The Perfect Storm of 2019: An immunological and phylodynamic analysis of Cambodia’s unprecedented dengue outbreak

The year 2019 witnessed the highest number of dengue cases ever reported globally. We analyzed epidemiological, serological, and phylogenomic data to investigate the drivers of the 2019 epidemic in Cambodia. Using epidemiological models fit to a 19-year national dataset, we identified an overall trend of declining annual force of infection (FOI) for dengue virus (DENV) in Cambodia, interspersed with FOI spikes corresponding to epidemic year caseloads that exceeded demographic predictions. We constructed time-resolved phylogenetic trees with 105 DENV genomes sequenced from the 2019 Cambodian epidemic, paired with historical Southeast Asian data, to document the first-recorded introduction of DENV-2 Cosmopolitan genotype into Cambodia. This introduction yielded highly localized transmission and decreased genomic diversity when compared to endemic DENV-1, supporting the hypothesis of epidemic invasion. Introduction of this genetically distinct lineage into a population with limited prior immunity—paired with a spike in FOI—was a key driver of the 2019 Cambodian epidemic. These studies were registered at [clinicaltrials.gov][1] under [NCT04034264][2] and [NCT03534245][3]. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the Division of Intramural Research at the National Institute of Allergy and Infectious Diseases at the National Institutes of Health and the Bill and Melinda Gates Foundation. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The National Ethics Committee for Human Research of the Cambodian Ministry of Health gave ethical approval for this work. The Institutional Review Board of the US National Institutes of Health gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All genome sequence data from this study have been submitted to the NCBI Sequence Read Archive under Bioproject ID PRJNA681566. Consensus DENV sequences are also available in GenBank, under the following accession numbers: DENV-1: [OK159935][4]-[OK159976][5], [OL411495][6]-[OL411499][7], and [OL412140][8], [OL412678][9], and [OL412703][10]; DENV-2: [OL414717][11]-[OL414765][12], [OL412740][13], [OL420733][14] and [OL435143][15]; DENV-4: [MZ976858][16]-[MZ976860][17]). [1]: http://clinicaltrials.gov [2]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT04034264&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [3]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT03534245&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [4]: /lookup/external-ref?link_type=GEN&access_num=OK159935&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [5]: /lookup/external-ref?link_type=GEN&access_num=OK159976&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [6]: /lookup/external-ref?link_type=GEN&access_num=OL411495&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [7]: /lookup/external-ref?link_type=GEN&access_num=OL411499&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [8]: /lookup/external-ref?link_type=GEN&access_num=OL412140&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [9]: /lookup/external-ref?link_type=GEN&access_num=OL412678&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [10]: /lookup/external-ref?link_type=GEN&access_num=OL412703&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [11]: /lookup/external-ref?link_type=GEN&access_num=OL414717&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [12]: /lookup/external-ref?link_type=GEN&access_num=OL414765&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [13]: /lookup/external-ref?link_type=GEN&access_num=OL412740&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [14]: /lookup/external-ref?link_type=GEN&access_num=OL420733&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [15]: /lookup/external-ref?link_type=GEN&access_num=OL435143&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [16]: /lookup/external-ref?link_type=GEN&access_num=MZ976858&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom [17]: /lookup/external-ref?link_type=GEN&access_num=MZ976860&atom=%2Fmedrxiv%2Fearly%2F2022%2F06%2F09%2F2022.06.08.22276171.atom