Mosquito Small RNA Responses to West Nile and Insect-Specific Virus Infections in Aedes and Culex Mosquito Cells

Göertz, Giel P.; Miesen, Pascal; Overheul, Gijs J.; Rij, Ronald P. van; Oers, Monique M. van; Pijlman, Gorben P.

doi:10.3390/v11030271

Cited by 75 publications

(93 citation statements)

References 77 publications

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“…2) come from four different studies and five different Culicinae mosquito species (Chandler et al 2015;Cook et al 2013;Shi et al 2016Shi et al , 2017; moreover, in several samples, viral RNA accounts for >0.1 per cent (in one case, >2%) of total non-ribosomal RNA reads, which may be unlikely if the virus is infecting a contaminant (Shi et al 2016(Shi et al , 2017. Very recently, another narnavirus in this clade (MK628543.1; Culex narnavirus 1; 97 per cent nt identity to KP642120.1) was found to persistently infect a Culex tarsalis cell culture and also give rise to typical 21nt viral siRNAs with equal coverage of both strands, indicative of active infection (Gö ertz et al 2019). An ONLV2-related EVE has been previously reported for arthropods (Shi et al 2016), and we also identified sequences that clustered with rORFcontaining narnaviruses in WGS assembly data sets from several species of ant, the seven spot ladybird and the glassy winged sharpshooter.…”

Section: Discussionmentioning

confidence: 97%

“…Since our original identification of long rORFs in the ONLV1 and ONLV2 genomes, besides sequences from Uromyces appendiculatus and Puccinia striiformis transcriptomes (Cook et al 2013), a number of other studies have discovered narnaviral genomes containing similar rORFs (Chandler et al 2015;Shi et al 2016Shi et al , 2017Viljakainen et al 2018;Gö ertz et al 2019). These rORFcontaining sequences appear not to form a monophyletic group, although they do show considerable phylogenetic clustering.…”

Section: Discussionmentioning

confidence: 99%

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OUP accepted manuscript

et al. 2020

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Positive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long ($1,000-codon) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae, form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverseframe ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

OUP accepted manuscript

et al. 2020

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“…More recently, evidence was put forward that at least some narnaviruses are true arthropod viruses: for example, the group of alphanarnaviruses comprising (Figure 2) come from four different studies and five different Culicinae mosquito species (Chandler et al 2015;Cook et al 2013;Shi et al 2016;Shi et al 2017); moreover, in several samples, viral RNA accounts for >0.1% (in one case, >2%) of total non-ribosomal RNA reads, which appears unlikely if the virus is infecting a contaminant (Shi et al 2016;Shi et al 2017). Very recently, another narnavirus in this clade (MK628543.1; Culex narnavirus 1; 97% nt identity to KP642120.1) was found to persistently infect a Culex tarsalis cell culture and also give rise to typical 21-nt viral siRNAs with equal coverage of both strands, indicative of active infection (Göertz et al 2019).…”

Section: Discussionmentioning

confidence: 99%

A case for a reverse-frame coding sequence in a group of positive-sense RNA viruses

Dinan

Lukhovitskaya

Olendraitė

et al. 2019

Preprint

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ABSTRACTPositive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (~1000 codons) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae, form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungi and plant transcriptomic datasets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95% of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes.

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“…These infections were first observed in cultured yeast 2,3 . Subsequent metagenomic sequencing revealed narnaviruses in other fungi 4 , oomycetes 5 , mosquitoes [6][7][8][9] , other arthropods 10 , algae 11 , trypanosomatids [12][13][14] and potentially apicomplexans 15 , although the precise host species is not always clear. The known examples of narnaviruses are approximately 3 kb in size and code for a single protein, an RNA-dependent RNA polymerase (RdRp), with the exception of two putative bipartite narnaviruses 12,14,15 .…”

Section: Introductionmentioning

confidence: 99%

An exploration of ambigrammatic sequences in narnaviruses

DeRisi

Huber

Kistler

et al. 2019

Preprint

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Narnaviruses have been described as positive-sense RNA viruses with a remarkably 10 simple genome of ∼ 3 kb, encoding only a highly conserved RNA-dependent RNA polymerase 11 (RdRp). Many narnaviruses, however, are 'ambigrammatic' and harbor an additional uninterrupted 12 open reading frame (ORF) covering almost the entire length of the reverse complement strand. No 13 function has been described for this ORF, yet the absence of stops is conserved across diverse 14 narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The > 3 kb 15 ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of 16 the constraints imposed or alleviated by the codon alignment. Here, we show that only when the 17 codon frames are aligned can all stop codons be eliminated from the reverse strand by 18 synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo 19 gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore 20 what implications this coding strategy has for other aspects of narnavirus biology. Beyond 21 narnaviruses, our rapidly expanding catalog of viral diversity may yet reveal additional examples of 22 this broadly-extensible principle for ambigrammatic-sequence development. 23 24 42 235 MW thanks the Chan Zuckerberg Biohub for its hospitality. Author contributions: MW, DY and GH 236 7 of 13 Manuscript submitted to eLife conceived of the proposal and performed reading frame analysis. HR analyzed sequencing data 237 that stimulated this investigation, and generated the figures. JLD and AK provided critical input on 238 viral biology. HR, MW and DY wrote the manuscript with input from all authors.

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Mosquito Small RNA Responses to West Nile and Insect-Specific Virus Infections in Aedes and Culex Mosquito Cells

Cited by 75 publications

References 77 publications

OUP accepted manuscript

OUP accepted manuscript

A case for a reverse-frame coding sequence in a group of positive-sense RNA viruses

An exploration of ambigrammatic sequences in narnaviruses

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