Isolation of Avian Paramyxovirus 1 from a Patient with a Lethal Case of Pneumonia

Goebel, Scott J.; Taylor, Jill; Barr, Bradd C.; Kiehn, Timothy E.; Castro‐Malaspina, Hugo; Hedvat, Cyrus V.; Rush-Wilson, Kim; Kelly, Christopher E.; Davis, Stephen W.; Samsonoff, William A.; Hurst, Kelley R.; Behr, Melissa; Masters, Paul S.

doi:10.1128/jvi.01406-07

Cited by 40 publications

(46 citation statements)

References 27 publications

(35 reference statements)

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“…Examples include hexamer [16], [17], [20], [26], [30], [34], [35], [36], [37], [38], octamer [19], [22], [23], [39], [40], [41], [42], nonamer [24], [43], [44], [45] and decamer random 3′ annealing parts [46]. Stangegaard and colleagues [47] studied the impact of different random primers (without 5′ specific amplification tag sequence) on the yield and quality of synthesized cDNA, concluding that reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA compared with hexa- and nonamers.…”

Section: Discussionmentioning

confidence: 99%

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing

et al. 2013

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Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3′ random part used to prime complementary DNA synthesis and a 5′ defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3′ part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides) and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5′ defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

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Section: Discussionmentioning

confidence: 99%

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing

et al. 2013

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“…Mild fever and respiratory involvement may rarely develop in humans, most frequently following aerosol exposure (Swayne and King, 2003) although some question the true frequency of this occurrence (Goebel et al, 2007). Highly pathogenic strains have largely been excluded from flocks within the United States.…”

Section: Mode Of Transmissionmentioning

confidence: 99%

Selected Zoonoses

Fox

Otto²,

Colby

2015

Laboratory Animal Medicine

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“…Moreover, the occurrence of a fatal human case due to pneumonia has proven that this disease is an important zoonosis (Greenacre;Goebel et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Avian Paramyxoviruses: Detection by Transmission Electron Microscopy Techniques

Catroxo¹,

Martins²,

Petrella³

et al. 2012

Int. J. Morphol.

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SUMMARY:Diseases caused by avian paramyxovirus (APMV) occur in commercial, captive and wild birds worldwide, demonstrating the significant economic and ecological importance of these agents. Paramyxoviruses belong to the Paramyxoviridae family, Paramyxovirinae subfamily and Avulavirus genus. During the period 2000 to 2011, stool and small intestine samples of 1647 birds species were sent to the Laboratory of Electron Microscopy, Biological Institute of São Paulo, Brazil, for diagnosis of viral agents. The samples were processed by negative staining (rapid preparation) and resin embedding techniques. Under the transmission electron microscope by negative staining technique, in 294 (17.8%) samples of 1647 were visualized paramyxovirus particles pleomorphic, roughly spherical or filamentous, measuring 100 to 500 nm of diameter containing an envelope covered with spikes and characteristic helical herring-bone-like nucleocapsid measuring 15 to 20 nm in diameter. Ultrathin sections of the small intestine fragments revealed the presence of amorphous granular intracytoplasmic inclusions surrounded by membrane and containing viral nucleocapsid measuring 10-14 nm in diameter. Immature particles budding from cell membranes, pleomorphic, spherical and tubular particles containing viral nucleocapsid strands, and the complete particles measured up to 170 nm in diameter were seen in the cytoplasm. Intranuclear inclusions containing viral nucleocapsid were also visualized. Nuclei showed a marginalized chromatin.

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Isolation of Avian Paramyxovirus 1 from a Patient with a Lethal Case of Pneumonia

Cited by 40 publications

References 27 publications

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing

Selected Zoonoses

Avian Paramyxoviruses: Detection by Transmission Electron Microscopy Techniques

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