Comparative genomic analysis of coxsackievirus A6 strains of different clinical disease entities

Abstract

Background: Studies regarding coxsackievirus A6 (CVA6) infection were limited. In Taiwan, outbreaks of CVA6 occurred in 2009 and 2010, respectively, but the clinical manifestations were markedly different. We conducted a study to compare the clinical features and genomic sequence between the two years.

Methodology/principal findings: In 2009 and 2010, 205 patients with coxsackievirus A6 (CVA6) infection were treated at Chang Gung Memorial Hospital. Detailed clinical features were obtained from 126 inpatients, 62 in 2009 and 64 in 2010. Between the inpatients in 2009 and 2010, no statistically significant difference was noted in terms of demographics, length of hospital stay and laboratory data. Significantly more patients in 2009 presented with herpangina (82%) while more patients in 2010 presented with hand-foot-mouth disease (HFMD; 67%) and skin rash beyond the typical sites for HFMD. Complete genomic sequences were determined and compared for three isolates from patients with herpangina in 2009 and three isolates from patients with HFMD in 2010. The complete sequences showed that 2009 and 2010 CVA6 isolates were indistinguishable by partial VP1 genes, but there were 5 unique nucleotide changes in 3' UTR, and 23 out of 2201 (1%) amino acids were different. 2010 viruses underwent the largest number of amino acid changes in 3CD protein, which is the precursor of both 3C protease and 3D polymerase.

Conclusions: Since 2008 in Finland, outbreaks of HFMD due to CVA6 were noted internationally. CVA6 of different genetic background may cause different clinical manifestations such as herpangina and HFMD.

Figure 1. Monthly Distribution of Cox-A6 infection children in 2009 and 2010.

Figure 2. Phylogenetic analysis of CVA6 VP1 genes.

Partial VP1 sequences (nt 2957 to 3306 according to Gdula numbering) of 6 CVA6 strains obtained from this study and 135 partial VP1 sequences of reference strains derived from GenBank were used to perform phylogenetic analysis. The phylogenetic tree was constructed using the neighbor-joining method with 1,000 bootstrap replications, as implemented in MEGA version 4. CVA16/G-10 (Accession No. U05876) was used as an outgroup. Bootstrap values over 70% are shown at the branch nodes. GenBank accession numbers are indicated after the slash. Open circle indicated 2009 CVA6 and black circle indicated 2010 CVA6. Abbreviations: CHN, China; ESP, Spain; FIN, Finland; FRA, France; IND, India; JPN, Japan; KOR, Korea; NOR, Norway; TW, Taiwan.

Figure 3. Alignment of the nucleotide sequences of 3′ UTR of CVA6.

The first three strains (Accession Nos. JQ946050–JQ946052) were isolated from HFMD patients with small skin rush in 2009, but other three strains (Accession Nos. JQ946053–JQ946053) were isolated from HFMD patients with onchomadesis in 2010. The ‘-‘ denotes a gap and the ‘.’ denotes sequence identity in the sequence. Numbering is based on coxsackievirus A6 strain Gdula (accession No. AY421764).