A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains

A new lineage nomenclature to aid genomic surveillance of dengue virus

Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propose adding two sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national and sub-national discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.

DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus

BACKGROUND

The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes.

RESULTS

We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments.

CONCLUSIONS

DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.

An outbreak of a novel lineage of dengue virus 2 in Vietnam in 2022

In 2022, a large dengue outbreak was reported in Vietnam, where dengue was endemic. A total of 1889 acute-phase serum samples were collected from patients with suspected dengue at Vung Tau General Hospital, the core hospital in Vung Tau Province, southern Vietnam. Among the 1889 samples analyzed for laboratory confirmation of dengue virus (DENV) infection, 339 positive cases were identified, of which 130 were primary infections and 209 were secondary infections. DENV-2 was the dominant serotype in both primary and secondary infection groups. Phylogenetic analysis based on sequences of the envelope protein-coding region revealed the emergence of a new DENV-2 lineage during this outbreak.

Liver Impairment and Elevated Aminotransferase Levels Predict Severe Dengue in Vietnamese Children

BACKGROUND

The degree of liver impairment in children with dengue infection varies from mild to severe injury. Aminotransferase levels may be useful in predicting severe dengue. This study aimed to evaluate the degree of liver impairment and determine whether elevated aminotransferases could be used to discriminate between non-severe and severe dengue in Vietnamese children.

METHODS

This was a prospective cohort study of pediatric patients with confirmed dengue infection who were admitted to Can Tho Children's Hospital, Vietnam. The receiver operating characteristic (ROC) curve was used to discriminate the power of Aspartate transaminase (AST) or Alanine transaminase (ALT) to predict severe dengue.

RESULTS

Two hundred and thirty confirmed dengue patients were enrolled, including 70% (161) patients with non-severe dengue and 30% (69) with severe dengue. This study indicates that 73.9% of patients had abnormal AST (＞40 U/L), and 34.8% of patients had abnormal ALT (＞40 U/L). The incidence of dengue patients with hepatitis (AST or ALT ≥ 4×ULN) and severe hepatitis (AST or ALT ≥ 10×ULN) were 18.7% and 17.0%, respectively. At a cut-off point of 120 U/L, AST's AUROC, sensitivity, and specificity were 0.93 (95% CI: 0.90-0.96), 82.5%, and 87.3%, respectively. At a cut-off point of 80 U/L, ALT's AUROC, sensitivity, and specificity were 0.89 (95% CI: 0.84-0,93), 87.5%, and 85.2%, respectively, for predicting severe dengue.

CONCLUSION

Elevated aminotransferase levels were associated with severe dengue, and AST/ALT were good markers for predicting severe dengue in Vietnamese children.