Phylodynamic Characterization of an Ocular-Tropism Coxsackievirus A24 Variant

Evolutionary Studies on the Coxsackievirus A-24 Variants Causing Acute Hemorrhagic Conjunctivitis with Emphasis on the Recent Outbreak of 2023 in India

Acute Hemorrhagic Conjunctivitis (AHC) is primarily caused by viral infections, with Coxsackievirus A-24v (CV-A24v) being a significant culprit. Enteroviruses, including CV-A24v, are responsible for global AHC outbreaks. Over time, CV-A24v has evolved, and genotype IV (GIV) has become the dominant strain. This study focused on examining the genetic features and evolutionary trends of CV-A24v responsible for the recent AHC outbreak of 2023 in India. Researchers isolated viral strains from ocular swabs and confirmed the presence of CV-A24v using reverse transcriptase quantitative PCR (RT-qPCR) and whole-genome sequencing. Genomic comparisons between isolates of 2023 and those from a previous outbreak in 2009 were conducted. Phylogenetic analysis revealed that the 2023 isolates formed a distinct cluster within GIV-5 and were related to recent strains from China and Pakistan. The older Indian isolates from 2009 grouped with GIV-3. New subclades, GIV-6 and GIV-7, were also identified in this study, indicating the diversification of CV-A24. Molecular clock and phylogeographic analysis traced the virus's circulation back to the 1960s, with the common ancestor likely to have originated in Singapore in 1968. The 2023 Indian strains probably originated from Thailand around 2014, with subsequent spread to China and Pakistan. This study concluded that the 2023 outbreak was caused by a genetically distinct CV-A24v strain with nine mutations, underlining the virus's ongoing evolution and adaptations and offering valuable insights for future outbreak control.

Molecular analysis of acute hemorrhagic conjunctivitis in a tertiary care hospital, Kalburgi district, Karnataka 2023

INTRODUCTION

Viral infections are the predominant cause of acute hemorrhagic conjunctivitis (AHC) across the globe. From July to August of 2023, a large-scale conjunctivitis outbreak was witnessed in India, affecting a large number of individuals. The present study was initiated to identify the causative agent responsible for the AHC outbreak in Kalburgi district of Karnataka state.

METHODOLOGY

Conjunctival and throat swabs were collected from AHC patients from a tertiary care hospital in Kalburgi from August to September 2023. After total viral RNA extraction from all the samples, reverse transcriptase PCR was performed using 5' non-coding regions of the enterovirus (EV) genome. The positive samples were further subjected to PCR using EV type-specific primers of Coxsackie A-24 variant (CA24v) and enterovirus-70 (EV-70). EV negative samples were also tested for human adenovirus. Five representative CA24v-positive samples were subjected to partial sequencing and phylogenetic analysis.

RESULTS

Thirty-three AHC patient samples were included in the testing and analysis. EV was detected among 54.5 % (18/33) of the patients and all were found to be CA24v, while no EV-70 or human adenovirus was detected. Partial 3C-proteinase sequencing revealed that the CA24v strains from Kalburgi were closely clustered and had 99 % sequence identity with CA24v strains reported from China in 2023. However, the Kalburagi strains were 90.3-93.2 % identical to previously reported Indian strains.

CONCLUSION

To summarize, CA24v was identified as an etiological agent responsible for the recent acute hemorrhagic conjunctivitis outbreak in Kalburgi. The CA24v strain detected was closely related to the currently circulating Asian strains.

Phylodynamic and Epistatic Analysis of Coxsackievirus A24 and Its Variant

Coxsackievirus A24 (CV-A24) is a human enterovirus that causes acute flaccid paralysis. However, a Coxsackievirus A24 variant (CV-A24v) is the most common cause of eye infections. The causes of these variable pathogenicity and tissue tropism remain unclear. To elucidate the phylodynamics of CV-A24 and CV-A24v, we analyzed a dataset of 66 strains using Bayesian phylodynamic approach, along with detailed sequence variation and epistatic analyses. Six CV-A24 strains available in GenBank and 60 CV-A24v strains, including 11 Taiwanese strains, were included in this study. The results revealed striking differences between CV-A24 and CV-A24v exhibiting long terminal branches in the phylogenetic tree, respectively. CV-A24v presented distinct ladder-like clustering, indicating immune escape mechanisms. Notably, 10 genetic recombination events in the 3D regions were identified. Furthermore, 11 missense mutation signatures were detected to differentiate CV-A24 and CV-A24v; among these mutations, the F810Y substitution may significantly affect the secondary structure of the GH loop of VP1 and subsequently affect the epitopes of the capsid proteins. In conclusion, this study provides critical insights into the evolutionary dynamics and epidemiological characteristics of CV-A24 and CV-A24v, and highlights the differences in viral evolution and tissue tropism.

Identification of coxsackievirus A-24 GIV C5 strain as the cause of acute hemorrhagic conjunctivitis outbreak in Hyderabad, India in 2022

Viral infection is frequently the cause for acute hemorrhagic conjunctivitis (AHC) epidemics. AHC can result from adenoviruses, with enterovirus 70 and coxsackievirus A24 being the primary agents. AHC was initially identified in Ghana in 1969, caused by enterovirus 70 and leading to a global pandemic. Since 2000, outbreaks of AHC linked to coxsackievirus A24 variant have been documented in Spain, Pakistan, Singapore, India, Korea, and China. A sudden surge of conjunctivitis cases reported in October 2022 in and out of the Hyderabad region. This infection presented with usual symptoms of redness of the eyes, discharge, pain in the eyes and crusting. Occular swab samples from 110 patients were collected in order to identify and characterize the virus that was causing the epidemic. We examined adenovirus, enterovirus, COVID-19 and Herpes Simplex Virus by using commercially kits available at the hospital. Conserved regions in the enteroviral 5'-UTR and VP2 gene were analyzed further for characterization of serotype at the National apex laboratory. None of them was found positive except Enterovirus in 16.36 % (18/110) of the patients. From enterovirus-positive samples, the coxsackievirus A24 was observed in all 18 positive samples. These clinical isolates constitute a new lineage cluster associated with genotype IV-C5, according to additional sequencing of the full-length VP2 genes and subsequent phylogenetic analysis. In conclusion, the current outbreak of acute haemorrhagic conjunctivitis in Hyderabad, India was traced to the coxsackievirus A24 strain GIV C5.

Molecular analysis of Coxsackievirus A24 variant isolates from three outbreaks of acute hemorrhagic conjunctivitis in 1988, 1994 and 2007 in Beijing, China

Coxsackievirus A24 variant (CVA24v) is a major pathogen that causes continued outbreaks and pandemics of acute hemorrhagic conjunctivitis (AHC). In China, the first confirmed outbreak of CVA24v-related AHC occurred in Beijing in 1988, followed by another two significant outbreaks respectively in 1994 and 2007, which coincides with the three-stage dynamic distribution of AHC in the world after 1970s. To illustrate the genetic characteristics of CVA24v in different periods, a total of 23 strains were isolated from those three outbreaks and the whole genome of those isolations were sequenced and analyzed. Compared with the prototype strain, the 23 strains shared four nucleotide deletions in the 5′ UTR except the 0744 strain isolated in 2007. And at the 98th site, one nucleotide insertion was found in all the strains collected from 2007. From 1994 to 2007, amino acid polarity in the VP1 region at the 25th and the 32nd site were changed. Both the 3C and VP1 phylogenetic tree indicated that isolates from 1988 and 1994 belonged to Genotype III (GIII), and 2007 strains to Genotype IV (GIV). According to the Bayesian analysis based on complete genome sequence, the most recent common ancestors for the isolates in 1988, 1994 and 2007 were respectively estimated around October 1987, February 1993 and December 2004. The evolutionary rate of the CVA24v was estimated to be 7.45 ​× ​10⁻³ substitutions/site/year. Our study indicated that the early epidemic of CVA24v in Chinese mainland was the GIII. Point mutations and amino acid changes in different genotypes of CVA24v may generate intensity differences of the AHC outbreak. CVA24v has been evolving constantly with a relatively rapid rate.

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The early epidemic of CVA24v in Chinese mainland is the Genotype III.

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Mutations may generate intensity differences of the AHC outbreak.

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CVA24v has been evolving constantly with a relatively rapid rate.

Molecular Characterization of Coxsackievirus A24v from Feces and Conjunctiva Reveals Epidemiological Links

Coxsackievirus A24 variant (CVA24v), the main causative agent of acute hemorrhagic conjunctivitis (AHC), can be isolated from both the eyes and lower alimentary tract. However, the molecular features of CVA24v in feces is not well-documented. In this study, we compared the VP1 and 3C sequences of CVA24v strains isolated from feces during AHC epidemics in Cuba in 1997, 2003, and 2008-2009 with those obtained from conjunctival swabs during the same epidemic period. The sequence analyses of the 3C and VP1 region of stool isolates from the three epidemics showed a high degree of nucleotide identity (ranging from 97.3-100%) to the corresponding conjunctival isolates. The phylogenetic analysis showed that fecal CVA24v isolates from the 1997 and 2003 Cuban outbreaks formed a clade with CVA24v strains isolated from conjunctival swabs in Cuba and other countries during the same period. There were three amino acid changes (3C region) and one amino acid change (VP1 region) in seven CVA24v strains isolated sequentially over 20 days from fecal samples of one patient, suggesting viral replication in the intestine. Despite these substitutions, the virus from the conjunctival swab and fecal samples were genetically very similar. Therefore, fecal samples should be considered as a reliable alternative sample type for the routine molecular diagnosis and molecular epidemiology of CVA24v, also during outbreaks of AHC.

Molecular evolution of coxsackievirus A24v in Cuba over 23-years, 1986-2009

Coxsackievirus A24 variant (CVA24v) is a major causative agent of acute hemorrhagic conjunctivitis outbreaks worldwide, yet the evolutionary and transmission dynamics of the virus remain unclear. To address this, we analyzed and compared the 3C and partial VP1 gene regions of CVA24v isolates obtained from five outbreaks in Cuba between 1986 and 2009 and strains isolated worldwide. Here we show that Cuban strains were homologous to those isolated in Africa, the Americas and Asia during the same time period. Two genotypes of CVA24v (GIII and GIV) were repeatedly introduced into Cuba and they arose about two years before the epidemic was detected. The two genotypes co-evolved with a population size that is stable over time. However, nucleotide substitution rates peaked during pandemics with 4.39 × 10-3 and 5.80 × 10-3 substitutions per site per year for the 3C and VP1 region, respectively. The phylogeographic analysis identified 25 and 19 viral transmission routes based on 3C and VP1 regions, respectively. Pandemic viruses usually originated in Asia, and both China and Brazil were the major hub for the global dispersal of the virus. Together, these data provide novel insight into the epidemiological dynamics of this virus and possibly other pandemic viruses.

Molecular epidemiology of acute hemorrhagic conjunctivitis caused by coxsackie A type 24 variant in China, 2004-2014

To understand control interventions, the molecular epidemiology of acute hemorrhagic conjunctivitis (AHC) was investigated from 2004 to 2014.A total of 613,485 AHC cases (annualized cases 55,771) with two deaths were included. Our findings showed that AHC was reported in all provinces, predominantly in Southern and Eastern China. The incidence rates were highest in 2007 (5.65/100,000) and 2010 (21.78/100,000) respectively. A clear seasonal pattern was identified with a peak from August to October. AHC cases occurred in all age groups; however, five to 14 years was the predominant group [23.06%, 133, 510/578,909]. The median age was 24 years (one month~97 years). The median duration from onset to diagnosis was 1.5 days, and there was no difference between the <15, 15~60 and >60-year-old patients [p = 0.0653]. The phylogenetic analysis of 100 nonstructural proteins (3C) and 84 structural proteins (VP1) revealed that AHC outbreaks were caused by Coxsackievirus A24 variant. Genotypes G4-c5a, G4-c5b, and G4-c3 co-circulated with both temporal and geographical overlaps. In conclusion, despite the overall steady decline in the number of AHC cases since the peak in 2010, it still remains a serious public health problem in Southern and Eastern China that targets on the school aged children under 15 years old.