Genomic Insights into the 2023 Outbreak of Acute Hemorrhagic Conjunctivitis in Pakistan: Identification of Coxsackievirus A24 Variant through Next Generation Sequencing

Acute Hemorrhagic Conjunctivitis (AHC) has caused a significant outbreak in Pakistan in 2023, leading to a surge in cases across various cities. To gain insights into the genetic makeup of the virus responsible for the outbreak, the National Institute of Health, Islamabad conducted a study involving twenty individuals with suspected conjunctivitis in Islamabad. Five of these samples underwent whole-genome sequencing for the first-time in Pakistan, revealing Coxsackievirus A24 variant (CVA24v), genotype IV. Phylogenetic analysis revealed a higher homology (99.38-99.43%) with isolates from Zhongshan, China, in June 2023, with notable mutations concentrated in the 3D and VP1 regions. The sample also exhibited a 94% homology with 2015 France isolates. Comparing the 2023 study sequence with partial 2005 Pakistan sequences revealed divergence in the VP1 region, marked by three non-synonymous mutations (“H25P,” “I89V,” and “I90L”), while no mutation was found in the VP3 region. Notably, no intertypic recombination events were detected. This study underscores the significance of genomic surveillance for effective understanding and management of infectious disease outbreaks, offering crucial insights for public health interventions.