title: Genotypic characterization of Orientia tsutsugamushi from patients in two geographical locations in Sri Lanka.
abstract: To date more than 20 antigenically distinct strains of Orientia tsutsugamushi (OT) reported within the tsutsugamushi triangle that cause an undifferentiated acute febrile illness in humans. Genotypic characterization of OT in different geographic regions or within the same country, is important in order to establish effective diagnostics, clinical management and to develop effective vaccines. Genetic and antigenic characterization of OT causing human disease in OT-endemic regions is not known for Sri Lanka.
  
  
  
  Adult patients and children who were admitted with an acute febrile illness and presumed to having acute scrub typhus based on presence of an eschar and other supporting clinical features were recruited. Eschar biopsies and buffy coat samples collected from patients who were confirmed having OT by IFA were further studied by real time PCR (Orientia 47 kD) and nested PCR (Orientia 56 kD) amplification. DNA sequences were obtained for 56 kD gene amplicons and phylogenetic comparisons were analyzed using currently available data in GenBank [Neucleotide substitution per 100 residues, 1000 Bootstrap Trials].
  
  
  
  Twenty eschar biopsies (Location1,19, Location 2,1) and eight buffy coat samples (Location1,6, Location2,2) examined by real time PCR revealed Orientia amplicons in 16 samples. DNA sequences were obtained for the 56 kD gene amplicons in 12 eschars and 4 buffy coat samples. The genotypes of the Location1 samples revealed that, 7 exhibiting close homology with JP1 [distantly related to UT177 Thai (Karp related)], five had close homology with Kato strain, two had close homology with JGv and JG AF [Distantly related to Kawasaki M63383] and one had close homology with Gilliam strain. The Location 2 strain was closely related to Kuroki-Boryong L04956, the genotype which is distributed in far eastern Asia. Similar to other patients in the cohort this patient also had never travelled out of Sri Lanka.
  
  
  
  We observed all three main OT genotypes in Sri Lanka, and the majority fell into Thai Karp related clade. These results demonstrate great antigenic diversity of OT in the studied areas of Sri Lanka.
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Kelaniya, Thalagolla Road, PO Box 6, Ragama, Sri Lanka. ranjanp64@gmail.com.
authors.forename: Ranjan
authors.identifier: 0000-0002-6588-9467
authors.initials: R
authors.lastname: Premaratna
authors.affiliation: Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA. Isblanto@utmb.edu.
authors.forename: Lucas S
authors.initials: LS
authors.lastname: Blanton
authors.affiliation: Medical Unit, Base Hospital, Balapitiya, Sri Lanka.
authors.forename: Dilhar N
authors.initials: DN
authors.lastname: Samaraweera
authors.affiliation: Paediatric Unit, Base Hospital, Balapitiya, Sri Lanka.
authors.forename: G Nalika N
authors.initials: GN
authors.lastname: de Silva
authors.affiliation: Department of Parasitology, Faculty of Medicine, Universityof Kelaniya, Thalagolla Road, PO Box 6, Ragama, Sri Lanka.
authors.forename: Nilmini T G A
authors.initials: NT
authors.lastname: Chandrasena
authors.affiliation: Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: Walker
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Kelaniya, Thalagolla Road, PO Box 6, Ragama, Sri Lanka.
authors.forename: H J
authors.initials: HJ
authors.lastname: de Silva
mesh_terms: D000328:Adult; D000940:Antigenic Variation; D002648:Child; D004269:DNA, Bacterial / Q000235:genetics*; D005838:Genotype; D006801:Humans; D012285:Orientia tsutsugamushi / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D060888:Real-Time Polymerase Chain Reaction; D012612:Scrub Typhus / Q000453:epidemiology / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013188:Sri Lanka / Q000453:epidemiology
chemical_list: D004269:DNA, Bacterial
keywords: Genotypes; Orientia tsutsugamushi; Scrub typhus; Sri Lanka