Genomic Epidemiology and Active Surveillance to Investigate Outbreaks of Hantaviruses

Kim, Won Keun; Cho, Seungchan; Lee, Seung Ho; No, Jin Sun; Lee, Geum Young; Park, Kyungmin; Lee, Dae-Sang; Jeong, Seong Tae; Song, Jin Won

doi:10.3389/fcimb.2020.532388

Cited by 14 publications

(15 citation statements)

References 94 publications

(78 reference statements)

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“…Phylogeographic analysis of SFTSV elucidated an epidemiological association between viral sequences from ROK Army soldier with SFTS and wild ticks collected from the putative infection site [ 35 ]. The additional genome sequences of SFTSV with geographical information enable to define the phylogenetic and spatial relationships of SFTS patients with infectious sources at high-resolution [ 50 , 51 ]. In this study, whole-genome sequences of SFTSV were newly obtained from ticks ( H .…”

Section: Discussionmentioning

confidence: 99%

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

et al. 2022

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Background Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK). Principal findings A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nanopore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S segments) sub-genotypes, indicating a natural reassortment between sub-genotypes. Conclusion/Significance Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.

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Section: Discussionmentioning

confidence: 99%

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

et al. 2022

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“…In addition, there have been signifi cant epidemic complications due to the spread of known EDIs, such as EVD [32], Chikungunya fever [29], new HFRS strains, etc. [33]. Antarctica and on March 11, the WHO declared a COVID-2019 pandemic [31].…”

Section: Modern Technologies In the Development Of Vaccines In View Of New Biological Threatsmentioning

confidence: 99%

Vaccination and Extremely Dangerous Infections: Achievements and Prospects

Vynograd¹,

Vasylyshyn²,

Kozak³

et al. 2021

PSSS MS

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Introduction. Infectious diseases have been a threat during all periods of human existence. Primary measures to protect against extremely dangerous pathogens included quarantine, observation and vaccination. Vaccination was crucial in the fight against smallpox - the only disease, which was eradicated on a global scale. The aim of the work was to identify the main stages of development and application of vaccines for the protection against extremely dangerous infections (EDI) and the contribution of Ukrainian scientists in the development of vaccines for EDI. Methods. An analysis using the Search Strategy of narrative reviews of literary sources and Internet resource was conducted to systematize data about the application of immunobiological preparations to create an active immunity against several actual EDI. The participation of scientists with Ukrainian roots in the creation of vaccines against this group of diseases is indicated. Results. Smallpox (variolation in China in the 11th century) is known as the first disease against which specific protection was created. Until the 20s century, the first five vaccines against EDI were developed: smallpox, rabies, anthrax, cholera, and plague. In the 20s century, the list was supplemented by vaccines against typhus, yellow fever, tick-borne encephalitis, tularemia, brucellosis, coxiellosis (Q-fever), hemorrhagic fever with renal syndrome (HFRS). The introduction of new technologies in the 21st century allowed improving existing preparations and creating new ones against Ebola viral disease (EVD), COVID-19 as EDIs relevant ones for the pandemic potential. Outstanding scientists with Ukrainian roots contributed to the creation of vaccines against EDI: V. Khavkin, D. Samoilovich, V. Zhdanov. Conclusion. Protection of the population against EDIs is limited by the number of available effective vaccines. The development of vaccines against COVID-19 has improved the prognosis for containment of the COVID-19 pandemic.

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“…The emergence and rise in the spread of RNA viruses in recent years have posed major threats to human life [ 1 ]. Hantaviruses are negative-sense, enveloped, single-stranded RNA viruses, hosted by small mammals such as rodents, shrews, bats, and moles [ 2 ]. They are responsible for the occurrence of a zoonotic disease named hantavirus cardiopulmonary syndrome (HCS) in America and haemorrhagic fever with renal syndrome (HFSR) in Europe.…”

Section: Introductionmentioning

confidence: 99%

Design of a Multi-Epitopes Vaccine against Hantaviruses: An Immunoinformatics and Molecular Modelling Approach

et al. 2022

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Hantaviruses are negative-sense, enveloped, single-stranded RNA viruses of the family Hantaviridae. In recent years, rodent-borne hantaviruses have emerged as novel zoonotic viruses posing a substantial health issue and socioeconomic burden. In the current research, a reverse vaccinology approach was applied to design a multi-epitope-based vaccine against hantavirus. A set of 340 experimentally reported epitopes were retrieved from Virus Pathogen Database and Analysis Resource (ViPR) and subjected to different analyses such as antigenicity, allergenicity, solubility, IFN gamma, toxicity, and virulent checks. Finally, 10 epitopes which cleared all the filters used were linked with each other through specific GPGPG linkers to construct a multi-antigenic epitope vaccine. The designed vaccine was then joined to three different adjuvants—TLR4-agonist adjuvant, β-defensin, and 50S ribosomal protein L7/L12—using an EAAAK linker to boost up immune-stimulating responses and check the potency of vaccine with each adjuvant. The designed vaccine structures were modelled and subjected to error refinement and disulphide engineering to enhance their stability. To understand the vaccine binding affinity with immune cell receptors, molecular docking was performed between the designed vaccines and TLR4; the docked complex with a low level of global energy was then subjected to molecular dynamics simulations to validate the docking results and dynamic behaviour. The docking binding energy of vaccines with TLR4 is −29.63 kcal/mol (TLR4-agonist), −3.41 kcal/mol (β-defensin), and −11.03 kcal/mol (50S ribosomal protein L7/L12). The systems dynamics revealed all three systems to be highly stable with a root-mean-square deviation (RMSD) value within 3 Å. To test docking predictions and determine dominant interaction energies, binding free energies of vaccine(s)–TLR4 complexes were calculated. The net binding energy of the systems was as follows: TLR4-agonist vaccine with TLR4 (MM–GBSA, −1628.47 kcal/mol and MM–PBSA, −37.75 kcal/mol); 50S ribosomal protein L7/L12 vaccine with TLR4 complex (MM–GBSA, −194.62 kcal/mol and MM–PBSA, −150.67 kcal/mol); β-defensin vaccine with TLR4 complex (MM–GBSA, −9.80 kcal/mol and MM–PBSA, −42.34 kcal/mol). Finally, these findings may aid experimental vaccinologists in developing a very potent hantavirus vaccine.

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Genomic Epidemiology and Active Surveillance to Investigate Outbreaks of Hantaviruses

Cited by 14 publications

References 94 publications

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

Vaccination and Extremely Dangerous Infections: Achievements and Prospects

Design of a Multi-Epitopes Vaccine against Hantaviruses: An Immunoinformatics and Molecular Modelling Approach

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