Scott T.W., Hay S.I. Refining the Global Spatial Limits of Dengue Virus Transmission by Evidence-Based Consensus. PLoS Negl. Trop. Dis. 2012;6:e1760. doi: 10.1371/journal.pntd.0001760. - DOI - PMC - PubMed
    1. Harapan H., Michie A., Sasmono R.T., Imrie A. Dengue: A Minireview. Viruses. 2020;12:829. doi: 10.3390/v12080829. - DOI - PMC - PubMed
    1. World Health Organization . Dengue Guidelines for Diagnosis, Treatment, Prevention and Control: New Edition. World Health Organization; Geneva, Switzerland: 2009. - PubMed

Publication types