A new lineage nomenclature to aid genomic surveillance of dengue virus

Shifting Dynamics of DENV2 in Costa Rica: Emergence of the Cosmopolitan Genotype (2024)

Dengue remains a major public health challenge. In Costa Rica, we implemented the first nationwide genomic surveillance to track the emergence of the DENV2 Cosmopolitan genotype. Phylogenetic and eco-epidemiological analyses revealed early detection, climate-linked spread, and spatial heterogeneity. Findings underscore the need for integrated surveillance to guide adaptive responses to emerging arboviral threats.

Clinico-genomic study reveals association of dengue virus genome high frequency mutations with dengue disease severity

Transmission of the dengue virus (DENV) places a huge burden on public health in several endemic regions. Like other RNA viruses, mutations in the DENV genome greatly governs its virulence, transmissibility, and interaction with the host immune system. Present study focuses on integrated analysis of mutation and clinical data accompanied at the onset of dengue fever. The findings from the associated clinical data with the variants of the DENV are critical for early detection of the disease and understanding the disease progression. RNA was isolated from the 1310 serum samples collected from the NS1-antigen positive dengue patients. Serotyping reveals that DENV-2 was predominant in circulation. The genome of 1305 DENV-2 was sequenced using Oxford Nanopore Technology and Illumina platforms. A total of 1023 DENV-2 demonstrated > 50% genome coverage. Mutation analysis across the 1023 DENV-2 genomes yielded a total of 2667 mutations including 627 non-synonymous and 2040 synonymous mutations. We observed a notable over-representation of synonymous mutations in prM and ancC genes while a higher occurrence of non-synonymous mutations was found in ancC, prM, and M proteins. Comparison of mutation frequency between mild and severe demonstrates higher mutation frequency in severe phenotype. Moreover, we observed a total of 56 significant mutations including 23 in severe, 17 in moderate and 16 in mild. The E-protein having non-synonymous mutations were docked with DC-SIGN with lower binding energy (ΔG = - 11.9 kcal/mol) for severe as compared to mild (ΔG = - 13.5 kcal/mol), suggesting lesser affinity of E-protein and DC-SIGN in case of severe as compared to the mild. We have identified the core set of high frequency mutations significantly associated with distinct dengue disease severity viz., mild, moderate and severe. Furthermore, in-silico protein modelling and docking studies demonstrate the potential functional role of the non-synonymous mutations identified across E-protein in severe dengue.

Whole genome characterization of Torque teno sus virus 1 (TTSuV1) in wild and domestic pigs: insights into genetic classification, host differentiation, and intra-host variation

Background

Torque teno sus virus 1 (TTSuV1), a member of the Anelloviridae family, is highly prevalent in swine populations and exhibits substantial genetic diversity. Despite its ubiquity, TTSuV1 remains understudied, particularly regarding its genetic diversity, host-specific differentiation, and intra-host variation. These characteristics are critical for understanding its evolution, transmission dynamics, and potential applications in biosecurity monitoring.

Methods

Field and laboratory protocols included capturing wild pigs, collecting whole blood samples, and screening for TTSuV1-positive samples through PCR. TOPO TA cloning was used to amplify individual viral variants within hosts, and whole genome sequencing (WGS) was performed on selected clones. A dated phylogenetic tree was reconstructed using TTSuV1 whole genome sequences obtained from wild pig samples in this study and all available sequences from NCBI. To evaluate genetic differentiation between wild and domestic pigs, partial viral sequences (~700 bp) were analyzed using phylogenetic D statistic and analysis of molecular variance (AMOVA). Intra-host variation was assessed by calculating pairwise identity percentages among viral clones from individual hosts and constructing haplotype networks.

Results

Phylogenetic analysis of whole genome sequences grouped TTSuV1 into four clades, with sequences from wild pigs distributed across all clades. Known subtypes 1a, 1b, and 1c were localized within Clades 3 and 4, leaving sequences in Clades 1 and 2 with unidentified subtypes. Partial sequence analysis revealed significant host-specific genetic differentiation: the D statistic confirmed a non-random association between host type (wild vs. domestic) and phylogeny, and AMOVA further showed contributions of both host type and geography to overall variation. Intra-host variation analysis provided evidence for multiple sources of genetic diversity within individual hosts. Pairwise identity percentages among viral clones ranged from 63.6% to 100%, with lower identity values indicating co-infection with distinct viral variants. Haplotype network analysis revealed mutational steps between haplotypes from the same host, suggesting that intra-host evolution also contributes to within-host genetic variation.

Conclusions

This study highlights the significant genetic diversity and host-specific differentiation of TTSuV1, with wild pigs playing a key role in its evolution. Both intra-host evolution and co-infection contribute to its diversity, underscoring its potential as a tool for monitoring biosecurity risks and cross-transmission between wild and domestic pigs.

Detection and molecular characterization of dengue among patients suspected of having malaria in Timika, Central Papua, Indonesia

BACKGROUND

Dengue and malaria are major public health problems in Indonesia. Dengue is hyperendemic nationwide, while malaria remains endemic in specific regions, especially in eastern Indonesia. Timika in Central Papua province is a highly malaria-endemic area; however, this city is historically known as a low endemic area for dengue. With the increasing incidence of dengue in Papua, this study aimed to assess dengue prevalence, possible co-infection and to molecularly characterize the dengue virus (DENV) in patients suspected of having malaria.

METHODS

Archived samples of patients suspected of having malaria were screened for dengue using RT-PCR. Dengue serological and antigen detection was performed and whole genome sequencing was employed to determine the genetic characteristics of viruses. Detection of other arboviruses was also performed.

RESULTS

Among 119 patients, 30 (25.2%) were positive for dengue. Most samples (n=29) were infected by DENV-3, while one was positive for DENV-2. Dengue and malaria co-infections were found in six patients. Phylogenetic analysis classified DENV-2 as the Cosmopolitan genotype that is closely related to strains from the Indonesian city of Makassar, while DENV-3 was classified as Genotype I, which is closely related to a strain from Singapore.

CONCLUSIONS

Dengue significantly contributes to febrile illness among patients suspected of having malaria in Timika, Central Papua. Virus importation from surrounding regions is likely to contribute to the dispersion of DENV into eastern parts of Indonesia. Our findings reveal the underestimation of this viral disease in a highly malaria-endemic area.

Genomic hotspots in the DENV-2 serotype (E, NS4B, and NS5 genes) are associated with dengue disease severity in the endemic region of India

Dengue virus (DENV) infection manifests a wide spectrum of clinical outcomes, ranging from mild fever to severe and potentially fatal disease, yet the factors driving this variability remain poorly understood. This study aims to unravel the relationship between clinical manifestations of dengue and the genetic diversity of the virus, providing insights into the genomic variability driving disease severity. To achieve this, serum samples were collected during a dengue outbreak in National Capital Region-Delhi, India, from June to November 2023. Serotyping of RNA isolated from 4,045 clinical serum samples revealed DENV-2 as the predominant serotype in circulation (n = 3702). Whole-genome sequencing for 3702 clinical samples was performed using Oxford Nanopore Technology (ONT) further yielding 3254 DENV-2 genomes with >50% coverage. However, all of them identified the cosmopolitan genotype of DENV-2, forming a distinct monophyletic cluster in the global phylogenetic tree. Comprehensive variant analysis uncovered 1,618,158 single nucleotide variations (SNVs) across the sequenced DENV-2 population. The clinico-genomic approach carried out in 1294 samples, mild (n = 473), moderate (n = 405) and clinically severe (n = 416), reveals a significant burden of SNVs in various genomic regions linked to differential disease outcomes. Statistical analyses, including Fisher's exact test and phi-correlation, identified hotspot regions in the Envelope (E), NS4B, and NS5 genes, where SNVs were strongly associated with mild and clinically severe phenotypes, providing insights into the genomic determinants of disease severity. Interestingly, the clustering of severity-associated SNVs in these genomic hotspot regions highlights their potential as therapeutic targets within the DENV genome. These findings offer a promising direction for developing early mitigation strategies and targeted interventions to manage the progression of severe DENV infections.

Reassessing the dengue virus type 4 in Brazil: Genomic sequencing and dispersion dynamics, 2011-2017

Orthoflavivirus denguei (Dengue virus) type 4; (DENV-4) has emerged as a significant public health concern in Brazil, particularly following its reintroduction in the early 21st century. This study provides a comprehensive analysis of DENV-4's genetic characterization and its spatiotemporal dynamics reassessment within Brazil, with a focus on the period between 2010 and 2017. We performed direct genomic sequencing on 24 human samples obtained from various Brazilian states using a multiplex sequencing approach on the Ion Torrent platform. Phylogenetic analysis revealed that the new isolates belong exclusively to the genotype 4II, lineage 4II_B.1.1, with no detection of genotype 4I, which was previously identified in Brazil. This absence of genotype 4I in our findings suggests a potential decline, not adaptation to mosquito host, sub endemic circulation or displacement of this genotype in the country. The phylogeographic analysis indicates multiple introduction events of genotype 4II into Brazil, with significant dispersion across different regions, including the North, Northeast, Midwest, and Southeast. The temporal analysis confirmed a robust evolutionary signal, supporting the observed phylogenetic clustering. Eighteen of the 24 genomes in this study had unique nonsynonymous mutations across the entire coding sequences and seven genomes showed mutations that altered the biochemical property of the amino acids at E, NS1, NS2B, NS3,and NS5 genes compared with genotype 4I. Our findings underscore the ongoing spread of DENV-4 within Brazil, and in the Americas driven by complex networks of viral dispersion, and highlight the dynamic nature of DENV-4 genotype distribution. This study emphasizes the importance of advanced direct genomic sequencing tools in understanding the DENV-4 dynamics and spreading, providing critical insights for public health strategies on genomic surveillance to control further dengue outbreaks.

The Genetic Evolution of DENV2 in the French Territories of the Americas: A Retrospective Study from the 2000s to the 2024 Epidemic, Including a Comparison of Amino Acid Changes with Vaccine Strains

BACKGROUND

Dengue virus type 2 (DENV2) is endemic to hyperendemic in the French territories of the Americas (FTAs), including French Guiana, Guadeloupe, Martinique, Saint-Barthelemy, and Saint-Martin. In 2023-2024, French Guiana, Martinique, and Guadeloupe experienced unprecedented dengue epidemics partly associated with this serotype. In response, we conducted a retrospective study of the diversity of DENV2 strains circulating in the FTAs from 2000 to 2024.

METHODS

To this end, we selected DENV2 samples from the collection at the National Research Center for Arboviruses in French Guiana (NRCA-FG) and sequenced them using Oxford Nanopore Technologies (ONT)-based next-generation sequencing (NGS).

RESULTS

Phylogenetic analysis revealed that (i) the 77 DENV2 sequences from the FTAs belong to two distinct genotypes-Asian American and Cosmopolitan; (ii) from the 2000s up to the 2019 epidemic in French Guiana, all sequenced strains belonged to the Asian American genotype; (iii) and from 2019 to 2020, strains circulating in Martinique and Guadeloupe belonged to the Cosmopolitan genotype, specifically the Indian subcontinent sublineage, while (iv) strains from the 2023-2024 outbreak in Martinique, Guadeloupe, and French Guiana fall within a distinct sublineage of the same genotype-Other Cosmopolitan. Additionally, we analyzed amino acid (AA) changes in FTA sequences compared to the Dengvaxia® and Qdenga® vaccines. The analysis of amino acid changes in FTA sequences compared to the vaccines (Dengvaxia® and Qdenga®) identified 42 amino acid changes in the prM/E regions (15 in the prM region and 27 in the E region) relative to CYD-2 Dengvaxia® and 46 amino acid changes in the prM/E regions relative to Qdenga®, including 16 in the prM region and 30 in the E region. Some of these AA changes are shared across multiple genotypes and sublineages, with 8 substitutions in the prM region and 18 in the E region appearing in both analyses. This raises questions about the potential impact of these changes on vaccine efficacy.

CONCLUSION

Overall, these findings provide a current overview of the genomic evolution of DENV2 in the FTA, which is crucial for developing more effective prevention and control strategies and for selecting future vaccines tailored to circulating strains.

Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022-2023

In Ethiopia, dengue virus (DENV) infections have been reported in several regions; however, little is known about the genetic diversity of circulating viruses. We conducted clinical surveillance of DENV during the 2023 nationwide outbreak in Ethiopia. We enrolled patients at 3 sentinel hospital sites. Using reverse transcription PCR, we screened serum samples for 3 arboviruses and then serotyped and whole-genome sequenced DENV-positive samples. We detected DENV-1 and DENV-3 serotypes. Phylogenetic analysis identified 1 transmission cluster for DENV-1 (genotype III major lineage A) and 2 clusters for DENV-3 (genotype III major lineage B). The first DENV-3 cluster was closely related to an isolate from a 2023 dengue outbreak in Italy; the second cluster was related to isolates from India. Co-circulation of DENV-1 and DENV-3 in Ethiopia highlights the potential for severe dengue. Intensified surveillance and coordinated public health responses are needed to address the threat of severe dengue outbreaks.

Lineage B Genotype III of Dengue Virus Serotype 3 (DENV-3III_B) Is Responsible for Dengue Outbreak in Dire Dawa City, Ethiopia, 2023

The eastern parts of Ethiopia, including Dire Dawa City, have experienced annual dengue fever (DF) outbreaks since 2013, leading to significant healthcare and economic impacts. However, comprehensive evidence on the specific dengue virus (DENV) serotypes and genotypes involved remains limited. During the 2023 DF outbreak, the National Arbovirus Laboratory received seventy serum samples from suspected DF patients. Positive samples underwent sequencing of the CprM region of the DENV genome, and the obtained sequences were analyzed phylogenetically. Among the patients, 32 (45.7%) displayed early warning signs of severe dengue, and 13 were hospitalized, most showing symptoms indicative of severe dengue. Out of 67 adequate samples, 44 (65.6%) tested positive for DENV RNA by RT-PCR, and 17 successfully underwent CprM sequencing. All sequenced samples were identified as DENV-3, genotype III, major lineage B (DENV-3III_B), with two distinct minor lineages (DENV-3III_B.2 and DENV-3III_B.3). Phylogenetic analysis showed that these lineages were closely related to sequences from the Afar region, suggesting interconnected outbreaks with multiple co-circulating lineages. This study identifies DENV-3III_B as the cause of the 2023 DF outbreak in Dire Dawa City and highlights the need for enhanced viral genomic surveillance in Africa.

Craft: A Machine Learning Approach to Dengue Subtyping

Motivation

The dengue virus poses a major global health threat, with nearly 390 million infections annually. A recently proposed hierarchical dengue nomenclature system enhances spatial resolution by defining major and minor lineages within genotypes, aiding efforts to track viral evolution. While current subtyping tools - Genome Detective, GLUE, and NextClade - rely on computationally intensive sequence alignment and phylogenetic inference, machine learning presents a promising alternative for achieving accurate and rapid classification.

Results

We present Craft (Chaos Random Forest), a machine learning framework for dengue subtyping. We demonstrate that Craft is capable of faster classification speeds while matching or surpassing the accuracy of existing tools. Craft achieves 99.5% accuracy on a hold-out test set and processes over 140 000 sequences per minute. Notably, Craft maintains remarkably high accuracy even when classifying sequence segments as short as 700 nucleotides.

Reemerging Infectious Diseases and Neuroimmunologic Complications

During the past decade (and beyond), neurologists have become aware of the emergence, persistence, and consequences of some familiar and new infections affecting the nervous system. Even among the familiar CNS infections, such as herpes virus, polyoma virus/JC, influenza, arbovirus, and hepatitis, challenges remain in developing effective antiviral treatments and treatments of postinfection sequelae. With the changing environment and increased global travel, arthropod vectors that mediate zoonotic disease transmission have spread unfamiliar viruses such as West Nile virus, dengue, chikungunya, equine encephalitis, and Zika, among others. Although the global health impact of these diseases has not risen to that of COVID-19 and HIV, it is likely to dramatically increase with continued spread of transmission vectors and the emergence of new zoonotic animal-to-human diseases mediated by those transmission vectors. Furthermore, specific virus-targeting treatments or effective vaccines for arboviral infections are not yet available, and this represents a major challenge in limiting the morbidity of these infections. By contrast, HIV-1, a disease that originated by direct transmission from nonhuman primates to humans (as early as the 1930s), after many years of intense study, is now targeted by highly specific and effective antiviral drugs that can limit the spread of infection and extend human life and health in all populations. Even with these dramatic therapeutic effects of suppressing HIV replication, neurologic dysfunction (primarily cognitive impairment) affects significant numbers of persons living with HIV. This emphasizes not only the importance of treating the underlying infection but also developing treatments for legacy effects of the initial infection even after antiviral therapy. Notably, the rapid emergence of SARS-CoV-2 infection was met with rapid implementation of highly effective and specific antiviral therapies. This resulted in early and dramatic lowering of the morbidity and mortality of SARS-CoV-2 infection. Nonetheless, the postinfectious complications of SARS-CoV-2 infection (long COVID) are now among the more costly consequences of emerging zoonotic infections worldwide. Developing new antiviral therapies that can penetrate the CNS, vaccines, and therapies that target host immune responses and metabolic dysfunction will be necessary for management of infectious and postinfectious complications of established and emerging infections.

Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa

Despite the increasing burden of dengue in Kenya and Africa, the introduction and expansion of the virus in the region remain poorly understood. The objective of this study is to examine the genetic diversity and evolutionary histories of dengue virus (DENV) serotypes 1 and 3 in Kenya and contextualize their circulation within circulation dynamics in the broader African region. Viral RNA was extracted from samples collected from a cohort of febrile patients recruited at clinical sites in Kenya from 2013 to 2022. Samples were tested by polymerase chain reaction (PCR) for DENV presence. Five DENV-positive samples were serotyped, and complete viral genomes for phylogenetic inference were obtained via sequencing on Illumina platforms. Sequences generated in our study were combined with global datasets of sequences, and Bayesian and maximum likelihood methods were used to infer phylogenetic trees and geographic patterns of spread with a focus on Kenya and Africa as a whole. Four new DENV-1 and one new DENV-3 genomes were successfully sequenced and combined with 328 DENV-1 and 395 DENV-3 genomes from elsewhere for phylogenetic analyses. The DENV-1 sequences from our study formed a monophyletic cluster with an inferred common ancestor in 2019 (most recent common ancestor 2019 and 95% high posterior density 2018-19), which was closely related to sequences from Tanzania. The single DENV-3 sequence clustered with sequences from Tanzania and Kenya, was collected between 2017 and 2019 and was related to recent outbreaks in the region. Phylogenetic trees resolved multiple clades of DENV-1 and DENV-3 concurrently circulating in Africa, introduced in the early-to mid-2000s. Three DENV-1 and four DENV-3 clades are highlighted, introduced between 2000 and 2015. Phylogeographic models suggest frequent, independent importations of DENV lineages into Kenya and Africa from East and South-East Asia via distinct geographic pathways. DENV-1 and DENV-3 evolutionary dynamics in Africa are characterized by the cocirculation of multiple recently introduced lineages. Circulating lineages are introduced via distinct geographic pathways that may be centered around regional nexus locations. Increased surveillance is required to identify key regional locations that drive spread, and dengue interventions should focus on interrupting spread at these locations.

PLOS Biology and the life sciences in 2024

As we reach the end of 2024, we celebrate an amazing year of science for PLOS Biology and the life sciences more broadly, and thank everyone who continues to support the journal.

Genomics-based timely detection of dengue virus type I genotypes I and V in Uruguay

This study details a genomics-based approach for the early detection of mosquito-borne pathogens, marked by Uruguay's first ever complete genomic sequencing of Dengue Virus type I genotypes I and V. This pioneering effort has facilitated the prompt identification of these genotypes within the country, enabling Uruguayan public health authorities to develop timely and effective response strategies. Further integrated into this approach is a climate-driven suitability measure, closely associated with Dengue case reports and indicative of the local climate's role in the virus's transmission in the country within the changing climate context. The detection of multiple DENV-1 genotypes co-circulating in Uruguay underscores the necessity for proactive surveillance, particularly at borders, to prevent the introduction and dissemination of novel viral strains within the country and the region. This approach aids in facilitating prompt public health responses and intervention strategies, which are crucial in mitigating the impact of dengue outbreaks.

Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023-2024

Dengue cases rose to record levels during 2023-2024. We investigated dengue in Valle del Cauca, Colombia, to determine if specific virus serotypes or lineages caused its large outbreak. We detected all 4 serotypes and multiple lineages, suggesting that factors such as climatic conditions were likely responsible for increased dengue in Colombia.

Genomic surveillance reveals a dengue 2 virus epidemic lineage with a marked decrease in sensitivity to Mosnodenvir

Dengue fever is the most important arbovirosis for public health, with more than 5 million cases worldwide in 2023. Mosnodenvir is the first anti-dengue compound with very high preclinical pan-serotype activity, currently undergoing phase 2 clinical evaluation. Here, by analyzing dengue virus (DENV) genomes from the 2023-2024 epidemic in the French Caribbean Islands, we show that they all exhibit mutation NS4B:V91A, previously associated with a marked decrease in sensitivity to mosnodenvir in vitro. Using antiviral activity tests on four clinical and reverse-genetic strains, we confirm a marked decrease in mosnodenvir sensitivity for DENV-2 ( > 1000 fold). Finally, combining phylogenetic analysis and experimental testing for resistance, we find that virus lineages with low sensitivity to mosnodenvir due to the V91A mutation likely emerged multiple times over the last 30 years in DENV-2 and DENV-3. These results call for increased genomic surveillance, in particular to track lineages with resistance mutations. These efforts should allow to better assess the activity profile of DENV treatments in development against circulating strains.

Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia

Dengue fever remains as a public health challenge in Colombia, standing as the most prevalent infectious disease in the country. The cyclic nature of dengue epidemics, occurring approximately every 3 years, is intricately linked to meteorological events like El Niño Southern Oscillation (ENSO). Therefore, the Colombian system faces challenges in genomic surveillance. This study aimed to evaluate local dengue virus (DENV) transmission and genetic diversity in four Colombian departments with heterogeneous incidence patterns (department is first-level territorial units in Colombia). For this study, we processed 266 serum samples to identify DENV. Subsequently, we obtained 118 genome sequences by sequencing DENV genomes from serum samples of 134 patients infected with DENV-1 and DENV-2 serotypes. The predominant serotype was DENV-2 (108/143), with the Asian-American (AA) genotype (91/118) being the most prevalent one. Phylogenetic analysis revealed concurrent circulation of two lineages of both DENV-2 AA and DENV-1 V, suggesting ongoing genetic exchange with sequences from Venezuela and Cuba. The continuous migration of Venezuelan citizens into Colombia can contribute to this exchange, emphasizing the need for strengthened prevention measures in border areas. Notably, the time to most recent common ancestor analysis identified cryptic transmission of DENV-2 AA since approximately 2015, leading to the recent epidemic. This challenges the notion that major outbreaks are solely triggered by recent virus introductions, emphasizing the importance of active genomic surveillance. The study also highlighted the contrasting selection pressures on DENV-1 V and DENV-2 AA, with the latter experiencing positive selection, possibly influencing its transmissibility. The presence of a cosmopolitan genotype in Colombia, previously reported in Brazil and Peru, raises concerns about transmission routes, emphasizing the necessity for thorough DENV evolution studies. Despite limitations, the study underscores genomic epidemiology's crucial role in early detection and comprehension of DENV genotypes, recommending the use of advanced sequencing techniques as an early warning system to help prevent and control dengue outbreaks in Colombia and worldwide.