Full genomic sequence characterization of the chikungunya virus from an imported case with serum viral concentration below culturable level

Chikungunya virus (CHIKV) infection, responsible for chikungunya fever and occasionally severe symptoms, has emerged as an increasing global health concern following several large-scale outbreaks from Africa, Asia, Europe, and America. Over the past two decades, South and Southeast Asia regions have gradually become hot spots for outbreaks involving multiple CHIKV lineages. In China, most CHIKV infections are imported, making it crucial to trace the origins and transmission routes for effective prevention and control. In January 2024, a case of imported chikungunya fever was confirmed in Guangzhou City, Guangdong Province, China. However, the serum CHIKV viral concentration was too low for cultivation [reverse transcription-polymerase chain reaction (RT-PCR) detection, cycle threshold = 32.62]. Despite this, we successfully obtained the viral genome sequence directly from the whole blood sample using an optimized metatranscriptomic sequencing strategy, achieving a full-length viral genome with an average depth of 54.3X. Further analysis confirmed that the CHIKV virus belonged to the Asian lineage, traced to Timor-Leste, where an endemic CHIKV outbreak had been reported in January 2024, consistent with the patient’s travel history. Finally, we analyzed genetic evolutionary trends and amino acid site variations. This study highlights the identification of a CHIKV infection origin using direct whole-blood metatranscriptomic sequencing, a valuable method for rapidly sequencing low viral-load samples.