Sequence and secondary structure analysis of the 5′-terminal region of flavivirus genome RNA

Brinton, Margo A.; Dispoto, Janice H.

doi:10.1016/0042-6822(88)90468-0

Cited by 172 publications

(149 citation statements)

References 29 publications

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“…In contrast, MA studies of the eukaryote Caenorhabditis elegans showed that only 1-4% of mutations have detectable effects on laboratory fitness (Davies et al 1999;Estes et al 2004). It is tempting to explain this difference by claiming that viral genomes are more compact than eukaryotic genomes or that viral genomes contain more functional RNA secondary structure (Brinton and Dispoto 1988;Brown et al 1992;Berkhout and Schoneveld 1993). However, it is also possible that the laboratory environment more closely mimics the natural environment of viruses than it does the natural environment of C. elegans.…”

Section: Discussionmentioning

confidence: 66%

Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus ϕ6

Burch¹,

Guyader²,

Samarov

et al. 2007

Genetics

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Although the frequency and effects of neutral and nearly neutral mutations are critical to evolutionary patterns and processes governed by genetic drift, the small effects of such mutations make them difficult to study empirically. Here we present the results of a mutation-accumulation experiment designed to assess the frequencies of deleterious mutations with undetectable effects. We promoted the accumulation of spontaneous mutations by subjecting independent lineages of the RNA virus f6 to repeated population bottlenecks of a single individual. We measured fitness following every bottleneck to obtain a complete picture of the timing and effects of the accumulated mutations with detectable effects and sequenced complete genomes to determine the number of mutations that were undetected by the fitness assays. To estimate the effects of the undetected mutations, we implemented a likelihood model developed for quantitative trait locus (QTL) data (Otto and Jones 2000) to estimate the number and effects of the undetected mutations from the measured number and effects of the detected mutations. Using this method we estimated a deleterious mutation rate of U ¼ 0.03 and a gamma effects distribution with mean s ¼ 0:093 and coefficient of variation ¼ 0.204. Although our estimates of U and s fall within the range of recent mutation rate and effect estimates in eukaryotes, the fraction of mutations with detectable effects on laboratory fitness (39%) appears to be far higher in f6 than in eukaryotes.

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Section: Discussionmentioning

confidence: 66%

Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus ϕ6

Burch¹,

Guyader²,

Samarov

et al. 2007

Genetics

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“…Extensive secondary structure has been predicted for the 3Ј UTR of flaviviruses, 33 which appears to be vital for its function in viral replication. One might speculate that for the 5Ј UTR, in addition to secondary structure, 34 nucleotide sequence may also play an important role in recognition by the viral polymerase complex and/or by the capsid protein during packaging.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic analysis of Japanese encephalitis virus: envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent.

Uchil¹,

Satchidanandam²

2001

The American Journal of Tropical Medicine and Hygiene

151

108

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Abstract. We report the analysis of the complete nucleotide sequence for the Indian isolate (P20778; Genbank Accession number AF080251) of Japanese encephalitis virus (JEV). The phylogenetic tree topology obtained using thirteen complete genome sequences of JEV was reproduced with the envelope, NS1, NS3, and NS5 genes and revealed extensive divergence between the two Indian strains included. A more exhaustive analysis of JEV evolution using 107 envelope sequences available for isolates from different geographic locations worldwide revealed five distinct genotypes of JEV, displaying a minimum nucleotide divergence of 7% with high bootstrap support values. The tree also revealed overall clustering of strains based on geographic location, as well as multiple introductions of JEV into the Indian subcontinent. Nonsynonymous nucleotide divergence rates of the envelope gene estimated that the ancestor common to all JEV genotypes arose within the last three hundred years.

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“…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: 98%

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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Sequence and secondary structure analysis of the 5′-terminal region of flavivirus genome RNA

Cited by 172 publications

References 29 publications

Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus ϕ6

Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus ϕ6

Phylogenetic analysis of Japanese encephalitis virus: envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent.

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

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