The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure

The complete sequence of 9871 nucleotides (nts) of parsnip yellow fleck virus (PYFV; isolate P-121) was determined from cDNA clones and by direct sequencing of viral RNA. The RNA contains a large open reading frame between nts 279 and 9362 which encodes a polyprotein of 3027 amino acids with a calculated Mr of 336212 (336K). A PYFV polyclonal antiserum reacted with the proteins expressed from phage carrying cDNA clones from the 5' half of the PYFV genome. Comparison of the polyprotein sequence of PYFV with other viral polyprotein sequences reveals similarities to the putative NTP-binding and RNA polymerase domains of cowpea mosaic comovirus, tomato black ring nepovirus and several animal picornaviruses. The 3' untranslated region of PYFV RNA is 509 nts long and does not have a poly(A) tail. The Y-terminal 121 nts may form a stem-loop structure which resembles that formed in the genomic RNA of mosquito-borne flaviviruses.

Section: Discussionmentioning

confidence: 88%

The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus

Turnbull-Ross¹,

Reavy²,

Mayo³

et al. 1992

“…The conservation of the 59-NCR length (constant 96 nt) compared with the 39-NCR (337 to 649 nt depending on strains) was previously demonstrated (Brinton, 2014). On the other hand, the 39-and 59-NCRs fold into RNA secondary structures whose deletion is lethal for WNV infectious clones (Anthony et al, 2009;Brinton & Dispoto, 1988;Brinton et al, 1986;Deas et al, 2005Deas et al, , 2007Elghonemy et al, 2005;Li et al, 2010;Yu & Markoff, 2005). This suggests that the length of the 39-NCR increases the chance that non-lethal mutations occur in this region, as we seem to observe in some of our samples.…”

Section: Previous Studies Documenting Wnv Quasispecies (Deardorff Et mentioning

confidence: 97%

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

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.

“…Flanking the ORF, the viral RNA contains two untranslated regions (UTRs) involved in various functions such as initiation and regulation of virus translation, replication and assembly (Lindenbach & Rice, 2001;Proutski et al, 1999). The 39UTR of DENV and other mosquito-borne flaviviruses contains a conserved stemloop structure within the last~96 nt (Brinton & Dispoto, 1988;Brinton et al, 1986;Grange et al, 1985;Mohan & Padmanabhan, 1991). Additionally, there are two pairs of conserved sequences (59CS1, 39CS1, 59UAR and 39UAR) that together induce DENV cyclization (Alvarez et al, 2005a, b; Hahn et al, 1987).…”

Section: Introductionmentioning

confidence: 99%

Polypyrimidine tract-binding protein is relocated to the cytoplasm and is required during dengue virus infection in Vero cells

Agis-Juárez

Galván²,

Medina

et al. 2009

The 39 untranslated region (39UTR) of the dengue virus (DENV) genome contain several sequences required for translation, replication and cyclization processes. This region also binds cellular proteins such as La, polypyrimidine tract-binding protein (PTB), Y box-binding protein 1, poly(A)-binding protein and the translation initiation factor eEF-1a. PTB is a cellular protein that interacts with the regulatory sequences of positive-strand RNA viruses such as several picornaviruses and hepatitis C virus. In the present report, it was demonstrated that PTB translocates from the nucleus to the cytoplasm during DENV infection. At 48 h post-infection, PTB, as well as the DENV proteins NS1 and NS3, were found to co-localize with the endoplasmic reticulum marker calnexin. Silencing of PTB expression inhibited virus translation and replication, whilst overexpression of PTB augmented these processes. Thus, these results provide evidence that, during infection, PTB moves from the nucleus to the cytoplasm and plays an important role in the DENV replicative cycle. INTRODUCTIONDengue virus (DENV), a member of the family Flaviviridae, is the causative agent of dengue fever, dengue haemorrhagic fever and dengue shock syndrome. The single-stranded, positive-polarity RNA genome of approximately 11 kb contains a type I cap at the 59 end and lacks a poly(A) tail at the 39 end. The single open reading frame (ORF) encodes a polyprotein that generates three structural proteins -envelope (E), membrane and capsid (C) -and seven non-structural proteins -NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5. Flanking the ORF, the viral RNA contains two untranslated regions (UTRs) involved in various functions such as initiation and regulation of virus translation, replication and assembly (Lindenbach & Rice, 2001;Proutski et al., 1999). The 39UTR of DENV and other mosquito-borne flaviviruses contains a conserved stemloop structure within the last~96 nt (Brinton & Dispoto, 1988;Brinton et al., 1986;Grange et al., 1985;Mohan & Padmanabhan, 1991). Additionally, there are two pairs of conserved sequences (59CS1, 39CS1, 59UAR and 39UAR) that together induce DENV cyclization (Alvarez et al., 2005a, b; Hahn et al., 1987). These motifs are essential for negativestrand RNA synthesis of DENV (Ackermann & Padmanabhan, 2001; Alvarez et al., 2005a, b;Villordo & Gamarnik, 2009;You & Padmanabhan, 1999) and other flaviviruses (Bredenbeek et al., 2003;Corver et al., 2003;Jones et al., 2005;Khromykh et al., 2001;Lo et al., 2003;Nomaguchi et al., 2004). On the other hand, sequences present within a large stem-loop structure located at the 59 end as well as a conserved oligo(U) track function as the promoter for viral polymerase activity (Lodeiro et al., 2009). Moreover, an RNA secondary structure present in the coding region of DENV type 2 (DENV-2) directs translation, start-codon selection and replication of the viral genome (Clyde & Harris, 2006;Clyde et al., 2008). Although it has been shown that the cyclization process does not require the presence of cellular or v...