A New Gilliam Genotypic Variant of <em>Orientia tsutsugamushi </em>in Human Scrub Typhus Cases from Southwestern Tamil Nadu, India

Scrub typhus, caused by Orientia tsutsugamushi (Ot), is a re‐emerging public health concern across Southeast Asia. Although multiple Ot strains have been identified in endemic regions, its genetic diversity in India remains limited. We analysed Ot strains from humans by targeting the conserved GroEL and variable 56‐kDa genes. A total of 105 serum samples were subjected to PCR amplification and phylogenetic analysis for the GroEL gene, of which 33 (31.4%) were positive. Phylogenetic reconstruction revealed four major clades: Karp, Kato, Ot‐TJTN, and Gilliam‐related. Among the 33‐PCR positive samples, 11 sequences formed a distinct monophyletic clade within the Gilliam‐related group, diverging significantly from classical Gilliam strains. The overall mean nucleotide diversity (&pi;) was 0.02 (2%), while the divergence between these 11 sequences and Gilliam‐ related strains was 0.039 (3.9%). This level of divergence supports the identification of a novel Gilliam‐descendant lineage, designated INDv‐Gilliam. Further analysis of the 56‐kDa gene from the 11 INDv‐Gilliam samples revealed genotypic incongruence, indicating antigenic reassortment involving three clades: Karp‐like (n = 7), Ot‐TJTN‐like (n = 3), and Gilliam (n = 1). Similarity plot and recombination analyses, using 56‐kDa Ot‐TJTN and Karp‐like clades as queries against Gilliam‐type references, provided evidence of recombination involving TA716‐Kato and Ikeda‐Karp strains. These findings highlight the role of recombination and antigenic shift in driving the evolutionary dynamics and genetic diversity of Ot in the region. Accordingly, the isolates (11 nos.) were classified as mixed recombinant genotypes: Indian variant Gilliam (INDv‐Gilliam), INDv‐Gilliam/Karp‐like, INDv‐ Gilliam/Ot‐TJTN, and INDv‐Gilliam/Gilliam‐type.