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. 2018 Apr 26;13(4):e0196240.
doi: 10.1371/journal.pone.0196240. eCollection 2018.

Complexity of type-specific 56 kDa antigen CD4 T-cell epitopes of Orientia tsutsugamushi strains causing scrub typhus in India

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Complexity of type-specific 56 kDa antigen CD4 T-cell epitopes of Orientia tsutsugamushi strains causing scrub typhus in India

Arunachalam Ramaiah et al. PLoS One. .

Abstract

Orientia tsutsugamushi (Ots) is an obligate, intracellular, mite-transmitted human pathogen which causes scrub typhus. Understanding the diversity of Ots antigens is essential for designing specific diagnostic assays and efficient vaccines. The protective immunodominant type-specific 56 kDa antigen (TSA) of Ots varies locally and across its geographic distribution. TSA contains four hypervariable domains. We bioinformatically analyzed 345 partial sequences of TSA available from India, most of which contain only the three variable domains (VDI-III) and three spacer conserved domains (SVDI, SVDII/III, SVDIII). The total number (152) of antigenic types (amino acid variants) varied from 14-36 in the six domains of TSA that we studied. Notably, 55% (787/1435) of the predicted CD4 T-cell epitopes (TCEs) from all the six domains had high binding affinities (HBA) to at least one of the prevalent Indian human leukocyte antigen (HLA) alleles. A surprisingly high proportion (61%) of such TCEs were from spacer domains; indeed 100% of the CD4 TCEs in the SVDI were HBA. TSA sequences from India had more antigenic types (AT) than TSA from Korea. Overall, >90% of predicted CD4 TCEs from spacer domains were predicted to have HBA against one or more prevalent HLA types from Indian, Korean, Asia-Pacific region or global population data sets, while only <50% of CD4 TCEs in variable domains exhibited such HBA. The phylogenetically and immunologically important amino acids in the conserved spacer domains were identified. Our results suggest that the conserved spacer domains are predicted to be functionally more important than previously appreciated in immune responses to Ots infections. Changes occurring at the TCE level of TSA may contribute to the wide range of pathogenicity of Ots in humans and mouse models. CD4 T-cell functional experiments are needed to assess the immunological significance of these HBA spacer domains and their role in clearance of Ots from Indian patients.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Structural illustration of TSA and prevalence and disparity of TSA ATs in Orientia tsutsugamushi from India.
A) Schematic representation of TSA and the boundaries of different variable domains (VDI—VDIV) and spacer domains (S-VDI–S-VDIII) in the Gilliam prototype strain (NCBI accession # DQ485289, length 521 AA, which was used as a reference strain to align all the Indian TSA amino acid sequences. The lengths of available Gilliam type strains vary from 516–541 AA. B) 345 TSA sequences were studied; number of TSA with sequences covering each of the six domains ranged from 96–243. The pie diagrams show that the prevalence (percentage of TSAs with a given AT type) of different antigenic (sequence) types (AT) ranged from 14–36 in each domain region of Indian TSA sequences. The thinnest slices are from single sequences while thicker colors are from TSA types with the same sequence). C) The scatter plots show the length of each AT type in amino acids (X axis), and number of Ots strains present with a particular AT type (Y axis). The dark blue circle indicates that several ATs were present with the same length and numbers of sequences. Greater disparity in the AT lengths was observed among the three variable domains than the three conserved spacer domains.
Fig 2
Fig 2. Prevalent HLA-DRB1 alleles in different geographical regions and domain prevalence of Indian 15-amino acid TSA peptides with predicted high binding affinities.
A) Top six most prevalent HLA-DRB1 alleles identified in populations in India, South Korea, Asia-Pacific region and global (http://allelefrequencies.net/), which were used to predict the binding affinity of all predicted 15 aa peptides from each AT from six domains of Indian TSA. B) The distribution of HBA T-cell epitopes predicted from Indian TSA antigenic types in each TSA domain. For each domain, the first set of bars shows the total number of predicted unique peptides and the number of these peptides identified with HBA to at-least one prevalent Indian HLA allele. Both the total number of predicted peptides and the peptides with HBA were further classified based on their presence in AT detected in single (SS) or multiple strains (MS) (bar pairs 2 and 3, respectively). C) Distribution (percentages) of peptides (15 aa) with HBAs from ATs identified in single (SS-uniquely present) and multiple (MS-shared sequences ≥2) Ots strains.The peptides present in both single and multiple strain sequences are highlighted in orange, the HBA peptides in SS and MS types are highlighted in purple and green, respectively.
Fig 3
Fig 3. Proportion of peptides with HBA (CD4 TCEs) from the six domains of TSA from India and South Korea.
The bar diagrams show that the proportion of predicted HBA peptides from all ATs from each of six domains from A) India TSA and B) South Korea TSA. Six prevalent HLA-DRB1 alleles from four different population sets (see Fig 2A) were used to identify the CD4 TSA TCEs with HBA.
Fig 4
Fig 4. Phylogenetic relationships of Ots TSA spacer domains.
All the ATs from each of three spacer domains S-VDI, S-VDII/III and S-VDIII of Indian and South Korean TSA were used for constructing individual Neighbor-Joining phylogenetic trees using their amino acid sequences. The TSA country of origin, the AT type and number of samples with that AT domain type are indicated for each unique AT type for each data set (S3 Table) (e.g., India-24-18). The pairs of identical 12 AT present in both India and South Korea TSAs are highlighted with red circles. Only the nodes with ≥70 bootstrap values are shown (1000 bootstraps). The bracket values show the scale for amino acid differences for each domain.
Fig 5
Fig 5. Properties of peptides exhibiting HBA from Indian and South Korean TSAs.
A) The mean binding affinity score was calculated from the binding affinity (score) of each predicted 15 aa peptides (sliding window approach) from ATs present in multiple strains with six prevalent HLA types studied from each country. A total of 7 and 5 ATs in S-VDI, 11 and 8 ATs in S-VDII/III and 13 and 8 ATs in S-VDIII were present in multiple Ots TSA sample sequences from India (blue) and South Korea (red), respectively. The overlapping 7 identical ATs present in multiple Ots strains from both India (blue dash lines) and Korea (red dash lines) TSA spacer domains are also shown. B) The range and the median average binding affinities of the peptides predicted from three spacer domains. C) Comparison of unique HBA TCEs from Indian and South Korean TSAs.

References

    1. Paris DH, Richards AL, Day NPJ. Orientia Chapter 112, pp. 2057–2096. In Molecular Medical Microbiology, Elsevier; 2015.
    1. Kelly DJ, Fuerst PA, Ching WM, Richards AL. Scrub typhus: the geographic distribution of phenotypic and genotypic variants of Orientia tsutsugamushi. Clinical Infectious Diseases. 2009; 48 Suppl 3: S203–230. doi: 10.1086/596576 - DOI - PubMed
    1. Shirai A, Wisseman CL Jr. Serologic classification of scrub typhus isolates from Pakistan. The American Journal of Tropical Medicine and Hygiene. 1975; 24:145–153. - PubMed
    1. Currie B. Medicine in tropical Australia. The Medical Journal of Australia. 1993; 158:612–615. - PubMed
    1. Graves S, Wang L, Nack Z, Jones S. Rickettsia serosurvey in Kimberley, Western Australia. The American Journal of Tropical Medicine and Hygiene. 1999; 60:786–789. - PubMed

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