An alternative method to determine the 5′ extremities of non-segmented, negative sense RNA viral genomes using positive replication intermediate 3′ tailing: Application to two members of the Paramyxoviridae family

Brown, Paul A.; Briand, François-Xavier; Guionie, Olivier; Lemaitre, Evelyne; Courtillon, Céline; Henry, Aurélie; Jestin, Véronique; Eterradossi, Nicolas

doi:10.1016/j.jviromet.2013.05.007

Cited by 11 publications

(10 citation statements)

References 18 publications

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“…In combination with sequences described previously [20], [24], [34], [35], this study completes the sequences of European AMPV-C (French duck isolate, Fr-AMPV-C) and D (French Turkey isolate, Fr-AMPV-D). Comparisons were made to full length sequences of European AMPV-A, B and US-C and of all HMPV-A and B sublineages.…”

Section: Introductionsupporting

confidence: 56%

“…We have previously described the 3′ and 5′ sequence extremities of Fr-AMPV-C [34] discussing. Here complete leader and trailer sequences showed varying levels of conservation amongst all MPV’s (67–97.5%).…”

Section: Resultsmentioning

confidence: 99%

“…Additional primers were defined from the newly determined sequences (sequence of all primers are available on request). Sequence of the leader and trailer as previously reported, based on 3′ tailing of the genome and its positive replication intermediate [34]. cDNA copies of the viral RNA were prepared using superscript II (Invitrogen, France) according to manufacturer’s recommendations.…”

Section: Methodsmentioning

confidence: 99%

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Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and –D Isolates, Further Supports Possible Subclassification within the MPV Genus

et al. 2014

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Four avian metapneumovirus (AMPV) subgroups (A–D) have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively) have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV) sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus “clusters” HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II.

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Section: Introductionsupporting

confidence: 56%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and –D Isolates, Further Supports Possible Subclassification within the MPV Genus

et al. 2014

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“…Nearly all of the short missing regions occurred at either the termini (a common issue in viral NGS sequencing) [46] or at one specific intergenic location in the genome between genes N and P which displayed extremely low coverage in all analyzed samples (possibly as a result of high GC content – 76%). For the purpose of submitting full-length NDV sequences to GenBank, we sequenced the termini using a previously described protocol [47] and primers designed for the current study (see Additional file 4: Table S3). The internal gaps, where necessary, were sequenced using PCR and Sanger sequencing (for primers sequences see Additional file 4: Table S3).…”

Section: Resultsmentioning

confidence: 99%

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Dimitrov

Sharma

Volkening

et al. 2017

Virol J

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BackgroundNext-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools.MethodsIn this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform.ResultsTwenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25–30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2–3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample.ConclusionsThis work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-017-0741-5) contains supplementary material, which is available to authorized users.

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“…Sequence data were assembled using MIRA version 3.4.1 (6) within a customized workflow on the Galaxy platform (7), as described previously (8). Missing positions at the 5′ and 3′ ends of the genomes were sequenced using Sanger technology, as described previously (9). …”

Section: Genome Announcementmentioning

confidence: 99%

Complete Genome Sequences of Four Avian Paramyxoviruses of Serotype 10 Isolated from Rockhopper Penguins on the Falkland Islands

et al. 2017

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An alternative method to determine the 5′ extremities of non-segmented, negative sense RNA viral genomes using positive replication intermediate 3′ tailing: Application to two members of the Paramyxoviridae family

Cited by 11 publications

References 18 publications

Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and –D Isolates, Further Supports Possible Subclassification within the MPV Genus

Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and –D Isolates, Further Supports Possible Subclassification within the MPV Genus

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Complete Genome Sequences of Four Avian Paramyxoviruses of Serotype 10 Isolated from Rockhopper Penguins on the Falkland Islands

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