Molecular evolution of VP3, VP1, 3C^pro and 3D^pol coding regions in coxsackievirus group A type 24 variant isolates from acute hemorrhagic conjunctivitis in 2011 in Okinawa, Japan

Abstract

A large acute hemorrhagic conjunctivitis (AHC) outbreak occurred in 2011 in Okinawa Prefecture in Japan. Ten strains of coxsackievirus group A type 24 variant (CA24v) were isolated from patients with AHC and full sequence analysis of the VP3, VP1, 3Cpro and 3D pol coding regions performed. To assess time-scale evolution, phylogenetic analysis was performed using the Bayesian Markov chain Monte Carlo method. In addition, similarity plots were constructed and pairwise distance (p-distance) and positive pressure analyses performed. A phylogenetic tree based on the VP1 coding region showed that the present strains belong to genotype 4 (G4). In addition, the present strains could have divided in about 2010 from the same lineages detected in other countries such as China, India and Australia. The mean rates of molecular evolution of four coding regions were estimated at about 6.15 to 7.86 Â 10 À3 substitutions/site/year. Similarity plot analyses suggested that nucleotide similarities between the present strains and a prototype strain (EH24/70 strain) were 0.77-0.94. The p-distance of the present strains was relatively short (<0.01). Only one positive selected site (L25H) was identified in the VP1 protein. These findings suggest that the present CA24v strains causing AHC are genetically related to other AHC strains with rapid evolution and emerged in around 2010.

Coxsackievirus A24 Variant Associated with Acute Haemorrhagic Conjunctivitis Cases, French Guiana, 2017

“…Table 1). This level of divergence is in line with that observed previously in Japan: during an AHC outbreak that occurred in Okinawa in 2011, the CV-A24v isolates collected in October featured between 21 and 30 nucleotide divergences with isolates collected 4 months before [12]. …”

A major outbreak of conjunctivitis caused by coxsackievirus A24, Réunion, January to April 2015

“…Within this group, the sequences from this study were most closely related to those of recent AHC outbreaks (i.e. China 2010, Egypt 2010 and Japan 2011), which belong to a sub-cluster that might have emerged between 2008 and 2009 [22].…”

“…CV-A24v belonging to genotype IV was identified in all the samples by sequencing of the VP1 coding region (Figure 4). The 10 VP1 partial nt sequences shared a 99.1 to 100% nt identity and had 95.1 to 97.9% nt similarity with sequences from genotype IV isolates previously identified in AHC outbreaks in Egypt (2010) [21], Japan (2011) [22], China (2007 and 2010) [23][24][25], Brazil (2009) [26], India (2007) and Singapore (2005) [27] (Figure 4). They also grouped in a larger cluster containing the VP1 sequence from a genotype IV isolate detected in a traveller returning from Comoros to France in 2012 (Figure 4; accession number JX196594).…”

“…They also grouped in a larger cluster containing the VP1 sequence from a genotype IV isolate detected in a traveller returning from Comoros to France in 2012 (Figure 4; accession number JX196594). Two whole genome sequences were generated by a metagenomic approach and showed a 97.2-97.3% similarity with sequences from Japanese strains detected in 2011 in Okinawa [22]. Similarity plots provided no evidence of recombination (data not shown).…”

Forecasting the incidence of acute haemorrhagic conjunctivitis in Chongqing: a time series analysis

“…The main symptoms are conjunctival congestion, burning feeling, photophobia, tears, feeling foreign body and so on. Outbreaks have been found in many countries, such as India, Senegal and so on [3][4][5]. Although cases occur every month, AHC incidence has obvious seasonal characteristics [6].…”