Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015–2019
Abstract
:1. Introduction
2. Results
2.1. Sample Demographics
2.2. Detection of Viral Pathogens
2.3. Detection of Wild-Type Rotavirus
2.4. Seasonal Variation of Wild-Type Rotavirus
2.5. Detection of Vaccine-Derived Rotavirus (Rotarix)
2.6. Distribution of Genotypes in Ireland
2.7. Comparison of the Genotype Diversity Pre- and Post-Vaccine
2.8. Detection of Human and Equine-Like Rotavirus G3
2.9. Genotypes Detected in Rotavirus Positive Samples from Those of Vaccine-Eligible Age
3. Discussion
4. Materials and Methods
4.1. Study Design
4.2. Annual Birth Cohort in Ireland
4.3. Data Analysis
4.4. Sampling Strategy for Genotyping and Sequencing of Samples
4.5. Seasonality
4.6. Vaccine Eligibility
4.7. Laboratory Methods
4.8. GenBank Accession Numbers
4.9. Statistical Analysis
4.10. Ethical Statement
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Results (%) by Year | Total | |||||
---|---|---|---|---|---|---|
Virus Detected | 2015 | 2016 | 2017 | 2018 | 2019 | |
Rotavirus-wild-type | 662 (15.03) | 519 (13.09) | 250 (15.49) | 53 (4.42) | 70 (5.93) | 1554 |
Rotavirus-Rotarix | 0 (0.00) | 1 (0.03) | 61 (3.78) | 49 (4.08) | 69 (5.84) | 180 |
Norovirus | 482 (10.94) | 492 (12.41) | 210 (13.01) | 158 (13.17) | 141 (11.94) | 1483 |
Adenovirus F | 156 (3.54) | 155 (3.91) | 101 (6.26) | 64 (5.33) | 47 (3.98) | 523 |
Sapovirus | 202 (4.59) | 167 (4.21) | 85 (5.27) | 72 (6.00) | 33 (2.79) | 559 |
Astrovirus | 197 (4.47) | 121 (3.05) | 77 (4.77) | 68 (5.67) | 53 (4.49) | 516 |
No virus detected | 2705 (61.42) | 2511 (63.31) | 830 (51.43) | 736 (61.33) | 768 (65.03) | 7550 |
Total samples tested | 4199 | 3787 | 1499 | 1159 | 1156 | |
Total results | 4404 a | 3966 b | 1614 c | 1200 d | 1181 e |
Year | Number of Wild-Type Rotavirus Positive Samples/Total Number of Samples Tested (%) | Median Age (IQR) | |||||||
---|---|---|---|---|---|---|---|---|---|
0–1 Year | 1–2 Years | 2–3 Years | 3–4 Years | 4–5 Years | 5–6 Years | Total | |||
Pre-vaccine | 2015 | 285/2280 (12.5) | 227/899 (25.3) | 90/413 (21.8) | 35/213 (16.4) | 17/213 (8.0) | 8/181 (4.4) | 662/4199 (15.8) | 1.17 (0.5-1.9) |
2016 | 200/2065 (9.7) | 217/792 (27.4) | 55/427 (12.9) | 24/224 (10.7) | 11/136 (8.1) | 12/143 (8.4) | 519/3787 (13.7) | 1.22 (0.8-1.8) | |
Post-vaccine | 2017 | 57/760 (7.5) | 110/374 (29.4) | 49/144 (34.0) | 19/105 (18.1) | 6/55 (10.9) | 9/61 (14.8) | 250/1499 (16.7) | 1.59 (1.0–2.4) |
2018 | 8/587 (1.4) | 12/272 (4.4) | 23/125 (18.4) | 2/62 (3.2) | 3/59 (5.1) | 5/54 (9.2) | 53/1159 (4.6) | 2.24 (1.6–2.9) | |
2019 | 4/608 (0.7) | 16/233 (6.9) | 16/129 (12.4) | 21/86 (24.4) | 6/58 (10.3) | 7/42 (16.7) | 70/1156 (6.1) | 2.90 (1.9–3.5) |
Age | ||||||
---|---|---|---|---|---|---|
2 mts | 3 mts | 4 mts | 5 mts | 6 mts | 7 mts | |
Rotarix detected/total number Rotarix detected (%) | 99/180 (55.0) | 41/180 (22.8) | 26/180 (14.4) | 11/180 (6.1) | 2/180 (1.1) | 1/180 (0.6) |
Pre-Vaccinen (%) | Post-Vaccinen (%) | Pre-Vaccine Data Combined | Post-Vaccine Data Combined | Pre vs. Post | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Genotype | 2015 | 2016 | 2017 | 2018 | 2019 | n (%) | CI 95% | n (%) | CI 95% | p = |
G1P[8] | 125 (42.7) | 172 (71.1) | 70 (51.9) | 7 (14.6) | 3 (4.4) | 297 (55.5) | 51.3–59.7 | 80 (31.9) | 26.4–37.9 | <0.0001 |
G2P[4] | 6 (2.0) | 16 (6.6) | 15 (11.1) | 7 (14.6) | 27 (39.7) | 22 (4.1) | 2.7–6.2 | 49 (19.5) | 15.1–24.9 | <0.0001 |
G3P[8] | 10 (3.4) | 9 (3.7) | 17 (12.6) | 7 (14.6) | 16 (23.5) | 19 (3.6) | 2.3–5.5 | 40 (15.9) | 11.9–21.0 | <0.0001 |
G4P[8] | 64 (21.8) | 0 (0.0) | 6 (4.4) | 11 (23.0) | 0 (0.0) | 64 (12.0) | 9.5–15.0 | 17 (6.8) | 4.3–10.6 | 0.0257 |
G9P[8] | 69 (23.5) | 34 (14.1) | 20 (14.8) | 10 (20.9) | 4 (5.9) | 103 (19.3) | 16.1–22.8 | 34 (13.6) | 9.9–18.3 | 0.0493 |
G12P[8] | 3 (1.0) | 4 (1.7) | 0 (0.0) | 1 (2.1) | 5 (7.4) | 7 (1.3) | 0.1–2.7 | 6 (2.4) | 1.1–5.1 | 0.2675 |
Mixed | 7 (2.4) | 3 (1.2) | 1 (0.7) | 1 (2.1) | 4 (5.9) | 10 (1.9) | 1–3.4 | 6 (2.4) | 1.1–5.1 | 0.0014 |
Uncommon | 2 (0.7) | 2 (0.8) | 1 (0.7) | 1 (2.1) | 8 (11.8) | 4 (0.8) | 0.03–1.9 | 10 (4.0) | 2.2–7.2 | 0.6295 |
Untypable | 7 (2.4) | 2 (0.8) | 5 (3.7) | 3 (6.3) | 1 (1.5) | 9 (1.7) | 0.9–3.2 | 9 (3.6) | 1.9–6.7 | n/a |
Total | 293 (100) | 242 (100) | 135 (100) | 48 (100) | 68 (100) | 535 (100) | n/a | 251 (100) | n/a | n/a |
Genotype | Classification of Genotype | Number of Samples (%) |
---|---|---|
G1P[8] | Common | 5 (13.5) |
G2P[4] | Common | 11 (29.7) |
G3P[8] | Common | 6 (16.2) |
G4P[8] | Common | 1 (2.7) |
G9P[8] | Common | 4 (10.8) |
G12P[8] | Common | 3 (8.1) |
G3P[4] | Uncommon | 3 (8.1) |
G9P[4] | Uncommon | 1 (2.7) |
G1/3 P[8] | Mixed | 1 (2.7) |
G9/12 P[8] | Mixed | 1 (2.7) |
G9 P untypable | Untypable | 1 (2.7) |
Total | 37 (100) |
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Yandle, Z.; Coughlan, S.; Dean, J.; Tuite, G.; Conroy, A.; De Gascun, C.F. Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015–2019. Pathogens 2020, 9, 449. https://doi.org/10.3390/pathogens9060449
Yandle Z, Coughlan S, Dean J, Tuite G, Conroy A, De Gascun CF. Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015–2019. Pathogens. 2020; 9(6):449. https://doi.org/10.3390/pathogens9060449
Chicago/Turabian StyleYandle, Zoe, Suzie Coughlan, Jonathan Dean, Gráinne Tuite, Anne Conroy, and Cillian F. De Gascun. 2020. "Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015–2019" Pathogens 9, no. 6: 449. https://doi.org/10.3390/pathogens9060449
APA StyleYandle, Z., Coughlan, S., Dean, J., Tuite, G., Conroy, A., & De Gascun, C. F. (2020). Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015–2019. Pathogens, 9(6), 449. https://doi.org/10.3390/pathogens9060449