Alphavirus genome organization pdf

Mayaro virus mayv togaviridae, genus alphavirus was first isolated in trinidad in 1954 from blood samples from five febrile patients. Structural and functional insights into alphavirus. Sarscov2 has recently emerged and has been declared as a pandemic by the world health organization. The genome size is similar to other alphaviruses at approximately 11900 nt. Structural and functional insights into alphavirus polyprotein processing and pathogenesis gyehwa shina,1,2, samantha a. Alphaviruses are mosquitoborne positive sense rna viruses that infect a wide range of vertebrate and invertebrate hosts. The genome is located inside the virion and consists of a single molecule of singlestranded rna. Table 2 and figure 1 both show the breadth of genes that can be encoded. They are dna sequences inserted between the exons and found in the orf.

Alphaviruses cause debilitating disease in humans and animals and are transmitted by bloodfeeding arthropods, typically mosquitoes. Their genomic organization is similar, but phylogenetic analyses have suggested that alphaviruses and rubiviruses are only distantly related koonin and dolja. Residuelevel resolution of alphavirus envelope protein interactions in phdependent fusion xiancheng zenga, suchetana mukhopadhyayb, and charles l. Shape data for the sindbis virus genome, represented by the local median 55nt window compared with the global median. Alphaviruses are organized with the nonstructural ns proteins at the end of the genome e ns proteins are translated from the genomic rna while the structural proteins are translated from a subgenomic rna that includes the.

Functional analysis of viral and host components of. Here we report the complete genome sequence of a chikungunya virus strain, gd052010, isolated in 2010 from a patient with chikungunya fever in guangdong, china. The genus alphavirus harbours mostly insecttransmitted viruses that cause severe disease in humans, livestock and wildlife. The genome is surrounded by 240 copies of the viral capsid protein c, which form a coat termed the capsid. Besides the coding exons, the noncoding dna in eukaryotes may fall in the following classes. Regions of nucleotide homology and regions regions of nucleotide homology and regions encoding homologous amino acid sequence within the nonstructural protein orf are shown. Salmonid alphavirus structure and replication the alphavirus genus is well studied and characterized, but little work has been done with regard to molecular characterization of sav in vitro. The alphavirus genome is a positivestrand rna molecule, approximately 1112 kb in length. These proteins, which serve as replicases, are translated as a single polypeptide which is first cleaved into functional intermediate proteins and then into the four functional nonstructural proteins. Pdf the alphavirus replicon technology has been utilized for many years to develop vaccines for both veterinary and human applications. These are synthesized principally as a polyprotein with an apparent molecular weight of 290,000 from which the final products are formed by proteolytic. Ncs isolated from alphavirusinfected cells are stable and have a sedimentation coefficient of 140 s.

Elrodb, arash grakouib, and joseph marcotrigianoa,3 acenter for advanced biotechnology and medicine, department of chemistry and chemical biology, rutgers university, piscataway, nj 08854. The disease shares some clinical signs with dengue and zika, and can be misdiagnosed in areas where. Structural divergence creates new functional features in. The comber alphavirus is a new member of the genus alphavirus, family togaviridae. Twothirds of the alphavirus genome, beginning at the 5 end, encode four nonstructural proteins. Four nonstructural proteins nsp14 are required for transcription and replication of viral rna, and three main structural proteins i. Structure and replication of the alphavirus genome springerlink. Virion and genome organization the alphavirus virion has icosahedral symmetry, and its diameter is 6570 nm.

Salmon pancreas disease virus, an alphavirus infecting. Chikungunya virus chikv, a member of the genus alphavirus and the family togaviridae, is the causative agent of chikungunya fever, which is characterized by fever, rash, myalgia, and arthralgia. Genomic characterization of sarscov2 has shown that it is of zoonotic origin. Purified capsid proteins oligomerize into corelike particles in vitro in the presence of singlestranded nucleic acid, and resemble the native ncs 172. Alphavirus genome organization and replication strategy. In general, the genome organization is less complex. Sindbis virus sinv is the prototype virus of the alphavirus genus and generally infects avian species 1,2. This book focuses on the genus alphavirus, which consists of small 45 to 75 nm in diameter, enveloped viruses, typically transmitted by arthropod vectors, including mosquitoes. Dec 14, 2018 alphaviruses are enveloped rna viruses that contain several human pathogens.

Ncs isolated from alphavirus infected cells are stable and have a sedimentation coefficient of 140 s. The development of new tools to investigate alphavirus replication kinetics nicole e. The salmonid alphaviruses and southern elephant seal virus, which cause disease in several species of fish and marine mammals, are exceptions because they seemingly lack an invertebrate vector. The genome of chikv has approximately 11,800 nucleotides. A structural and functional perspective of alphavirus. Packaging signal attenuating mutations replicon rna capsid protein envelope glycoproteins packaged rp split helper rnas nsp14 foreign gene e3e26ke1 c 26s promoter fig. Brooks iiia,1 adepartment of chemistry and biophysics program, university of michigan, ann arbor, mi 48109. Model for the processing of the alphavirus nonstructural polyprotein during replication. Plaskon thesis submitted to the faculty of virginia polytechnic institute and state university in partial fulfillment of the requirement for the degree of master of science in life science kevin m. There are 31 alphaviruses, which infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses, as well as invertebrates. The expression and organization of the alphavirus genome. The alphavirus nc contains a single copy of the rna genome complexed with 240 copies of cp. Genome organization refers to the sequential, not the structural organization of the genome.

The sindbis virus genome contains a multitude of diverse rna structures. It is transmitted by an arthropod vector, usually haemagogus sp. Interestingly, changes in ion concentration in host cells. No of sequence data on plant virus genome generated over the last one decade 1st viral genome sequenced was dna of camv franck et al. Viral vectors based on the alphaviruses can take advantage of this genome organization in multiple ways including replication competent vectors wherein a. Complete genome sequence of a chikungunya virus isolated in. These viruses are 70nm in diameter, have an enveloped icosahedral capsid and have a positive polarity singlestranded rna the genomic rna itself is the messenger rna. Spurgers and glass j bioterr biodef 2011, s1 bioterrorism. Residuelevel resolution of alphavirus envelope protein. Using fulllength sequences of all known alphaviruses, we produced a robust and comprehensive phylogeny of the alphavirus genus, presenting a more complete evolutionary history of these viruses compared to previous studies based on partial sequences.

The development of new tools to investigate alphavirus. Complete genome sequence of a chikungunya virus isolated. The organization of their respective genomes is similar, but phylogenetic analysis shows that alphaviruses and rubiviruses are quite divergent koonin and dolja, 1993. This allows the virus to be internalized and transported into the acidic intracellular vesicles. Only a single contig with a length comparable to the. Structural differences observed in arboviruses of the. Chapter 5 structure and function of alphavirus proteases shailly tomar, megha aggarwal indian institute of technology, roorkee, uttarakhand, india 1. When low levels of p123 are present, ciscleavage of p1234 generates the minusstrand rna replicase of the virus. With a traditional focus on two models, sindbis virus and semliki forest virus, alphavirus research has significantly intensified in the last decade partly due to the reemergence and dramatic expansion of chikungunya virus in asia, europe, and the americas. Structure and replication of the alphavirus genome. The alphaviruses have a positive strand rna genome about 12,000 nucleotides in length. The fully proteolyzed nonstructural protein nsp1, nsp2, nsp3, nsp4 synthesize progeny, positive strands and subgenomic rna, which encode for the viral structural protein. Alphaviruses are organized with the nonstructural ns proteins at the 5. Abstract sarscov2 is a singlestranded rna virus of 30 kb genome size which belongs to genus coronavirus and family coronaviridae.

The 5 end of the genome encodes the nonstructural proteins nsp1nsp4. The alphavirus genome consists of two open reading frames encoding nonstructural and structural polyproteins. Review article structural differences observed in arboviruses. There are no effective vaccines or specific antivirals available for the treatment of alphavirusrelated infections. The mrna encoding the structural proteins is transcribed from a replication intermediate not shown and the 26s subgenomic rna promoter. Alphavirus particles are roughly spherical, with three principal substructuresan outer glycoprotein shell, a lipid bilayer, and an rnacontaining core nucleocapsid. Aetiological agent, agent strains sav is an enveloped, spherical, singlestranded, positivesense rna virus, approximately 6070 nm in diameter, with a genome of 12 kb. May 22, 2012 chikungunya virus belongs to the genus alphavirus in the family togaviridae. Genome organization and viral replication chikv and mayv are members of the family togaviridae, genus alphavirus. The virus was isolated in c636 mosquito cells, and full genome sequencing revealed an 11 468 nt long genome with maximum pairwise nucleotide identity of 62.

Alphaviruses are, for the most part, arthropodborne viruses which replicate in both their invertebrate vectors and their vertebrate hosts. Doing that, the viral rna genome starts to be released into the cytoplasm and is translated into two polyproteins and structural proteins, after which the viral genome begins to replicate inside. In this study, we found a novel alphavirus in one culex. Genomic sequence of a new alphavirus detected in comber. Agua salud alphavirus defines a novel lineage of insect. The comber alphavirus was isolated from a fish cell line from the brain of an apparently healthy serranus cabrilla specimen collected during wild fish surveillance in southern italy. Genetic stability within the norwegian subtype of salmonid alphavirus family togaviridae. The alphavirus structural protein genes correspond to the 3 onethird of the viral genome and are transcribed from a subgenomic rna promoter. The alphavirus genome consists of singlestranded, positivesense rna of.

Salmon pancreas disease virus, an alphavirus infecting farmed. In this study, we found a novel alphavirus in one culex declarator mosquito sampled in panama. Genome characterization of flatfish alphavirus and its. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Drosophila melanogaster clipdomain serine proteases. The sequence information is important for surveillance of this emerging arboviral infection in china. The genus alphavirus comprises a diverse group of viruses, including some that cause severe disease. Facts of genome molecular wt of nucleotide pair 650 da wt of chromosome varies greatly no. The symptoms of mayv infection include fever, headache, myalgia, diarrhea, skin rash, and arthralgia. This results in primarily negative sense rna being generated from the incoming genomic rna of the virus upper panel. Determination of the complete sequence of virus genomes coupled with mapping of the virusencoded proteins on those genomes has resulted in a wealth of information about the structure of the genome, the nature of the encoded proteins, the translation strategy used by the virus, and the nature of proteolytic processing or other modification. The radial organization of these components is summarized in fig.

Structure and function of alphavirus proteases pdf free. However, sinv can spill over into humans, where it causes symptoms such as fever, rash, myalgia, and arthralgia. Alphavirus infection an overview sciencedirect topics. The positive strand, rna genome is transcribed into a minus strand by the cleavage intermediate nsp23 and nsp4.

The mrna encoding the structural proteins is transcribed from a replication intermediate. The 3 terminal region encodes the structural proteins. The symptoms of mayv infection include fever, headache, myalgia, diarrhea, skin rash. Genomescale phylogeny of the alphavirus genus suggests a. Alphaviruses are enveloped rna viruses that contain several human pathogens. Chapter 3 morphology, genome organization, replication. The alphavirus infection cycle begins when e2 binds to receptors on the surface of a host cell. Chikungunya is a viral disease transmitted to humans by infected mosquitoes. Alphaviruses are arthropodborne viruses that can cause fever, rash, arthralgias, and encephalitis. The most extensive structural studies have been carried out on sindbis virus and semliki forest virus sfv. Joint pain is often debilitating and can vary in duration. It consists of a positive sense singlestranded, non. The mosquito species aedes aegypti and aedes albopictus are the most frequent transmitters of alphaviruses.

Structure and function of alphavirus proteases chapter 5 structure and function of alphavirus proteases shailly tomar, megha aggarwal indian institute of technology, roorkee, uttarakhand, india 1. The 5 orf is directly translated from the genomic rna into a polyprotein that contains the four. Alphavirus and rubivirus schlesinger and schlesinger, 2001. Implication for alphavirus hostcell entry and assembly. Alphavirus is a genus of rna viruses, the sole genus in the togaviridae family. Alphaviruses belong to group iv of the baltimore classification of viruses, with a positivesense, singlestranded rna genome. The cdna copy of the alphavirus genome is placed on a plasmid under the sp6 or t7 promoter at the 5. Chikv is transmitted to humans by infected mosquitoes, and it has emerged and reemerged in africa, south america, and southern and southeastern asia, with a. Complete genome sequence of mayaro virus togaviridae. Clone pbs38r was produced using a 39 race reaction, the success of which depended on the spdv genome possessing a polyadenylated tract at its 39 terminus fig. The genomic rna has a methyl guanine cap mg, and a polyadenylated tail a n. Research article a phylogenomic study of the genus alphavirus. As the term implies, large genome dna viruses can also encode many more proteins.