Background
Methods
Study sample
RNA extraction and cDNA synthesis
PCR Amplification of VP6, VP7 and VP4 genes
Gene | Primer (Polarity) | Sequence (5′–3′) | Position | Reference |
---|---|---|---|---|
VP7 | VP7 FP-1 BMJ-13 | 5′-GGC ATT TAA AAA AGA AGA AGC TG-3′ 5′-AGC CAC ATG ATC TTG TTT -3′ | 1–23 | Jiang et al.,1995 |
1063–1046 | ||||
BMJ-107 BMJ-13 | 5′ TGT TTG GAG ATG TGA TGA -3′ 5′-AGC CAC ATG ATC TTG TTT-3′ | 546–563 | Jiang et al.,1995 | |
1063–1046 | ||||
VP6 | VP6 FP-1 BMJ-44 | 5′- GCA TTT AAA ATC TCA TTC ACA A-3′ 5′-AGC CAC ATA GTT CAC ATT TCA-3′ | 2–22 | Jiang et al.,1995 |
1353–1333 | ||||
BMJ-145 BMJ-144 | 5′-AGT CCG TTC TAT GTG ATT C-3′ 5′-CCT TCT GGG GAT CAT CCA T-3′ | 1014–1032 | Jiang et al.,1995 | |
1331–1313 | ||||
VP4 | GCVP4-1FP GCVP4-12RP | 5′- GGC TTA AAA AAT AGA GAT CGA TGG CG -3′ 5′- CAT AAA CAA GTT GCA ACC TTG ATG -3′ | 1–26 | Yamamoto et al., 2011 |
1275–1252 | ||||
GCVP4-2FP GCVP4-12RP | 5′- GTA AGG ACT CAT TGT GGC AAG A -3′ 5′- CAT AAA CAA GTT GCA ACC TTG ATG -3′ | 843–820 | Yamamoto et al., 2011 | |
1275–1252 |
Statistical analysis
Results
Rotavirus detection
Phylogenetic and sequence analysis of VP6 gene
Strain | Human | Bovine | Porcine | Human/India | Study Samples | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Bristol | BCN9 | OH567 | Wu82 | BS347 | Jajeri | Toyama | RVC | V460 | V508 | ND-056 | ND-061 | ND-204 | ND-237 | ND-240 | ND-398 | |
Bristol | 92.10% | 96.90% | 92.10% | 96.90% | 92.40% | 79.00% | 79.30% | 92.40% | 92.10% | 99.00% | 99.00% | 98.70% | 99.00% | 98.70% | 98.70% | |
BCN9 | 97.80% | 92.70% | 97.60% | 93.20% | 98.50% | 84.80% | 84.20% | 99.10% | 98.80% | 96.70% | 96.70% | 97.70% | 96.70% | 97.70% | 97.70% | |
OH567 | 92.10% | 90.60% | 93.80% | 97.50% | 93.00% | 78.70% | 79.30% | 93.50% | 92.70% | 95.30% | 95.30% | 96.30% | 95.30% | 96.30% | 96.30% | |
Wu82 | 96.70% | 93.30% | 94.20% | 92.10% | 97.90% | 84.50% | 84.50% | 98.50% | 97.60% | 95.30% | 95.30% | 97.10% | 95.30% | 97.10% | 97.10% | |
BS347 | 91.10% | 90.50% | 93.00% | 97.60% | 93.00% | 79.80% | 79.80% | 93.50% | 93.20% | 96.90% | 96.90% | 96.90% | 96.90% | 96.90% | 96.90% | |
Jajeri | 92.60% | 95.20% | 90.40% | 94.20% | 92.50% | 84.80% | 84.80% | 98.80% | 98.50% | 98.60% | 98.60% | 99.70% | 98.60% | 99.70% | 99.70% | |
Toyama | 68.60% | 67.10% | 62.30% | 66.10% | 61.40% | 66.10% | 88.90% | 84.80% | 85.10% | 77.00% | 77.00% | 78.70% | 77.00% | 78.70% | 78.70% | |
RVC | 66.60% | 67.10% | 60.40% | 64.20% | 61.40% | 66.10% | 88.00% | 84.80% | 83.90% | 77.00% | 77.00% | 78.70% | 77.00% | 78.70% | 78.70% | |
V460 | 95.30% | 94.80% | 95.30% | 92.90% | 91.10% | 95.30% | 64.80% | 64.80% | 99.10% | 90.90% | 90.90% | 93.00% | 90.90% | 93.00% | 93.00% | |
V508 | 96.20% | 92.00% | 96.20% | 91.60% | 95.80% | 93.50% | 63.50% | 61.60% | 92.90% | 90.60% | 90.60% | 92.70% | 90.60% | 92.70% | 92.70% | |
ND-056 | 96.20% | 95.10% | 96.00% | 95.70% | 96.20% | 97.60% | 67.60% | 66.60% | 96.40% | 95.10% | 100.00% | 98.60% | 100.00% | 98.60% | 98.60% | |
ND-061 | 96.20% | 95.10% | 96.00% | 95.70% | 96.20% | 97.60% | 67.60% | 66.60% | 96.40% | 95.10% | 100.00% | 98.60% | 100.00% | 98.60% | 98.60% | |
ND-204 | 95.40% | 93.20% | 93.20% | 95.30% | 92.10% | 96.40% | 61.40% | 60.20% | 95.20% | 96.60% | 97.20% | 97.20% | 97.20% | 100.00% | 100.00% | |
ND-237 | 96.20% | 95.10% | 96.00% | 95.70% | 96.20% | 97.60% | 67.60% | 66.60% | 96.40% | 95.10% | 100.00% | 100.00% | 98.60% | 98.60% | 97.20% | |
ND-240 | 95.40% | 93.20% | 93.20% | 95.30% | 92.10% | 96.40% | 61.40% | 60.20% | 95.20% | 96.60% | 97.20% | 97.20% | 100.00% | 97.20% | 100.00% | |
ND-398 | 95.40% | 93.20% | 93.20% | 95.30% | 92.10% | 96.40% | 61.40% | 60.20% | 95.20% | 96.60% | 97.20% | 97.20% | 100.00% | 97.20% | 100.00% |
Phylogenetic and sequence analysis of VP7 gene
Strain | Human | Porcine | Bovine | Human/India | Study Samples | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Bristol | BCN9 | OH567 | Wu82 | BS347 | C13 | S-1 | Cowden | Shintoku | V460 | V508 | ND-061 | ND-240 | ND-237 | |
Bristol | 96.70% | 98.20% | 98.20% | 96.70% | 96.30% | 98.20% | 75.10% | 79.00% | 96.70% | 96.70% | 97.10% | 98.40% | 97.10% | |
BCN9 | 90.70% | 95.30% | 95.30% | 97.30% | 96.90% | 95.30% | 74.20% | 78.60% | 97.60% | 97.60% | 97.70% | 98.90% | 97.70% | |
OH567 | 95.00% | 95.80% | 100.00% | 95.70% | 95.30% | 98.80% | 75.50% | 79.40% | 95.70% | 96.10% | 96.20% | 97.40% | 96.20% | |
Wu82 | 95.00% | 93.80% | 100.00% | 95.70% | 95.30% | 98.80% | 75.50% | 79.40% | 95.70% | 96.10% | 96.20% | 97.00% | 96.20% | |
BS347 | 91.90% | 93.80% | 91.50% | 93.30% | 99.60% | 96.10% | 75.00% | 78.40% | 99.20% | 98.40% | 98.40% | 98.60% | 98.40% | |
C13 | 90.70% | 92.60% | 93.30% | 91.50% | 98.70% | 95.70% | 74.60% | 78.00% | 98.80% | 98.00% | 98.00% | 98.20% | 98.00% | |
S-1 | 95.00% | 95.80% | 96.20% | 96.20% | 90.70% | 94.50% | 75.70% | 79.80% | 96.10% | 96.10% | 99.20% | 94.80% | 99.20% | |
Cowden | 70.70% | 73.80% | 78.20% | 78.20% | 76.70% | 75.10% | 76.50% | 79.40% | 75.10% | 75.10% | 73.00% | 74.10% | 73.00% | |
Shintoku | 71.30% | 74.40% | 70.00% | 79.10% | 76.90% | 75.70% | 70.00% | 76.90% | 78.80% | 78.20% | 77.80% | 78.40% | 77.80% | |
V460 | 94.80% | 92.50% | 95.40% | 95.40% | 94.40% | 94.00% | 96.00% | 75.00% | 75.40% | 98.80% | 97.60% | 97.80% | 97.60% | |
V508 | 95.10% | 97.50% | 96.70% | 95.70% | 97.10% | 97.80% | 98.30% | 77.10% | 76.70% | 98.70% | 96.90% | 97.10% | 96.90% | |
ND-061 | 95.50% | 97.40% | 96.40% | 96.40% | 96.90% | 95.70% | 97.60% | 75.60% | 73.80% | 92.50% | 90.90% | 98.20% | 100.00% | |
ND-240 | 98.80% | 97.70% | 95.70% | 95.80% | 95.10% | 96.20% | 97.00% | 75.00% | 73.20% | 97.90% | 96.50% | 96.20% | 98.20% | |
ND-237 | 95.50% | 97.40% | 96.40% | 96.40% | 96.90% | 95.70% | 97.60% | 75.60% | 73.80% | 92.50% | 90.90% | 100.00% | 96.50% |
Phylogenetic and sequence analysis of VP4 gene
Strains | Human | Porcine | Bovine | Human/India | Study Samples | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Bristol | BCN9 | OH567 | Wu82 | BS347 | CAU 10–312 | Cowden | Shintoku | V460 | V508 | ND-061 | ND-240 | ND-237 | |
Bristol | 97.00% | 97.00% | 97.60% | 96.10% | 96.50% | 69.20% | 65.20% | 96.60% | 97.00% | 98.40% | 99.90% | 98.40% | |
BCN9 | 91.90% | 97.80% | 98.50% | 97.80% | 97.40% | 68.80% | 64.40% | 98.30% | 98.70% | 97.90% | 98.20% | 97.90% | |
OH567 | 91.90% | 94.60% | 99.30% | 97.00% | 97.00% | 69.00% | 65.00% | 97.40% | 98.20% | 98.20% | 98.40% | 98.20% | |
Wu82 | 93.20% | 95.90% | 98.60% | 97.60% | 97.60% | 69.20% | 65.00% | 98.00% | 98.50% | 97.70% | 98.90% | 97.70% | |
BS347 | 89.90% | 93.90% | 92.60% | 93.90% | 97.40% | 68.80% | 64.40% | 97.80% | 97.80% | 97.10% | 98.40% | 97.10% | |
CAU 10–312 | 91.20% | 92.60% | 92.60% | 93.90% | 93.20% | 69.20% | 65.20% | 97.80% | 97.40% | 98.70% | 99.50% | 98.70% | |
Cowden | 69.70% | 69.10% | 69.70% | 69.70% | 67.20% | 60.30% | 75.70% | 69.00% | 69.20% | 66.80% | 67.80% | 66.80% | |
Shintoku | 69.00% | 67.80% | 69.00% | 69.00% | 67.80% | 69.60% | 77.30% | 64.60% | 64.80% | 63.20% | 63.60% | 63.20% | |
V460 | 90.60% | 94.60% | 93.30% | 94.60% | 94.00% | 94.00% | 69.10% | 67.80% | 98.30% | 97.30% | 98.00% | 97.30% | |
V508 | 92.60% | 96.60% | 95.30% | 96.60% | 94.60% | 93.20% | 69.10% | 67.80% | 95.30% | 98.10% | 97.40% | 98.10% | |
ND-061 | 92.50% | 95.90% | 94.50% | 95.90% | 95.90% | 98.20% | 68.10% | 66.80% | 97.30% | 96.50% | 97.20% | 100.00% | |
ND-240 | 93.80% | 97.20% | 95.90% | 97.20% | 97.20% | 97.60% | 68.70% | 67.40% | 96.30% | 97.90% | 99.50% | 98.20% | |
ND-237 | 92.50% | 95.90% | 94.50% | 95.90% | 95.90% | 98.20% | 68.10% | 66.80% | 97.30% | 96.50% | 100.00% | 99.50% |
Human Strains | Bovine | Porcine | ||||
---|---|---|---|---|---|---|
Gene | Nucleotide | Amino acid | Nucleotide | Amino acid | Nucleotide | Amino acid |
VP4 | 96.10–100 | 89.90–100 | 63.20–65.20 | 66.80–69.60 | 66.80–69.20 | 60.30–69.70 |
VP6 | 90.60–100 | 90.40–100 | 77.0–85.80 | 61.40–68.60 | 77.0–84.80 | 60.20–67.10 |
VP7 | 94.10–100 | 91.50–100 | 77.8–79.4 | 70.0–79.1 | 83.80–85.50 | 70.70–78.20 |
Parameters | RVC negative | RVC positive | |
---|---|---|---|
patients (n = 344) | patients (n = 6) | ||
Gender (Male/Female) | 64.8% / 35.17% | 66.7% / 33.3% | |
Age (mean ± SD) (months) | 12.39 (±8.41) | 17 (±11.15) |
p (0.09) |
Days of Diarrhea (mean ± SD) | 2.85 ± 1.95 | 4.33 ± 2.94 |
p (0.06) |
Episodes (mean ± SD) | 16.08 ± 8.05 | 20.67 ± 10.72 |
p (0.16) |
Severe Dehydration | 72.20% | 100% | |
Days of vomiting (mean ± SD) | 1.95 ± 1.70 | 1 ± 1.26 |
p (0.17) |
Episodes/day (mean ± SD) | 5.26 ± 4.26 | 4.5 ± 5.92 |
p (0.67) |
Treatment (Oral/Intravenous) | 24.7% / 75.29% | 16.6% / 83.3% |