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      Complete Genome Sequence of Mumps Virus Genotype G from a Vaccinated Child in Franceville, Southeastern Gabon, in 2013

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          Abstract

          The genome of mumps virus (MuV), a member of the family Paramyxoviridae of the genus Rubulavirus, consists of a single-stranded, negative-sense, nonsegmented RNA. Here, we report the first whole-genome sequence of 15,263 nucleotides of a mumps virus strain from a 6-year-old vaccinated boy in Franceville, southeastern Gabon.

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          Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR

          Nicolas Berthet, Anita K Reinhardt, India Leclercq … (2008)
          Background Phi29 polymerase based amplification methods provides amplified DNA with minimal changes in sequence and relative abundance for many biomedical applications. RNA virus detection using microarrays, however, can present a challenge because phi29 DNA polymerase cannot amplify RNA nor small cDNA fragments (<2000 bases) obtained by reverse transcription of certain viral RNA genomes. Therefore, ligation of cDNA fragments is necessary prior phi29 polymerase based amplification. We adapted the QuantiTect Whole Transcriptome Kit (Qiagen) to our purposes and designated the method as Whole Transcriptome Amplification (WTA). Results WTA successfully amplified cDNA from a panel of RNA viruses representing the diversity of ribovirus genome sizes. We amplified a range of genome copy numbers from 15 to 4 × 107 using WTA, which yielded quantities of amplified DNA as high as 1.2 μg/μl or 1010 target copies. The amplification factor varied between 109 and 106. We also demonstrated that co-amplification occurred when viral RNA was mixed with bacterial DNA. Conclusion This is the first report in the scientific literature showing that a modified WGA (WTA) approach can be successfully applied to viral genomic RNA of all sizes. Amplifying viral RNA by WTA provides considerably better sensitivity and accuracy of detection compared to random RT-PCR.
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            Author and article information

            Journal
            Journal ID (nlm-ta): Genome Announc
            Journal ID (iso-abbrev): Genome Announc
            Journal ID (hwp): ga
            Journal ID (pmc): ga
            Journal ID (publisher-id): GA
            Title: Genome Announcements
            Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
            ISSN (Electronic): 2169-8287
            Publication date (Electronic): 26 November 2014
            Publication date Collection: Nov-Dec 2014
            Volume: 2
            Issue: 6
            Electronic Location Identifier: e00972-14
            Affiliations
            [a ]Centre International de Recherches Médicales de Franceville (CIRMF), Département Zoonose et Maladies Emergentes, Franceville, Gabon
            [b ]CIRMF, Unité de Recherche et d’Analyse Médicale, Franceville, Gabon
            [c ]Aix Marseille University, URMITE unit, Marseille, France
            [d ]Imagine, Institut des Maladies Génétiques - Plateforme Génomique, Hôpital Necker, Enfants Malades, Paris, France
            [e ]Institut de Recherche pour le Développement (IRD), UMR 224, Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), IRD/CNRS/UM1/UM2, Montpellier, France
            [f ]Centre National de la Recherche Scientifique, UMR 3569, Paris, France
            Author notes
            Address correspondence to Gael D. Maganga, gael_maganga@ 123456yahoo.fr .

            G.D.M. and B.A.I. contributed equally to this work.

            Article
            Publisher ID: genomeA00972-14
            DOI: 10.1128/genomeA.00972-14
            PMC ID: 4246153
            PubMed ID: 25428961
            SO-VID: 4ba5c050-408f-4150-94bd-ca0d97f3106f
            Copyright © Copyright © 2014 Maganga et al.
            License:

            This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

            History
            Date received : 21 August 2014
            Date accepted : 21 October 2014
            Page count
            Pages: 2
            Categories
            Subject: Viruses
            Custom metadata
            cover-date November/December 2014
            access-type free

            ScienceOpen disciplines: Genetics
            Data availability:
            ScienceOpen disciplines: Genetics

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