Rotavirus A Infection Prevalence and Spatio-Temporal Genotype Shift among Under-Five Children in Amhara National Regional State, Ethiopia: A Multi-Center Cross-Sectional Study
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design and Settings
2.2. Sociodemographic and Clinical Data Collection
2.3. Nutritional Assessment and Clinical Severity Scorning of Diarrhea
2.4. Sample Collection, Transport, and Storage
2.5. RNA Extraction and RVA Detection
2.6. RNA Shipment for Genotyping and Sequencing
2.7. VP7 (G) and VP4 (P) Based Genotyping PCR
2.8. Gel Electrophoresis and Sequencing
2.9. Genotyping and Phylogenetic Analysis
2.10. VP7 and VP4 Protein Modeling
2.11. Statistical Analysis
3. Results
3.1. Sociodemographic and Clinical Characteristics
3.2. Rotavirus A Prevalence
3.3. Genotypic Distribution of RVAs
3.4. Phylogenetic Analysis of VP7 Gene of the Circulating RVA Strains
3.5. Phylogenetic Analysis of VP4 Gene of the Circulating RVA Strains
3.6. Comparison of the VP7 Antigenic Epitopes with Vaccine Strains
3.7. Comparison of VP4 Antigenic Epitopes with Vaccine Strains
4. Discussion
5. Conclusions and Recommendation
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Variables | Frequency (%) |
---|---|
Age in months (mean ± SD) 26.4 ± 15.2 range 2–59 MO | |
Sex | |
Male | 308 (57.4) |
Female | 229 (42.6) |
Residence | |
Urban | 494 (92) |
Rural | 43 (8.0) |
Immunization | |
Yes | 524 (97.6) |
No | 13 (2.4) |
Admission status | |
Yes | 41 (7.6) |
No | 496 (92.4) |
Vomiting | |
Yes | 233 (43.4) |
No | 304 (56.6) |
Child’s thirst status | |
Drink normally | 366 (68.2) |
Thirsty/drink eagerly | 152 (28.3) |
Drink poorly/not able to drink | 13 (2.4) |
N/A | 6 (1.1) |
Sunken eyes | |
Yes | 83 (15.5) |
No | 454 (84.5) |
Irritable/restless | |
Yes | 133 (24.8) |
No | 404 (75.2) |
Lethargic | |
Yes | 108 (20.1) |
No | 429 (79.9) |
Mental status of the child | |
Normal | 528 (98.3) |
Altered | 9 (1.7) |
Fever | |
Yes | 182 (33.9) |
No | 355 (66.1) |
Dehydration status | |
No dehydration | 496 (92.2) |
Some dehydration | 40 (7.4) |
Severe dehydration | 1 (0.2) |
Given IV fluid | |
Yes | 57 (10.6) |
No | 480 (89.4) |
Vesikari clinical severity | |
Mild | 198 (36.9) |
Moderate | 257 (47.9) |
Severe | 82 (15.2) |
Variables | RVA | ||
---|---|---|---|
Positive (%) | Negative (%) | p-Value | |
Study locations | |||
Gondar | 44 (16.9) | 217 (83.1) | 0.001 |
Bahir Dar | 41 (29.3) | 99 (70.7) | |
Debre Markos | 9 (6.6) | 127 (93.4) | |
Age (in months) | |||
0–11 | 17 (19.8) | 69 (80.2) | 0.04 |
12–23 | 46 (23.8) | 147 (76.2) | |
24–59 | 31 (12.0) | 227 (88.0) | |
Vomiting | |||
Yes | 54 (23.2) | 179 (76.8) | 0.002 |
No | 30 (13.2) | 263 (86.8) | |
Sunken eyes | |||
Yes | 22 (26.5) | 61 (73.5) | 0.019 |
No | 72 (15.9) | 382 (84.1) | |
IV fluid given | |||
Yes | 16 (28.1) | 41 (71.9) | 0.026 |
No | 78 (16.2) | 402 (83.8) | |
Vesikari clinical severity | |||
Mild | 23 (11.6) | 175 (88.4) | 0.006 |
Moderate | 49 (19.1) | 208 (80.9) | |
Severe | 22 (26.8) | 60 (73.2) | |
Stunting (HFA) | |||
Normal | 63 (16.8) | 313 (83.2) | 0.329 |
Moderately stunted | 14 (15.9) | 74 (84.1) | |
Severely stunted | 15 (24.2) | 47 (75.8) | |
Weight (WFA) | |||
Normal | 75 (16.8) | 372 (83.2) | 0.005 |
Moderately underweight | 10 (15.4) | 55 (84.6) | |
Severely underweight | 7 (50) | 7 (50) | |
Wasting (WFH) | |||
Normal | 75 (16.6) | 376 (83.4) | 0.007 |
Moderately wasted | 8 (14.8) | 46 (85.2) | |
Severely wasted | 9 (42.9) | 12 (57.1) |
G/P Combinations | Isolates (n = 67) | Proportion (%) |
---|---|---|
G1P[6] | 1 | 1.5 |
G1P[8] | 13 | 19.4 |
G2P[4] | 5 | 7.5 |
G3P[8] | 22 | 32.8 |
G9P[4] | 5 | 7.5 |
G9P[6] | 1 | 1.5 |
G12P[6] | 19 | 28.4 |
G12P[8] | 1 | 3 |
Total | 67 | 100 |
Strain (No. of Sequences) | Lineage | Epitope 7-1a | Epitope 7-1b | Epitope 7-2 | ||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
87 | 91 | 94 | 96 | 97 | 98 | 99 | 100 | 104 | 123 | 125 | 129 | 130 | 291 | 201 | 211 | 212 | 213 | 238 | 242 | 143 | 145 | 146 | 147 | 148 | 190 | 217 | 221 | 264 | ||
Rotarix/A41CB052A/G1P[8] | II | T | T | N | G | E | W | K | D | Q | S | V | V | D | K | Q | N | V | D | N | T | K | D | Q | N | L | S | M | N | G |
RotaTeq/W179-9/G1P7[5] | III | T | T | N | G | D | W | K | D | Q | S | V | V | D | K | Q | N | V | D | N | T | K | D | Q | S | L | S | M | N | G |
GR36/2021/G1P8 (12) | II | T | T | N | G | E | W | K | D | Q | S | V | V | D | K | Q | N | V | D | N | T | K | D | Q | N | L | S | M | N | G |
BD44/2021/G1P6 (1) | II | T | T | N | G | E | W | K | D | Q | S | V | V | D | K | Q | N | V | D | N | T | K | D | Q | N | L | S | M | N | G |
RotaTeq/SC2-9/G2P7[5] | II | A | N | S | D | E | W | E | N | Q | D | T | M | N | K | Q | D | T | M | N | K | Q | D | V | S | N | S | R | D | N |
GR13/2021/G2P4 (5) | IV | T | N | S | N | E | W | E | N | Q | D | T | M | N | K | Q | D | V | D | N | N | R | D | N | T | S | D | I | S | G |
RotaTeq/wi78-8/G3P7[5] | II | T | T | N | N | S | W | K | D | Q | D | A | V | D | K | Q | D | A | N | K | D | K | D | A | T | L | S | E | A | G |
GR03/2021/G3P8 (11) | I | T | N | N | N | S | W | K | D | Q | D | A | V | D | K | Q | D | T | N | N | N | K | D | A | T | L | S | E | A | G |
GR10/2021/G3P8 (1) | I | T | N | D | N | S | W | K | D | Q | D | A | V | D | K | Q | D | T | N | N | N | K | D | A | T | L | S | E | A | G |
BD34/2021/G3P8 (12) | I | T | T | N | N | S | W | K | D | Q | D | A | V | D | K | Q | D | T | N | N | N | K | D | A | T | L | S | E | D | G |
DM01/2021/G9P4 (5) | I | T | T | G | T | E | W | K | D | Q | D | A | I | D | K | Q | N | T | A | D | N | K | D | S | T | L | S | E | S | G |
DM31/2021/G9P6 (1) | I | T | T | G | T | E | W | K | D | Q | D | A | I | D | K | Q | N | T | A | D | N | K | D | S | T | L | S | E | S | G |
RotaTeq/Br-B-9/G4P7[5] | II | S | T | S | T | E | W | K | D | Q | N | L | I | D | K | Q | D | T | A | D | T | R | A | S | G | E | S | T | S | G |
RotaTeq/WI79-4/G6P1A[8] | - | V | N | A | T | E | W | K | D | Q | D | A | V | E | K | Q | N | P | D | N | A | K | D | S | T | Q | S | T | T | G |
BD33/2021/G12P6 (18) | S | T | T | P | D | W | T | N | Q | D | S | V | D | K | Q | D | V | T | N | N | Q | Q | N | S | L | S | E | A | G | |
BD49/2021/G12P8 (1) | S | T | T | P | D | W | T | N | Q | D | S | V | D | K | Q | D | V | T | N | N | Q | Q | N | S | L | S | E | A | G | |
BD104/2022/G12P6 (1) | S | T | T | P | D | W | T | S | Q | D | S | V | D | E | Q | D | V | T | N | N | Q | Q | N | S | L | S | E | A | G |
Strain (No. of Sequences) | Lineage | Epitope 8-1 | Epitope 8-2 | Epitope 8-3 | Epitope 8-4 | |||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
100 | 146 | 148 | 150 | 188 | 190 | 192 | 193 | 194 | 195 | 196 | 180 | 183 | 113 | 114 | 115 | 116 | 125 | 131 | 132 | 133 | 135 | 86 | 87 | 88 | 89 | 90 | ||
Rotarix/A41CB52A/G1P[8] | I | D | S | Q | E | S | T | N | L | N | N | I | T | A | N | P | V | D | S | S | N | D | N | S | N | T | N | G |
RotaTeq/WI79-4/G6P1A[8] | II | D | S | Q | E | S | T | N | L | N | D | I | T | A | N | P | V | D | N | R | N | D | D | S | N | T | N | G |
GR03/2021/G3P8 (12) | III | D | S | Q | D | S | T | N | L | D | G | I | T | A | N | P | V | D | N | N | N | D | D | S | N | T | N | G |
BD34/2021/G3P8 (9) | III | D | S | Q | D | S | T | N | L | N | G | I | T | A | N | P | V | D | N | N | N | D | D | S | N | T | N | G |
BD63/2021/G3P8 (1) | III | D | S | Q | D | S | T | N | L | N | G | I | T | A | N | P | V | D | N | R | N | D | D | S | N | T | N | G |
GR36/2021/G1P8 (1) | IV | D | S | Q | E | S | T | N | L | T | S | I | T | A | N | P | V | D | S | S | N | D | N | S | N | T | N | G |
GR38/2021/G1P8 (10) | IV | D | S | Q | E | S | T | D | L | T | S | I | T | A | D | P | V | D | S | S | N | D | N | S | N | T | N | G |
BD49/2021/G12P8 (1) | IV | D | S | Q | E | S | T | D | L | T | S | I | T | A | D | P | V | D | S | S | N | D | N | S | N | T | N | G |
RotaTeq-WI79-9/G1P7[5] | G | T | I | G | R | I | T | N | Y | A | S | E | N | T | S | E | T | S | S | N | A | D | P | T | G | P | G | |
BD33/2021/G12P6 (19) | - | D | N | N | E | S | T | N | L | S | E | V | T | A | T | N | Q | S | V | E | N | N | N | P | T | N | Q | Q |
DM31/2021/G9P6 (1) | - | D | N | N | E | S | T | N | L | S | E | V | T | A | T | N | Q | S | V | E | N | N | N | P | T | N | Q | Q |
BD44/2021/G1P6 (1) | - | D | N | N | E | S | T | N | L | S | E | V | T | A | T | N | Q | S | V | E | N | N | N | P | T | N | Q | Q |
GR13/2021/G2P4 (5) | - | D | S | Q | D | S | T | D | L | N | N | I | T | A | S | Q | T | N | N | E | N | S | D | S | N | T | D | G |
DM01/2021/G9P4 (5) | - | D | S | Q | D | S | T | D | L | N | N | I | T | A | S | Q | T | N | N | E | N | S | D | S | N | T | D | G |
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Damtie, D.; Gelaw, A.; Wondimeneh, Y.; Aleka, Y.; Kick, M.K.; Tigabu, Z.; Sack, U.; Mekuria, Z.H.; Vlasova, A.N.; Tessema, B. Rotavirus A Infection Prevalence and Spatio-Temporal Genotype Shift among Under-Five Children in Amhara National Regional State, Ethiopia: A Multi-Center Cross-Sectional Study. Vaccines 2024, 12, 866. https://doi.org/10.3390/vaccines12080866
Damtie D, Gelaw A, Wondimeneh Y, Aleka Y, Kick MK, Tigabu Z, Sack U, Mekuria ZH, Vlasova AN, Tessema B. Rotavirus A Infection Prevalence and Spatio-Temporal Genotype Shift among Under-Five Children in Amhara National Regional State, Ethiopia: A Multi-Center Cross-Sectional Study. Vaccines. 2024; 12(8):866. https://doi.org/10.3390/vaccines12080866
Chicago/Turabian StyleDamtie, Debasu, Aschalew Gelaw, Yitayih Wondimeneh, Yetemwork Aleka, Maryssa K. Kick, Zemene Tigabu, Ulrich Sack, Zelalem H. Mekuria, Anastasia N. Vlasova, and Belay Tessema. 2024. "Rotavirus A Infection Prevalence and Spatio-Temporal Genotype Shift among Under-Five Children in Amhara National Regional State, Ethiopia: A Multi-Center Cross-Sectional Study" Vaccines 12, no. 8: 866. https://doi.org/10.3390/vaccines12080866