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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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Jiang L, Xu Q, Wu Y, Zhou X, Chen Z, Sun Q, Wen J. Characterization of a Straboviridae phage vB_AbaM-SHI and its inhibition effect on biofilms of Acinetobacter baumannii. Front Cell Infect Microbiol 2024; 14:1351993. [PMID: 38524182 PMCID: PMC10958429 DOI: 10.3389/fcimb.2024.1351993] [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: 12/15/2023] [Accepted: 02/22/2024] [Indexed: 03/26/2024] Open
Abstract
Acinetobacter baumannii (A. baumannii) is a popular clinical pathogen worldwide. Biofilm-associated antibiotic-resistant A. baumannii infection poses a great threat to human health. Bacteria in biofilms are highly resistant to antibiotics and disinfectants. Furthermore, inhibition or eradication of biofilms in husbandry, the food industry and clinics are almost impossible. Phages can move across the biofilm matrix and promote antibiotic penetration. In the present study, a lytic A. baumannii phage vB_AbaM-SHI, belonging to family Straboviridae, was isolated from sauce chop factory drain outlet in Wuxi, China. The DNA genome consists of 44,180 bp which contain 93 open reading frames, and genes encoding products morphogenesis are located at the end of the genome. The amino acid sequence of vB_AbaM-SHI endolysin is different from those of previously reported A. baumannii phages in NCBI. Phage vB_AbaM-SHI endolysin has two additional β strands due to the replacement of a lysine (K) (in KU510289.1, NC_041857.1, JX976549.1 and MH853786.1) with an arginine (R) (SHI) at position 21 of A. baumannii phage endolysin. Spot test showed that phage vB_AbaM-SHI is able to lyse some antibiotic-resistant bacteria, such as A. baumannii (SL, SL1, and SG strains) and E. coli BL21 strain. Additionally, phage vB_AbaM-SHI independently killed bacteria and inhibited bacterial biofilm formation, and synergistically exerted strong antibacterial effects with antibiotics. This study provided a new perspective into the potential application value of phage vB_AbaM-SHI as an antimicrobial agent.
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Affiliation(s)
- Liming Jiang
- School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Qian Xu
- Department of Blood Transfusion, Hubei No. 3 People’s Hospital of Jianghan University, Wuhan, Hubei, China
| | - Ying Wu
- Department of Rheumatology Immunology, The First People’s Hospital of Hefei, Hefei, Anhui, China
| | - Xianglian Zhou
- Department of Rheumatology Immunology, The First People’s Hospital of Hefei, Hefei, Anhui, China
| | - Zhu Chen
- Department of Laboratory, Ningbo No.2 Hospital, Ningbo, Zhejiang, China
| | - Qiangming Sun
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jinsheng Wen
- School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
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Amorim MT, Naveca FG, Hernández LHA, da Paz TYB, da Silva de Oliveira CC, da Conceição Miranda Santos A, Queiroz ALN, Wanzeller ALM, da Silva EVP, da Silva FS, da Silva SP, Nunes BTD, Cruz ACR. Detection of a Multiple Circulation Event of Dengue Virus 2 Strains in the Northern Region of Brazil. Trop Med Infect Dis 2024; 9:17. [PMID: 38251214 PMCID: PMC10818346 DOI: 10.3390/tropicalmed9010017] [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: 11/08/2023] [Revised: 12/10/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
Dengue virus serotype 2 (DENV-2) is responsible for dengue epidemics on a global scale and is associated with severe cases of the disease. This study conducted a phylogenetic investigation of DENV-2 isolates from 2017 to 2021 originating from the northern states of Brazil. A total of 32 samples from DENV-2 isolates were analyzed, including 12 from Acre, 19 from Roraima, and one from Tocantins. Only one lineage of the Asian-American genotype and one lineage of the cosmopolitan genotype were observed: Lineage 1, Asian-American genotype (connection to Puerto Rico); Lineage 5, cosmopolitan genotype (connection to Peru). Our results provide important data regarding the study of DENV genotypes and lineage distribution and open up possibilities for probable introduction and dissemination routes.
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Affiliation(s)
- Murilo Tavares Amorim
- Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil;
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Felipe Gomes Naveca
- Laboratory of Infectious Diseases Ecology in Amazon, Leonidas and Maria Deane Institute, Fiocruz, Manaus 69057-070, Brazil;
- Arbovirus and Hemorrhagic Virus Laboratory, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Leonardo Henrique Almeida Hernández
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Thito Yan Bezerra da Paz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | | | - Alessandra da Conceição Miranda Santos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Alice Louize Nunes Queiroz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Ana Lucia Monteiro Wanzeller
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Eliana Vieira Pinto da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Fábio Silva da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Sandro Patroca da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Bruno Tardelli Diniz Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Ana Cecília Ribeiro Cruz
- Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil;
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
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Sun H, Yao W, Siddique A, He F, Yue M. Genomic characterization of dengue virus serotype 2 during dengue outbreak and endemics in Hangzhou, Zhejiang (2017-2019). Front Microbiol 2023; 14:1245416. [PMID: 37692383 PMCID: PMC10485828 DOI: 10.3389/fmicb.2023.1245416] [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: 06/23/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction Dengue fever (DF) is a mosquito-borne viral disease caused by the dengue virus (DENV). In recent years, Hangzhou has undergone a DF epidemic, particularly in 2017, with an outbreak of 1,128 patients. The study aimed to investigate the genetic diversity and molecular evolution among the DF clinical isolates during and after the outbreak to aid in mapping its spread. Methods To understand the genetic diversity, 74 DENV-2 strains were isolated from DF epidemic cases between 2017 and 2019. Combining whole genome sequencing (WGS) technology, additional phylogenetic, haplotype, amino acid (AA) substitution, and recombination analyses were performed. Results The results revealed that strains from 2017 were closely related to those from Singapore, Malaysia, and Thailand, indicating an imported international transmission. Local strains from 2018 were clustered with those recovered from 2019 and were closely associated with Guangzhou isolates, suggesting a within-country transmission after the significant outbreak in 2017. Compared to DENV-2 virus P14337 (Thailand/0168/1979), a total of 20 AA substitutions were detected. Notably, V431I, T2881I, and K3291T mutations only occurred in indigenous cases from 2017, and A1402T, V1457I, Q2777E, R3189K, and Q3310R mutations were exclusively found in imported cases from 2018 to 2019. The recombination analysis indicated that a total of 14 recombination events were observed. Conclusion This study may improve our understanding of DENV transmission in Hangzhou and provide further insight into DENV-2 transmission and the local vaccine choice.
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Affiliation(s)
- Hua Sun
- Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, China
| | - Wenwu Yao
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Abubakar Siddique
- Hainan Institute of Zhejiang University, Sanya, China
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Fan He
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya, China
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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Xiong N, Sun Q. Identification of stage-related and severity-related biomarkers and exploration of immune landscape for Dengue by comprehensive analyses. Virol J 2022; 19:130. [PMID: 35918744 PMCID: PMC9344228 DOI: 10.1186/s12985-022-01853-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background At present, there are still no specific therapeutic drugs and appropriate vaccines for Dengue. Therefore, it is important to explore distinct clinical diagnostic indicators. Methods In this study, we combined differentially expressed genes (DEGs) analysis, weighted co-expression network analysis (WGCNA) and Receiver Operator Characteristic Curve (ROC) to screen a stable and robust biomarker with diagnosis value for Dengue patients. CIBERSORT was used to evaluate immune landscape of Dengue patients. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene set enrichment analysis (GSEA) were applied to explore potential functions of hub genes. Results CD38 and Plasma cells have excellent Area Under the Curve (AUC) in distinguishing clinical stages for Dengue patients, and activated memory CD4+ T cells and Monocytes have good AUC for this function. ZNF595 has acceptable AUC in discriminating dengue hemorrhagic fever (DHF) from dengue fever (DF) in whole acute stages. Analyzing any serotype, we can obtain consistent results. Negative inhibition of viral replication based on GO, KEGG and GSEA analysis results, up-regulated autophagy genes and the impairing immune system are potential reasons resulting in DHF. Conclusions CD38, Plasma cells, activated memory CD4+ T cells and Monocytes can be used to distinguish clinical stages for dengue patients, and ZNF595 can be used to discriminate DHF from DF, regardless of serotypes. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01853-8.
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Affiliation(s)
- Nan Xiong
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Kunming Medical University, Kunming, 650500, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.
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7
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Han A, Sun B, Sun Z, Xu X, Yang Q, Xie D, Guan W, Lou Y. Molecular Characterization and Phylogenetic Analysis of the 2019 Dengue Outbreak in Wenzhou, China. Front Cell Infect Microbiol 2022; 12:829380. [PMID: 35663472 PMCID: PMC9161089 DOI: 10.3389/fcimb.2022.829380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
In 2019, a dengue outbreak occurred with 290 confirmed cases in Wenzhou, a coastal city in southeast China. To identify the origin of the dengue virus (DENV) from this outbreak, viral RNA was extracted from four serum samples and sequenced for whole genome analysis. Then, phylogenetic analysis, gene mutation, secondary structure prediction, selection pressure analysis, and recombination analysis were performed. DENV strains Cam-03 and Cam-11 were isolated from patients traveling from Cambodia, while ZJWZ-18 and ZJWZ-62 strains were isolated from local patients without a record of traveling abroad. The whole genome sequence of all four strains was 10,735 nucleotides long. Phylogenetic tree analysis showed that the four strains belonged to genotype 1 of DENV-1, but the local Wenzhou strains and imported strains clustered in different branches. ZJWZ-18 and ZJWZ-62 were closely related to strain MF033254-Singapore-2016, and Cam-03 and Cam-11 were closely related to strain AB608788-China : Taiwan-1994. A comparison of the coding regions between the local strains and the DENV-1 standard strain (EU848545-Hawaii-1944) showed 82 amino acid mutations between the two strains. A total of 55 amino acid mutations were found between the coding regions of the local and imported strains. The overall secondary structure of the 3' UTR of the local strains had changed: apparent changes in the head and tail position were observed when compared to DENV-1 standard strain. Furthermore, selection pressure analysis and recombination detection using the 4 isolates and 41 reference strains showed two credible positive selection sites and eight credible recombination events, which warrant further studies. This study may enhance the understanding of viral replication, infection, evolution, virulence, and pathogenicity of DENV.
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Affiliation(s)
- Axiang Han
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Baochang Sun
- Department of Laboratory, Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Zhewei Sun
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xuelian Xu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiongying Yang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Danli Xie
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wanchun Guan
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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Wang X, Li T, Shu Y, Zhang J, Shan X, Li D, Ma D, Long S, Pan Y, Chen J, Liu P, Sun Q. Clinical Characteristics and Risk Factors for Severe Dengue Fever in Xishuangbanna, During the Dengue Outbreak in 2019. Front Microbiol 2022; 13:739970. [PMID: 35359722 PMCID: PMC8960845 DOI: 10.3389/fmicb.2022.739970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/25/2022] [Indexed: 12/17/2022] Open
Abstract
BackgroundDengue poses a large burden on the public health systems worldwide. severe dengue (SD) could lead to more serious clinical symptoms and even death. This study aimed to identify the cause of SD in a clinical trial during the dengue outbreak in Xishuangbanna in 2019, and could provide new insights into the pathogenic mechanisms of SD.MethodsMosquito-borne viral (DENV, JEV, and CHIKV) infections were identified. The epidemiological factors and clinical symptoms of inpatients in Xishuangbanna were recorded. The IgG and IgM levels in the serum of dengue inpatients were evaluated, and secondary infections were identified. Then, the structural proteins (C/PrM/E) were sequenced and compared with those of the same type of DENV in the same area as before, and their structures were predicted by the SWISS-MODEL (expasy.org). The full-length viral genomes were sequenced and aligned with representative strains by BioEidt or MEGA 5.0.ResultsIn this outbreak, the clinical symptoms were more serious in SD. The proportion of SD inpatients of male and Han nationality was larger than that of dengue fever (DF) inpatients (p < 0.05). DENV-2 infection was the majority in DF, with 45 inpatients. However, DENV-1 infection was the most common SD, with 54 inpatients. There were 3 DENV-3-positive inpatients in the DF group and 6 ZIKV-positive inpatients in the SD group. A secondary infection accounted for 76.47% (78 cases) of SD inpatients, but secondary infections were only in 20% (17 cases) of DF inpatients. In the three-dimensional structure of protein analysis, the C/PrM/E of DENV-1 and DENV-2 showed more stability than previous epidemic strains, while DENV-3 in 2019 showed a looser spatial structure. After a complete genome sequencing and analysis, all six DENV-2 strains belonged to cosmopolitan, five of which clustered into one branch. The GC/AT of the five strains decreased from 2014 to 2018. Compared with DF strains, SD strains had no mutations of commonness.ConclusionsSD may related to secondary heteromorphic dengue in Xishuangbanna in 2019. The coinfection of ZIKV could be another related factor for SD. The currently datas were very limited and only suggestive.
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Affiliation(s)
- Xiaodan Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
- Yunnan Key Laboratory of Vector-Borne Infectious Disease, Kunming, China
| | - Tingting Li
- Xishuangbanna Dai Autonomous Prefecture People’s Hospital, Jinhong, China
| | - Yun Shu
- Xishuangbanna Dai Autonomous Prefecture People’s Hospital, Jinhong, China
| | - Juan Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
- Yunnan Key Laboratory of Vector-Borne Infectious Disease, Kunming, China
- Kunming Medical University, Kunming, China
| | - Xiyun Shan
- Xishuangbanna Dai Autonomous Prefecture People’s Hospital, Jinhong, China
| | - Daiying Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
- Yunnan Key Laboratory of Vector-Borne Infectious Disease, Kunming, China
| | - Dehong Ma
- Xishuangbanna Dai Autonomous Prefecture People’s Hospital, Jinhong, China
| | | | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
- Yunnan Key Laboratory of Vector-Borne Infectious Disease, Kunming, China
| | - Junying Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
- Yunnan Key Laboratory of Vector-Borne Infectious Disease, Kunming, China
| | - Pinghua Liu
- Xishuangbanna Dai Autonomous Prefecture People’s Hospital, Jinhong, China
- Pinghua Liu,
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
- Yunnan Key Laboratory of Vector-Borne Infectious Disease, Kunming, China
- *Correspondence: Qiangming Sun,
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Ma Y, Li M, Xie L, Gao N, Fan D, Feng K, Yao Y, Zhou Y, Sheng Z, Zhou H, Chen H, An J. Seroepidemiologic study on convalescent sera from dengue fever patients in Jinghong, Yunnan. Virol Sin 2022; 37:19-29. [PMID: 35234619 PMCID: PMC8922416 DOI: 10.1016/j.virs.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/28/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Yingshuo Ma
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Man Li
- Yunnan Institute of Parasitic Diseases, Pu'er, 665000, China
| | - Lyu Xie
- Yunnan Institute of Parasitic Diseases, Pu'er, 665000, China
| | - Na Gao
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Dongying Fan
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Kaihao Feng
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yao Yao
- People's Hospital of Xishuangbanna Dai Autonomous Prefecture, Xishuangbanna, 666100, China
| | - Yong Zhou
- Xishuangbanna Mental Health Center, Xishuangbanna, 666100, China
| | - Ziyang Sheng
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Pu'er, 665000, China; Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research and Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control (YPCICPHDPC), Pu'er, 665000, China.
| | - Hui Chen
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China; Experimental Center for Basic Medical Teaching, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
| | - Jing An
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
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Calvez E, Bounmany P, Balière C, Somlor S, Viengphouthong S, Xaybounsou T, Keosenhom S, Fangkham K, Brey PT, Caro V, Lacoste V, Grandadam M. Using Background Sequencing Data to Anticipate DENV-1 Circulation in the Lao PDR. Microorganisms 2021; 9:microorganisms9112263. [PMID: 34835389 PMCID: PMC8617722 DOI: 10.3390/microorganisms9112263] [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: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
Since its first detection in 1979, dengue fever has been considered a major public health issue in the Lao People’s Democratic Republic (PDR). Dengue virus (DENV) serotype 1 was the cause of an epidemic in 2010–2011. Between 2012 and 2020, major outbreaks due successively to DENV-3, DENV-4 and recently DENV-2 have been recorded. However, DENV-1 still co-circulated in the country over this period. Here, we summarize epidemiological and molecular data of DENV-1 between 2016 and 2020 in the Lao PDR. Our data highlight the continuous circulation of DENV-1 in the country at levels ranging from 16% to 22% among serotyping tests. In addition, the phylogenetic analysis has revealed the circulation of DENV-1 genotype I at least since 2008 with a co-circulation of different clusters. Sequence data support independent DENV-1 introductions in the Lao PDR correlated with an active circulation of this serotype at the regional level in Southeast Asia. The maintenance of DENV-1 circulation over the last ten years supports a low level of immunity against this serotype within the Lao population. Thereby, the risk of a DENV-1 epidemic cannot be ruled out in the future, and this emphasizes the importance of maintaining an integrated surveillance approach to prevent major outbreaks.
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Affiliation(s)
- Elodie Calvez
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
- Correspondence:
| | - Phaithong Bounmany
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Charlotte Balière
- Environment and Infectious Risks Unit, Institut Pasteur, 75015 Paris, France; (C.B.); (V.C.)
| | - Somphavanh Somlor
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Souksakhone Viengphouthong
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Thonglakhone Xaybounsou
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Sitsana Keosenhom
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Kitphithak Fangkham
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
- Lao Army Institute for Preventive Medicine, Vientiane 01030, Laos
| | - Paul T. Brey
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane 01030, Laos;
| | - Valérie Caro
- Environment and Infectious Risks Unit, Institut Pasteur, 75015 Paris, France; (C.B.); (V.C.)
| | - Vincent Lacoste
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
| | - Marc Grandadam
- Arbovirus and Emerging Viral Diseases Laboratory, Institut Pasteur du Laos, Vientiane 01030, Laos; (P.B.); (S.S.); (S.V.); (T.X.); (S.K.); (K.F.); (V.L.); (M.G.)
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11
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Calvez E, Somlor S, Viengphouthong S, Balière C, Bounmany P, Keosenhom S, Caro V, Grandadam M. Rapid genotyping protocol to improve dengue virus serotype 2 survey in Lao PDR. PLoS One 2020; 15:e0237384. [PMID: 32764809 PMCID: PMC7413503 DOI: 10.1371/journal.pone.0237384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 12/30/2022] Open
Abstract
Dengue fever is one of the major public health problems in Lao PDR. Over the last decade, dengue virus (DENV) epidemics were characterized by a novel predominant serotype accompanied by at least two other serotypes. Since 2008, DENV-2 circulated at a low level in Lao PDR but its epidemiologic profile changed at the end of 2018. Indeed, the number of confirmed DENV-2 cases suddenly increased in October 2018 and DENV-2 became predominant at the country level in early 2019. We developed a Genotype Screening Protocol (GSP) to determine the origin(s) of the Lao DENV-2 and study their genetic polymorphism. With a good correlation with full envelope gene sequencing data, this molecular epidemiology tool evidence the co-circulation of two highly polymorphic DENV-2 genotypes, i.e. Asian I and Cosmopolitan genotypes, over the last five years, suggesting multiple introductions of DENV-2 in the country. GSP approach provides relevant first line information that may help countries with limited laboratory resources to reinforce their capabilities to DENV-2 and to follow the epidemics progresses and assess situations at the regional level.
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Affiliation(s)
- Elodie Calvez
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
- * E-mail:
| | - Somphavanh Somlor
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
| | | | | | | | - Sitsana Keosenhom
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
| | | | - Marc Grandadam
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
- Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
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Hwang EH, Kim G, Oh H, An YJ, Kim J, Kim JH, Hwang ES, Park JH, Hong J, Koo BS. Molecular and evolutionary analysis of dengue virus serotype 2 isolates from Korean travelers in 2015. Arch Virol 2020; 165:1739-1748. [PMID: 32409874 PMCID: PMC7351809 DOI: 10.1007/s00705-020-04653-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/10/2020] [Indexed: 12/17/2022]
Abstract
In Korea, dengue infection has been frequently reported in travelers to tropical and subtropical countries. Global warming increases the probability of autochthonous dengue outbreaks in Korea. In this report, the molecular and evolutionary properties of four dengue virus (DENV) type 2 isolates from Korean overseas travelers were examined. Three of these isolates were classified as Cosmopolitan genotypes and further divided into sublineages 1 (43,253, 43,254) and 2 (43,248), while the other isolate (KBPV-VR29) was related to American genotypes. The variable amino acid motifs related to virulence and replication were identified in the structural and non-structural proteins. A negative selection mechanism was clearly verified in all of the DENV proteins. Potential recombination events were identified in the NS5 protein of the XSBN10 strain. The substitution rate (5.32 × 10-4 substitutions per site) and the time of the most recent common ancestor (TMRCA) for each evolutionary group were determined by the Bayesian skyline coalescent method. This study shows that DENV type 2 strains with distinct phylogenetic, evolutionary, and virulence characteristics have been introduced into Korea by overseas travelers and have the potential to trigger autochthonous dengue outbreaks.
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Affiliation(s)
- Eun-Ha Hwang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Green Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Hanseul Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - You Jung An
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Jiyeon Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Jung Heon Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Eung-Soo Hwang
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Jong-Hwan Park
- Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - JungJoo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.
| | - Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.
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13
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Kar M, Nisheetha A, Kumar A, Jagtap S, Shinde J, Singla M, M S, Pandit A, Chandele A, Kabra SK, Krishna S, Roy R, Lodha R, Pattabiraman C, Medigeshi GR. Isolation and molecular characterization of dengue virus clinical isolates from pediatric patients in New Delhi. Int J Infect Dis 2018; 84S:S25-S33. [PMID: 30528666 DOI: 10.1016/j.ijid.2018.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVE To characterize the in vitro replication fitness, viral diversity, and phylogeny of dengue viruses (DENV) isolated from Indian patients. METHODS DENV was isolated from whole blood collected from patients by passaging in cell culture. Passage 3 viruses were used for growth kinetics in C6/36 mosquito cells. Parallel efforts also focused on the isolation of DENV RNA from plasma samples of the same patients, which were processed for next-generation sequencing. RESULTS It was possible to isolate 64 clinical isolates of DENV, mostly DENV-2. Twenty-five of these were further used for growth curve analysis in vitro, which showed a wide range of replication kinetics. The highest viral titers were associated with isolates from patients with dengue with warning signs and severe dengue cases. Full genome sequences of 21 DENV isolates were obtained. Genome analysis mapped the circulating DENV-2 strains to the Cosmopolitan genotype. CONCLUSIONS The replication kinetics of isolates from patients with mild or severe infection did not differ significantly, but the viral titers varied by two orders of magnitude between the isolates, suggesting differences in replication fitness among the circulating DENV-2.
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Affiliation(s)
- Meenakshi Kar
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amul Nisheetha
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Anuj Kumar
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Jitendra Shinde
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Mohit Singla
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Saranya M
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, ICGEB Campus, New Delhi, India
| | - Sushil K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sudhir Krishna
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India; Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India; Center for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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