{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:08:00Z","timestamp":1785434880807,"version":"3.56.0"},"reference-count":49,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T00:00:00Z","timestamp":1779321600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"armasuisse W+T, the Swiss Federal Office for Defence Procurement","award":["PN R-3210\/045-13"],"award-info":[{"award-number":["PN R-3210\/045-13"]}]},{"award":["PN R-3210\/045-13"],"award-info":[{"award-number":["PN R-3210\/045-13"]}],"id":[{"id":"https:\/\/ror.org\/00pw7mk43","id-type":"ROR","asserted-by":"publisher"}]},{"name":"INOVEC","award":["101086257"],"award-info":[{"award-number":["101086257"]}]},{"name":"Rudolf Geigy Foundation","award":["200902"],"award-info":[{"award-number":["200902"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Dengue virus (DENV) poses a growing risk in Tanzania, yet its genetic diversity in mosquito populations remains poorly understood. Using Nanopore sequencing, we recovered full coding sequences from six DENV-2 positive mosquito pools collected in Dar es Salaam outside recognized outbreak periods. Phylogenetic analysis placed these sequences in a distinct monophyletic clade within genotype II, separate from strains linked to Tanzania\u2019s 2014 outbreak. Instead, they clustered with Asian lineages and showed the closest relatedness to DENV-2 strains from Kenya (2013) and India (2014), with divergence estimated to have occurred around 2010. Variant profiling identified 212 low-frequency intra-pool variants, predominantly non-synonymous changes in the NS3, NS4B, and NS5 coding regions. These results suggest a previously unrecognized introduction of genotype II that is now circulating silently within local mosquito populations. Our findings highlight the value of genomic surveillance in mosquito vectors for early detection of arboviral threats, even in the absence of reported human cases.<\/jats:p>","DOI":"10.3390\/v18050585","type":"journal-article","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T16:46:18Z","timestamp":1779381978000},"page":"585","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Evidence for Novel Introduction and Intra-Host Diversity of DENV-2 in Dar es Salaam, Tanzania"],"prefix":"10.3390","volume":"18","author":[{"given":"Silvan","family":"H\u00e4lg","sequence":"first","affiliation":[{"name":"Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland"},{"name":"Faculty of Science, University of Basel, 4051 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank S. C.","family":"Tenywa","sequence":"additional","affiliation":[{"name":"Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland"},{"name":"Faculty of Science, University of Basel, 4051 Basel, Switzerland"},{"name":"Ifakara Health Institute, Bagamoyo P.O. Box 74, Tanzania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4354-2419","authenticated-orcid":false,"given":"Nicole","family":"Liechti","sequence":"additional","affiliation":[{"name":"Spiez Laboratory, 3700 Spiez, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Beuret","sequence":"additional","affiliation":[{"name":"Spiez Laboratory, 3700 Spiez, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0938-6654","authenticated-orcid":false,"given":"Sarah J.","family":"Moore","sequence":"additional","affiliation":[{"name":"Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland"},{"name":"Faculty of Science, University of Basel, 4051 Basel, Switzerland"},{"name":"Ifakara Health Institute, Bagamoyo P.O. Box 74, Tanzania"},{"name":"Nelson Mandela African Institute of Science and Technologys, Tengeru P.O. Box 447, Tanzania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0181-5781","authenticated-orcid":false,"given":"Pie","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland"},{"name":"Faculty of Science, University of Basel, 4051 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"22592","DOI":"10.1038\/srep22592","article-title":"Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission","volume":"6","author":"Hapuarachchi","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1508","DOI":"10.1038\/s41564-019-0476-8","article-title":"The current and future global distribution and population at risk of dengue","volume":"4","author":"Messina","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_3","unstructured":"WHO (2025, August 08). Dengue and Severe Dengue: World Health Organization. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/dengue-and-severe-dengue."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1146\/annurev-ento-011019-024918","article-title":"The Global Expansion of Dengue: How Aedes aegypti Mosquitoes Enabled the First Pandemic Arbovirus","volume":"65","author":"Brady","year":"2020","journal-title":"Annu. Rev. Entomol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1016\/S0140-6736(14)60572-9","article-title":"Dengue","volume":"385","author":"Guzman","year":"2015","journal-title":"Lancet"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1038\/nrmicro2460","article-title":"Dengue: A continuing global threat","volume":"8","author":"Guzman","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.antiviral.2013.03.018","article-title":"Dengue virus neutralization and antibody-dependent enhancement activities of human monoclonal antibodies derived from dengue patients at acute phase of secondary infection","volume":"98","author":"Sasaki","year":"2013","journal-title":"Antivir. Res."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1099\/vir.0.060384-0","article-title":"Demonstration of marmosets (Callithrix jacchus) as a non-human primate model for secondary dengue virus infection: High levels of viraemia and serotype cross-reactive antibody responses consistent with secondary infection of humans","volume":"95","author":"Moi","year":"2014","journal-title":"J. Gen. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/0042-6822(90)90102-W","article-title":"Molecular evolution and distribution of dengue viruses type 1 and 2 in nature","volume":"174","year":"1990","journal-title":"Virology"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/S1567-1348(03)00004-2","article-title":"The origin, emergence and evolutionary genetics of dengue virus","volume":"3","author":"Holmes","year":"2003","journal-title":"Infect. Genet. Evol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.meegid.2015.03.006","article-title":"Genomic analysis and growth characteristic of dengue viruses from Makassar, Indonesia","volume":"32","author":"Sasmono","year":"2015","journal-title":"Infect. Genet. Evol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"veaa026","DOI":"10.1093\/ve\/veaa026","article-title":"Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype lineages","volume":"6","author":"Langat","year":"2020","journal-title":"Virus Evol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kelly, M.E., Msafiri, F., Affara, M., Gehre, F., Moremi, N., Mghamba, J., Misinzo, G., Thye, T., Gatei, W., and Whistler, T. (2023). Molecular Characterization and Phylogenetic Analysis of Dengue Fever Viruses in Three Outbreaks in Tanzania Between 2017 and 2019. PLoS Neglected Trop. Dis., 17.","DOI":"10.1371\/journal.pntd.0011289"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Mustafa, U.K., Kreppel, K.S., and Sauli, E. (2024). Dengue virus transmission during non-outbreak period in Dar Es Salaam, Tanzania: A cross-sectional survey. BMC Infect. Dis., 24.","DOI":"10.1186\/s12879-024-10109-5"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Tenywa, F.S.C., H\u00e4lg, S., Makame, H., Moore, J., Dogan, O., Mapipi, H.I., Machange, J.J., Lilolime, N.S., Hofer, L.M., and Batao, L.D. (2025). DENV-2 Circulation and Host Preference Among Highly Anthropophilic, Outdoor-Biting Aedes aegypti in Dar es Salaam, Tanzania. Viruses, 17.","DOI":"10.20944\/preprints202504.2031.v1"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Nonyong, P., Ekalaksananan, T., Phanthanawiboon, S., Overgaard, H.J., Alexander, N., Thaewnongiew, K., Sawaswong, V., Nimsamer, P., Payungporn, S., and Phadungsombat, J. (2023). Intrahost Genetic Diversity of Dengue Virus in Human Hosts and Mosquito Vectors under Natural Conditions Which Impact Replicative Fitness In Vitro. Viruses, 15.","DOI":"10.3390\/v15040982"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.chom.2017.08.003","article-title":"Intrahost Selection Pressures Drive Rapid Dengue Virus Microevolution in Acute Human Infections","volume":"22","author":"Parameswaran","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Morrison, A.C., Zielinski-Gutierrez, E., Scott, T.W., and Rosenberg, R. (2008). Defining challenges and proposing solutions for control of the virus vector Aedes aegypti. PLoS Med., 5.","DOI":"10.1371\/journal.pmed.0050068"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e01210-22","DOI":"10.1128\/spectrum.01210-22","article-title":"Serotype-specific and multiplex PCR method for whole genome sequencing of Dengue virus directly from clinical samples","volume":"10","author":"Su","year":"2022","journal-title":"ASM Microbiol. Spectr."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet.journal Tech. Notes"},{"key":"ref_21","unstructured":"Wick, R. Filtlong, GitHub repository. Available online: https:\/\/github.com\/rrwick\/Filtlong."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar","volume":"20","author":"Grubaugh","year":"2019","journal-title":"Genome Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Bouckaert, R., Vaughan, T.G., Barido-Sottani, J., Duchene, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kuhnert, D., and De Maio, N. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol., 15.","DOI":"10.1371\/journal.pcbi.1006650"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"veaf013","DOI":"10.1093\/ve\/veaf013","article-title":"Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis","volume":"11","author":"Sun","year":"2025","journal-title":"Virus Evol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"ref_29","unstructured":"Rambaut, A. (2010). FigTree, v1.4.1, Institute of Evolutionary Biology, University of Edinburgh."},{"key":"ref_30","unstructured":"Wickham, H. (2016). Elegant Graphics for Data Analysis, Springer Nature."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"ref_32","unstructured":"Krassowski, M. ComplexUpset: Flexible UpSet plots for set visualization. R package version (CRAN). Available online: https:\/\/cran.r-project.org\/package=ComplexUpset."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: Visualization of Intersecting Sets","volume":"20","author":"Lex","year":"2014","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"895","DOI":"10.3201\/eid2205.151462","article-title":"Clinical, Virologic, and Epidemiologic Characteristics of Dengue Outbreak, Dar es Salaam, Tanzania, 2014","volume":"22","author":"Vairo","year":"2016","journal-title":"Emerg. Infect. Dis."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Phadungsombat, J., Nakayama, E.E., and Shioda, T. (2024). Unraveling Dengue Virus Diversity in Asia: An Epidemiological Study through Genetic Sequences and Phylogenetic Analysis. Viruses, 16.","DOI":"10.3390\/v16071046"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Masika, M.M., Korhonen, E.M., Smura, T., Uusitalo, R., Vapalahti, K., Mwaengo, D., Jaaskelainen, A.J., Anzala, O., Vapalahti, O., and Huhtamo, E. (2020). Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya. PLoS Neglected Trop. Dis., 14.","DOI":"10.1371\/journal.pntd.0008099"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"7832","DOI":"10.1038\/s41467-024-51018-0","article-title":"Molecular epidemiology and evolutionary characteristics of dengue virus 2 in East Africa","volume":"15","author":"Nyathi","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.ijid.2023.04.391","article-title":"Phylogeographic analysis of dengue virus serotype 1 and cosmopolitan serotype 2 in Africa","volume":"133","author":"Selhorst","year":"2023","journal-title":"Int. J. Infect. Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e1043","DOI":"10.1016\/S2542-5196(24)00272-9","article-title":"Dengue virus importation risks in Africa: A modelling study","volume":"8","author":"Poongavanan","year":"2024","journal-title":"Lancet Planet Health"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Drumond, B.P., Mondini, A., Schmidt, D.J., de Morais Bronzoni, R.V., Bosch, I., and Nogueira, M.L. (2013). Circulation of different lineages of Dengue virus 2, genotype American\/Asian in Brazil: Dynamics and molecular and phylogenetic characterization. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0059422"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1006\/viro.1997.8504","article-title":"Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas","volume":"230","author":"Harrison","year":"1997","journal-title":"Virology"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s13059-016-0907-2","article-title":"Genomic approaches for understanding dengue: Insights from the virus, vector, and host","volume":"17","author":"Sim","year":"2016","journal-title":"Genome Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"11296","DOI":"10.1128\/JVI.77.20.11296-11298.2003","article-title":"Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus","volume":"77","author":"Holmes","year":"2003","journal-title":"J. Virol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S0065-3527(03)59002-9","article-title":"Molecular biology of flaviviruses","volume":"59","author":"Lindenbach","year":"2003","journal-title":"Adv. Virus Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1016\/j.tim.2018.02.007","article-title":"Within-Host Evolution of Human Influenza Virus","volume":"26","author":"Xue","year":"2018","journal-title":"Trends Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"8546","DOI":"10.1128\/JVI.00736-12","article-title":"Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity","volume":"86","author":"Parameswaran","year":"2012","journal-title":"J. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Salvo, M.A., Aliota, M.T., Moncla, L.H., Velez, I.D., Trujillo, A.I., Friedrich, T.C., and Osorio, J.E. (2019). Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic area in Colombia. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0212947"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1016\/S1473-3099(16)30473-X","article-title":"Dengue: Knowledge gaps, unmet needs, and research priorities","volume":"17","author":"Katzelnick","year":"2017","journal-title":"Lancet Infect. Dis."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Napit, R., Elong Ngono, A., Mihindukulasuriya, K.A., Pradhan, A., Khadka, B., Shrestha, S., Droit, L., Paredes, A., Karki, L., and Khatiwada, R. (2024). Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10879-x"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/5\/585\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T02:39:01Z","timestamp":1780454341000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/5\/585"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,21]]},"references-count":49,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["v18050585"],"URL":"https:\/\/doi.org\/10.3390\/v18050585","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.11.17.688789","asserted-by":"object"}]},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,21]]}}}