RNA virus replication, transcription and recombination

White, K. Andrew; Enjuanes, Luis; Berkhout, Ben

doi:10.4161/rna.8.2.15663

Cited by 23 publications

(15 citation statements)

References 13 publications

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“…This is consistent with the literature showing that differences in coverage of overlapping sequences can lead to the split of supposedly contiguous sequences into different contigs [19]. This is a problem mainly when assembling viral genomes from RNAs since viral genes can show different transcription profiles [37,38]. To overcome this limitation, we decided to use contigs derived from the "meta" strategy as trusted contigs trying to extend these contiguous sequences.…”

Section: Resultssupporting

confidence: 75%

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics

Sardi

Carvalho

Pacheco

et al. 2020

Viruses

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Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from metatranscriptomics data is key to the development of new control strategies for these diseases. Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification.

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Section: Resultssupporting

confidence: 75%

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics

Sardi

Carvalho

Pacheco

et al. 2020

Viruses

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“…Worobey and Holmes [ 43 ] mention that segmental exchange recombination in phi6 RNA virus is impossible or very rare. They go on to state that template switching by viral replicase may be inhibited by physical constraints such as the ribonucleoprotein packaging in the case of negative-strand RNA viruses, also corroborated by White et al [ 42 ] as mentioned earlier. However, one other physical constraint mentioned by them, viz., the extent of sequence dissimilarity between potentially recombining genomes, is obviated in our case by our imposed condition that potential matches ensure identical sequences between parent and daughter segments.…”

Section: Introductionmentioning

confidence: 58%

“…Homologous recombination is well documented in the case of eukaryote and bacterial genomes [ 29 ], but is controversial in cases of negative stranded RNA viruses [ 18 ]. Such viruses are believed to be rapidly packed with ribonucleoprotein after being transcribed and it then becomes difficult, but perhaps not impossible, for RNA polymerase to ‘jump’ from one strand to another to search for similar sequences [ 42 ]. In mammalian genes and chromosomes, recombination can take place through one or more cross-overs during replication [ 29 ].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatics studies of Influenza A hemagglutinin sequence data indicate recombination-like events leading to segment exchanges

Sarkar

Nandy

2016

BMC Res Notes

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BackgroundThe influenza genome is highly variable due primarily to two mechanisms: antigenic drift and antigenic shift. A third mechanism for genetic change, known as copy choice or template switching, can arise during replication when, if two viral strains infect a cell, a part of a gene from the second viral strain can be copied into the growing progeny of a gene of the first viral strain as replacement leading to a new variety of the virus. This template switching between the same genes of the two strains is known as homologous recombination. While genetic drift and shift are well-understood, the presence or absence of intra-segment homologous recombination in influenza genomes is controversial.Context and purpose of studyWe are interested to study the possibility of subunit-wise homologous recombination. The idea is that where well-defined subunits are separated by consensus sequences, it might be possible for template switching to take place at such junctions. The influenza hemagglutinin gene has basically two subunits, HA1 and HA2, with HA1 being mostly surface exposed and containing the active site for binding to cells, while HA2 secures the hemagglutinin to the viral coat. We undertook a thorough search of the major human infecting influenza hemagglutinin gene sequences, viz., the H1N1, H5N1, H3N2 and H7N9 subtypes, over the period 2010–2014 in Asia to determine if certain sequences could be identified that had HA1 from a previous strain and HA2 from another.ResultsOur search yielded several instances where sequence identities between segments of various strains could be interpreted as indicating possibilities of segment exchange. In some cases, on closer examination they turn out to differ by a few mutations in each segment, due perhaps to the short time span of our database.Conclusions and potential implicationsThe study reported here, and in combination with our earlier observations on the neuraminidase, shows that subunit-wise recombination-like events in the influenza genes may be occurring more often than have been accounted for and merits further detailed studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2017-3) contains supplementary material, which is available to authorized users.

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“…The majority of viruses infecting animals are RNA viruses. All RNA virus replication proceeds through a RNA strand complimentary intermediate, except for in retroviruses where the intermediate is DNA [ 66 ]. Despite differences in genomic features and replication strategies, immediately after virus infection, all RNA viruses trigger evolutionarily conserved innate immune responses that serve as a first line of defense against infection.…”

Section: Intracellular Immune Ecosystem Of Virus-infected Cellsmentioning

confidence: 99%

Immune Ecosystem of Virus-Infected Host Tissues

Maarouf

Raj

Goraya

et al. 2018

IJMS

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Virus infected host cells serve as a central immune ecological niche during viral infection and replication and stimulate the host immune response via molecular signaling. The viral infection and multiplication process involves complex intracellular molecular interactions between viral components and the host factors. Various types of host cells are also involved to modulate immune factors in delicate and dynamic equilibrium to maintain a balanced immune ecosystem in an infected host tissue. Antiviral host arsenals are equipped to combat or eliminate viral invasion. However, viruses have evolved with strategies to counter against antiviral immunity or hijack cellular machinery to survive inside host tissue for their multiplication. However, host immune systems have also evolved to neutralize the infection; which, in turn, either clears the virus from the infected host or causes immune-mediated host tissue injury. A complex relationship between viral pathogenesis and host antiviral defense could define the immune ecosystem of virus-infected host tissues. Understanding of the molecular mechanism underlying this ecosystem would uncover strategies to modulate host immune function for antiviral therapeutics. This review presents past and present updates of immune-ecological components of virus infected host tissue and explains how viruses subvert the host immune surveillances.

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RNA virus replication, transcription and recombination

Cited by 23 publications

References 13 publications

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics

Bioinformatics studies of Influenza A hemagglutinin sequence data indicate recombination-like events leading to segment exchanges

Immune Ecosystem of Virus-Infected Host Tissues

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