The six codons containing UpA (UUA, CUA, GUA, UAU, UAC and AUA) were also under-represented (RSCU<1.6) and were not preferred codons for their respective amino acids. The outbreak has since spread to 38 regions in the Americas. This volume covers multidisciplinary approaches on various aspects of Chikungunya Virus (CHIKV) research that was brought together from leading laboratories across the globe. Our data suggested that codon usage in CHIKV is undergoing an evolutionary process, probably reflecting a dynamic process of mutation and natural selection to re-adapt its codon usage to different environments and hosts. https://doi.org/10.1371/journal.pone.0090905.g007, https://doi.org/10.1371/journal.pone.0090905.t004. Found insideAedes albopictus have been seen in outbreaks of chikungunya virus and in some parts ... Slight variations in the genome size has been observed from samples ... Found inside – Page 37[83] Rager M, Vongpunsawad S, Duprex WP, Cattaneo R. Polyploid measles virus with hexameric genome length. EMBO J 2002;21(10):2364–72. Vector Borne Zoonotic Dis. Schnierle BS. The CAI is used as a quantitative method of predicting the expression level of a gene based on its codon sequence. These results indicated that, although natural selection has influenced codon usage of CHIKV genomes to some extent, it is much weaker compared with mutational pressure. However, this theory cannot explain under-representation of CpGs in RNA viruses. 27. A simplified phylogenetic tree of Alphaviruses assuming their New World origin, adapted from…, Organization of the CHIKV genome and gene products. https://doi.org/10.1371/journal.pone.0090905.g002. CHIKV belongs to the Alphavirus genus, and is an enveloped, single-stranded positive-sense RNA virus (Strauss & Strauss, 1994). Funding: This research was supported by grants from the National Hi-Tech Research and Development (863) Program of China (No. The virion is 70 nm in diameter and it is composed of repeating units of the E1 and E2 transmembrane glycoproteins (240 heterodimers of E2/E1 arranged as trimeric spikes on its surface), the capsid (C), a host-derived lipid bilayer, and a single molecule of genome RNA. In comparison to the ENC, which is another way of calculating codon usage bias and measures deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes [32]. Allow 30 minutes of contact time before disposal and cleanup of spill materials. 2013) . Chikungunya virus (CHIKV), one of the most relevant arbovirus currently known, is a re-emergent virus that causes a disease named chikungunya fever, characterized by a severe arthralgia (joint pains) that can persist for several months or years in some individuals. Similarly, the eight codons containing CpA (UCA, CCA, ACA, GCA, CAA, CAG, CAU and CAC) and five codons containing UpG (UUG, CUG, GUG, UGU and UGC) were also over-represented compared with the rest of the codons for their respective amino acids and a majority of them were also preferential codons for their respective amino acids, based on RSCU analysis (Table 2). The bar plot shows the cumulative number of Zika virus (ZIKV) genomes from each World Health Organization (WHO) geographic region (see key).The dashed black line indicates the cumulative number of countries affected by the 2015–2016 ZIKV epidemic as of 14 July 2016 []. aegypti (ID # 7) and chikungunya-infected Ae. In late 2013, the first local transmission of chikungunya virus in the Americas was identified in Caribbean countries and territories. Local transmission means that mosquitoes in the area have been infected with the virus and are spreading it to people. The virus then spread throughout most of the Americas. ( See data from PAHO ). As for the effects of the two primates on the formation of the overall codon usage of CHIKV, the strongest effect of H. sapiens was on the Asian genotype, closely followed by the ECSA and WA genotypes. Two more cases were reported in 1981. We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, web-based pipeline for real-time bioinformatics analysis on a computational server or laptop (MetaPORE). Delatte H, Paupy C, Dehecq JS, Thiria J, Failloux AB, Fontenille D. Parasite. Schematic representation of the capsid protein with the main interaction domains. The molecular architecture of the plasma membrane-associated replication complex from the Chikungunya virus is unknown. Insects. The synonymous codons with RSCU values >1.0 have positive codon usage bias and were defined as abundant codons, while those with RSCU values <1.0 have negative codon usage bias and were defined as less-abundant codons. It has been proposed that CpG deficiency in pathogens is associated with the immunostimulatory properties of unmethylated CpGs, which are recognized by the host’s innate immune system as a pathogen signature [28]. G3% was positively correlated with G% (r = 0.658, P<0.01) U% (r = 0.354, P<0.01), and negatively correlated with C% (r = −0.377, P<0.01) and A% (r = −0.610, P<0.01); the correlation with the GC% was non-significant. The genome is capped at the 50end and polyadenylated at the 30 end. Found insideThese diseases are called vector-borne zoonotic diseases. This book is meant to be used by veterinarians, medical doctors, entomologists, and other experts, as well as students, animal owners, nature lovers, etc. This ongoing outbreak has spread to >8 other provinces and has had a harmful effect on public health. Although information available on CHIKV is growing quite rapidly, we are still far from understanding the strategies required for the ecologic success of this virus, virus replication, its interactions with its vertebrate hosts and arthropod vectors, and its genetic evolution. Structural Virology covers a wide range of topics and is split into three sections. The remaining 52 codons had RSCU values between 0.6–1.6 (Figure 1 and Table 2). The GC1 ranged from 50.6% to 53.8%, with a mean of 53.56% and an SD 0.27. Chikungunya virus and the mosquito vector Aedes aegypti in New Caledonia (South Pacific Region). GENOME ANNOUNCEMENT. Discover a faster, simpler path to publishing in a high-quality journal. Found inside – Page 71Crystallography does not have any inherent size restrictions, ... The same in principle applies to viral genome, which is present in one unique copy in ... Chikungunya virus is an enveloped plus-strand RNA virus with icosahedral symmetry. In detail, the preferred codons for 12 out of 18 amino acids were common between CHIKV and H. sapiens. It has been suggested that if synonymous codon usage bias is affected by mutational pressure alone, then the frequency of nucleotides A and U/T should be equal to that of C and G at the synonymous codon third position [26]. Found insideThis book investigates how this facilitates the design and development of potent antiviral agents used against life-threatening viruses. GENOME ANNOUNCEMENT. Here we use a genome-wide … In addition, contributions of other factors, including hosts, geography, dinucleotides composition and natural selection, are also evident from our analysis. Genome announcements. here. Found inside – Page 1006It has a genome size of w12 kb, and it consists of 2 open reading frames cleaved ... Transmission, and Chikungunya Virus Outbreaks Human cases of CHIK have ... Background. This analysis showed that the three different genotypes of CHIKV might have common ancestor. These findings suggested that despite being an RNA virus with a high mutation rate in its lifecycle, CHIKV has evolved to form a relatively stable genetic composition at some specific levels of synonymous codon usage. https://doi.org/10.1371/journal.pone.0090905.t007. Genes, whose codon choice is constrained only by a mutation bias, will lie on or just below the curve of the expected ENC values. C3% had significant positive correlation with C% (r = 0.621, P<0.01), A (r = 0.261, P<0.01) and GC% (r = 0.798, P<0.01), and negative correlations with U% (r = −0.5877, P<0.01) and G% (r = −0.217, P<0.01). On the other hand, despite slight over-representation of the GpC dinucleotide, all GpC-containing codons were also under-represented (RSCU<1.6) and were not preferred codons for their respective amino acids, with two exceptions; GCA (Ala, RSCU = 1.43) and UGC (Cys, RSCU = 1.33) (Table 2). De novoassembly and mapping of each sequence was performed using the velvet assembler and bowtie enabled by Pipeline Pilot, with hash size = 31 and insert size = 150. Genome announcements. It is a member of the Semliki Forest virus complex and is closely related to Ross River virus, O'nyong'nyong virus, and Semliki Forest virus. Panel E illustrates one example of the presence of CHIKV particles within cellular vacuoles. 11.7 kilobases long. A subgenomic positive-strand mRNA referred to as 26S RNA, is transcribed from a negative-stranded-RNA intermediate and serves as the mRNA for the synthesis of the viral structural proteins. Yes Furthermore, all common preferred codons between CHIKV and H. sapiens were G/C- ended (C-ended: 7; G-ended: 4), with exception of an A-ended preferred codon for amino acid Arg. Zika virus (ZIKV), chikungunya virus (CHIKV) and dengue virus (DENV) have similar epidemiology, transmission cycles in urban environments and clinical symptoms at onset (although complications vary markedly). The ENC is used to quantify the absolute codon usage bias of the gene (s) of interest, irrespective of gene length and the number of amino acids [30]. Detection of Chikungunya Virus E1 by Western Blot. In case of the two transmission vectors, 10 out of 18 preferred codons were common among both mosquito species and CHIKV. Zhang et al. Adapted after Zhao et al. (2010) Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. The chikungunya (CHIKV) viral infection is a global health burden characterized by the neurologic complications with CHIKV infection. This book intends to fill this gap by considering the patterns and processes of viral evolution at all its spatial and temporal scales. a The Illumina mapping data presented in the table were obtained in 2017 on samples that had been collected and found positive for chikungunya or dengue virus by real-time reverse transcription-PCR in 2016. b ‘R1 + R2’ indicates paired-end sequencing. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.) Two different types of particles can be observed, viral particles of about 65 nm with an electron-dense capsid of 32 nm (white arrow) and particles of about 76 nm showing only a small electron-dense material in the middle very similar to the most frequent particles observed in CHIKV-infected HEK-293 T cells. 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