Nucleotide and Complete Amino Acid Sequences of Kunjin Virus: Definitive Gene Order and Characteristics of the Virus-specified Proteins

Coia, Gregory; Parker, Michael D.; Speight, Graham; Byrne, Mary E.; Westaway, E. G.

doi:10.1099/0022-1317-69-1-1

Cited by 228 publications

(164 citation statements)

References 56 publications

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“…NS1 is a multifunctional viral glycoprotein that is highly conserved among flaviviruses (Coia et al, 1988). Interestingly, most of the WNV variants that were shared between all samples in this study occurred in the NS1-coding region.…”

Section: Previous Studies Documenting Wnv Quasispecies (Deardorff Et mentioning

confidence: 95%

Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model

Dridi

Rosseel

Orton

et al. 2015

Journal of General Virology

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West Nile virus (WNV) occurs as a population of genetic variants (quasispecies) infecting a single animal. Previous low-resolution viral genetic diversity estimates in sampled wild birds and mosquitoes, and in multiple-passage adaptation studies in vivo or in cell culture, suggest that WNV genetic diversification is mostly limited to the mosquito vector. This study investigated genetic diversification of WNV in avian hosts during a single passage using next-generation sequencing. Wild-captured carrion crows were subcutaneously infected using a clonal MiddleEast WNV. Blood samples were collected 2 and 4 days post-infection. A reverse-transcription (RT)-PCR approach was used to amplify the WNV genome directly from serum samples prior to next-generation sequencing resulting in an average depth of at least 7006 in each sample. Appropriate controls were sequenced to discriminate biologically relevant low-frequency variants from experimentally introduced errors. The WNV populations in the wild crows showed significant diversification away from the inoculum virus quasispecies structure. By contrast, WNV populations in intracerebrally infected day-old chickens did not diversify from that of the inoculum. Where previous studies concluded that WNV genetic diversification is only experimentally demonstrated in its permissive insect vector species, we have experimentally shown significant diversification of WNV populations in a wild bird reservoir species.

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Section: Previous Studies Documenting Wnv Quasispecies (Deardorff Et mentioning

confidence: 95%

Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model

Dridi

Rosseel

Orton

et al. 2015

Journal of General Virology

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“…Alignment of the amino acid sequences of the E proteins of flaviviruses within the type-specific hypervariable domain proposed for TBE and dengue viruses. Sequences of LI (Shiu et al, 1991), TBE (Mandl et al, 1988;Ptetnev et al, 1990), LGT (Mandl et al, 1991), DEN1 (Mason et al, 1987), DEN2 (Deubel et al, 1986;Hahn et al, 1988), DEN3 (Osatomi & Sumiyoshi, 1990), DEN4 (Zhao et al, 1986), West Nile (WN) (Castle et al, 1985), Kunjin (KUN) (Coia et al, 1988), Japanese encephalitis (JE) (Sumiyoshi et al, 1987), Murray Valley encephalitis (MVE) (Dalgarno et al, 1986), St Louis encephalitis (SLE) (Trent et al, 1987) and yellow fever (Rice et al, 1985) viruses are aligned. The amino acids are numbered according to their positions in the respective E proteins.…”

Section: S S T ---A 232 Mve 228 P As T ---E 232 Sle 228 P At T ---D 2mentioning

confidence: 99%

Envelope protein sequences of dengue virus isolates TH-36 and TH-Sman, and identification of a type-specific genetic marker for dengue and tick-borne flaviviruses

Shiu

Jiang

Porterfield³

et al. 1992

Journal of General Virology

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Complementary DNAs were synthesized from the envelope protein genes of two isolates of dengue virus (TH-36 and TH-Sman, previously suggested as possible dengue virus type 5 and dengue virus type 6 respectively) and amplified by the polymerase chain reaction using sense and antisense primers designed from conserved dengue virus gene sequences. The amplified cDNA clones were sequenced in both directions by double-stranded dideoxynucleotide sequencing. Alignment with published dengue virus sequences enabled us to assign these viruses accurately to classified serotypes, confirming that TH-36 and THSman are strains of dengue virus type 2 and dengue virus type 1 respectively. Amino acid changes between the proteins encoded by these two isolates and strains of their respective serotypes may account for the significant antigenic differences observed during previous serological typing of these viruses. Moreover, sequence alignment of flavivirus envelope proteins revealed a hypervariable region, within which members of the dengue and tick-borne virus antigenic complexes show unique peptide sequences. This type-specific hypervariable domain may be useful as a genetic marker for typing dengue and tick-borne flaviviruses.Dengue viruses, mosquito-borne members of the family Flaviviridae (Westaway et al., 1985), are responsible for classic dengue fever and for the associated conditions dengue haemorrhagic fever (DHF) and dengue shock syndrome, each of which has a high level of morbidity and mortality in the tropics. There is evidence suggesting that the more severe forms of dengue fever occur when individuals (usually children) with cross-reactive but non-protective antibodies, acquired maternally or induced by prior infection with a different serotype, are naturally exposed to dengue virus infection (Halstead, 1981(Halstead, , 1988. Despite much research, effective dengue virus vaccines are not yet available, so the antigenic properties of dengue viruses have received much attention.Currently, four distinct dengue virus serotypes (types 1 to 4; DEN1 to DEN4) can be distinguished by complement fixation (CF), haemagglutination-inhibition and neutralization tests (Porterfield, 1980). Two Thai isolates are of particular interest. Strain TH-36 wasThe sequence data reported in this article have been deposited with the DDBJ, EMBL and GenBank databases under the accession numbers D01073 (TH-Sman) and D01074 (TH-36). isolated in 1958 by Hammon and co-workers from a patient with DHF in Bangkok, and TH-Sman was isolated from a similar patient by Dr Sman Vardhanabhuti. Strain TH-36 was initially identified as DEN2 and TH-Sman as DEN 1, but both were shown to differ to a significant degree from the respective prototype strains by CF, plaque neutralization, immunodiffusion and immunoelectrophoresis tests (Hammon et al., 1961; Hammon & Sather, 1964a, b; Ibrahim & Hammon, 1968a, b;Ibrahim et al., 1968). Tests using the soluble complement-fixing antigen also showed that strain THSman differed from the prototype DEN1 virus, but TH-36 was ind...

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Section: Methodsmentioning

confidence: 99%

“…Viral strains, locations, years of isolation, and GenBank accession numbers of the E sequences utilized in the phylogenetic analyses are listed in Table I. Sequences from Japanese encephalitis virus (JEV) (Accession # M55506 (Nitayaphan et al 1990); West Nile virus (WNV) Accession # M12294 (Castle et al 1985); Kunjin virus (KUNV) Accession # D000246 (Coia et al 1988), and Murray Valley encephalitis virus (MVEV), Accession # X03467 (Dalgarno et al 1986) were used as outgroups in the phylogenetic analysis.RT-PCR and nucleotide sequencing -Viral RNA was isolated from first passage cell culture supernatant using the QIAmp Viral RNA Extraction Kit (QIAGEN, Valencia, Phylogenetic analysis -Sequence alignment was performed using the multiple sequence alignment method implemented in CLUSTALX (Thompson et al 1997). Accuracy of nucleotide sequence alignment was examined using amino acid sequence alignment.…”

mentioning

confidence: 99%

Genetic characterization of St. Louis encephalitis virus isolated from human in São Paulo, Brazil

Santos

Sallum

Franco

et al. 2006

Mem. Inst. Oswaldo Cruz

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(Calisher et al. 1989). The genome of flaviviruses contains a single-stranded positive sense RNA, about 10,800 nucleotides long that encodes 10 distinct proteins in a single reading frame (Chambers et al. 1990). SLEV is the etiologic agent of St. Louis encephalitis, a disease of epidemiological importance in North America. This virus was first isolated in the United States of America (US) in 1933, during an outbreak, which occurred in St. Louis and Kansas City, Mo. (Muckenfuss et al. 1934). In the US intermittent and unpredictable epidemics have been occurring during the last decades. The majority of SLEV infections is sub clinical or result in mild illness. The severity of infections is strongly dependent on the age of a patient, and the case fatality rate during epidemics ranges from 2% in young adults to more than 22% in the elders (Monath & Heinz 1996). In spite of being endemic in Central and South America, causing sporadic illness, occurrence of SLEV outbreaks is unknown (Spence 1980, Monath & Heinz 1996.The biological cycle of SLEV in nature involves primarily wild birds and several mosquito species; humans and other mammals are considered to be incidental hosts (Monath & Heinz 1996). In the US, Culicinae mosquitoes and birds, Passeriformes and Columbiformes, are involved in the dynamics of SLEV transmission. The transmission Financial support: Fapesp (no. 2004/07819-6) and CNPq (no. 305339/2003-6) cycle varies regionally, depending on the biology of mosquito species, virulence of SLEV strains and susceptibility to infection of vertebrate hosts (Monath & Tsai 1987, Day 2001, Reisen 2003. In Central and South America SLEV transmission cycle is not well defined, but it may include mosquito species of the genera Culex, Mansonia, Haemagogus, and Sabethes. A variety of bird taxa, including herons, egrets, and cormorant may be virus reservoirs (Spence 1980, Monath & Heinz 1996, Reisen 2003.The occurrence of SLEV in Brazil was recorded in 1953, by the finding of antibodies to this virus in residents of the Amazon Valley (Causey & Theiller 1958). A pool of mosquito Sabethes belisarioi, captured along the Belém-Brasília highway, was the source for the first isolation of a SLEV strain (Causey et al. 1964). Later in 1970 and 1978 two strains were recovered from human blood in Amazon region. In both cases the patients developed a febrile illness with jaundice, neither of them presenting neurological involvement (Pinheiro et al. 1981, Vasconcelos et al. 1998. SLEV was also found in the Southeast region of Brazil where it was isolated from wild birds, rodents, and sentinel mice during a surveillance program on arbovirus activity carried out in the state of São Paulo from 1967 to 1969 (Lopes et al. 1979).In the summer of 2004, after more than two decades of the last human Brazilian report, a clinical case of infection by SLEV was detected in the state of São Paulo. Epidemiologic data about the SLEV case was fully detailed by Rocco et al. (2005). Briefly, a patient, suffering from severe uncharacterized febrile illnes...

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Nucleotide and Complete Amino Acid Sequences of Kunjin Virus: Definitive Gene Order and Characteristics of the Virus-specified Proteins

Cited by 228 publications

References 56 publications

Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model

Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model

Envelope protein sequences of dengue virus isolates TH-36 and TH-Sman, and identification of a type-specific genetic marker for dengue and tick-borne flaviviruses

Genetic characterization of St. Louis encephalitis virus isolated from human in São Paulo, Brazil

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