Whole-Genome sequencing of Chikungunya Virus (CHIKV) from Pakistan: Detection of the East/Central/South African (ECSA) genotype during the 2024 outbreak in Mansehra

Abstract

The 2024 chikungunya virus (CHIKV) outbreak in Mansehra, Khyber Pakhtunkhwa, Pakistan, marked a significant public health event, providing a unique opportunity to investigate the genomic diversity and evolutionary dynamics of circulating strains. Using metagenomic next-generation sequencing (mNGS), we analyzed serum samples from patients presenting with acute febrile illness and joint pain, identifying 16 CHIKV-positive cases, six of which yielded near-complete genomes. Phylogenetic analysis revealed that all isolates belonged to the East/Central/South African (ECSA) genotype, closely related to strains from India (2020–2024) and China (2017). Notably, this study represents the first comprehensive whole-genome sequencing of CHIKV in Pakistan, uncovering unique mutations in structural (E1: I28V, V290I; E2: Y39H, D54E) and non-structural proteins (NSP1: I167V, M376T; NSP4: G27R, P52S, I403V), suggesting potential viral adaptations to local environmental and vector conditions. The absence of the E1-A226V mutation, associated with enhanced transmission by Aedes albopictus, highlights the need for continued genomic surveillance to monitor emerging variants. Additionally, the detection of a GB virus-C co-infection in one case underscores the utility of mNGS in identifying co-circulating pathogens. This study provides critical insights into the genomic landscape of CHIKV in Pakistan, emphasizing the importance of enhanced surveillance, diagnostics, and vector control strategies to mitigate future outbreaks. The findings underscore the necessity of regional collaboration and genomic monitoring to address the evolving threat of CHIKV in South Asia.