Sequencing of the Viral UL111a Gene Directly from Clinical Specimens Reveals Variants of HCMV-Encoded IL-10 That Are Associated with Altered Immune Responses to HCMV
Abstract
:1. Introduction
2. Results
2.1. Most Clinical Samples Contain More Than One Variant of HCMV
2.2. Several Polymorphisms Were Group-Specific
2.3. Amino Acid Haplotypes Differ between Samples from Australia and Indonesia
2.4. UL111a Variations Are Associated with Levels of HCMV-Reactive Antibody
3. Discussion
4. Materials and Methods
4.1. RTR and Healthy Controls from Perth, Western Australia
4.2. People with HIV from Jakarta, Indonesia
4.3. Australia Neonates
4.4. Extraction and Detection of HCMV DNA
4.5. Targeted Whole Gene Amplification
4.6. Preparation of Ion Ampliseq™ DNA Libraries
4.7. Libraries Were Sequenced Using an Ion Proton Sequencer
4.8. Immunological Assessments of HCMV
4.9. Assessment of Vascular Pathology
4.10. Data Analysis
4.11. Statistical Analyses
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Residue Position | Toledo Reference | Neonates n = 4 | Adults n = 55 | Australian n = 28 | Indonesian n = 27 | Buffy Coat n = 31 | Saliva n = 24 |
---|---|---|---|---|---|---|---|
9 | S | S | S/T | S/T | S/T | S/T | S/T |
16 | F | F | F/L | F/L | F | F/L | F/L |
30 | I | I/T/M | I/T/M | I/T/M | I | I/T/M | I/T/M |
41 | D | D | D/N | D/N | D | D/N | D/N |
73 | S | S/Y | S/Y | S/Y | S/Y | S/Y | S/Y |
83 | P | P | P/L | P/L | P/L | P/L | P/L |
99 | G | G | G/V | G/V | G/V | G/V | G/V |
109 | H | H | H/Y | H/Y | H/Y | H/Y | H/Y |
114 | K | E | K/E | E/K | E/K | K/E | K/E |
122 | P | P/S | P/S | P/S | P/S | P/S | P/S |
123 | R | R | R/C | R/C | R/C | R/C | R/C |
126 | P | P | P/T/S | P/T/S | P/T | P/T/S | P/S/T |
127 | R | R | R/G | R/G | R/G | R/G | R/G |
128 | L | L | L/Q/V | L/Q/V | L/Q/V | L/Q/V | L/Q/V |
129 | S | S | S/F/A/C | S/F/A/C | S/F/A/C | S/F/A/C | S/F/A/C |
130 | R | R | R/L/G | R/L/G | R/L/G | R/L/G | R/L/G |
131 | T | T | T/A/S/P | T/A/S/P | T/A/S/P | T/A/S/P | T/A/S/P |
132 | Q | Q/* | Q/* | Q/* | Q/* | Q/* | Q/* |
147 | Q | Q | Q/* | Q/* | Q/* | Q/* | Q/* |
153 | R | R | R/C | R/C | R/C | R/C | R/C |
163 | A | A | A/T | A/T | A/T | A/T | A/T |
170 | * | * | */Q | */Q | */Q | */Q | */Q |
174 | L | L/F | L/F | L/F/W | L/F/W | L/F/W | L/F/W |
180 | Q | Q | Q/H/L/R | Q/H/R | Q/H/L/R | Q/H/L/R | Q/H/R |
181 | P | P | P/L/T | P/L/T | P/L/T | P/L/T | P/L/T |
182 | L | L | L/V/Q | L/V/Q | L/V/Q | L/V/Q | L/V/Q |
183 | L | L | L/F/S | L/F | L/F/S | L/F/S | L/F |
184 | G | G | G/V | G/V | G/V | G/V | G/V |
185 | C | C | C/G/S/F | C/S/F | C/G/S/F | C/G/S/F | C/S/F |
186 | G | G | G/P/R | G | G/P/R | G/P/R | G |
189 | S | S | S/T | S | S/T | S/T | S |
214 | D | D | D/N | D | D/N | D/N | D |
Position Toledo Variant | 9 | 16 | 41 | 73 | 83 | 99 | 109 | 114 | 122 | 123 | 127 | 153 | 170 | 174 | 184 | 189 | 214 | Indo (n = 27) | Aus (n = 28) | p a |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
S | F | D | S | P | G | H | K | P | R | R | R | * | L | G | S | D | ||||
T | L | N | Y | L | V | Y | E | S | C | G | C | Q | F/W | V | T | N | ||||
Haplotypes | ||||||||||||||||||||
UL111a-1 | S | F | D | S | P | G | H | E | P | R | R | R | * | L | G | S | D | 12 | 12 | 0.99 |
UL111a-2 | S | F | D | S | L | G | H | E | P | R | R | R | * | L | G | S | D | 14 | 5 | 0.01 |
UL111a-3 | S | F | D | S | P | G | H | E | P | R | R | R | * | F/W | G | S | D | 3 | 3 | 0.99 |
UL111a-4 | S | F | D | Y | P | G | H | E | P | R | R | R | * | L | G | S | D | 2 | 3 | 0.99 |
UL111a-5 | S | F | D | S | P | G | H | E | S | R | R | R | * | L | G | S | D | 1 | 0 | 0.49 |
UL111a-6 | S | F | D | S | L | V | H | E | P | R | R | R | * | L | G | S | D | 1 | 1 | 0.99 |
UL111a-7 | S | F | N | Y | P | G | H | E | P | R | R | R | * | L | G | S | D | 0 | 5 | 0.05 |
UL111a-8 | S | F | D | S | P | G | H | E | S | R | R | C | * | L | G | S | D | 0 | 3 | 0.24 |
UL111a-9 | S | F | D | S | L | G | H | E | P | R | R | R | Q | L | G | S | D | 2 | 0 | 0.24 |
UL111a-10 | S | L | D | S | P | G | H | E | S | R | R | C | * | L | G | S | D | 0 | 2 | 0.49 |
UL111a-11 | S | F | D | S | P | G | Y | E | S | R | R | C | * | L | G | S | D | 1 | 1 | 0.99 |
UL111a-12 | S | F | D | S | L | G | Y | E | P | R | R | R | * | L | G | S | D | 1 | 1 | 0.99 |
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Waters, S.; Lee, S.; Ariyanto, I.; Kresoje, N.; Leary, S.; Munyard, K.; Gaudieri, S.; Irish, A.; Keil, A.D.; Allcock, R.J.N.; et al. Sequencing of the Viral UL111a Gene Directly from Clinical Specimens Reveals Variants of HCMV-Encoded IL-10 That Are Associated with Altered Immune Responses to HCMV. Int. J. Mol. Sci. 2022, 23, 4644. https://doi.org/10.3390/ijms23094644
Waters S, Lee S, Ariyanto I, Kresoje N, Leary S, Munyard K, Gaudieri S, Irish A, Keil AD, Allcock RJN, et al. Sequencing of the Viral UL111a Gene Directly from Clinical Specimens Reveals Variants of HCMV-Encoded IL-10 That Are Associated with Altered Immune Responses to HCMV. International Journal of Molecular Sciences. 2022; 23(9):4644. https://doi.org/10.3390/ijms23094644
Chicago/Turabian StyleWaters, Shelley, Silvia Lee, Ibnu Ariyanto, Nina Kresoje, Shay Leary, Kylie Munyard, Silvana Gaudieri, Ashley Irish, Anthony D. Keil, Richard J. N. Allcock, and et al. 2022. "Sequencing of the Viral UL111a Gene Directly from Clinical Specimens Reveals Variants of HCMV-Encoded IL-10 That Are Associated with Altered Immune Responses to HCMV" International Journal of Molecular Sciences 23, no. 9: 4644. https://doi.org/10.3390/ijms23094644
APA StyleWaters, S., Lee, S., Ariyanto, I., Kresoje, N., Leary, S., Munyard, K., Gaudieri, S., Irish, A., Keil, A. D., Allcock, R. J. N., & Price, P. (2022). Sequencing of the Viral UL111a Gene Directly from Clinical Specimens Reveals Variants of HCMV-Encoded IL-10 That Are Associated with Altered Immune Responses to HCMV. International Journal of Molecular Sciences, 23(9), 4644. https://doi.org/10.3390/ijms23094644