Nationwide Distribution of Dengue Virus Type 3 (DENV-3) Genotype I and Emergence of DENV-3 Genotype III during the 2019 Outbreak in Bangladesh

Re-Emergence of DENV-3 in French Guiana: Retrospective Analysis of Cases That Circulated in the French Territories of the Americas from the 2000s to the 2023-2024 Outbreak

French Guiana experienced an unprecedented dengue epidemic during 2023-2024. Prior to the 2023-2024 outbreak in French Guiana, DENV-3 had not circulated in an epidemic manner since 2005. We therefore studied retrospectively the strains circulating in the French Territories of the Americas (FTA)-French Guiana, Guadeloupe, and Martinique-from the 2000s to the current epidemic. To this end, DENV-3 samples from the collection of the National Reference Center for Arboviruses in French Guiana (NRCA-FG) were selected and sequenced using next-generation sequencing (NGS) based on Oxford Nanopore Technologies, ONT. Phylogenetic analysis showed that (i) the 97 FTA sequences obtained all belonged to genotype III (GIII); (ii) between the 2000s and 2013, the regional circulation of the GIII American-I lineage was the source of the FTA cases through local extinctions and re-introductions; (iii) multiple introductions of lineages of Asian origin appear to be the source of the 2019-2021 epidemic in Martinique and the 2023-2024 epidemic in French Guiana. Genomic surveillance is a key factor in identifying circulating DENV genotypes, monitoring strain evolution, and identifying import events.

Identifying the panorama of potential pandemic pathogens and their key characteristics: a systematic scoping review

The globe has recently seen several terrifying pandemics and outbreaks, underlining the ongoing danger presented by infectious microorganisms. This literature review aims to explore the wide range of infections that have the potential to lead to pandemics in the present and the future and pave the way to the conception of epidemic early warning systems. A systematic review was carried out to identify and compile data on infectious agents known to cause pandemics and those that pose future concerns. One hundred and fifteen articles were included in the review. They provided insights on 25 pathogens that could start or contribute to creating pandemic situations. Diagnostic procedures, clinical symptoms, and infection transmission routes were analyzed for each of these pathogens. Each infectious agent's potential is discussed, shedding light on the crucial aspects that render them potential threats to the future. This literature review provides insights for policymakers, healthcare professionals, and researchers in their quest to identify potential pandemic pathogens, and in their efforts to enhance pandemic preparedness through building early warning systems for continuous epidemiological monitoring.

Genetic Characterization of the Dengue Virus Type 3 Genotype I Prevailing in Dhaka, Bangladesh, 2021

Background: In Bangladesh, dengue has been prevalent since its resurgence in 2018, and the dominant causative virus in 2019 was considered dengue virus serotype 3 (DENV-3). However, limited information is available for DENV serotype/genotype circulating after 2020. Materials and Methods: Viral RNA was extracted from NS1 antigen-positive blood samples of febrile patients in Dhaka, in 2021. DENV gene was detected by semi-nested RT-PCR, and sequences of envelope (E) gene and C-prM gene were determined by direct sequencing of RT-PCR products for genetic analysis. Results: Among 172 NS1-positive samples collected, 91 samples were assigned to DENV-3 and DENV-2 (88 and 3 samples, respectively) by RT-PCR targeting the C-prM gene. Phylogenetic analysis of the E gene for the 17 representative DENV-3 samples showed that all the viruses belonged to genotype I, forming a cluster (B-cluster) with those of DENV-3 reported in Bangladesh in 2017. Analysis of the deduced amino acid sequences of E protein revealed 16 amino acid substitutions, including two novel ones (G221W, L285P), and a substitution T223I that was specifically found in DENV-3 B-cluster. Conclusion: This study showed the persistent predominance of DENV-3 genotype I in Bangladesh having unique genetic traits in the E gene. (Approval number: MMC/IRB/2022/468).

Molecular surveillance of dengue virus in field-collected Aedes mosquitoes from Bhopal, central India: evidence of circulation of a new lineage of serotype 2

Introduction

Dengue fever is hyperendemic in several Southeast and South Asian countries, including India, with all four serotypes (DENV 1-4) circulating at different periods and in different locations. Sustainable and improved virological and entomological surveillance is the only tool to prevent dengue and other vector-borne diseases.

Objectives

The present study has been carried out to detect and characterize the circulating dengue virus (DENV) in field-collected Aedes mosquitoes in Bhopal, Central India.

Methods

Aedes mosquitoes were collected from 29 localities within Bhopal city during October 2020 to September 2022. DENV infection was assessed in the individual head and thorax regions of Aedes mosquitoes using reverse transcriptase PCR. Positive samples were sequenced, and the circulating serotypes and genotypes were determined using phylogenetic analysis.

Results

DENV RNA was detected in 7 Aedes aegypti and 1 Aedes albopictus, with infection rates of 0.59 and 0.14%, respectively. Phylogenetic analysis revealed all the isolates belonged to DENV serotype 2 and distinctly clustered with the non-Indian lineage (cosmopolitan genotype 4a), which was not recorded from the study area earlier. The time to most common recent ancestor (TMRCA) of these sequences was 7.4 years old, with the highest posterior density (HPD) of 3.5-12.2 years, indicating that this new lineage emerged during the year 2014. This is the first report on the DENV incrimination in both Ae. aegypti and Ae. albopictus mosquitoes collected from Bhopal, Central India.

Conclusion

The observed emergence of the non-Indian lineage of DENV-2 in Bhopal, which again is a first report from the area, coincides with the gradual increase in DENV cases in Bhopal since 2014. This study emphasizes the importance of DENV surveillance and risk assessment in this strategically important part of the country to decipher its outbreak and severe disease-causing potential.

Twenty-two years of dengue outbreaks in Bangladesh: epidemiology, clinical spectrum, serotypes, and future disease risks

Dengue is the most rapidly spreading mosquito-borne disease and has become a major public health threat, particularly for tropical and subtropical countries including Bangladesh. This comprehensive review aims to summarize the overall scenario of dengue, including disease burden, clinical spectrum, seroprevalence, circulating serotypes/genotypes, and spatial distribution since the first recorded outbreak in Bangladesh. Since the first recorded outbreak in 2000, dengue epidemiology has shown the typical epidemic pattern with more frequent and bigger outbreaks and gradual geographic expansion to non-endemic regions in Bangladesh. For instance, highly confined Rohingya refugee camps that provide shelters to nearly 1.2 million forcibly displaced vulnerable Myanmar nationals in Cox's Bazar district confronted a massive outbreak in 2022. Recent major outbreaks are found to be associated with the emergence of serotype DENV-3, which was undetected for a long time. Consequently, changes in serotypes might be attributed to increased severity in clinical manifestation in recent years. The existing weak surveillance and risk management systems are inadequate to deal with impending dengue risks. The healthcare system, particularly at the district level, is not prepared to manage impending large-scale dengue outbreaks in Bangladesh. Our findings would contribute to the development of strategies for dengue control and management in Bangladesh as well as other similar settings elsewhere in the world.

Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh

Background

The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever.

Methods

In this study, blood serum RNA was extracted from 21 dengue patients and 3 healthy individuals. Total transcriptomic data were analyzed for phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools.

Results

The viral genome sequence revealed dengue viral genome size ranges 10647 to 10707 nucleotide. Phylogenetic and phylodynamic analysis showed that the 2021 epidemic isolates were DENV-3 genotype-I and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis showed a total of 2686 genes were DEG in dengue patients compared to control with a q-value < 0.05. DESeq2 plot counts function of the top 24 genes with the smallest q-values of differential gene expression of RNA-seq data showed that 11 genes were upregulated, whereas 13 genes were downregulated. GO analysis showed a significant upregulation (p = < 0.001) in a process of multicellular organismal, nervous system, sensory perception of chemical stimulus, and G protein-coupled receptor signaling pathways in the dengue patients. However, there were a significant downregulation (p = < 0.001) of intracellular component, cellular anatomical entity, and protein-containing complex in dengue patients. Most importantly, there was a significant increase of a class of immunoregulatory proteins in dengue patients in compared to the controls, with increased GO of immune system process. In addition, upregulation of toll receptor (TLR) signaling pathways were found in dengue patients. These TLR pathways were particularly involved for the activation of innate system coupled with adaptive immune system that probably involved the rapid elimination of dengue virus infected cells. These differentially expressed genes could be further investigated for target based prophylactic interventions for dengue.

Conclusion

This is a first report describing DENV complete genomic features and differentially expressed genes in patients in Bangladesh. These genes may have diagnostic and therapeutic values for dengue infection. Continual genomic surveillance is required to further investigate the shift in dominant genotypes in relation to viral pathogenesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-023-02030-1.

Genetic Analysis of Dengue Virus in Severe and Non-Severe Cases in Dhaka, Bangladesh, in 2018-2022

Dengue virus (DENV) infections have unpredictable clinical outcomes, ranging from asymptomatic or minor febrile illness to severe and fatal disease. The severity of dengue infection is at least partly related to the replacement of circulating DENV serotypes and/or genotypes. To describe clinical profiles of patients and the viral sequence diversity corresponding to non-severe and severe cases, we collected patient samples from 2018 to 2022 at Evercare Hospital Dhaka, Bangladesh. Serotyping of 495 cases and sequencing of 179 cases showed that the dominant serotype of DENV shifted from DENV2 in 2017 and 2018 to DENV3 in 2019. DENV3 persisted as the only representative serotype until 2022. Co-circulation of clades B and C of the DENV2 cosmopolitan genotype in 2017 was replaced by circulation of clade C alone in 2018 with all clones disappearing thereafter. DENV3 genotype I was first detected in 2017 and was the only genotype in circulation until 2022. We observed a high incidence of severe cases in 2019 when the DENV3 genotype I became the only virus in circulation. Phylogenetic analysis revealed clusters of severe cases in several different subclades of DENV3 genotype I. Thus, these serotype and genotype changes in DENV may explain the large dengue outbreaks and increased severity of the disease in 2019.

Prevalence of dengue virus in Haripur district, Khyber Pakhtunkhwa, Pakistan

Dengue virus (DENV) has caused about 12 large outbreaks in Pakistan, resulting in 286,262 morbidities and 1108 deaths. The most affected province is Khyber Pakhtunkhwa (KP). This study was conducted to determine the average DENV prevalence in different areas of the Haripur endemic district of KP and the causing factors of DENV.

METHODS

This work was a cross-sectional study that was performed in the DENV endemic district Haripur. A total of 761 individuals were included in this study. The data were categorized according to sex, age and symptoms (like fever, body aches, bleeding, and skin rash). For data analysis, SPSS 23 version was applied. ArcGIS version 10.8 was used to map the study area.

RESULTS

In this study, there were 716 confirmed cases of DENV fever, including 421 males (58.8%) and 295 females (41.2%). The most affected age range, 16-30 years, reported by 301 (42.0%), was followed by 31-45 years, 184 (25.7%), above 46 years, 132 (18.4%), and 0-15 years, 99 (13.8%). The positive IgG cases were 581(81.0%). Those whose age ranges from 1 to 15 years 82 (8.7%) cases, 16-30 years 244 (34.1%), 31-45 years 156 (21.8%), above 46-year age 99 (13.8%) cases. In addition, this suggests that those between the ages of 16 and 30 are at the highest risk for DENV infection. However, this might be the fact that individuals in this age range are more likely to be out in the environment, making them more vulnerable to the virus.

CONCLUSION

Over the past ten years, DENV fever has become increasingly prevalent in Pakistan. The risk is substantially higher for males. Dengue outbreaks hit those between the ages of 16 and 30 the hardest. The proper monitoring and assessment of DENV are necessary for prevention and controlling the disease. Disease surveillance includes identification and molecular characterization of infected persons and monitoring mosquito populations in high-risk locations for the purpose of vector surveillance. In order to assess the community's willingness to participate in DENV preventive efforts, behavioral impact surveillance is also necessary.

Clinical spectrum and predictors of severity of dengue among children in 2019 outbreak: a multicenter hospital-based study in Bangladesh

BACKGROUND

The mosquito-borne arboviral disease dengue has become a global public health concern. However, very few studies have reported atypical clinical features of dengue among children. Because an understanding of various spectrums of presentation of dengue is necessary for timely diagnosis and management, we aimed to document the typical and atypical clinical features along with predictors of severity among children with dengue during the largest outbreak in Bangladesh in 2019.

METHODS

We conducted a cross-sectional study between August 15 and September 30, 2019. in eight tertiary level hospitals in Dhaka city. Children (aged < 15 years) with serologically confirmed dengue were conveniently selected for data collection through a structured questionnaire. Descriptive, inferential statistics, and multivariable logistic regression were used to analyze data.

RESULTS

Among the 190 children (mean age 8.8 years, and male-female ratio 1.22:1) included in the analysis, respectively 71.1 and 28.9% children had non-severe and severe dengue. All children had fever with an average temperature of 103.3 ± 1.2 F (SD). Gastrointestinal symptoms were the most common associated feature, including mostly vomiting (80.4%), decreased appetite (79.5%), constipation (72.7%), and abdominal pain (64.9%). Mouth sore, a less reported feature besides constipation, was present in 28.3% of children. Atypical clinical features were mostly neurological, with confusion (21.3%) being the predominant symptom. Frequent laboratory abnormalities were thrombocytopenia (87.2%), leucopenia (40.4%), and increased hematocrit (13.4%). Age (AOR 0.86, 95%CI 0.75-0.98, p = 0.023), mouth sore (AOR 2.69, 95%CI 1.06-6.96, p = 0.038) and a decreased platelet count (< 50,000/mm3) with increased hematocrit (> 20%) (AOR 4.94, 95%CI 1.48-17.31, p = 0.01) were significant predictors of severity.

CONCLUSIONS

Dengue in children was characterized by a high severity, predominance of gastrointestinal symptoms, and atypical neurological presentations. Younger age, mouth sores, and a decreased platelet with increased hematocrit were significant predictors of severity. Our findings would contribute to the clinical management of dengue in children.