| Literature DB >> 23521862 |
Kanti Pabbaraju1, Sallene Wong, Eve N Y Chan, Raymond Tellier.
Abstract
BACKGROUND: An unusually high incidence of aseptic meningitis caused by enteroviruses was noted in Alberta, Canada between March and October 2010. Sequence based typing was performed on the enterovirus positive samples to gain a better understanding of the molecular characteristics of the Coxsackie A9 (CVA-9) strain responsible for most cases in this outbreak.Entities:
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Year: 2013 PMID: 23521862 PMCID: PMC3620579 DOI: 10.1186/1743-422X-10-93
Source DB: PubMed Journal: Virol J ISSN: 1743-422X Impact factor: 4.099
Figure 1Distribution of the different serotypes detected in the sequenced samples. A indicates serotype distribution in samples from patients less than one year and B from patients over one year old.
Figure 2Phylogenetic tree including representatives of the different serotypes detected and corresponding prototype sequences . The alignment used for the phylogenetic tree included 173 bases of the VP2 region from the clinical specimens, the same region from the prototype strains is also included. The Genbank accession number for the prototype strains is included in legend for Table 2. Patient samples are identified using a laboratory number followed by the enterovirus type.
Closest neighbour to the 2003 and 2010 samples based on phylogenetic analysis
| 5’NCR | EV74 | EV74 |
| VP4 | EV101 | EV101 |
| VP2 | CVA-9 | CVA-9 |
| VP3 | CVA-9 | CVA-9 |
| VP1 | CVA-9 | CVA-9 |
| 2A Protease | Echo 25 | Echo 25 |
| 2B Protein | CVB-5 and echo14 | CVB-5 and echo14 |
| 2C Helicase | Echo 25 | CVB-6 |
| 3A protein | Echo 16 and CVB-6 | EV 86 |
| 3B Protein (VPg) | Echo 14 and CVB-5 | Echo 14 and CVB-5 |
| 3C Protease | Echo 13 | EV 100 |
| 3D Protein (Pol) | Echo 13 | EV 86 |
Phylogenetic analysis was performed using all the available prototype sequences belonging to enterovirus species B.
Phylogenetic tree is based on complete nucleotide sequence of the VP2 and VP4 genes; GenBank numbers for the prototype sequences used were D00627_CVA-9; M16560_CVB1; AF085363_CVB2; M16572_CVB3; X05690_CVB4; AF114383_CVB5; AF105342_CVB6; AF029859_E1; AY302545_E2; AY302553_E3; AY302557_E4; AF083069_E5; AY302558_E6; AY302559_E7; X84981_E9; X80059_E11; X79047_E12; AY302539_E13; AY302540_E14; AY302541_E15; AY302542_E16; AY302543_E17; AF317694_E18; AY302544_E19; AY302546_E20; AY302547_E21; AY302548_E24; AY302549_E25; AY302550_E26; AY302551_E27; AY302552_E29; AF162711_E30; AY302554_E31; AY302555_E32; AY302556_E33; AY302560_EV69; AF241359_EV73; AY556057_EV74; AY556070_EV75; AJ493062_EV77; AY843297_EV79; AY843298_EV80; AY843299_EV81; AY843300_EV82; AY843301_EV83; DQ902712_EV84; AY843303_EV85; AY843304_EV86; AY843305_EV87; AY843306_EV88; AY843307_EV97; NC_013115.1_EV107; DQ902713_EV100; AY843308_EV101. The GenBank numbers for the in-house sequenced samples from 2003 and 2010 are JQ837913 and JQ837914.
Figure 3Age distribution of patients positive for enterovirus CVA-9. The bars represent the total number of samples positive for CVA-9 and the broken line indicates the percentage of samples positive for CVA-9 among the serotyped samples in each age group. The solid line indicates the percentage of samples positive for all enteroviruses in each age group based on the number of CSF samples tested within that age group.
Percent identity comparison of nucleotide and amino acid sequences for isolates from 2003 (JQ837913), 2010 (JQ837914) and prototype CVA-9 sequence (D00627)
| | ||||||
|---|---|---|---|---|---|---|
| 5’NCR | 96.5 | N/A | 84.93 | N/A | 85.5 | N/A |
| VP4 | 92.65 | 94.29 | 79.9 | 94.12 | 77.94 | 94.12 |
| VP2 | 94.76 | 94.03 | 80.95 | 88.85 | 80.95 | 89.23 |
| VP3 | 95.24 | 97.51 | 81.37 | 98.74 | 81.65 | 98.32 |
| VP1 | 94.92 | 95.47 | 82 | 93.38 | 81.24 | 92.05 |
| 2A Protease | 96.15 | 97.31 | 77.78 | 93.88 | 79.14 | 95.24 |
| 2B Protein | 93.6 | 83.33 | 79.46 | 91.92 | 80.47 | 96.97 |
| 2C Helicase | 82.19 | 92.96 | 82.07 | 97.26 | 80.87 | 96.35 |
| 3A protein | 81.34 | 93.48 | 73.03 | 91.01 | 74.63 | 89.89 |
| 3B Protein (VPg) | 74.63 | 86.36 | 79.1 | 90.91 | 70.15 | 86.36 |
| 3C Protease | 77.78 | 91.62 | 81.75 | 97.27 | 79.02 | 95.63 |
| 3D Protein (Pol) | 80.19 | 92.09 | 76.81 | 96.32 | 73.69 | 95.89 |
Figure 4Simplot analysis of full genome sequences of CVA-9_2003, CVA-9_2010 and related species B sequences. Genomic regions are indicated at the bottom of each panel based on numbering of the prototype CVA-9 (D00627) 5’UTR:1–722; VP4:723–929; VP2:930–1712; VP3:1713–2426; VP1:2427–3332; 2A:3333–3773; 2B:3774–4069; 2C:4070–5057; 3A:5058–5323; 3B:5324–5390; 3C:5391–5938; 3D:5939–7324; 3’UTR:7325 - >7403. The query sequences used are CVA-9_2003 in panel 4A and CVA-9_2010 in panels 4B and 4C. Arrows in panels 4A and 4B indicate recombination with EV-101 in the VP4 region.