Analysis of Genetic Diversity in Indian Isolates of Rhipicephalus microplus Based on Bm86 Gene Sequence
Abstract
:1. Introduction
2. Materials and Methods
2.1. Tick Samples
2.2. Study Area
2.3. RNA Isolation and cDNA Synthesis
2.4. Amplification of Full-Length IVRI-I Bm86 (orf) Gene, Cloning and Sequencing
2.5. Amplification of the Bm86 Conserved Sequence
2.6. Phylogenetic Analysis
2.7. In Silico Prediction of Linear B-Cell Epitopes on IVRI-IBm86 Protein
2.8. Evaluation of Degree of Conservation of Linear B-Cell Epitopes
3. Results
3.1. Sequence Analysis
3.2. Phylogenetic Analysis
3.3. In Silico Analysis of IVRI-I Bm86 Protein
- 1.
- Two deletions in IVRI-I epitopes (G177-D224) showed increased antigenicity to Yeerongpilly and Camcord strains;
- 2.
- same VaxiJen scores were observed in four epitopes (T18-D45, D519-K554, C598-T606, T609-K623) of IVRI-I, Yeerongpilly and Camcord strains; the same score may be due to 100% similarity in the epitope sequence;
- 3.
- the substitutions/ mutations can increase (G177-D224, W280-R311) or decrease (D97-G129, K319-K501, H563-Q587) the antigenicity (VaxiJen scores) of IVRI-I epitopes when compared to the same epitopes in Yeerongpilly and Camcord strains (Supplementary Table S5).
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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A | B | C | D | E | F | G | H | I | J | K | L | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
A | ID | 100 | 93.2 | 94.4 | 90.1 | 96.7 | 97.8 | 93 | 93.3 | 28.6 | 93.5 | 90.7 |
B | 100 | ID | 93.2 | 94.4 | 90.1 | 96.7 | 97.8 | 93 | 93.3 | 28.6 | 93.5 | 90.7 |
C | 93.2 | 93.2 | ID | 97 | 86.9 | 93.6 | 92.4 | 96.3 | 96.6 | 28.3 | 89.3 | 87.5 |
D | 94.4 | 94.4 | 97 | ID | 88.7 | 95.5 | 93.5 | 94.6 | 94.9 | 29.3 | 91.5 | 89 |
E | 90.1 | 90.1 | 86.9 | 88.7 | ID | 92.9 | 89.5 | 86.4 | 86.7 | 27 | 93.5 | 99 |
F | 96.7 | 96.7 | 93.6 | 95.5 | 92.9 | ID | 95.8 | 93.2 | 93.5 | 28.6 | 93.8 | 93.5 |
G | 97.8 | 97.8 | 92.4 | 93.5 | 89.5 | 95.8 | ID | 91.8 | 92.1 | 27.6 | 92.6 | 89.8 |
H | 93 | 93 | 96.3 | 94.6 | 86.4 | 93.2 | 91.8 | ID | 98.9 | 27.5 | 88.9 | 87 |
I | 93.3 | 93.3 | 96.6 | 94.9 | 86.7 | 93.5 | 92.1 | 98.9 | ID | 27.5 | 89.2 | 87.3 |
J | 28.6 | 28.6 | 28.3 | 29.3 | 27 | 28.6 | 27.6 | 27.5 | 27.5 | ID | 26.1 | 27.3 |
K | 93.5 | 93.5 | 89.3 | 91.5 | 93.5 | 93.8 | 92.6 | 88.9 | 89.2 | 26.1 | ID | 93 |
L | 90.7 | 90.7 | 87.5 | 89 | 99 | 93.5 | 89.8 | 87 | 87.3 | 27.3 | 93 | ID |
A | B | C | D | E | F | G | H | I | J | K | L | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
A | ID | 100 | 95 | 95.6 | 91.3 | 98.1 | 98.6 | 95.5 | 95.5 | 28.9 | 94.8 | 91.7 |
B | 100 | ID | 95 | 95.6 | 91.3 | 98.1 | 98.6 | 95.5 | 95.5 | 28.9 | 94.8 | 91.7 |
C | 95 | 95 | ID | 97.3 | 88.4 | 95.1 | 94.8 | 97.5 | 97.5 | 28.6 | 91.9 | 88.7 |
D | 95.6 | 95.6 | 97.3 | ID | 89.6 | 96.3 | 95.6 | 96.4 | 96.4 | 29.2 | 92.7 | 89.7 |
E | 91.3 | 91.3 | 88.4 | 89.6 | ID | 93.1 | 90.6 | 88.7 | 88.7 | 27.5 | 94.5 | 99.4 |
F | 98.1 | 98.1 | 95.1 | 96.3 | 93.1 | ID | 97.2 | 95.5 | 95.5 | 28.9 | 95 | 93.4 |
G | 98.6 | 98.6 | 94.8 | 95.6 | 90.6 | 97.2 | ID | 94.9 | 94.9 | 28.3 | 94 | 90.8 |
H | 95.5 | 95.5 | 97.5 | 96.4 | 88.7 | 95.5 | 94.9 | ID | 99.5 | 28.3 | 92.2 | 89 |
I | 95.5 | 95.5 | 97.5 | 96.4 | 88.7 | 95.5 | 94.9 | 99.5 | ID | 28.3 | 92.2 | 89 |
J | 28.9 | 28.9 | 28.6 | 29.2 | 27.5 | 28.9 | 28.3 | 28.3 | 28.3 | ID | 26.4 | 27.5 |
K | 94.8 | 94.8 | 91.9 | 92.7 | 94.5 | 95 | 94 | 92.2 | 92.2 | 26.4 | ID | 94.2 |
L | 91.7 | 91.7 | 88.7 | 89.7 | 99.4 | 93.4 | 90.8 | 89 | 89 | 27.5 | 94.2 | ID |
B- Cell Epitope Sequence | Length | IEDB Server Score | VaxiJen Score |
---|---|---|---|
18TAESSICSDFGNEFCRNAECEVVPGAE45 | 28 | 0.52 | 0.795 (Probable ANTIGEN) |
24DNMYFNAAEKQCEYKDTCKTRECS77 | 24 | 0.54 | Probable NON-ANTIGEN |
83QSNP86 | 4 | 0.5 | Probable NON-ANTIGEN |
97DTLTLQCNIKDDYATDCRNSGGTAKLRTDGVIG129 | 33 | 0.58 | 1.3361 (Probable ANTIGEN) |
136EWGAMNKTTRN146 | 11 | 0.52 | Probable NON-ANTIGEN |
152CLRPDLTCKDLCEKNLLQRDSR173 | 22 | 0.55 | Probable NON-ANTIGEN |
175C175 | 1 | 1.0 | Probable NON-ANTIGEN |
177GWNSPKCSAPADSYCSPGSPKGPDGQCKDACKTKEAG FVCKHGCRSTD224 | 48 | 0.54 | 0.9020 (Probable ANTIGEN) |
235FTVAEDGITCKSIPYTGGCTVEQKQTCR262 | 28 | 0.54 | Probable NON-ANTIGEN |
280WNQHLVGDKCIGDCVENKCHGEFTDCGVYMNR311 | 32 | 0.536 | 1.3679 (Probable ANTIGEN) |
319KSRKPGPNVNINECLLNEYYYTVSFTPNISLDSDHCDWYED RVLEAIRTSIGKEVFKVEILNCTQDIKARLIAEKPLSKHVL RKLQACEHPIGEWCMMYPKLLIKKNSATEIEEENLCDSLLK NQEAAYKGQNKCVKVDNLFWFQCADGYTTTYEMTRGRLR RSVCKAGVSCNENEQLECADK501 | 183 | 0.57 | 0.6052 (Probable ANTIGEN) |
507YEN509 | 3 | 0.50 | Probable NON-ANTIGEN |
511K511 | 1 | 1.0 | Probable NON-ANTIGEN |
519DTKPGEIGCIERTTCNPKEIQECQDKKLECVYKNHK554 | 36 | 0.56 | 0.8751 (Probable ANTIGEN) |
563HECSREPAKDSCSEEDNGKCQSSGQ587 | 25 | 0.55 | 1.4514 (Probable ANTIGEN) |
598CKEKSEATT606 | 9 | 0.510 | 1.4151 (Probable ANTIGEN) |
609TTTTKAKDKDPDPGK623 | 15 | 0.58 | 0.7273 (Probable ANTIGEN) |
Predicted IVRI-I Bm86 B-cell Epitopes | Yeerongpilly | Thailand M1 | Thailand M2 | Thailand S1 | USA (Hidalgo) | USA (Zapta 1) | USA (Starr 2) | China |
---|---|---|---|---|---|---|---|---|
Bm86 | 93% | 96.4% | 96.1% | 96.3% | 97.0% | 93.5% | 93.3% | 92.3% |
Bm86(T18-D45) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
Bm86(D97-G129) | 84.8% | 96.9% | 96.9% | 93.9% | 84.8% | 81.8% | 81.8% | 78.7% |
Bm86(G177-D224) | 82.0% | 84% | 84% | 84% | 97.9% | 84% | 84% | 82% |
Bm86(W280-R311) | 81.2% | 93.7% | 90.6% | 93.7% | 93.7% | 81.2% | 81.2% | 81.2% |
Bm86(K319-K501) | 97.8% | 97.2% | 96.7% | 97.8% | 98.9% | 97.2% | 96.7% | 98.3% |
Bm86(D519-K554) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
Bm86(H563-Q587) | 100% | 100% | 100% | 100% | 100% | 96% | 100% | 100% |
Bm86(C598-K606) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 88.8% |
Bm86(T609-K623) | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 86.6% |
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Parthasarathi, B.C.; Kumar, B.; Nagar, G.; Manjunathachar, H.V.; de la Fuente, J.; Ghosh, S. Analysis of Genetic Diversity in Indian Isolates of Rhipicephalus microplus Based on Bm86 Gene Sequence. Vaccines 2021, 9, 194. https://doi.org/10.3390/vaccines9030194
Parthasarathi BC, Kumar B, Nagar G, Manjunathachar HV, de la Fuente J, Ghosh S. Analysis of Genetic Diversity in Indian Isolates of Rhipicephalus microplus Based on Bm86 Gene Sequence. Vaccines. 2021; 9(3):194. https://doi.org/10.3390/vaccines9030194
Chicago/Turabian StyleParthasarathi, Balasamudram Chandrasekhar, Binod Kumar, Gaurav Nagar, Haranahally Vasanthachar Manjunathachar, José de la Fuente, and Srikant Ghosh. 2021. "Analysis of Genetic Diversity in Indian Isolates of Rhipicephalus microplus Based on Bm86 Gene Sequence" Vaccines 9, no. 3: 194. https://doi.org/10.3390/vaccines9030194