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Balingit JC, Denis D, Suzuki R, Hayati RF, Ngwe Tun MM, Takamatsu Y, Masyeni S, Sasmono RT, Morita K. Impact of pre-existing cross-reactive antibodies on cyclic dengue outbreaks in the hyperendemic region of Bali, Indonesia. Virus Res 2024; 348:199445. [PMID: 39089369 DOI: 10.1016/j.virusres.2024.199445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
The four serotypes of the dengue virus (DENV) cause a range of diseases ranging from mild fever to severe conditions. Understanding the immunological interactions among the four serotypes is crucial in comprehending the dynamics of serotype shifting during outbreaks in areas where all four serotypes co-circulate. Hence, we evaluated the neutralizing antibody and antibody-dependent enhancement responses against the four DENV serotypes using acute-phase plasma samples collected from 48 laboratory-confirmed dengue patients during a dengue outbreak in Bali, Indonesia in 2022. Employing single-round infectious particles to exclusively investigate immunogenicity to the structural surface proteins of DENV, which are the targets of antibodies, we found that individuals with a probable prior history of DENV-1 infection exhibited increased susceptibility to secondary DENV-3 infection, attributed to cross-reactive antibodies with limited neutralizing activity against DENV-3 (geometric mean 50 % neutralization titer (GMNT50) = 47.6 ± 11.5). This susceptibility was evident in vitro, with a mean fold enhancement of 28.4 ± 33.9. Neutralization titers against DENV-3 were significantly lower compared to other serotypes (DENV-1 GMNT50 = 678.1 ± 9.0; DENV-2 GMNT50 = 210.5 ± 8.7; DENV-4 GMNT50 = 95.14 ± 7.0). We demonstrate that prior immunity to one serotype provides limited cross-protection against the other serotypes, influencing the dominant serotype in subsequent outbreaks. These findings underscore the complexity of dengue immunity and its implications for vaccine design and transmission dynamics in hyperendemic regions.
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Affiliation(s)
- Jean Claude Balingit
- Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | | | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | | | - Mya Myat Ngwe Tun
- Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 690-8504, Japan
| | - Yuki Takamatsu
- Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Sri Masyeni
- Department of Internal Medicine, Faculty of Medicine and Health Science, Universitas Warmadewa, Bali 80239, Indonesia
| | - R Tedjo Sasmono
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency (BRIN), Jakarta 10340, Indonesia
| | - Kouichi Morita
- Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan.
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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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Jahan A, Paul SK, Nasreen SA, Haque N, Roy S, Sultana M, Hossain T, Nila SS, Ahmad FU, Ahmed S, Aung MS, Kobayashi N. Genetic Characterization of the Dengue Virus Type 3 Genotype I Prevailing in Dhaka, Bangladesh, 2021. Vector Borne Zoonotic Dis 2023; 23:634-638. [PMID: 37603293 DOI: 10.1089/vbz.2023.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023] Open
Abstract
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).
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Affiliation(s)
- Afsana Jahan
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
- Pabna Medical College, Pabna, Bangladesh
| | - Shyamal Kumar Paul
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
- Netrokona Medical College, Netrokona, Bangladesh
| | | | - Nazia Haque
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Sangjukta Roy
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Monira Sultana
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
- Nilphamari Medical College, Nilphamari, Bangladesh
| | - Tasmia Hossain
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | | | | | - Salma Ahmed
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
- Mugda Medical College, Dhaka, Bangladesh
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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Suppiah J, Ali EZ, Mohd Khalid MKN, Mohd Ghazali S, Tee KK, Zulkifli MMS, Ramli N, Adiee AH, Ramly MN, Robert F, Lakha Singh SS, Mohd Zain R, Thayan R. Resurgence of Dengue Virus Serotype 4 in Malaysia: A Comprehensive Clinicodemographic and Genomic Analysis. Trop Med Infect Dis 2023; 8:409. [PMID: 37624348 PMCID: PMC10458033 DOI: 10.3390/tropicalmed8080409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Dengue virus serotype 4 (DENV-4) has been the rarest circulating serotype in Malaysia, resulting in it being an understudied area. A recent observation from institutional surveillance data indicated a rapid increase in DENV-4-infected cases. The present study aimed to investigate the resurgence of DENV-4 in relation to the demographic, clinical and genomic profiles of 75 retrospective dengue samples. First, the demographic and clinical profiles obtained between 2017 and July 2022 were statistically assessed. Samples with good quality were subjected to full genome sequencing on the Illumina Next Seq 500 platform and the genome data were analysed for the presence of mutations. The effect of the mutations of interest was studied via an in silico computational approach using SWISS-MODEL and AlphaFold2 programs. The predominance of DENV-4 was discovered from 2021 to 2022, with a prevalence of 64.3% (n = 9/14) and 89.2% (n = 33/37), respectively. Two clades with a genetic divergence of 2.8% were observed within the dominant genotype IIa. The majority of DENV-4-infected patients presented with gastrointestinal symptoms, such as vomiting (46.7%), persistent diarrhoea (30.7%) and abdominal pain (13.3%). Two mutations, His50Tyr and Pro144Ser, located at the wing domain of the NS1 protein were discovered to be unique to the recently sequenced DENV-4.
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Affiliation(s)
- Jeyanthi Suppiah
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
| | - Ernie Zuraida Ali
- Inborn Error of Metabolism and Genetic Unit, Nutrition, Metabolic & Cardiovascular Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia
| | - Mohd Khairul Nizam Mohd Khalid
- Inborn Error of Metabolism and Genetic Unit, Nutrition, Metabolic & Cardiovascular Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia
| | - Sumarni Mohd Ghazali
- Biomedical Epidemiology Unit, Special Resource Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Murni Maya Sari Zulkifli
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
| | - Nuraisyah Ramli
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
| | - Amir Hussin Adiee
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
| | - Muhamad Nurrani Ramly
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
| | - Fionie Robert
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
| | - Sarbhan Singh Lakha Singh
- Biomedical Epidemiology Unit, Special Resource Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia
| | - Rozainanee Mohd Zain
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
| | - Ravindran Thayan
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam 40170, Selangor, Malaysia; (M.M.S.Z.)
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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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Annan E, Nguyen USDT, Treviño J, Wan Yaacob WF, Mangla S, Pathak AK, Nandy R, Haque U. Moderation effects of serotype on dengue severity across pregnancy status in Mexico. BMC Infect Dis 2023; 23:147. [PMID: 36899304 PMCID: PMC9999597 DOI: 10.1186/s12879-023-08051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/02/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Pregnancy increases a woman's risk of severe dengue. To the best of our knowledge, the moderation effect of the dengue serotype among pregnant women has not been studied in Mexico. This study explores how pregnancy interacted with the dengue serotype from 2012 to 2020 in Mexico. METHOD Information from 2469 notifying health units in Mexican municipalities was used for this cross-sectional analysis. Multiple logistic regression with interaction effects was chosen as the final model and sensitivity analysis was done to assess potential exposure misclassification of pregnancy status. RESULTS Pregnant women were found to have higher odds of severe dengue [1.50 (95% CI 1.41, 1.59)]. The odds of dengue severity varied for pregnant women with DENV-1 [1.45, (95% CI 1.21, 1.74)], DENV-2 [1.33, (95% CI 1.18, 1.53)] and DENV-4 [3.78, (95% CI 1.14, 12.59)]. While the odds of severe dengue were generally higher for pregnant women compared with non-pregnant women with DENV-1 and DENV-2, the odds of disease severity were much higher for those infected with the DENV-4 serotype. CONCLUSION The effect of pregnancy on severe dengue is moderated by the dengue serotype. Future studies on genetic diversification may potentially elucidate this serotype-specific effect among pregnant women in Mexico.
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Affiliation(s)
- Esther Annan
- Department of Biostatistics & Epidemiology, University of North Texas Health Science Center, Fort Worth, TX, USA. .,Center for Health and Wellbeing, School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
| | - Uyen-Sa D T Nguyen
- Department of Biostatistics & Epidemiology, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jesús Treviño
- Department of Urban Affairs at the School of Architecture, Universidad Autónoma de Nuevo León, 66455, San Nicolás de los Garza, Nuevo Léon, México
| | - Wan Fairos Wan Yaacob
- Mathematical Sciences Studies, College of Computing, Informatics and Media, Universiti Teknologi MARA Cawangan Kelantan, Lembah Sireh, Kampus Kota Bharu, 15150, Kota Bharu, Kelantan, Malaysia.,Institute for Big Data Analytics and Artificial Intelligence (IBDAAI), Universiti Teknologi MARA, Kompleks Al- Hawarizmi, 40450, Shah Alam, Selangor, Malaysia
| | - Sherry Mangla
- International Institute for Population Sciences, Mumbai, Maharashtra, 400088, India
| | - Ashok Kumar Pathak
- Department of Mathematics and Statistics, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Rajesh Nandy
- Department of Biostatistics & Epidemiology, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Ubydul Haque
- Rutgers Global Health Institute, New Brunswick, NJ, USA.,Department of Biostatistics and Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ, USA
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Wardhani P, Yohan B, Tanzilia M, Sunari EP, Wrahatnala BJ, Hakim FKN, Rohman A, Husada D, Hayati RF, Santoso MS, Sievers JTO, Aryati A, Sasmono RT. Genetic characterization of dengue virus 4 complete genomes from East Java, Indonesia. Virus Genes 2023; 59:36-44. [PMID: 36266496 PMCID: PMC9584228 DOI: 10.1007/s11262-022-01942-4] [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: 08/11/2022] [Accepted: 10/05/2022] [Indexed: 01/13/2023]
Abstract
Dengue is an endemic arboviral disease with continuous transmission in Indonesia for more than five decades. A recent outbreak in Jember, East Java province, demonstrated the predominance of DENV-4, a serotype known for its low global spread and limited transmission. While epidemiological factors such as new serotype introduction and lacking herd immunity may explain its predominance, viral factors may also contribute. Using next-generation sequencing, we generated 13 representative complete genomes of DENV-4 responsible for the outbreak. Phylogenetic and evolutionary analyses on complete genomes were performed to understand the spatial and temporal dynamics of the viruses. Further analyses were done to study amino acid variations in DENV genes, as well as the potential events of recombination and selection pressure within the genomes. We revealed the DENV-4 genetic factors that may lead to its predominance in the 2019 Jember dengue outbreak. A combination of selection pressure and mutational genetic changes may contribute to the DENV-4 predominance in East Java, Indonesia. The possible intra-serotype recombination events involving the non-structural protein 5 (NS5) gene were also observed. Altogether, these genetic factors may act as additional factors behind the complex dengue outbreak mechanism.
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Affiliation(s)
- Puspa Wardhani
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XInstitute for Tropical Diseases, Universitas Airlangga, Surabaya, 60115 Indonesia ,Dr. Soetomo General Academic Hospital, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XPost Graduate School, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Benediktus Yohan
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia ,grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | - Mayfanny Tanzilia
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Eka Putri Sunari
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Billy J. Wrahatnala
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Faradila K. N. Hakim
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Ali Rohman
- grid.440745.60000 0001 0152 762XDepartment of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, 60115 Indonesia
| | - Dominicus Husada
- Dr. Soetomo General Academic Hospital, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XDepartment of Pediatric, Faculty of Medicine Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Rahma F. Hayati
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
| | - Marsha S. Santoso
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
| | - Justus T. O. Sievers
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
| | - A. Aryati
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XInstitute for Tropical Diseases, Universitas Airlangga, Surabaya, 60115 Indonesia ,Dr. Soetomo General Academic Hospital, Surabaya, 60286 Indonesia
| | - R. Tedjo Sasmono
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
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Saqallah FG, Abbas MA, Wahab HA. Recent advances in natural products as potential inhibitors of dengue virus with a special emphasis on NS2b/NS3 protease. PHYTOCHEMISTRY 2022; 202:113362. [PMID: 35948138 DOI: 10.1016/j.phytochem.2022.113362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Dengue virus (DENV) is an arbovirus widespread through tropical and subtropical areas. It is transmitted to humans through Aedes mosquitoes. Infections with DENV can lead to a series of complications, including dengue fever, dengue haemorrhagic fever, or dengue shock syndrome, which might manifest through secondary infections because of a vulnerable immune system. To date, only one tetravalent DENV vaccine is approved to be administered to children whom have been previously DENV-infected and between 9 and 16 years of age. One of the key targets in discovering DENV antiviral agents is the NS2b/NS3 protease. This protease is a crucial enzyme complex for the proteolytic and cleavage activities of the translated polyprotein during DENV life cycle. Several studies were conducted to discover potential antivirals from natural sources or synthetic compounds and peptides. In this review, we describe the recent studies from the past five years dealing with isolated natural products as potential inhibitors of DENV with a greater focus on inhibiting the NS2b/NS3 protease. This review describes recent discoveries in anti-DENV potential of isolated phytochemicals belonging to different groups including fatty acids, glucosides, terpenes and terpenoids, flavonoids, phenolics, chalcones, acetamides, and peptides. Curcumin, quercetin, and myricetin were found to act as non-competitive inhibitors for the NS2b/NS3 protease enzyme. In some studies, the molecular targets of some of these compounds are yet to be identified using in-silico and in-vitro approaches. So far, none of the isolated natural products was tested clinically for the management of DENV infections. The discussed studies demonstrate that natural products are a rich source of potential anti-DENV compounds. However, not all of these compounds were studied for their kinetic molecular mechanism and type of inhibition. In-silico studies provided an ample number of phytochemical hits to be tested experimentally as DENV protease inhibitors. In conclusion, derivatives of these natural products can be designed and synthesised, which could enhance their specificity and efficacy towards the protease. Other sources of natural products, such as fungi, bacterial toxins, marine organisms, and animals, should also be explored towards discovering more potential and effective DENV NS2b/NS3 protease inhibitors.
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Affiliation(s)
- Fadi G Saqallah
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; Discipline of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | - Manal A Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328, Amman, Jordan; Pharmacological and Diagnostic Research Lab, Al-Ahliyya Amman University, 19328, Amman, Jordan.
| | - Habibah A Wahab
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; Discipline of Pharmaceutical Technology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines. Vaccines (Basel) 2022; 10:vaccines10081259. [PMID: 36016147 PMCID: PMC9415047 DOI: 10.3390/vaccines10081259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022] Open
Abstract
Dengue is a viral mosquito-borne disease that rapidly spreads in tropical and subtropical countries, including the Philippines. One of its most distinguishing characteristics is the ability of the Dengue Virus (DENV) to easily surpass the innate responses of the body, thus activating B cells of the adaptive immunity to produce virus-specific antibodies. Moreover, Dengvaxia® is the only licensed vaccine for DENV, but recent studies showed that seronegative individuals become prone to increased disease severity and hospitalization. Owing to this limitation of the dengue vaccine, this study determined and compared consensus and unique B cell epitopes among each DENV (1–4) Philippine isolate to identify potential areas of interest for future vaccine studies and therapeutic developments. An in silico-based epitope prediction of forty (40) DENV 1–4 strains, each serotype represented by ten (10) sequences from The National Center for Biotechnology Information (NCBI), was conducted using Kolaskar and Tongaonkar antigenicity, Emini surface accessibility, and Parker hydrophilicity prediction in Immune Epitope Database (IEDB). Results showed that five (5) epitopes were consensus for DENV-1 with no detected unique epitope, one (1) consensus epitope for DENV-2 with two (2) unique epitopes, one (1) consensus epitope for DENV-3 plus two (2) unique epitopes, and two (2) consensus epitopes and one (1) unique epitope for DENV-4. The findings of this study would contribute to determining potential vaccine and diagnostic marker candidates for further research studies and immunological applications against DENV (1–4) Philippine isolates.
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Arguni E, Indriani C, Rahayu A, Supriyati E, Yohan B, Hayati RF, Wardana S, Tantowijoyo W, Anshari MR, Rahayu E, Ahmad RA, Utarini A, Simmons CP, Sasmono RT. Dengue virus population genetics in Yogyakarta, Indonesia prior to city-wide Wolbachia deployment. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105308. [PMID: 35644356 DOI: 10.1016/j.meegid.2022.105308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/29/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Dengue has been endemic in Yogyakarta, Indonesia for decades. Here, we report the dengue epidemiology, entomology, and virology in Yogyakarta in 2016-2017, prior to the commencement of the Applying Wolbachia to Eliminate Dengue (AWED) randomized trial. Dengue epidemiological data were compiled and blood samples from dengue-suspected patients were tested for dengue virus (DENV). Ae. aegypti mosquito samples were caught from the field using BG-Sentinel traps and tested for the presence of DENV infection. Sequencing of the DENV E gene was used to determine the phylogeny and genotypes of circulating DENV. Within the last decade, the 2016-2017 dengue incidence was considered very high. Among the 649 plasma samples collected between March 2016-February 2017; and 36,910 mosquito samples collected between December 2016-May 2017, a total of 197 and 38 samples were DENV-positive by qRT-PCR, respectively. All four DENV serotypes were detected, with DENV-3 (n = 88; 44.67%) and DENV-1 (n = 87; 44.16%) as the predominant serotype, followed by DENV-4 (n = 12; 6.09%) and DENV-2 (n = 10; 5.08%). The Yogyakarta DENV-1 isolates were classified into Genotype I and IV, while DENV-2, DENV-3, and DENV-4 isolates were classified into the Cosmopolitan genotype, Genotype I, and Genotype II, respectively. Yogyakarta DENV isolates were closely related to Indonesian strains from neighboring Javanese cities, consistent with the endemic circulation of DENV on this highly populous island. Our study provides comprehensive baseline information on the DENV population genetic characteristics in Yogyakarta, which are useful as baseline data for the AWED trial and the future DENV surveillance in the city in the presence of a Wolbachia-infected Ae. aegypti population.
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Affiliation(s)
- Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Citra Indriani
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Biostatistics, Epidemiology and Population Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Satrio Wardana
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Warsito Tantowijoyo
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Ridwan Anshari
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endang Rahayu
- Disease Control Department, Yogyakarta District Health Office, Yogyakarta, Indonesia
| | - Riris Andono Ahmad
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Biostatistics, Epidemiology and Population Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Adi Utarini
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Health Policy and Management, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Cameron P Simmons
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Clayton, Victoria 3800, Australia
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
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Genetic Diversity of Hepatitis E Virus Type 3 in Switzerland-From Stable to Table. Animals (Basel) 2021; 11:ani11113177. [PMID: 34827909 PMCID: PMC8614342 DOI: 10.3390/ani11113177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The main hosts of hepatitis E virus (HEV) genotype 3 are porcine species. Transmission of the virus to humans, for example via undercooked meat, may cause acute or chronic hepatitis. To determine sources and routes of infection, comparing the viruses present in humans to the ones present in main hosts is a helpful tool. However, it requires knowledge of the genetic diversity of the circulating viruses. Therefore, we tested Swiss pigs and wild boars for HEV and determined the virus subtype and part of its genome. In addition, we determined the HEV subtype present in 11 positive meat products. One pig liver from the slaughterhouses (0.3%) and seven livers from a carcass collection (13%) as well as seven wild boar livers (5.8%) were found HEV positive. The same virus subtypes were found in Swiss pigs, wild boars, and meat products. Most of the viruses belonged to a Swiss-specific cluster within the subtype 3h. In addition, one pig liver and one wild boar liver were found positive for 3l and two meat products from Germany for 3c. Our data indicate that Switzerland has its “own” HEV viruses that circulate independent from the rest of Europe. Abstract Hepatitis E caused by hepatitis E viruses of the genotype 3 (HEV-3) is a major health concern in industrialized countries and due to its zoonotic character requires a “One Health” approach to unravel routes and sources of transmission. Knowing the viral diversity present in reservoir hosts, i.e., pigs but also wild boars, is an important prerequisite for molecular epidemiology. The aim of this study was to gain primary information on the diversity of HEV-3 subtypes present along the food chain in Switzerland, as well as the diversity within these subtypes. To this end, samples of domestic pigs from slaughterhouses and carcass collection points, as well as from hunted wild boars, were tested for HEV RNA and antibodies. HEV positive meat products were provided by food testing labs. The HEV subtypes were determined using Sanger and next generation sequencing. The genetic analyses confirmed the predominance of a Swiss-specific cluster within subtype HEV-3h in pigs, meat products, and wild boars. This cluster, which may result from local virus evolution due to the isolated Swiss pig industry, supports fast differentiation of domestic and imported infections with HEV.
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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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Molecular epidemiology of dengue in North Kalimantan, a province with the highest incidence rates in Indonesia in 2019. INFECTION GENETICS AND EVOLUTION 2021; 95:105036. [PMID: 34411743 DOI: 10.1016/j.meegid.2021.105036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Dengue is endemic to Indonesia, a country that has largely varied geographical and demographic conditions across different regions. In 2019, dengue epidemic occurred in North Kalimantan province and recorded as the highest incidence rate in Indonesia. This study aims to investigate the molecular epidemiology of dengue during outbreak in the province and compare the epidemiological characteristics between two cities/towns in North Kalimantan, namely Malinau, an inland town surrounded by a dense rainforest, and Tarakan, an island city. METHODS A cross sectional study was conducted between September 2018 and July 2019. Dengue-like illness patients were recruited in hospitals and tested for dengue NS1 and IgG/IgM. Serological prevalence was measured using IgG ELISA, dengue virus (DENV) serotyping was conducted using RT-PCR and Envelope gene sequencing was performed to infer the virus origins and phylogeny. Clinical, demographical, and diagnostics data were also recorded and analyzed. RESULTS We recruited 523 patients, 261 from Malinau and 262 from Tarakan. Among them, 349 patients were confirmed dengue. Cases in Malinau had a higher proportion of confirmed dengue (82.0%) compared to those in Tarakan (51.5%). Cases in Malinau were more likely to be dengue hemorrhagic fever with more severe hematological features compared to those in Tarakan. All four DENV serotypes were detected in both cities, the most prevalent serotype being DENV-2. The genetic characteristics of the viruses in the two towns was similar except for DENV-3. No sylvatic DENV was detected as well as alphaviruses and non-dengue flaviviruses during the outbreak. CONCLUSIONS The molecular epidemiology of dengue in North Kalimantan revealed the similar virological characteristics but different clinical and demographic aspects in Malinau and Tarakan. The distinct dengue dynamics between different regions of Indonesia is prominent and this knowledge will be important for understanding future patterns of DENV transmission in the region.
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