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. 2006 Sep;72(9):6381-7.
doi: 10.1128/AEM.02621-05.

Molecular epidemiology of echoviruses 11 and 13, based on an environmental surveillance conducted in Toyama Prefecture, 2002-2003

Masae Iwai  1 , Hiromu Yoshida, Kumiko Matsuura, Tsuguto Fujimoto, Hiroyuki Shimizu, Takenori Takizawa, Yoshiyuki Nagai
Affiliations

Molecular epidemiology of echoviruses 11 and 13, based on an environmental surveillance conducted in Toyama Prefecture, 2002-2003

Masae Iwai et al. Appl Environ Microbiol. 2006 Sep.

Abstract

Nineteen echovirus 11 (E11) and 12 E13 isolates were isolated from three rivers in Toyama Prefecture, Japan, during an environmental surveillance conducted from April 2002 to March 2003. The nucleotide sequences of E13 isolates were closely related to those from patients with aseptic meningitis, with less than 1.3% divergence in the VP1 region of the viral capsid gene, and belonged to the same clade responsible for a worldwide outbreak that started in 2000. In contrast, E11 isolates were clustered into three genomic groups and were not closely related to echovirus strains isolated from patients. These results suggest that the combination of both virus isolation from environmental sources and phylogenetic analysis could be complementary assessment approaches to trace prevalent and minor circulating enteroviruses in the human population.

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Figures

FIG. 1.
FIG. 1.
Locations of the three rivers (Itachi [I], Oyabe [O], and Sembo [S]) in Toyama Prefecture. Squares (▪) indicate the fixed points for water sampling. Circles (○) indicate the locations of hospitals where aseptic meningitis patients were admitted. Double lines indicate distance.
FIG. 2.
FIG. 2.
Total numbers of virus isolates from three rivers from April 2002 (Apr) to March 2003 (Mar). Waters from fixed points of three rivers were collected on the indicated dates. CB2, coxsackievirus type B2; Polio2, poliovirus type 2; Reo1, reovirus type 1.
FIG. 3.
FIG. 3.
(a) Phylogenetic relationships between the Japanese isolates. Phylogenetic trees for E13 using the partial VP1 region (703 bp) were generated by the neighbor-joining method with 36 strains: 17 Toyama isolates (12 from river samples and 5 from patients) and 19 other Japanese isolates (GenBank accession no. AB086858, AB092984, AB092985, AB109377 to AB109382, AB109384 to AB109386, AB112409, AB112411, AB112412, AB167996, and AB178768 to AB178770). Bootstrap values (in percentages) for 1,000 replicated trees are indicated. Circles and triangles specify patient isolates and environmental isolates, respectively. S, O, and I indicate Sembo, Oyabe, and Itachi, respectively. (b) Phylogenetic trees were reconstructed using 61 strains (accession no. AB112410, AJ537604 to AJ537609, AY227334 to AY227347, AY268561, AY268563 to AY268569, AY268571 to AY268580, AY680685, AY680686, and AJ241427 from GenBank and including the 19 other Japanese isolates). Bootstrap values (in percentages) for 1,000 replicated trees are indicated. The major genomic group isolated during 2000 to 2002 was compressed within the same cluster (2000-2002 cluster). Arrows from tree a to tree b indicate that Japanese isolates in tree a are included in the compressed cluster. The strains are represented as accession no./country or city/year/strain code using the reference or Web data in GenBank.
FIG. 4.
FIG. 4.
Phylogenetic tree for E11 using the partial VP1 region (561 bp) generated by the neighbor-joining method with 78 strains: 19 Toyama River isolates, 8 patient isolates from Hyogo, and 51 other isolates (accession no. AY121373 to AY121405, AY121407 to AY121418, AY121420, AY121422, AY121423, AB167806, AF295498, and AF081326 from GenBank). Circles and triangles indicate viruses isolated from patients and the environment, respectively. Bootstrap values (in percentages) for 1,000 replicated trees are indicated. Subgenomic groups I to IV in this study are shown, with D4 and D5 clusters being named as suggested previously by Oberste et al. (25). The strains are represented as accession no./country or city/year/strain code using the reference or Web data in GenBank. Isolate identifiers consist of a three-letter country abbreviation (ARG, Argentina; AUS, Australia; BAN, Bangladesh; COL, Colombia; DOR, Dominican Republic; ZAI, Democratic Republic of Congo; IRQ, Iraq; KUW, Kuwait; NET, The Netherlands; OMA, Oman; PAR, Paraguay; PER, Peru; SOA, South Africa; TUN, Tunisia; Tur, Turkey; or USA, United States), with two-letter abbreviations for U.S. states. The viral isolate from Fukuoka City (accession no. AB167806) is indicated by arrows (Japan/01).
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