Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan
Abstract
:1. Introduction
2. Results
2.1. Sample Characteristics
2.2. Phylogenetic Analysis and Nucleotide (nt) Identities of Individual ORFs
2.3. Comparative Analysis of the ORF1
2.4. Comparative Analysis of the ORF2
2.5. Comparative Analysis of the ORF3
3. Discussion
4. Materials and Methods
4.1. Sample Selection and RNA Extraction
4.2. Next-Generation Sequencing (NGS)
4.3. Phylogenetic Analysis
4.4. Nucleotide Accession Number
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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ID | Place | Collection Date | Age (m) | NoV Genotype | Characteristics | Coinfection | GenBank Accession Number |
---|---|---|---|---|---|---|---|
12241 | Kyoto | 23 October 2013 | 14 | GII.P31-GII.4 | Epidemic | - | OR844370 |
12283 | Kyoto | 12 February 2014 | 16 | GII.P31-GII.4 | Epidemic | - | OR844371 |
12286 | Kyoto | 4 March 2014 | 7 | GII.P31-GII.4 | Epidemic | - | OR844372 |
14146 | Kyoto | 1 December 2015 | 18 | GII.P31-GII.4 | Epidemic | - | OR844373 |
14147 | Kyoto | 1 December 2015 | 23 | GII.P31-GII.4 | Epidemic | - | OR844374 |
14157 | Kyoto | 1 December 2015 | 18 | GII.P31-GII.4 | Epidemic | - | OR844375 |
14307 | Kyoto | 1 January 2016 | 22 | GII.P31-GII.4 | Epidemic | - | OR844376 |
14311 | Kyoto | 1 February 2016 | 10 | GII.P31-GII.4 | Epidemic | - | OR844377 |
17378 | Kyoto | 11 January 2019 | 21 | GII.P31-GII.4 | Non-epidemic | - | OR844378 |
18792 | Kyoto | 17 September 2021 | 27 | GII.P31-GII.4 | Epidemic | Ast1 | OR844379 |
18794 | Kyoto | 17 September 2021 | 26 | GII.P31-GII.4 | Epidemic | Ast1 | OR844380 |
18821 | Kyoto | 8 October 2021 | 20 | GII.P31-GII.4 | Epidemic | Ast1 | OR844381 |
18958 | Shizuoka | 27 January 2022 | 9 | GII.P31-GII.4 | Epidemic | Ast1 | OR844382 |
18968 | Shizuoka | 10 February 2022 | 40 | GII.P31-GII.4 | Epidemic | - | OR844383 |
Collection Year | ID/Collection Year | Nucleotide Identity | |||||
---|---|---|---|---|---|---|---|
ORF1 | ORF2 | ORF3 | |||||
JX459908 | AB972502 | JX459908 | AB972502 | JX459908 | AB972502 | ||
99.29 | 98.95 | 98.88 | |||||
12241/2013 | 98.98 | 99.65 | 99.01 | 99.69 | 98.63 | 99.75 | |
2013–2016 | 12283/2014 | 99.02 | 99.68 | 98.71 | 99.14 | 98.51 | 99.63 |
12286/2014 | 99.04 | 99.63 | 98.52 | 99.2 | 97.76 | 98.63 | |
14146/2015 | 98.8 | 99.39 | 98.15 | 98.83 | 98.13 | 99.25 | |
14147/2015 | 98.8 | 99.39 | 98.15 | 98.83 | 98.13 | 99.25 | |
14157/2015 | 98.82 | 99.49 | 98.34 | 99.01 | 98.38 | 99.5 | |
14307/2016 | 98.72 | 99.31 | 98.21 | 98.64 | 98.13 | 99.25 | |
14311/2016 | 98.74 | 99.33 | 97.97 | 98.64 | 98.13 | 99.25 | |
Average | 98.9 | 99.5 | 98.4 | 99.0 | 98.2 | 99.3 | |
17378/2019 | 97.62 | 98.07 | 96.79 | 97.47 | 95.9 | 97.01 | |
2019–2022 | 18792/2021 | 97.81 | 98.31 | 97.29 | 97.72 | 95.52 | 96.64 |
18794/2021 | 97.81 | 98.31 | 97.29 | 97.72 | 95.52 | 96.64 | |
18821/2021 | 97.77 | 98.27 | 97.23 | 97.66 | 95.65 | 96.77 | |
18958/2022 | 97.62 | 98.13 | 96.73 | 97.29 | 96.39 | 97.51 | |
18968/2022 | 97.72 | 98.27 | 96.61 | 97.16 | 96.89 | 98.01 | |
Average | 97.7 | 98.2 | 97.0 | 97.5 | 96.0 | 97.1 |
ORF1 | p48 | NTPase | p22 | Vpg | Pro | RdRp | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
29 | 50 | 67 | 84 | 90 | 118 | 161 | 286 | 389 | 429 | 433 | 497 | 711 | 761 | 763 | 774 | 779 | 783 | 784 | 788 | 842 | 845 | 847 | 850 | 875 | 961 | 1044 | 1045 | 1052 | 1315 | 1346 | 1368 | 1514 | 1522 | 1547 | 1647 | 1648 | 1653 | |
JX459908 | L | K | K | N | S | S | L | I | K | K | A | K | I | N | S | S | K | A | I | N | K | V | D | E | T | K | S | A | P | M | S | K | V | I | K | K | I | I |
12241/Kyoto/Oct/2013–2014 | F | R | G | T | S | R | G | N | R | |||||||||||||||||||||||||||||
12283/Kyoto/Feb/2013–2014 | F | R | G | T | G | N | ||||||||||||||||||||||||||||||||
12286/Kyoto/Mar/2013–2014 | R | R | S | G | T | G | N | |||||||||||||||||||||||||||||||
14146/Kyoto/Dec/2015–2016 | F | R | G | R | T | A | G | K | N | |||||||||||||||||||||||||||||
14147/Kyoto/Dec/2015–2016 | F | R | G | R | T | A | G | K | N | |||||||||||||||||||||||||||||
14157/Kyoto/Dec/2015–2016 | F | I | R | G | V | T | A | D | G | N | I | |||||||||||||||||||||||||||
14307/Kyoto/Jan/2015–2016 | F | R | G | R | T | A | G | T | K | N | ||||||||||||||||||||||||||||
14311/Kyoto/Feb/2015–2016 | F | E | R | G | R | T | A | G | K | N | ||||||||||||||||||||||||||||
17378/Kyoto/Jan/2018–2019 | F | E | N | F | T | R | G | T | R | G | N | V | R | |||||||||||||||||||||||||
18792/Kyoto/Sep/2021–2022 | F | F | R | V | G | N | T | G | N | R | R | V | V | |||||||||||||||||||||||||
18794/Kyoto/Sep/2021–2022 | F | F | R | V | G | N | T | G | N | R | R | V | V | |||||||||||||||||||||||||
18821/Kyoto/Oct/2021–2022 | F | F | R | V | G | N | T | G | V | N | R | R | V | V | ||||||||||||||||||||||||
18958/Shizuoka/Jan/2021–2022 | F | N | V | R | T | R | G | T | N | G | N | R | ||||||||||||||||||||||||||
AB972502/Niigata/JP/2011 | F | R | G | T | G | N | ||||||||||||||||||||||||||||||||
KM272334/KR/2012 | F | R | G | T | S | G | N | |||||||||||||||||||||||||||||||
KT202795/CHN/2014 | F | R | G | T | G | N | ||||||||||||||||||||||||||||||||
MH702269/Hu/Bhutan/2012 | F | R | G | T | G | N | ||||||||||||||||||||||||||||||||
MF140672/Hu/NL/2013 | F | A | R | G | T | G | N | |||||||||||||||||||||||||||||||
MN897754/Hu/US/2018 | F | N | R | G | T | G | N |
ORF2 | NTA | S | P1 | P2 | P1 | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8 | 9 | 17 | 98 | 119 | 231 | 244 | 285 | 297 | 309 | 310 | 333 | 340 | 372 | 373 | 377 | 378 | 393 | 395 | 407 | 414 | 460 | 534 | 540 | |
JX459908 | A | N | N | G | V | V | I | T | R | N | D | V | T | D | R | A | N | G | T | S | H | Y | T | V |
12241/Kyoto/Oct/2013–2014 | S | N | S | A | P | L | ||||||||||||||||||
12283/Kyoto/Feb/2013–2014 | N | H | S | P | L | |||||||||||||||||||
12286/Kyoto/Mar/2013–2014 | S | H | S | N | H | T | S | P | L | |||||||||||||||
14146/Kyoto/Dec/2015–2016 | S | N | M | A | H | S | P | L | ||||||||||||||||
14147/Kyoto/Dec/2015–2016 | S | N | M | A | H | S | P | L | ||||||||||||||||
14157/Kyoto/Dec/2015–2016 | S | S | N | H | S | P | L | |||||||||||||||||
14307/Kyoto/Jan/2015–2016 | V | N | M | A | H | S | P | L | ||||||||||||||||
14311/Kyoto/Feb/2015–2016 | S | N | M | A | H | I | S | P | L | |||||||||||||||
17378/Kyoto/Jan/2018–2019 | V | I | H | S | N | M | N | N | P | A | L | |||||||||||||
18792/Kyoto/Sep/2021–2022 | A | H | S | N | M | N | N | P | A | L | ||||||||||||||
18794/Kyoto/Sep/2021–2022 | A | H | S | N | M | N | N | P | A | L | ||||||||||||||
18821/Kyoto/Oct/2021–2022 | A | H | S | N | M | N | N | P | A | L | ||||||||||||||
18958/Shizuoka/Jan/2021–2022 | V | H | S | N | M | N | N | P | A | L | ||||||||||||||
18968/Shizuoka/Feb/2021–2022 | S | S | I | H | S | N | M | S | N | T | G | P | H | A | L | |||||||||
AB972502/Niigata 2011/JP | S | N | S | P | L | |||||||||||||||||||
KM272334/KR/2012 | N | H | ||||||||||||||||||||||
KJ649702/Hu/HKG/2014 | S | N | M | S | P | L | ||||||||||||||||||
KJ451059/2013/TW | S | S | N | S | P | L | ||||||||||||||||||
LC133344/Osaka/2014/JP | S | N | P | L | ||||||||||||||||||||
LC005734/Hu/JP/2013 | N | H | S | P | L | |||||||||||||||||||
KX354113/2014/USA | S | S | N | H | P | L | ||||||||||||||||||
OM373200/2018/CHN | V | H | S | N | M | N | N | P | A | L | ||||||||||||||
LC699533/Tokyo/2021 | A | H | S | N | M | N | N | P | A | L | ||||||||||||||
OK148516/Hu/GZ19/2018/CHN | V | H | S | N | M | N | N | P | A | L | ||||||||||||||
AB933699/Akita/2011/2006b | I | I | N | G | E | N | T | H | P | H | L | |||||||||||||
AB933761/Osaka/2011/2009 | I | S | N | T | S | L |
ORF3 | 4 | 13 | 23 | 73 | 78 | 82 | 92 | 101 | 112 | 134 | 137 | 141 | 145 | 146 | 149 | 150 | 159 | 164 | 174 | 181 | 183 | 191 | 211 | 241 | 247 | 268 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
JX459908 | A | V | N | K | M | K | F | I | S | P | S | P | N | L | A | V | S | T | T | T | V | F | S | V | G | A |
12241/Kyoto/Oct/2013–2014 | R | R | S | G | F | I | ||||||||||||||||||||
12283/Kyoto/Feb/2013–2014 | R | S | N | G | F | I | ||||||||||||||||||||
12286/Kyoto/Mar/2013–2014 | S | R | V | S | N | A | G | S | F | I | S | |||||||||||||||
14146/Kyoto/Dec/2015–2016 | R | S | L | G | F | I | S | |||||||||||||||||||
14147/Kyoto/Dec/2015–2016 | R | S | L | G | F | I | ||||||||||||||||||||
14157/Kyoto/Dec/2015–2016 | R | S | N | G | F | I | S | |||||||||||||||||||
14307/Kyoto/Jan/2015–2016 | R | S | L | G | F | I | S | |||||||||||||||||||
14311/Kyoto/Feb/2015–2016 | R | S | L | G | F | I | ||||||||||||||||||||
17378/Kyoto/Jan/2018–2019 | I | R | S | S | P | F | F | A | G | F | I | V | ||||||||||||||
18792/Kyoto/Sep/2021–2022 | T | R | S | T | - | - | A | I | G | F | I | V | ||||||||||||||
18794/Kyoto/Sep/2021–2022 | T | R | S | T | - | - | A | I | G | F | I | V | ||||||||||||||
18821/Kyoto/Oct/2021–2022 | T | R | S | T | - | - | A | I | G | F | I | V | ||||||||||||||
18958/Shizuoka/Jan/2021–2022 | R | S | F | I | A | G | F | I | V | |||||||||||||||||
18968/Shizuoka/Feb/2021–2022 | R | S | T | A | I | G | F | I | V | |||||||||||||||||
AB972502/Niigata 2011/JP | R | S | G | F | I | |||||||||||||||||||||
KM272334/KR/2012 | R | S | G | F | ||||||||||||||||||||||
LC726073/Tokyo/2021 | R | S | F | I | A | G | F | I | V | |||||||||||||||||
MH979230/2018/TW | R | S | I | G | F | I | V | |||||||||||||||||||
MK928496/TH/2018 | R | S | F | G | F | I | V | |||||||||||||||||||
OM386670/CHN/2019 | R | S | F | G | F | I | V | |||||||||||||||||||
MH702270/Hu/Bhutan/2012 | R | S | G | F | I | |||||||||||||||||||||
AB933699/Akita/2011/2006b | R | S | P | V | G | F | V | |||||||||||||||||||
AB933761/Osaka/2011/2009 | R | S | G | F | V |
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Ushijima, H.; Hoque, S.A.; Akari, Y.; Pham, N.T.K.; Phan, T.; Nishimura, S.; Kobayashi, M.; Sugita, K.; Okitsu, S.; Komoto, S.; et al. Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan. Int. J. Mol. Sci. 2024, 25, 3619. https://doi.org/10.3390/ijms25073619
Ushijima H, Hoque SA, Akari Y, Pham NTK, Phan T, Nishimura S, Kobayashi M, Sugita K, Okitsu S, Komoto S, et al. Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan. International Journal of Molecular Sciences. 2024; 25(7):3619. https://doi.org/10.3390/ijms25073619
Chicago/Turabian StyleUshijima, Hiroshi, Sheikh Ariful Hoque, Yuki Akari, Ngan Thi Kim Pham, Tung Phan, Shuichi Nishimura, Masaaki Kobayashi, Kumiko Sugita, Shoko Okitsu, Satoshi Komoto, and et al. 2024. "Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan" International Journal of Molecular Sciences 25, no. 7: 3619. https://doi.org/10.3390/ijms25073619
APA StyleUshijima, H., Hoque, S. A., Akari, Y., Pham, N. T. K., Phan, T., Nishimura, S., Kobayashi, M., Sugita, K., Okitsu, S., Komoto, S., Thongprachum, A., Khamrin, P., Maneekarn, N., & Hayakawa, S. (2024). Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan. International Journal of Molecular Sciences, 25(7), 3619. https://doi.org/10.3390/ijms25073619