To investigate the extent of intrahost sequence variation of other dengue viral genes, we examined in this study the capsid c gene and the nonstructural gene, ns2b, derived directly from plasma dengue viruses from 18. Integrating dengue virus whole genome annotation with disease ontology. Backgroundpythium species are a kind of the funguslike oomycetes presenting in soil and aquatic environments latijnhouwers et al. On the basis of phylogenetic analyses, these isolates were assigned genotype 1. Feat provides insights into west nile, yellow fever and other flaviviruses. Although dengue is an old disease, recent decades have seen an unprecedented increase in the geographic range, incidence, and severity of infection. Anatomy of a killer understanding sarscov2 and the drugs that. Dengue virus denv is a positivesense, singlestranded rna virus of the family flaviviridae. Jun 15, 2016 backgroundpythium species are a kind of the funguslike oomycetes presenting in soil and aquatic environments latijnhouwers et al. Dengue virus 3 genotype 1 associated with dengue fever and. Molecular basis for specific viral rna recognition and o. New dengue virus strain complete genome sequence lc. Genome organization and genome mapping of all serotypes of dengue virus to sort out comparative genome analysis. Dengue fever remains a serious public health threat throughout the world.
Virus pathogen database and analysis resource vipr. Proteins, nucleic acids, serology, replication of plant viruses in vectors, insect tissue cultures as a tool for studying plant viruses, virus induced mutations in maize, noncapsid viral proteins, viruses infecting eukaryotic chlorellalike green algae, application of recombinant dna techniques to. The dataset of complete genome sequences from 990 strains of dengue virus serotype 2 used in this study. Here we report a newly detected strain of chik, zhejiangchiksy2012, in china, a nonindigenous region for chik, using a modified approach based on the classic cdnaaflp. The incidence and geographic range of dengue have increased dramatically in recent decades.
To compare the genetic relatedness of the partial virus genome. Malaria remains a major global health threat with an estimated 300 500 million cases per year and deaths of. Ns3 protease from flavivirus as a target for designing. Several quantitative trait loci qtl underlying variation in ae. Molecular epidemiology of dengue viruses from complete. The incidence of dengue has increased remarkably in recent decades singh 2014. Dengue virus is spherical enveloped viruses with approximately 4060 nm in diameter. Dengue virus, full genome, phylogenetic analysis, diversity, jeddah, saudi arabia background dengue virus denv is a positive sense singlestranded rna virus belonging to the flaviviridae family. Distribution of structural and nonstructural proteins on the basis of size. These studies were confirmed and extended by simpson and hirst 1961, taking advantage of the plaque technique, which became available for influenza viruses at this time. The viral genomes resource is a collection of viral genomic sequences that is a part of the entrez genomes, which provides curated sequence data and annotations of complete genomes to.
Mutations can be deleterious, neutral, or occasionally favorable. Circulation of dengue virus type 3 genotype iii in africa. Pdf complete genome sequence of chikungunya virus isolated. The flavivirus genus includes other important human pathogens such as yellow fever yfv, west nile wnv, japanese encephalitis jev, and tick borne encephalitis tbev.
Mar 16, 2015 a crystal structure of the dengue virus ns5 protein reveals a novel interdomain interface essential for protein flexibility and virus replication. Complete genome sequence and phylogenetic analysis. The raw fastq files for each virus sample were filtered using previously. The virus is in the family flaviviridae of the genus flavivirus, and the typespecific virus is yellow fever. Frontiers genome sequence of dengue virus 3 from the. Introduction of ns5 mutations into genome length denv cdnamutations encoding changes in ns3 and ns5 amino acids were introduced into the genomic length denv2 strain new guinea c ngc cdna clone pdvws601, which yields the virus v601 32, 33. Model answers to the exercises are given in answers to the exercises on dna sequence statistics 2. Complete genome analysis of dengue virus type 3 isolated from. Figure genome analysis of mayaro virus imported to.
Integrating dengue virus whole genome annotation with disease. The surface proteins are arranged in an icosahedrallike symmetry. Dengue virus denv genome amplification is a process that involves the viral rna, cellular and viral proteins, and a complex architecture of cellular membranes. Background chikungunya chik virus is a mosquitoborne emerging pathogen presenting great health challenges worldwide, particularly in tropical zones. The four denv serotypes denv1, 2, 3, and 4 are primarily transmitted between humans by the mosquito aedes aegypti, with aedes albopictus as a secondary vector. The table lists the assigned serial number, genbank accession number, strain name, genotype, country, collection date and the subpopulationlineage. Structure mapping of dengue and zika viruses reveals. Opening doors to the possibility of developing new vaccines and antiviral agents to fight a host of insectborne diseases, scientists have, for the first time, determined the structure of a family of viruses known as the flaviviruses. To analyse the molecular evolution of the virus, a phylogenetic tree can be constructed using specific regions of the denv genome, such as the fulllength sequence, e, or ens1 huang et al. Remarkably, for a virus that is considered a categorya pathogen and that infects 100 million people each year, there are only 96 whole genome sequences 10.
By analyzing a conserved region of the denv genome 504 nt of cprm gene and a more variable region 1,023 nt of the envelope gene, we veri. We report the solution structure of the 200residue homodimer of dengue 2 c. The viral rna is not a passive template during this process. Dengue virus denv, a mosquitoborne flavivirus, is the causative agent of dengue fever, currently one of the most significant emerging disease challenges to global public health. Proteins, nucleic acids, serology, replication of plant viruses in vectors, insect tissue cultures as a tool for studying plant viruses, virusinduced mutations in maize, noncapsid viral proteins, viruses infecting eukaryotic chlorellalike green algae, application of recombinant dna techniques to. Vipr uses phyml guindon and gascuel, 2003 and offers multiple evolutionary models to infer phylogenies. New york genomeweb gene variants with different prevalence among world populations affect susceptibility to classic dengue fever or dengue shock syndrome, a new study has found. Download genbank file sequence header bit score e value ext702037 gi702037 country. Dengue serotype 3 viruses were isolated from patients in brazil from 2002 through 2004. Dengue virus has singlestranded positivesense rna genome of about 11 kbp long, surrounded by a nucleocapsid and covered by a lipid envelope that contains the viral glycoproteins. The main objectives of this book are to proved annotation of dengue virus serotypes genomes at nucleotide level for better understanding and ease organization.
Out of which 3 are structural proteins and 7 are non structural proteins. In order to analyze the complete genome sequence of a den2 brazilian strain br6402298, we designed primers to amplify contiguous segments of approximately 500 base pairs across the entire sequence of the viral genome. Molecular characterization and phylogenetic analysis of. Virus dengue is known to be caused by a singlestranded rna virus approximately 11 kilobases long with an icosahedral nucleocapsid and covered by a lipid envelope. According to the world health organization, dengue virus incidence has increased 30fold over the past 50 years, with up to 50 to 100 million infections occurring annually in over 100 endemic countries. Highthroughput screening using dengue virus reporter genomes.
Dengue virus denv is a member of the flavivirus genus of the flaviviridae family. The malaria parasite is one of the most widespread eukaryotic pathogens in the world today. Amongst the denv proteins, nonstructural protein 1 ns1 is one of the most enigmatic, being required for rna replication, but also secreted from infected cells to. Dengue fever df is common mosquito born disease caused by dengue virus 1. Jun 15, 2017 complete genome analysis of dengue virus type 3 isolated from the 20 dengue outbreak in yunnan, china author links open overlay panel xiaodan wang a b c 1 dehong ma d 1 xinwei huang a b c lihua li c duo li a b c yujiao zhao a b c lijuan qiu a b c yue pan a b c junying chen a b c juemin xi a b c xiyun shan d qiangming sun a b c. Chikungunya is caused by the chikungunya virus chikv, an arthropodborne virus arbovirus. Jul 28, 2018 the epidemic of dengue virus infections has spread markedly in yunnan province of china in recent years due to an increase in the number of imported dengue cases. Perspectives on progress in plant virology pdf 21p this note describes the following topics. Flaviviruses are enveloped viruses with a single stranded.
A recentstudy is the first to report a whole genome sequence and molecular characterization of an imported denv4 isolate from thailand. Climate change, rapid urbanization and increased global travel have facilitated the spread of both efficient mosquito vectors and the four dengue virus serotypes between population centers. The comparison of nucleotide sequences 240 bp from the ens1 gene region of the dengue virus genome has been shown to reflect evolutionary relationships and geographic origins of dengue virus. It is caused by the 4 serotype of dengue virus and is transmitted with in human through female aedes mosquito. A computational research on dengue virus zulkifal yousaf on. Complete nucleotide sequence analysis of a brazilian. This structure captures the viral enzyme in the act of transferring a methyl group to the 2. As a virus invades the body and begins to massproduce itself by manipulating the replication machinery of the bodys own cells, the virus can make mistakes while replicating the genome, leading to defective viral genomes dvgs present in some cells. Dengue fever is a selflimiting viral infection in the majority of cases. Structure of influenza viruses, connected with influenza life.
Presence of a segmented singlestranded rna genome in influenza c virus. Viral genetics medical microbiology ncbi bookshelf. Complete genome sequence of chikungunya virus isolated in the article pdf available in genome announcements 23. Oribose of the first nucleotide of the viral genome, providing an atomiclevelunderstandingofspecific2. The ability to monitor such epidemics would be enhanced by characterizing the viral populations that circulate within infected individuals. Author summary dengue viruses denv are viruses that can cause asymptomatic infection to lifethreatening haemorrhagic fever disease. Molecular epidemiology of dengue viruses from complete genome. Current concepts in dengue pathogenesis pdf 92p download book. Author summary chikungunya virus is a reemerging and rapidly spreading arbovirus that has caused several outbreaks in the last decade with the most recent in the caribbean islands and the americas beginning in 20 infecting over 1 million individuals. Dengue virus genome structure with the structural and nonstructural genes the life cycle of dengue involves endocytosis via a cell surface receptor see video 1 and figure 3. Wholegenome sequencing analysis from the chikungunya virus. Although several aspects in dengue virus replication are known, many others are yet to be understood. Mature virions contain two virus encoded membrane proteins m and e, while immature virions contain a membrane protein precursor. Research open access complete genome sequencing and phylogenetic analysis of dengue type 1 virus isolated from jeddah, saudi arabia esam i azhar1,2,anwarmhashem1,3, sherif a elkafrawy1,saidabolela1, adly mm abdalla4, sayed sartaj sohrab1, suha a farraj1, norah a othman1,hudagbenhelaby1, ahmed ashshi5,tariqamadani6 and ghazi jamjoom1 abstract.
Previously, we studied the envelope e gene of dengue virus and reported that dengue3 virus is present as a quasispecies. Author summary dengue virus denv is a major arthropodborne human pathogen, infecting more than 400 million individuals annually worldwide. China destroyed samples of the virus and ordered their doctors to stop testing in december. They are regarded as serious plant pathogens, resulting in economic losses of many crops. Twenty fragments amplified by reverse transcriptasepcr were. Targeted full genome amplification and sequencing of. We present the global characteristics of the rna genome of zika virus zikv, an emerging pathogen within the flavivirus genus. Under genome selection reference genome, click upload genome file and browse to the saved reference.
We then performed etiological and phylogenetic analyses to better. There are 29 different types of alphaviruses that cause diseases in humans and other. Genomic characterisation and epidemiology of 2019 novel. Sep 07, 20 carries a single stranded rna as its genome. The genome of 10,672 base pairs was studied with reference to global and the regional genomes of dengue3 virus. In many cities, rapid urbanization has resulted in densely packed human and mosquito populations and in an increased. Various sorts of virus, though, store their genes on rna. Assembly of all sequenced overlapping fragments obtained by rtpcr resulted in a genome of 10,622 nts with a complete coding region encoding for 3392 amino acids aa flanked by 94 and 349 nts at the 5 utr and 3 utr, respectively. Identification of zika virus and dengue virus dependency. The virus uncoats intracellularly via a specific process.
Structure of influenza viruses, connected with influenza. Structure, function, and uses molecular cell biology. Dengue virus denv is a member of the genus flavivurs, family flaviviridae. This genotype had never been reported in south america before. Complete nucleotide sequence analysis of a brazilian dengue. Maquart m, caro v, jaffarbandjee mc, dosso m, et al. There are 29 different types of alphaviruses that cause diseases in humans and other mammals. Currently, more than 40% of the worlds population is at risk for dengue virus denv infection, and there is no. Bayesian maximum clade credibility tree representing the timescale phylogeny of mayaro virus mayv by analysis of 2kb genomic fragments, including the 3. At the same time, significant advances in genomics approaches have provided insights into hostpathogen. In the infectious form of the virus, the envelope protein lays flat on the surface of the virus. Circulation of dengue virus type 3 genotype iii in africa since 2008 211.
The dengue virus genome encodes an uninterrupted open reading frame of 10,173 nucleotides that is translated into a polyprotein precursor 3391 amino acids long. Nucleotide composition of the zika virus rna genome and its. A recent study is the first to report a whole genome sequence and molecular characterization of an imported denv4. Using modeling frameworks to map the global distribution of dengue risk. Rna viruses have genomes with a distinct nucleotide composition and codon usage. Dengue virus is the most common mosquitoborne viral disease and infects about 390 million people each year. Studies on imported dengue cases can provide useful information about the geographic distribution. In order to characterize the denv1jeddah12011 isolate, the full genome was sequenced. Dengue virus is responsible for 50100 million infections, resulting in nearly 24,000 deaths annually. Infectious disease epidemiology of aedes aegyptiborne dengue. The availability of whole genome sequencing has contributed to many aspects of dengue research, and its use in dengue virus denv surveillance for early epidemic warning has been proposed. Till 2001, eight genome segments influenza a and b, and ten proteins, encoded by them, were descri bed. Do you see any regions of unusual dna content in the genome eg. The epidemic of dengue virus infections has spread markedly in yunnan province of china in recent years due to an increase in the number of imported dengue cases.
Dengue virus nonstructural protein 1 modulates infectious. Methods to sequence the genomes of individual dengue serotypes have been described previously, but no single method is known to be applicable for all four. Mature viral protein products resulting from protease and selfcleavage of the polyprotein are displayed according to their location in the genome and the polyprotein. Nextgeneration whole genome sequencing of dengue virus article pdf available in methods in molecular biology clifton, n. Zikv was first isolated in 1947 in uganda, caused a widespread epidemic in south and central america and the caribbean in 2015 and has recently been associated with microcephaly in. Analysis of genotype diversity and evolution of dengue virus.
Quantitative genetics of aedes aegypti vector competence for. Draw a sliding window plot of gc content in the den1 dengue virus genome, using a window size of 200 nucleotides. This means the ssrna that enters the host may immediately be translated. Fever, body aches, gastro intestinal symptoms, headache, and skin rash and chest symptoms. Viruses like hiv, which causes aids, make dna copies of their rna genome once. Chikungunya is a member of the alphavirus genus in the family togaviridae. Although denv are not classically known to infect and invade central nervous system cns in human, numerous cases of denv infection in the cns have been reported with limited information about the characteristics of the infecting virus. Mutagenesisofthedenguevirustype2ns5 methyltransferasedomain s. Complete genome sequencing and phylogenetic analysis of. The seven non structural proteins ns1, ns2a, ns2b, ns3, ns4a, ns4b, ns5 known as. Dengue denv and zika zikv viruses are clinically important members of the flaviviridae family with an 11 kb positive strand rna genome that folds to enable virus function.
Pdf investigation of polymorphisms in the genome of. A method for full genome sequencing of all four serotypes. Isolation and complete genome analysis of neurotropic dengue. Defective viral genomes help infections linger immunology. Solution structure of dengue virus capsid protein reveals. Clinical manifestations of dengue can have a wide range of outcomes varying from a mild febrile illness to a lifethreatening condition. The genome of influenza viruses is a linear, segmented and formed by ssrna. The viral genomes resource is a collection of viral genomic sequences that is a part of the entrez genomes, which provides curated sequence data and annotations of complete genomes to the scientific community.
According to the world health organization, dengue viruses denvs family flaviviridae. Nucleotide composition of the zika virus rna genome and. The flaviviruses latin flavus meaning yellow, because of the jaundice induced by yellow fever virus comprise a large genus of medically important, arthropodtransmitted, enveloped viruses with members that include yellow fever, dengue, west nile, tickborne encephalitis tbev, and japanese encephalitis viruses burke and monath 2001, lindenbach and rice 2001. Pdf nextgeneration whole genome sequencing of dengue virus. As rna viruses, coronaviruses rely on rnadependent rna. Decoration options let you color tree leaves by metadata. Isolation and complete genome analysis of neurotropic. Integrating dengue virus whole genome annotation with. First study of complete genome of dengue3 virus from. First study on the complete genome characterization of dengue3 virus is reported from dengue endemic state rajasthan, india. The capsid c protein of dengue virus is essential for speci. This article aims to summarize the advances in the understanding of dengue virus genome replication, highlighting the cis as well as trans elements that may have key roles in this process. This enveloped virus contains a positive singlestranded rna genome. From origin to outbreak provides a detailed accounting of one of the worlds fastest growing infections.
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