Molecular identification of coxsackievirus A24 variant, isolated from an outbreak of acute hemorrhagic conjunctivitis in Singapore in 2005

Abstract

An outbreak of acute hemorrhagic conjunctivitis (AHC) was reported in Singapore military camps in the year 2005. A total of 103 conjunctival swab specimens were collected from military personnel diagnosed clinically with AHC. PCR testing on these conjunctival specimens revealed the presence of an enterovirus, and this was confirmed by virus isolation. Molecular typing using a partial VP1 gene confirmed a variant of coxsackievirus A24 (CA24v) as the most likely etiological agent for the outbreak. Full-length genome sequencing was carried out on 2 selected virus strains, DSO-26SIN05 and DSO-52SIN05. Sequence comparison and phylogenetic analyses of the VP4, VP1 and 3Cpro gene regions were performed, clustering the Singapore CA24v strains with viruses originating from Asia in the post-2000 era. In addition, we report evolution rates of 4.2 x 10(-3) and 1.0 x 10(-3) nucleotide/year, respectively, for the VP4 capsid and 3Cpro gene regions. Our result shows a focal evolutionary point around 1965-1966, suggesting that the CA24v virus has been evolving constantly since its emergence in Singapore, nearly 40 years ago.

Molecular epidemiology of the attachment glycoprotein (G) gene in respiratory syncytial virus in children with acute respiratory infection in Japan in 2009/2010

“…In general, the evolutionary rate of structural proteincoding genes may be faster than non-structural proteincoding genes in various viruses (Yeo et al, 2007). Previous reports suggest that every virus shows a unique rate of evolution of structural protein-coding genes.…”

Molecular Analysis of Enteroviruses

“…Additional mutations encoding amino acid substitutions in the capsid region (including VP1) contribute to and stabilize the attenuated phenotype [122]. In CV-A24 variant strains, the estimated evolutionary rates were 1.0 -4.1 × 10 -3 or 6.27 -6.67 × 10 -4 per nucleotide per year based on the 3C protease gene [94,[123][124][125], 4.2 × 10 -3 per nucleotide per year based on the VP4 gene [123], and 1.83-2.17 × 10 -3 per nucleotide per year based on the 3' VP1 gene [125].…”

Molecular Analysis of Enterovirus C Species Using the 5’ Untranslated Region and VP1 Region

“…In CVA24 variant strains, the estimated evolutionary rates are 1.0 -4.1 × 10-3 or 6.27 -6.67 × 10-4 per nucleotide per year based on the 3C protease gene [39,66,68,69], 4.2 × 10-3 per nucleotide per year based on the VP4 gene [39], and 1.83 -2.17 × 10-3 per nucleotide per year based on the 3' VP1 gene [69].…”

“…The partial VP1 nucleotide and amino acid identities of both CVA24 local strains (labelled 'g', with 100% VP1 nucleotide identity) to the prototype CVA24 Joseph strain were 77.4% and 91.5%, respectively. Furthermore, both CVA24 local strains had 97.7% and 98.0% VP1 nucleotide identities to another two CVA24 strains (DQ443001 and DQ443002, labelled 'j') isolated in Singapore in 2005 [39], respectively. Compared to the other groups, the structure of CVA11 was uncomplicated, and only comprised four strains (a local strain [labelled'd'], the prototype CVA11 Belgium-1 strain and two Bangladeshi strains).…”

“…The CVA24 variant, together with EV70, has caused several outbreaks of acute hemorrhagic conjunctivitis [39,61]. CVA24 can occasionally be associated with acute flaccid paralysis [62], while CVA21 induces mainly mild respiratory infections and can be associated with encephalitis [63].…”