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Phadungsombat J, Nakayama EE, Shioda T. Unraveling Dengue Virus Diversity in Asia: An Epidemiological Study through Genetic Sequences and Phylogenetic Analysis. Viruses 2024; 16:1046. [PMID: 39066210 PMCID: PMC11281397 DOI: 10.3390/v16071046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Dengue virus (DENV) is the causative agent of dengue. Although most infected individuals are asymptomatic or present with only mild symptoms, severe manifestations could potentially devastate human populations in tropical and subtropical regions. In hyperendemic regions such as South Asia and Southeast Asia (SEA), all four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) have been prevalent for several decades. Each DENV serotype is further divided into multiple genotypes, reflecting the extensive diversity of DENV. Historically, specific DENV genotypes were associated with particular geographical distributions within endemic regions. However, this epidemiological pattern has changed due to urbanization, globalization, and climate change. This review comprehensively traces the historical and recent genetic epidemiology of DENV in Asia from the first time DENV was identified in the 1950s to the present. We analyzed envelope sequences from a database covering 16 endemic countries across three distinct geographic regions in Asia. These countries included Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka from South Asia; Cambodia, Laos, Myanmar, Thailand, and Vietnam from Mainland SEA; and Indonesia, the Philippines, Malaysia, and Singapore from Maritime SEA. Additionally, we describe the phylogenetic relationships among DENV genotypes within each serotype, along with their geographic distribution, to enhance the understanding of DENV dynamics.
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Affiliation(s)
| | | | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (J.P.); (E.E.N.)
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Prakash O, Verma AK, Paliwal A, Abbas F, Srivastava AK, Mishra VK, Radera S, Jain A. Circulating serotypes and genotypes of dengue virus in North India: An observational study. J Vector Borne Dis 2024; 61:117-122. [PMID: 38648413 DOI: 10.4103/0972-9062.392258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND OBJECTIVES This study reports observation on circulating serotypes and genotypes of Dengue Virus in North India. METHODS Serum samples were obtained from suspected cases of dengue referred to the virus diagnostic laboratory during 2014 to 2022. All samples were tested for anti-dengue virus IgM antibodies and NS1Ag by ELISA. NS1Ag positive samples were processed for serotyping and genotyping. RESULTS Total 41,476 dengue suspected cases were referred to the laboratory of which 12,292 (29.6%) tested positive. Anti-Dengue Virus IgM antibodies, NS1Ag, both IgM and NS1Ag, were positive in 7007 (57.4%); 3200 (26.0%) and 2085 (16.0%) cases respectively. Total 762 strains were serotyped during 9-year period. DENV-1, DENV-2, DENV-3 and DENV-4 serotypes were found in 79 (10.37%), 506 (66.40%), 151 (19.82%) and 26 (3.41%) cases respectively. DENV-1, DENV-2 and DENV-3 were in circulation throughout. Total 105 strains were genotyped. Genotype IV of DENV-1 serotype was circulating till 2014 which was later replaced by genotype V. A distinct seasonality with increase in number of cases in post-monsoon period was seen. INTERPRETATION CONCLUSION DENV-1, DENV-2 and DENV-3 were found to be in circulation in North India. Predominant serotype/genotype changed at times, but not at regular intervals.
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Affiliation(s)
- Om Prakash
- Department of Microbiology, King George's Medical University, Lucknow, India
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Islam A, Deeba F, Tarai B, Gupta E, Naqvi IH, Abdullah M, Dohare R, Ahmed A, Almajhdi FN, Hussain T, Parveen S. Global and local evolutionary dynamics of Dengue virus serotypes 1, 3, and 4. Epidemiol Infect 2023; 151:e127. [PMID: 37293986 PMCID: PMC10540175 DOI: 10.1017/s0950268823000924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/01/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Evolutionary studies on Dengue virus (DENV) in endemic regions are necessary since naturally occurring mutations may lead to genotypic variations or shifts in serotypes, which may lead to future outbreaks. Our study comprehends the evolutionary dynamics of DENV, using phylogenetic, molecular clock, skyline plots, network, selection pressure, and entropy analyses based on partial CprM gene sequences. We have collected 250 samples, 161 in 2017 and 89 in 2018. Details for the 2017 samples were published in our previous article and that of 2018 are presented in this study. Further evolutionary analysis was carried out using 800 sequences, which incorporate the study and global sequences from GenBank: DENV-1 (n = 240), DENV-3 (n = 374), and DENV-4 (n = 186), identified during 1944-2020, 1956-2020, and 1956-2021, respectively. Genotypes V, III, and I were identified as the predominant genotypes of the DENV-1, DENV-3, and DENV-4 serotypes, respectively. The rate of nucleotide substitution was found highest in DENV-3 (7.90 × 10-4 s/s/y), followed by DENV-4 (6.23 × 10-4 s/s/y) and DENV-1 (5.99 × 10-4 s/s/y). The Bayesian skyline plots of the Indian strains revealed dissimilar patterns amongst the population size of the three serotypes. Network analyses showed the presence of different clusters within the prevalent genotypes. The data presented in this study will assist in supplementing the measures for vaccine development against DENV.
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Affiliation(s)
- Arshi Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Farah Deeba
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Bansidhar Tarai
- Department of Microbiology and Infection Control, Max Superspeciality Hospital, New Delhi, India
| | - Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Irshad H. Naqvi
- Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Mohd. Abdullah
- Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fahad N. Almajhdi
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Tajamul Hussain
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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OUP accepted manuscript. Trans R Soc Trop Med Hyg 2022; 116:900-909. [DOI: 10.1093/trstmh/trac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/11/2021] [Accepted: 01/09/2022] [Indexed: 11/13/2022] Open
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Alagarasu K, Patil JA, Kakade MB, More AM, Yogesh B, Newase P, Jadhav SM, Parashar D, Kaur H, Gupta N, Vijay N, Narayan J, Shah PS. Serotype and genotype diversity of dengue viruses circulating in India: a multi-centre retrospective study involving the Virus Research Diagnostic Laboratory Network in 2018. Int J Infect Dis 2021; 111:242-252. [PMID: 34428547 DOI: 10.1016/j.ijid.2021.08.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES A retrospective study was undertaken to investigate the circulating dengue virus (DENV) serotypes and genotypes in India in 2018. METHODS In total, 4963 samples referred to virus research diagnostic laboratories (n=21), the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV) and ICMR-NIV field units (n=2) for diagnosis of dengue in 2018 were tested using a real-time reverse transcription polymerase chain reaction assay for the presence of DENV serotypes. Representative samples were sequenced for the envelope (E) gene. RESULTS Regional diversity was observed with regard to the dominant circulating serotypes. DENV-2 was found to be the most common serotype in many states. Thrombocytopenia, petechiae and malaise were associated with DENV-2 infection. Phylogenetic analyses of DENV E gene sequences revealed the circulation of genotypes I and V of DENV-1, two lineages of DENV-2 genotype IV, DENV-3 genotype III and DENV-4 genotype I. CONCLUSIONS This study found regional differences in the prevalence of circulating DENV serotypes in India, and provides baseline data for continuous molecular surveillance. Molecular surveillance may have implications for predicting large-scale outbreaks of dengue if regional shifts in the predominantly circulating serotypes and genotypes are detected during the early phase of the dengue season.
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Affiliation(s)
- K Alagarasu
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.
| | - J A Patil
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - M B Kakade
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A M More
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - B Yogesh
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - P Newase
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - S M Jadhav
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - D Parashar
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - H Kaur
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - N Gupta
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - N Vijay
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - J Narayan
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - P S Shah
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
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Näslund J, Ahlm C, Islam K, Evander M, Bucht G, Lwande OW. Emerging Mosquito-Borne Viruses Linked to Aedes aegypti and Aedes albopictus: Global Status and Preventive Strategies. Vector Borne Zoonotic Dis 2021; 21:731-746. [PMID: 34424778 DOI: 10.1089/vbz.2020.2762] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Emerging mosquito-borne viruses continue to cause serious health problems and economic burden among billions of people living in and near the tropical belt of the world. The highly invasive mosquito species Aedes aegypti and Aedes albopictus have successively invaded and expanded their presence as key vectors of Chikungunya virus, dengue virus, yellow fever virus, and Zika virus, and that has consecutively led to frequent outbreaks of the corresponding viral diseases. Of note, these two mosquito species have gradually adapted to the changing weather and environmental conditions leading to a shift in the epidemiology of the viral diseases, and facilitated their establishment in new ecozones inhabited by immunologically naive human populations. Many abilities of Ae. aegypti and Ae. albopictus, as vectors of significant arbovirus pathogens, may affect the infection and transmission rates after a bloodmeal, and may influence the vector competence for either virus. We highlight that many collaborating risk factors, for example, the global transportation systems may result in sporadic and more local outbreaks caused by mosquito-borne viruses related to Ae. aegypti and/or Ae. albopictus. Those local outbreaks could in synergy grow and produce larger epidemics with pandemic characters. There is an urgent need for improved surveillance of vector populations, human cases, and reliable prediction models. In summary, we recommend new and innovative strategies for the prevention of these types of infections.
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Affiliation(s)
- Jonas Näslund
- Swedish Defence Research Agency, CBRN, Defence and Security, Umeå, Sweden
| | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umea, Sweden.,Arctic Research Centre at Umeå University, Umea, Sweden
| | - Koushikul Islam
- Department of Clinical Microbiology, Umeå University, Umea, Sweden
| | - Magnus Evander
- Department of Clinical Microbiology, Umeå University, Umea, Sweden.,Arctic Research Centre at Umeå University, Umea, Sweden
| | - Göran Bucht
- Department of Clinical Microbiology, Umeå University, Umea, Sweden
| | - Olivia Wesula Lwande
- Department of Clinical Microbiology, Umeå University, Umea, Sweden.,Arctic Research Centre at Umeå University, Umea, Sweden
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Rai P, Kille S, Kotian A, Kumar BK, Deekshit VK, Ramakrishna MS, Karunasagar I, Karunasagar I. Molecular investigation of the dengue outbreak in Karnataka, South India, reveals co-circulation of all four dengue virus serotypes. INFECTION GENETICS AND EVOLUTION 2021; 92:104880. [PMID: 33905893 DOI: 10.1016/j.meegid.2021.104880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/20/2022]
Abstract
The growing incidence of dengue outbreaks in the state of Karnataka prompted us to study the circulating dengue virus (DENV) and their proportion among the suspected cases of dengue patients during the disease outbreak at Mysuru district of Southern India. The presence of the DENV in a patient's serum sample was identified by RT-PCR using previously published primer pairs targeting CprM gene. DENV serotyping was carried out by semi-nested multiplex PCR using serotype-specific primers and nucleotide sequencing. Three hundred fifty-five samples of serum from suspected dengue cases were collected, and 203 samples (57.18%) were found positives. In 2016, DENV-4 (97.87%) was found to be the most dominant DENV serotype either alone or as co-infection, followed by DENV-2 (8.51%) and DENV-3 (4.25%). In 47 positive cases, co-infection with more than one serotype was detected in 4 cases (8.51%). The analysis of the dengue cases in 2017, DENV-4 was dominating serotype (33.97%), followed by the emergence of DENV-2 (32.05%), DENV-3 (25.64%), and DENV-1 (25.00%). Our study also reports the circulation of all four DENV serotypes in the Mysuru district of Southern India, with concurrent infections rate of 16.66% in 2017. The present study provides information regarding the genetic variation among the circulating DENV serotype in an Indian state of Karnataka. The need for the studying genetic diversity of DENV will be useful during the continuous monitoring for disease burden as well as the development of appropriate prophylactic measures to control the spread of dengue infection.
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Affiliation(s)
- Praveen Rai
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru 575018, Karnataka, India.
| | - Sonam Kille
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru 575018, Karnataka, India
| | - Akshatha Kotian
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru 575018, Karnataka, India
| | - Ballamoole Krishna Kumar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru 575018, Karnataka, India
| | - Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru 575018, Karnataka, India
| | - Mysore Shivalingappa Ramakrishna
- 306/A, 3(rd) Stage Main, 9(th) Cross A-1BLOCK Vijay Nagar, 3(rd) Stage, Behind Clear medi Radiant Hospital, Mysuru 570030, Karnataka, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru 575018, Karnataka, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru 575018, Karnataka, India
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Murugesan A, Aridoss D, Senthilkumar S, Sivathanu L, Sekar R, Shankar EM, Manickan E. Molecular diversity of dengue virus serotypes 1-4 during an outbreak of acute dengue virus infection in Theni, India. Indian J Med Microbiol 2020; 38:401-408. [PMID: 33154254 DOI: 10.4103/ijmm.ijmm_20_89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Dengue fever (DF) is caused by an arthropod-borne dengue virus (DENV), has four serotypes and several genotypes. Although having clinical and epidemiological significance, the information on the circulating serotypes/genotypes is scarce in India. Materials and Methods Blood specimens were collected from the patients suspected of DF and they are tested for DENV NS1 antigen and DENV IgM by ELISA. Antigen-positive samples were further serotyped by reverse transcriptase polymerase chain reaction. Representative samples from each serotype were sequenced to identify the genotypes. Results All the four DENV serotypes were detected with the pre-dominance of DENV-1 (n = 49; 41.9%). Cases with multiple DENV serotype infections were also identified. Genotyping showed that DENV-1 belonging to genotype I, DENV-2 cosmopolitan (IV), DENV-3 genotype III and DENV-4 genotype I were active in the circulation during the outbreak in 2017. Conclusion Our study documents the molecular characteristics of DENV circulating in our geographical locality. The detection of heterologous DENV serotypes highlights the importance of regular molecular monitoring for the early recognition of any switch in pre-dominant serotype.
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Affiliation(s)
- Amudhan Murugesan
- Department of Microbiology, Government Theni Medical College, Theni; Department of Microbiology, Dr ALM PG IBMS, University of Madras, Chennai; Department of Microbiology, Virus Research and Diagnostic Laboratory, Government Theni Medical College, Theni, Tamil Nadu, India
| | - Dhanasezhian Aridoss
- Department of Microbiology, Government Theni Medical College, Theni; Department of Microbiology, Dr ALM PG IBMS, University of Madras, Chennai; Department of Microbiology, Virus Research and Diagnostic Laboratory, Government Theni Medical College, Theni, Tamil Nadu, India
| | - Swarna Senthilkumar
- Department of Microbiology; Department of Microbiology, Virus Research and Diagnostic Laboratory, Government Theni Medical College, Theni, Tamil Nadu, India
| | - Lallitha Sivathanu
- Department of Microbiology; Department of Microbiology, Virus Research and Diagnostic Laboratory, Government Theni Medical College, Theni, Tamil Nadu, India
| | - Ramalingam Sekar
- Department of Microbiology; Department of Microbiology, Virus Research and Diagnostic Laboratory, Government Theni Medical College, Theni, Tamil Nadu, India
| | - Esaki M Shankar
- Infection Biology, Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Elanchezhiyan Manickan
- Department of Microbiology, Dr ALM PG IBMS, University of Madras, Chennai, Tamil Nadu, India
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