20 research outputs found

    Predicted HRV-QPM pentamers compared to representative major (HRV-14) and minor (HRV-2) group HRV pentamers derived from crystallography data.

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    <p>(A) HRV-QPM versus HRV-14 SimPlot data projected onto a space filling depiction of the predicted HRV-QPM pentamer. Shading represents the amino acid identity (26–69%). The yellow dashed triangle represents a single icosahedral asymmetric unit (T = p3 conformation) composed of VP1 and VP2 from the same protomer and VP3 for an adjacent protomer. The major group domains of interest are divided between two asymmetric units for ease of viewing. Receptor (white) and antigenic (red) sites are shown in outline. (B) Top view ribbon depiction of a major group HRV pentamer (HRV-14; gray) with labelled antigenic neutralisation sites (NImIA-III, green) and combined HRV A (HRV-16) and B (HRV-14)ICAM-1 receptor footprints (red) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#pone.0001847-Laine1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#pone.0001847-Lole1" target="_blank">[37]</a>. Magnified areas of interest (boxed) highlight computer-based predictive comparisons to the equivalent HRV-QPM (orange) structures of interest. Arrows indicate structures and corresponding sequences of interest (refer to text). (C) HRV-QPM versus HRV-2 SimPlot data projected onto the HRV-QPM pentamer. The domains of interest are mostly shown within a single asymmetric unit. (D) A minor group pentamer (HRV-2; gray) including antigenic sites (sites A–C, green) and VLDL-R footprint (red) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#pone.0001847-Hofer1" target="_blank">[10]</a>. Attachment of the VLDL-R involves adjacent VP1 molecules. Magnified VP1 area represents one half of a VLDL-R footprint <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#pone.0001847-Stanway1" target="_blank">[42]</a>. Amino acid substitutions (arrowed) contributed to the differences between minor group sites B and C.</p

    Neighbour-joining phylogeny based on representative full-length picornavirus polyprotein sequences.

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    <p>Trees are unrooted and relevant nodes are labelled with bootstrap values (%) (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#s4" target="_blank">materials and methods</a> for details). Species are indicated next to vertical bars. CV-Coxsackievirus A; EV-Echovirus; HEV-Enterovirus; HPV-Poliovirus.</p

    Demographic and clinical characteristics of 96 patients randomized to treatment of Azithromycin (n = 50) or placebo (n = 46) and by ethnicity.

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    <p><b>Median and IQR (25–75) for continuous variables. Actual numbers for categorical variables and percentages.</b></p><p><b>NB</b>: Missing variables described.</p><p><b>Azithromycin</b>: Gestational age  = 3 (6%). Birth weight  = 6 (12%). Mother smoked during pregnancy  = 3 (6%). Exposure to household smoke  = 2 (4%), <b>Placebo</b>: Gestational age:  = 2 (4%). Birth weight  = 3 (6.5%).</p><p><b>Indigenous children</b>: Gestational age  = 2 (3.3%). Birth weight  = 4 (6.5%). Mother smoked during pregnancy  = 2 (3%). Exposure to household smoke  = 1 (1.6%): <b>Non Indigenous children</b>: Gestational age:  = 3 (8.6%). Birth weight  = 5 (14.3%) Mother smoked during pregnancy  = 1 (3%). Exposure to household smoke  = 1 (3%).</p

    HRV-QPM detections and association of co-morbidities and severity of respiratory illness upon discharge.

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    <p>HMPV-Human metapneumovirus, HCoV-229E or -NL63-Human coronaviruses, HBoV-Human bocavirus, WUPyV-WU polyomavirus. Labs-Myco/Pert- laboratory testing for <i>Mycoplasma spp.</i> or <i>Bordetella pertussis.</i><sup>1</sup>Steroids, <sup>2</sup>adrenalin or <sup>3</sup>bronchodilators administered, <sup>4</sup>Comparison of severity score using Wilcoxon rank-sum test for HRV-QPM cases with and without co-detection, p = 0.88. <sup>5</sup>Recorded as ‘zero’ due to the patient being admitted for cardiac surgery and all criteria were in relation to the surgery and not the ARTI. <sup>*</sup> Not admitted. CF-cystic fibrosis. NC-No chart could be obtained for review, CHD-congenital heart disease. NN-No notes were available from presentation during the preliminary study.</p

    Comparison of predicted protomers.

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    <p>(A) A simplified depiction of two protomers in opposition on a viral capsid (shaded areas, adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#pone.0001847-Lole1" target="_blank">[37]</a>). As a guide for visualising loop length, a dashed and a dotted line are spaced equidistantly and represent proximal and distal positions from the virion core, respectively. (B) Ribbon depiction of two opposing viral protomers from HRV-QPM, HRV-2 (minor group) and HRV-14 (major group). HRV-QPM proteins were predicted by <i>in silico</i> matching to the empirically derived HRV-16 and HRV-14 structure (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#s4" target="_blank">materials and methods</a>). Protomers consist of one copy each of VP1, VP2, VP3 and VP4. β-sheets are depicted as flat arrows and α-helices as coiled ribbons. The formation of VP1-VP3 into eight anti-parallel β-sheets is indicative of the ‘jellyroll’ conformation typical in picornaviruses. Major differences in the predicted HRV-QPM VP1 include the shortened external loops between β-sheets (asterisk) and an additional C-terminal sheet-loop-sheet formation (arrow indicates the same location on all protomers for comparison).</p

    Comparison of HRV-QPM and HEV structures at the sites comprising HEV receptor footprints.

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    <p>Figures indicate comparison of the predicted structures of HRV-QPM (orange) with representative HEVs (gray) in regions identified as HEV receptor footprints (red) across VP1, VP2 and VP3 proteins. RMSD values shown for conformational comparison of CAR and HRV-QPM structures, in angstroms.</p

    Criteria used to determine the severity[60] of respiratory illness upon discharge, in patients presenting to Queensland hospitals who tested positive for HRV-QPM.

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    1<p>Respiratory support by oxygen therapy and/or mechanical ventilation, <sup>2</sup>Supplementary fluids delivered by either intravenous and/or nasogastric route, <sup>3</sup><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#pone.0001847-Wainwright1" target="_blank">[61]</a>.</p

    Adherence of the newly identified HRV A2s to the ICTV species demarcation criteria.

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    <p>Numbers next to species indicates the number of polyprotein sequences included in the comparison. Bracketed percentages indicate G+C content variation of the HRV A2 polyprotein coding region to reference species. TD-to be determined. <sup>*</sup> See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001847#pone-0001847-g006" target="_blank">Figure 6</a> for accession numbers.</p
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