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Important Variable Sites: An analysis of Sites of Variation among Coxsackievirus A24 variant Isolates

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Coxsackievirus A24 variant (Coxsackievirus A24v; CVA24v) is an antigenic variant of the species Coxsackievirus A24 (CVA24) which is one of the etiological agents of Acute Hemorrhagic Conjunctivitis (AHC). AHC is a contagious disease of the eye characterized by red eyes and a sudden onset of pain th

at may rapidly develop into subconjunctival hemorrhage and conjunctivitis. Ever since the first outbreak of CVA24v-related AHC in 1970, a record of CVA24v sequences has been deposited into the National Center for Biotechnology (NCBI) database by studies conducting molecular and phylogenic analysis r

esearch on strains isolated during these outbreaks. Most molecular and phylogenic studies simply report the amino acid change at sites of variation among CVA24v sequences, however, no study has explicitly analyzed these sites of variations. This study aimed to analyze the sites of variations among C

oxsackievirus A24 variant isolates to determine any evolutionary significant patterns of variations. Complete coding sequencing of the ORF polyprotein, VP1 protein, and 3C protein of Coxsackievirus A24v isolates from 1970-2018 was extracted from the NCBI database to form the respective sequence data

sets. The sequence datasets were first processed using the Single-Likelihood Ancestor Counting (SLAC) tool from the Datamonkey evolutionary adaptive server to analyze the synonymous and non-synonymous substitutions occurring at each site within the datasets. The synonymous and non-synonymous substit

utions counting data were analyzed using EXCEL to identify sites of variations. The amino acid variations at each identified site for each dataset were examined to determine patterns of variation among compared sites. The results of the study revealed that most amino acid sites of the Coxsackievirus

A24v ORF polyprotein remain conserved except for a few sites which exhibit special patterns of variation referred to in this study as Important Variable Sites (IVS). IVS are amino acid sites within the virus proteins that show a distinct pattern of variation over time. The study further explored th

e evolutionary significance of these sites and found that some IVS have evolved under positive selection. Furthermore, IVS has a high positional correlation to the Neighborhood Joining phylogenic tree. An investigation into the practical applications of IVS showed that IVS can be used as a method fo

r estimating the year of isolation and genotype of unknown sequences. IVS can also be used together with sequencing and phylogenic analysis to characterize outbreaks of Coxsackievirus A24v. The analysis of sites of variation among Coxsackievirus A24v sequences reveals Important sites of variation (I

VS) which are epidemiologically, phylogenetically, and evolutionarily significant and have practical application for scientific research.