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Prajapati S, Ngono AE, Cauley MM, Timis J, Shrestha S, Bastola A, Mandal SK, Yadav SR, Napit R, Moi ML, Yamabhai M, Sessions OM, Shresta S, Manandhar KD. Genomic sequencing and neutralizing serological profiles during acute dengue infection: A 2017 cohort study in Nepal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597174. [PMID: 38895290 PMCID: PMC11185687 DOI: 10.1101/2024.06.03.597174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus that poses a threat to nearly 50% of the global population. DENV has been endemic in Nepal since 2006; however, little is known about how DENV is evolving or the prevalence of anti-DENV immunity within the Nepalese population. To begin to address these gaps, we performed a serologic and genetic study of 49 patients from across Nepal who presented at central hospitals during the 2017 dengue season with suspected DENV infection. Of the 49 subjects assessed, 21 (43%) were positive for DENV NS1 antigen; of these; 5 were also anti-DENV IgM + IgG + ; 7 were DENV IgM + IgG - , 2 were IgM - IgG + , and 7 were IgM - IgG - by specific ELISAs. Seven of the 21 NS1+ sera were RNA+ by RT-PCR (six DENV2, one DENV3), suggesting that DENV2 was the dominant serotype in our cohort. Whole-genome sequencing of two DENV2 isolates showed similarity with strains circulating in Singapore in 2016, and the envelope genes were also similar to strains circulating in India in 2017. DENV-neutralizing antibodies (nAbs) were present in 31 of 47 sera tested (66%); among these, 20, 24, 26, and 12 sera contained nAbs against DENV1, 2, 3, and 4 serotypes, respectively. Serology analysis suggested that 12 (26%) and 19 (40%) of the 49 subjects were experiencing primary and secondary DENV infections, respectively. Collectively, our results provide evidence for current and/or past exposure to multiple DENV serotypes in our cohort, and the RNA analyses further indicate that DENV2 was the likely dominant serotype circulating in Nepal in 2017. These data suggest that expanded local surveillance of circulating DENV genotypes and population immunity will be important to effectively manage and mitigate future dengue outbreaks in Nepal.
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Napit R, Ngono AE, Mihindukulasuriya KA, Pradhan A, Khadka B, Shrestha S, Droit L, Paredes A, Karki L, Khatiwada R, Tamang M, Chalise BS, Rawal M, Jha B, Wang D, Handley SA, Shresta S, Manandhar KD. Dengue Virus Surveillance in Nepal Yields the First On-Site Whole Genome Sequences of Isolates from the 2022 Outbreak. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597008. [PMID: 38895410 PMCID: PMC11185532 DOI: 10.1101/2024.06.02.597008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. Methods and Results During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1 + participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. Conclusion These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
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Fraenkel S, Nabeshima T, Xayavong D, Nguyen TTN, Xu Q, Kapandji M, Yamao K, Balingit JC, Pandey BD, Morita K, Hasebe F, Ngwe Tun MM, Takamatsu Y. The Development of New Primer Sets for the Amplification and Sequencing of the Envelope Gene of All Dengue Virus Serotypes. Microorganisms 2024; 12:1092. [PMID: 38930474 PMCID: PMC11205395 DOI: 10.3390/microorganisms12061092] [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: 04/28/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Dengue virus (DENV) poses a significant threat to global health, infecting approximately 390 million people annually. This virus comprises four serotypes capable of causing severe disease. Genetic analyses are crucial for understanding the epidemiology, evolution, and spread of DENV. Although previous studies have focused on the envelope protein-coding (E) gene, only a few primers can efficiently detect and amplify the viral genes from multiple endemic countries simultaneously. In this study, we designed degenerate primer pairs for each DENV serotype to amplify and sequence the entire E gene, using globally representative sequences for each serotype. These primers were validated using DENV isolates from various Asian countries and demonstrated broad-spectrum detection capabilities and high-quality sequences. The primers provide effective tools for genetic analysis in the regions affected by dengue, aiding strain identification and epidemiological studies during outbreaks.
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Affiliation(s)
- Stefania Fraenkel
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- School of Tropical Medicine and Global Health (TMGH), Nagasaki University, Nagasaki 852-8523, Japan
| | - Takeshi Nabeshima
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Kenya Research Station, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan
| | - Dalouny Xayavong
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Thi Thanh Ngan Nguyen
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Qiang Xu
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Merveille Kapandji
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Kano Yamao
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Dental School, Nagasaki University, Nagasaki 852-8588, Japan
| | - Jean Claude Balingit
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
| | - Basu Dev Pandey
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
- Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 690-8504, Japan
| | - Futoshi Hasebe
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Vietnam Research Station, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan
| | - Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, 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 Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
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Rimal S, Shrestha S, Paudel SW, Shah Y, Bhandari G, Pandey K, Kharbuja A, Kapandji M, Gautam I, Bhujel R, Takamatsu Y, Bhandari R, Klungthong C, Shrestha SK, Fernandez S, Malavige GN, Pandey BD, Urano T, Morita K, Ngwe Tun MM, Dumre SP. Molecular and Entomological Characterization of 2023 Dengue Outbreak in Dhading District, Central Nepal. Viruses 2024; 16:594. [PMID: 38675935 PMCID: PMC11053854 DOI: 10.3390/v16040594] [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: 03/12/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
In 2023, Nepal faced its second largest dengue outbreak ever, following a record-breaking number of dengue cases in 2022, characterized by the expansion of infections into areas of higher altitudes. However, the characteristics of the 2023 circulating dengue virus (DENV) and the vector density remain poorly understood. Therefore, we performed DENV serotyping, clinical and laboratory assessment, and entomological analysis of the 2023 outbreak in central Nepal. A total of 396 fever cases in Dhading hospital suspected of being DENV positive were enrolled, and blood samples were collected and tested by different techniques including PCR. Of these, 278 (70.2%) had confirmed DENV infection. Multiple serotypes (DENV-1, -2, and -3) were detected. DENV-2 (97.5%) re-emerged after six years in Dhading while DENV-3 was identified for the first time. Dengue inpatients had significantly higher frequency of anorexia, myalgia, rash, diarrhea, nausea, vomiting, abdominal pain, and thrombocytopenia (p < 0.05). In this area, Aedes mosquitoes largely predominated (90.7%) with the majority being A. aegypti (60.7%). We also found high levels of Aedes index (20.0%) and container index (16.7%). We confirmed multiple DENV serotype circulation with serotype re-emergence and new serotype introduction, and high vector density in 2023. These findings call for the urgent initiation and scaling up of DENV molecular surveillance in human and mosquito populations for dengue control and prevention in Nepal.
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Affiliation(s)
- Sandesh Rimal
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal; (S.R.); (S.S.); (A.K.); (R.B.)
| | - Sabin Shrestha
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal; (S.R.); (S.S.); (A.K.); (R.B.)
| | | | | | - Govinda Bhandari
- Dhading Hospital, Dhading Besi 45100, Nepal; (S.W.P.); (G.B.); (R.B.)
| | - Kishor Pandey
- Central Department of Zoology, Tribhuvan University, Kathmandu 44601, Nepal;
| | - Anjana Kharbuja
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal; (S.R.); (S.S.); (A.K.); (R.B.)
| | - Merveille Kapandji
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.K.); (Y.T.); (K.M.)
| | - Ishan Gautam
- Natural History Museum, Tribhuvan University, Swayambhu, Kathmandu 44620, Nepal;
| | - Rajshree Bhujel
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal; (S.R.); (S.S.); (A.K.); (R.B.)
| | - Yuki Takamatsu
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.K.); (Y.T.); (K.M.)
| | | | - Chonticha Klungthong
- Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand; (C.K.); (S.F.)
| | | | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand; (C.K.); (S.F.)
| | | | - Basu Dev Pandey
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan; (B.D.P.); (T.U.)
| | - Takeshi Urano
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan; (B.D.P.); (T.U.)
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.K.); (Y.T.); (K.M.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan; (B.D.P.); (T.U.)
- Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 690-8504, Japan
- Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.K.); (Y.T.); (K.M.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan; (B.D.P.); (T.U.)
- Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 690-8504, Japan
- Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Shyam Prakash Dumre
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal; (S.R.); (S.S.); (A.K.); (R.B.)
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Sarkar MMH, Rahman MS, Islam MR, Rahman A, Islam MS, Banu TA, Akter S, Goswami B, Jahan I, Habib MA, Uddin MM, Mia MZ, Miah MI, Shaikh AA, Khan MS. Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh. Virol J 2023; 20:127. [PMID: 37337232 PMCID: PMC10278332 DOI: 10.1186/s12985-023-02030-1] [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: 12/28/2022] [Accepted: 04/04/2023] [Indexed: 06/21/2023] Open
Abstract
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.
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Affiliation(s)
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Arafat Rahman
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Mohammad Mohi Uddin
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Zakaria Mia
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Md Ibrahim Miah
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh.
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Rauniyar R, Prajapati S, Manandhar B, Bastola A, Chalise BS, Shrestha S, Khanal C, Thapa M, Napit R, Bajracharya AM, Shrestha S, Adhikari A, Das Manandhar K. Dengue virus infection during window period of consecutive outbreaks in Nepal and assessment of clinical parameters. Sci Rep 2023; 13:9262. [PMID: 37286625 DOI: 10.1038/s41598-023-35928-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023] Open
Abstract
Nepal is an endemic country for dengue infection with rolling of every 3 year's clear cyclic outbreaks with exponential growth since 2019 outbreak and the virus gearing towards the non-foci temperate hill regions. However, the information regarding circulating serotype and genotype is not frequent. This research discusses on the clinical features, diagnosis, epidemiology, circulating serotype and genotype among 61 dengue suspected cases from different hospitals of Nepal during the window period 2017-2018 between the two outbreaks of 2016 and 2019. E-gene sequences from PCR positive samples were subjected to phylogenetic analysis under time to most recent common ancestor tree using Markov Chain Monte Carlo (MCMC) and BEAST v2.5.1. Both evolution and genotypes were determined based on the phylogenetic tree. Serotyping by Real-time PCR and Nested PCR showed the co-circulation of all the 3 serotypes of dengue in the year 2017 and only DENV-2 in 2018. Genotype V for DENV-1 and Cosmopolitan Genotype IVa for DENV-2 were detected. The detected Genotype V of DENV-1 in Terai was found close to Indian genotype while Cosmopolitan IVa of DENV-2 found spreading to geographically safe hilly region (now gripped to 9 districts) was close to South-East Asia. The genetic drift of DENV-2 is probably due to climate change and rapid viral evolution which could be a representative model for high altitude shift of the infection. Further, the increased primary infection indicates dengue venturing to new populations. Platelets count together with Aspartate transaminase and Aalanine transaminase could serve as important clinical markers to support clinical diagnosis. The study will support future dengue virology and epidemiology in Nepal.
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Affiliation(s)
- Ramanuj Rauniyar
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sabita Prajapati
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Binod Manandhar
- Department of Mathematical Sciences, Clark Atlanta University, Atlanta, USA
| | - Anup Bastola
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital (STIDH), Teku, Kathmandu, Nepal
| | - Bimal Sharma Chalise
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital (STIDH), Teku, Kathmandu, Nepal
| | - Srijan Shrestha
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Chetana Khanal
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Machchhendra Thapa
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rajindra Napit
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Molecular Biology and Virology, Centre for Molecular Dynamics Nepal (CMDN), Thapathali, Kathmandu, Nepal
| | | | - Shova Shrestha
- Microbiology Department, Trichandra Multiple Campus, Kathmandu, Nepal
| | - Anurag Adhikari
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences (KRIBS), Lalitpur, Nepal
| | - Krishna Das Manandhar
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal.
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Yang X, Qin S, Liu X, Zhang N, Chen J, Jin M, Liu F, Wang Y, Guo J, Shi H, Wang C, Chen Y. Meta-Viromic Sequencing Reveals Virome Characteristics of Mosquitoes and Culicoides on Zhoushan Island, China. Microbiol Spectr 2023; 11:e0268822. [PMID: 36651764 PMCID: PMC9927462 DOI: 10.1128/spectrum.02688-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mosquitoes and biting Culicoides species are arbovirus vectors. Effective virome profile surveillance is essential for the prevention and control of insect-borne diseases. From June to September 2021, we collected eight species of female mosquito and Culicoides on Zhoushan Island, China, and used meta-viromic sequencing to analyze their virome compositions and characteristics. The classified virus reads were distributed in 191 genera in 66 families. The virus sequences in mosquitoes with the largest proportions were Iflaviridae (30.03%), Phasmaviridae (23.09%), Xinmoviridae (21.82%), Flaviviridae (13.44%), and Rhabdoviridae (8.40%). Single-strand RNA+ viruses formed the largest proportions of viruses in all samples. Blood meals indicated that blood-sucking mosquito hosts were mainly chicken, duck, pig, and human, broadly consistent with the habitats where the mosquitoes were collected. Novel viruses of the Orthobunyavirus, Narnavirus, and Iflavirus genera were found in Culicoides by de-novo assembly. The viruses with vertebrate hosts carried by mosquitoes and Culicoides also varied widely. The analysis of unclassified viruses and deep-learning analysis of the "dark matter" in the meta-viromic sequencing data revealed the presence of a large number of unknown viruses. IMPORTANCE The monitoring of the viromes of mosquitoes and Culicoides, widely distributed arbovirus transmission vectors, is crucial to evaluate the risk of infectious disease transmission. In this study, the compositions of the viromes of mosquitoes and Culicoides on Zhoushan Island varied widely and were related mainly to the host species, with different host species having different core viromes. and many unknown sequences in the Culicoides viromes remain to be annotated, suggesting the presence of a large number of unknown viruses.
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Affiliation(s)
- Xiaojing Yang
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shiyu Qin
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xiong Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Na Zhang
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jiali Chen
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Meiling Jin
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Fangni Liu
- School of Public Health, China Medical University, Shenyang, Liaoning Province, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yong Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jinpeng Guo
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hua Shi
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Changjun Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yong Chen
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
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8
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Rimal S, Shrestha S, Pandey K, Nguyen TV, Bhandari P, Shah Y, Acharya D, Adhikari N, Rijal KR, Ghimire P, Takamatsu Y, Pandey BD, Fernandez S, Morita K, Ngwe Tun MM, Dumre SP. Co-Circulation of Dengue Virus Serotypes 1, 2, and 3 during the 2022 Dengue Outbreak in Nepal: A Cross-Sectional Study. Viruses 2023; 15:507. [PMID: 36851721 PMCID: PMC9958792 DOI: 10.3390/v15020507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
The largest dengue outbreak in the history of Nepal occurred in 2022, with a significant number of casualties. It affected all 77 districts, with the nation's capital, Kathmandu (altitude 1300 m), being the hardest hit. However, the molecular epidemiology of this outbreak, including the dengue virus (DENV) serotype(s) responsible for this epidemic, remain unknown. Here, we report the epidemic trends, clinico-laboratory features, and virus serotypes and their viral load profiles that are associated with this outbreak in Nepal. Dengue-suspected febrile patients were investigated by routine laboratory, serological, and molecular tools, including a real-time quantitative polymerase chain reaction (qRT-PCR). Of the 538 dengue-suspected patients enrolled, 401 (74.5%) were diagnosed with dengue. Among these dengue cases, 129 (32.2%) patients who required hospital admission had significant associations with myalgia, rash, diarrhea, retro-orbital pain, bleeding, and abdominal pain. DENV-1, -2, and -3 were identified during the 2022 epidemic, with a predominance of DENV-1 (57.1%) and DENV-3 (32.1%), exhibiting a new serotype addition. We found that multiple serotypes circulated in 2022, with a higher frequency of hospitalizations, more severe dengue, and more deaths than in the past. Therefore, precise mapping of dengue and other related infections through integrated disease surveillance, evaluation of the dynamics of population-level immunity and virus evolution should be the urgent plans of action for evidence-based policy-making for dengue control and prevention in the country.
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Affiliation(s)
- Sandesh Rimal
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal
| | - Sabin Shrestha
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal
| | - Kishor Pandey
- Central Department of Zoology, Tribhuvan University, Kathmandu 44601, Nepal
| | - Thanh Vu Nguyen
- Institute of Tropical Medicine, DEJIMA Infectious Disease Research Allience, Nagasaki University, Nagasaki 852-8523, Japan
| | - Parmananda Bhandari
- Sukraraj Tropical and Infectious Diseases Hospital, Teku, Kathmandu 44600, Nepal
| | | | - Dhiraj Acharya
- Cleveland Clinic, Florida Research and Innovation Center, Port Saint Lucie, FL 34987, USA
| | - Nabaraj Adhikari
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal
| | - Komal Raj Rijal
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal
| | - Prakash Ghimire
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal
| | - Yuki Takamatsu
- Institute of Tropical Medicine, DEJIMA Infectious Disease Research Allience, Nagasaki University, Nagasaki 852-8523, Japan
| | - Basu Dev Pandey
- Department of Molecular Epidemiology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand
| | - Kouichi Morita
- Institute of Tropical Medicine, DEJIMA Infectious Disease Research Allience, Nagasaki University, Nagasaki 852-8523, Japan
| | - Mya Myat Ngwe Tun
- Institute of Tropical Medicine, DEJIMA Infectious Disease Research Allience, Nagasaki University, Nagasaki 852-8523, Japan
| | - Shyam Prakash Dumre
- Central Department of Microbiology, Tribhuvan University, Kathmandu 44601, Nepal
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9
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Dieng I, Barry MA, Talla C, Sow B, Faye O, Diagne MM, Sene O, Ndiaye O, Diop B, Diagne CT, Fall G, Sall AA, Loucoubar C, Faye O. Analysis of a Dengue Virus Outbreak in Rosso, Senegal 2021. Trop Med Infect Dis 2022; 7:tropicalmed7120420. [PMID: 36548675 PMCID: PMC9781526 DOI: 10.3390/tropicalmed7120420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Senegal is hyperendemic for dengue. Since 2017, outbreaks have been noticed annually in many regions around the country, marked by the co-circulation of DENV1-3. On 8 October 2021, a Dengue virus outbreak in the Rosso health post (sentinel site of the syndromic surveillance network) located in the north of the country was notified to the WHO Collaborating Center for arboviruses and hemorrhagic fever viruses at Institut Pasteur de Dakar. A multidisciplinary team was then sent for epidemiological and virologic investigations. This study describes the results from investigations during an outbreak in Senegal using a rapid diagnostic test (RDT) for the combined detection of dengue virus non-structural protein 1 (NS1) and IgM/IgG. For confirmation, samples were also tested by real-time RT-PCR and IgM ELISA at the reference lab in Dakar. qRT-PCR positive samples were subjected to whole genome sequencing using nanopore technology. Virologic analysis scored 102 positives cases (RT-PCR, NS1 antigen detection and/or IgM) out of 173 enrolled patients; interestingly, virus serotyping showed that the outbreak was caused by the DENV-1, a serotype different from DENV-2 involved during the outbreak in Rosso three years earlier, indicating a serotype replacement. Nearly all field-tested NS1 positives samples were confirmed by qRT-PCR with a concordance of 92.3%. Whole genome sequencing and phylogenetic analysis of strains suggested a re-introduction in Rosso of a DENV-1 strain different to the one responsible for the outbreak in the Louga area five years before. Findings call for improved dengue virus surveillance in Senegal, with a wide deployment of DENV antigenic tests, which allow easy on-site diagnosis of suspected cases and early detection of outbreaks. This work highlights the need for continuous monitoring of circulating serotypes which is crucial for a better understanding of viral epidemiology around the country.
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Affiliation(s)
- Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
- Correspondence: ; Tel.: +221-76-1912447
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Talla
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Bocar Sow
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Moussa Moise Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Ousseynou Sene
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Ndiaye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Boly Diop
- Ministry of Health, Direction of Prevention, Dakar 220, Senegal
| | - Cheikh Tidiane Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
- DIATROPIX, Institute Pasteur de Dakar, Dakar 12900, Senegal
| | - Gamou Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Amadou Alpha Sall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
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10
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Ngwe Tun MM, Pandey K, Nabeshima T, Kyaw AK, Adhikari M, Raini SK, Inoue S, Dumre SP, Pandey BD, Morita K. An Outbreak of Dengue Virus Serotype 2 Cosmopolitan Genotype in Nepal, 2017. Viruses 2021; 13:v13081444. [PMID: 34452310 PMCID: PMC8402744 DOI: 10.3390/v13081444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Dengue virus (DENV) is one of the most prevalent neglected tropical diseases, with half of the world's population at risk of infection. In Nepal, DENV was first reported in 2004, and its prevalence is increasing every year. The present study aimed to obtain and characterize the full-length genome sequence of DENV from the 2017 outbreak. Hospital-based surveillance was conducted in two provinces of Nepal during the outbreak. Acute-phase serum samples were collected from 141 clinically suspected dengue patients after the rainy season. By serological and molecular techniques, 37 (26.9%) and 49 (34.8%), respectively, were confirmed as dengue patients. The cosmopolitan genotype of DENV-2 was isolated from 27 laboratory-confirmed dengue patients. Genomic analysis showed many amino acid substitutions distributed mainly among the E, NS3, and NS5 genes. Phylogenetic analyses of the whole genome sequence revealed two clades (Asian and Indian) among DENV-2 isolates from Nepal. The DENV isolates from hilly and Terai areas were similar to Asian and Indian strains, respectively. Further genomic study on different DENV serotypes is warranted to understand DENV epidemics in Nepal, where there are limited scientific resources and infrastructure.
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Affiliation(s)
- Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.M.N.T.); (T.N.); (A.K.K.); (S.K.R.); (S.I.)
| | - Kishor Pandey
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44060, Nepal;
| | - Takeshi Nabeshima
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.M.N.T.); (T.N.); (A.K.K.); (S.K.R.); (S.I.)
| | - Aung Kyaw Kyaw
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.M.N.T.); (T.N.); (A.K.K.); (S.K.R.); (S.I.)
| | - Mandira Adhikari
- Shi-Gan International College of Science and Technology, Kathmandu 44060, Nepal;
| | - Sandra Kendra Raini
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.M.N.T.); (T.N.); (A.K.K.); (S.K.R.); (S.I.)
| | - Shingo Inoue
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.M.N.T.); (T.N.); (A.K.K.); (S.K.R.); (S.I.)
| | - Shyam Prakash Dumre
- Central Department of Microbiology, Institute of Science and Technology, Tribhuvan University, Kirtipur 44618, Nepal;
| | - Basu Dev Pandey
- Ministry of Health and Population, Kathmandu 44060, Nepal
- Correspondence: (B.D.P.); (K.M.); Tel.: +977-9851065451 (B.D.P.); +81-95-819-7827 (K.M.)
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; (M.M.N.T.); (T.N.); (A.K.K.); (S.K.R.); (S.I.)
- Correspondence: (B.D.P.); (K.M.); Tel.: +977-9851065451 (B.D.P.); +81-95-819-7827 (K.M.)
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11
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Tsheten T, Gray DJ, Clements ACA, Wangdi K. Epidemiology and challenges of dengue surveillance in the WHO South-East Asia Region. Trans R Soc Trop Med Hyg 2021; 115:583-599. [PMID: 33410916 DOI: 10.1093/trstmh/traa158] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/02/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022] Open
Abstract
Dengue poses a significant health and economic burden in the WHO South-East Asia Region. Approaches for control need to be aligned with current knowledge on the epidemiology of dengue in the region. Such knowledge will ensure improved targeting of interventions to reduce dengue incidence and its socioeconomic impact. This review was undertaken to describe the contemporary epidemiology of dengue and critically analyse the existing surveillance strategies in the region. Over recent decades, dengue incidence has continued to increase with geographical expansion. The region has now become hyper-endemic for multiple dengue virus serotypes/genotypes. Every epidemic cycle was associated with a change of predominant serotype/genotype and this was often associated with severe disease with intense transmission. Classical larval indices are widely used in vector surveillance and adult mosquito samplings are not implemented as a part of routine surveillance. Further, there is a lack of integration of entomological and disease surveillance systems, often leading to inaction or delays in dengue prevention and control. Disease surveillance does not capture all cases, resulting in under-reporting, and has thus failed to adequately represent the true burden of disease in the region. Possible solutions include incorporating adult mosquito sampling into routine vector surveillance, the establishment of laboratory-based sentinel surveillance, integrated vector and dengue disease surveillance and climate-based early warning systems using available technologies like mobile apps.
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Affiliation(s)
- Tsheten Tsheten
- Department of Globa l Health, Research School of Population Health, Australian National University, Canberra, Australia.,Royal Centre for Disease Control, Ministry of Health, Bhutan
| | - Darren J Gray
- Department of Globa l Health, Research School of Population Health, Australian National University, Canberra, Australia
| | - Archie C A Clements
- Faculty of Health Sciences, Curtin University, Perth, Australia.,Telethon Kids Institute, Nedlands, Australia
| | - Kinley Wangdi
- Department of Globa l Health, Research School of Population Health, Australian National University, Canberra, Australia
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