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Khare K, Imran M, Ravi V, Mohite R, Halder S, Mishra P, Tarai B, Budhiraja S, Sethi T, Pandey R. Inter-host diversity associated with age, sex, and menstrual cycle modulates clinical manifestations in DENV-2 patients. iScience 2025; 28:112478. [PMID: 40395667 PMCID: PMC12090246 DOI: 10.1016/j.isci.2025.112478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 02/28/2025] [Accepted: 04/15/2025] [Indexed: 05/22/2025] Open
Abstract
Dengue virus (DENV-2) remains a global threat, yet the influence of age, sex, and menstrual status on its epidemiology and genetic diversity is underexplored. We analyzed 2136 hospitalized DENV-2 patients (ages 0-86) using whole-genome sequencing (WGS) to examine how these host factors shape interhost viral diversity and clinical manifestations. Young adult males (19-35 years) had the highest prevalence with sex-based clinical differences where females exhibited severe hematological changes, while males showed increased hepatic injury. Premenopausal females harbored more diverse viral populations, whereas postmenopausal women experienced pronounced platelet depletion. Dengue virus WGS identified 1100336 single nucleotide variants (SNVs) across 2932 genomic positions, with greater viral diversity in adults and females. Significant SNV burdens were observed in the E, NS3, and NS5 genes of the virus. These interconnected findings underscore the profound impact of age, sex, and menstrual status on DENV-2 epidemiology which merits inclusion into the disease pathophysiology.
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Affiliation(s)
- Kriti Khare
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Md Imran
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, Delhi 110007, India
| | - Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, Delhi 110007, India
- Indraprastha Institute of Information Technology Delhi, New Delhi, Delhi 110020, India
| | - Ramakant Mohite
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, Delhi 110007, India
| | - Sayanti Halder
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, Delhi 110007, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, Delhi 110007, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, Delhi 110017, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, New Delhi, Delhi 110017, India
| | - Tavpritesh Sethi
- Indraprastha Institute of Information Technology Delhi, New Delhi, Delhi 110020, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Ravi V, Khare K, Mohite R, Mishra P, Halder S, Shukla R, Liu CSC, Yadav A, Soni J, Kanika, Chaudhary K, Neha, Tarai B, Budhiraja S, Khosla P, Sethi T, Imran M, Pandey R. Genomic hotspots in the DENV-2 serotype (E, NS4B, and NS5 genes) are associated with dengue disease severity in the endemic region of India. PLoS Negl Trop Dis 2025; 19:e0013034. [PMID: 40299925 PMCID: PMC12040166 DOI: 10.1371/journal.pntd.0013034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Accepted: 04/04/2025] [Indexed: 05/01/2025] Open
Abstract
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.
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Affiliation(s)
- Varsha Ravi
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Indraprastha Institute of Information Technology, Delhi, India
| | - Kriti Khare
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Pallavi Mishra
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Sayanti Halder
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Richa Shukla
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Chinky Shiu Chen Liu
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Aanchal Yadav
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jyoti Soni
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kanika
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Komal Chaudhary
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | - Neha
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India,
| | | | | | - Md Imran
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
| | - Rajesh Pandey
- Division of Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Giri S, Anirvan P, Vaidya A, Praharaj DL. Dengue-related acute liver failure-A scoping review. Indian J Gastroenterol 2024; 43:407-424. [PMID: 38687431 DOI: 10.1007/s12664-024-01570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/09/2024] [Indexed: 05/02/2024]
Abstract
Infection by dengue virus is common in tropical countries. Hepatic involvement in dengue can range from asymptomatic elevation of transaminases to life-threatening acute liver failure (ALF). Dengue-related ALF (DALF) is responsible for significant morbidity and mortality, especially in Southeast Asia. However, there is a scarcity of literature on DALF, necessitating a thorough examination of its clinical determinants and management strategies. All relevant studies related to DALF were reviewed until December 2023. Case reports, case series and studies reporting ALF in dengue infection were included. Demographics, clinical profiles, management and outcomes of DALF cases were analyzed, which revealed a predominance of DALF incidence in pediatric patients (1.1% to 15.8%) and an upward trend over the years, particularly in India. The proportion of ALF cases attributable to dengue was also higher among pediatric ALF patients (6.7% to 34.3%). Age ≤ 40 years, persistent nausea, vomiting and elevated serum bilirubin and alkaline phosphatase (ALP) with aspartate aminotransferase (AST) > 1000 IU/mL within the first five days of illness, more than 10% of atypical lymphocytes in peripheral blood, platelet count of < 50,000/cu·mm, severe hepatitis at presentation and baseline model for end-stage liver disease (MELD) > 15 were the risk factors for the development of DALF. Histopathological features of DALF included multi-lobular hepatic necrosis, steatosis and occasional cholestasis. Mortality in DALF ranged from 0% to 80%; admission pH and lactate strongly predicted mortality, while mortality was found to be significantly higher in patients with cirrhosis. N-Acetyl cysteine (NAC) has been used as a treatment modality with varying results. There is limited evidence regarding the use of extra-corporeal support systems, while candidate selection for liver transplantation (LT) in DALF remains poorly defined.
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Affiliation(s)
- Suprabhat Giri
- Department of Gastroenterology and Hepatology, Kalinga Institute of Medical Sciences, Bhubaneswar, 751 024, India
| | - Prajna Anirvan
- Kalinga Gastroenterology Foundation, Cuttack, 753 001, India
| | - Arun Vaidya
- Department of Gastroenterology, Seth G S Medical College and K E M Hospital, Mumbai, 400 012, India
| | - Dibya Lochan Praharaj
- Department of Gastroenterology and Hepatology, Kalinga Institute of Medical Sciences, Bhubaneswar, 751 024, India.
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