Genetic analysis of recent Taiwanese isolates of a variant of coxsackievirus A24

Abstract

Epidemics of acute hemorrhagic conjunctivitis (AHC) caused by a variant of coxsackievirus A24 (CA24v) reappeared in Taiwan in 1990 and 1994, following the first two epidemics of 1985--86 and 1988--89. To analyze the genetic diversity of recent CA24v in Taiwan, 7 Taiwanese strains isolated during the 1990--94 period were studied together with one Japanese and two Thai strains isolated in 1993. A fragment of 674 nucleotides between the carboxy terminal 3A and the amino terminal 3D polymerase, including the entire 3C protease (3C(pro)), was amplified by a reverse transcription-polymerase chain reaction (RT-PCR) and the nucleotide sequences were determined. In the 549 nucleotides (183 amino acids) of the entire 3C(pro), we found nucleotide differences at 80 positions between 10 strains and the prototype strain, EH24/70, one of the earliest strains of CA24v. Most of the nucleotide changes were synonymous substitutions and only nine amino acid changes were found. The nucleotide sequence homologies among 71 strains worldwide were 88-100%. These 71 nucleotide sequences were then analyzed by Neighbor-joining method and phylogenetically separated into three distinct genotypes. Genotype I consisted of early strains isolated in 1970--71 from Singapore and Hong Kong. Genotype II included isolates from Singapore and Thailand obtained in 1975. Genotype III comprised strains from the eastern hemisphere isolated in 1985--94 from Japan, Taiwan, China, Hong Kong, Thailand, Singapore, Pakistan and Ghana. They were further divided chronologically into six clusters. The recent isolates from Taiwan obtained in 1985/1986, 1988/1989 and 1990--94 were classified into genotype III Clusters 1, 5, and 6 respectively. The evolutionary rate was re-estimated to be 3 x 10(- 3) 30 years after the emergence of the virus.

Phylogenetic analysis of complete VP1 sequences of echoviruses 11 and 6: high genetic diversity and circulation of genotypes with a wide geographical and temporal range

“…In some cases, like that of poliovirus, the different genotypes cluster geographically and, even if long-range importations do occur, a genotype remains specific to a given geographical region (Kew et al, 1995). In contrast, other enteroviruses, such as coxsackieviruses A24 and E30, have temporal genotypes, each having circulated during a given period of time, and seem to have become extinct in favour of newly emerging genotypes (Lin et al, 2001;Oberste et al, 2003;Triki et al, 2007). The present work shows that, for both E6 and E11, genotypes containing isolates with wide geographical and temporal ranges can be found, meaning that some genotypes can persist over a long period of time and have a wide geographical range of circulation.…”

Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan

“…Phylogenetic analysis by the NJ method is frequently used in molecular epidemiological studies of various viruses (Lin et al, 2001;Parveen et al, 2006;Vicente et al, 2011). The viral evolutionary rate and cluster classification can be obtained from phylogenetic trees using this method.…”

Molecular Analysis of Enteroviruses

“…CV-A11 groups together with the strains of subgroups B or C depending on the method of phylogenetic tree construction [93]. The major worldwide CV-A24 epidemics have been attributed to four genotypes of CV-A24 variant strains (I to IV) on the basis of phylogenetic analysis of the 3C protease or VP1 region [94,95].…”

“…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].…”