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      Novel avian paramyxovirus (APMV-15) isolated from a migratory bird in South America

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          Abstract

          A novel avian paramyxovirus (APMV) isolated from a migratory bird cloacal swab obtained during active surveillance in April 2012 in the Lagoa do Peixe National Park, Rio Grande do Sul state, South of Brazil was biologically and genetically characterized. The nucleotide sequence of the full viral genome was completed using a next-generation sequencing approach. The genome was 14,952 nucleotides (nt) long, with six genes (3’-NP-P-M-F-HN-L-5’) encoding 7 different proteins, typical of APMV. The fusion (F) protein gene of isolate RS-1177 contained 1,707 nucleotides in a single open reading frame encoding a protein of 569 amino acids. The F protein cleavage site contained two basic amino acids (VPKER↓L), typical of avirulent strains. Phylogenetic analysis of the whole genome indicated that the virus is related to APMV-10, -2 and -8, with 60.1% nucleotide sequence identity to the closest APMV-10 virus, 58.7% and 58.5% identity to the closest APMV-8 and APMV-2 genome, respectively, and less than 52% identity to representatives of the other APMVs groups. Such distances are comparable to the distances observed among other previously identified APMVs serotypes. These results suggest that unclassified/calidris_fuscicollis/Brazil/RS-1177/2012 is the prototype strain of a new APMV serotype, APMV-15.

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          Precision Farming: Technologies and Information as Risk-Reduction Tools

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            Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses.

            We have developed a set of reverse transcription-PCR assays for the detection and identification of known and novel paramyxoviruses in clinical specimens. Primers were designed from the conserved motifs of the polymerase pol gene sequences to detect members of the Paramyxovirinae or Pneumovirinae subfamily or groups of genera within the Paramyxovirinae subfamily. The consensus-degenerate hybrid oligonucleotide primer design and seminested or nested PCR assay design were used to enhance the breadth of reactivity and sensitivity of the respective assays. Using expressed RNA and 10-fold dilution series of virus-infected tissue culture isolates from different members of the family or genera, these assays were able to detect on average between 100 and 500 copies of template RNA. The assays were specific to the respective group of genera or subfamily viruses. This set of primers enhances our ability to look for novel viruses in outbreaks and diseases of unknown etiology.
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              Viral genome sequencing by random priming methods

              Background Most emerging health threats are of zoonotic origin. For the overwhelming majority, their causative agents are RNA viruses which include but are not limited to HIV, Influenza, SARS, Ebola, Dengue, and Hantavirus. Of increasing importance therefore is a better understanding of global viral diversity to enable better surveillance and prediction of pandemic threats; this will require rapid and flexible methods for complete viral genome sequencing. Results We have adapted the SISPA methodology [1-3] to genome sequencing of RNA and DNA viruses. We have demonstrated the utility of the method on various types and sources of viruses, obtaining near complete genome sequence of viruses ranging in size from 3,000–15,000 kb with a median depth of coverage of 14.33. We used this technique to generate full viral genome sequence in the presence of host contaminants, using viral preparations from cell culture supernatant, allantoic fluid and fecal matter. Conclusion The method described is of great utility in generating whole genome assemblies for viruses with little or no available sequence information, viruses from greatly divergent families, previously uncharacterized viruses, or to more fully describe mixed viral infections.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                9 May 2017
                2017
                : 12
                : 5
                : e0177214
                Affiliations
                [1 ]Laboratorio de Virologia Clinica e Molecular do Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Sao Paulo, Brazil
                [2 ]Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
                [3 ]Laboratório Nacional Agropecuário, Campinas, Sao Paulo, Brazil
                [4 ]Universidade do Vale do Rio dos Sinos, Sao Leopoldo, Rio Grande do Sul, Brazil
                SWEDEN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: LMT JdA TF DW MVP ELD RJW.

                • Formal analysis: LMT TF RJW.

                • Funding acquisition: LMT ELD JdA.

                • Investigation: LMT JdA TF DW MVP ELD RJW DR.

                • Methodology: LMT JdA TF DW TO CMB DR.

                • Project administration: ELD LMT.

                • Resources: LMT JdA TF DW MVP ELD RJW DR.

                • Software: LMT JdA TF DW MVP ELD RJW.

                • Supervision: ELD DR.

                • Writing – original draft: LMT TF RJW.

                • Writing – review & editing: LMT TF RJW.

                Author information
                http://orcid.org/0000-0002-9157-6122
                Article
                PONE-D-16-41742
                10.1371/journal.pone.0177214
                5423646
                28486490
                b45d2edf-4d6d-49b8-957c-5d2d9cbd7b2d
                © 2017 Thomazelli et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 19 October 2016
                : 24 April 2017
                Page count
                Figures: 1, Tables: 0, Pages: 7
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001807, Fundação de Amparo à Pesquisa do Estado de São Paulo;
                Award ID: 2013/05485-2
                Award Recipient :
                This work has been funded in part by the Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP 2013/05485-2), Conselho Nacional de Desenvolvimento a Pesquisa (CNPq) and the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, under contract number HHSN266200700005C and ALSAC. The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.
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                The complete genome sequence was deposited in GenBank database (Accession number: KX932454).

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