A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand
Abstract
1. Introduction
2. Materials and Methods
2.1. CHIKV Samples
2.2. CHIKV Genome Sequencing
2.3. Nucleotide Sequence Accession Numbers
2.4. Phylogenetic Analyses
2.5. Selection Analyses
3. Results
3.1. ECSA-IOL CHIKVs in Bangladesh and Thailand During 2017–2019
3.2. Evolution of the ECSA-CHIKV IOL Sub-Lineage
3.3. Signature Mutations Related to CHIKV ECSA-IOL Sub-Lineages among CHIKV Outbreak Strains
3.4. Selection Analyses
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Strain | Collection Date | Location | Country | Sample Type | Passage History | Accession No. |
---|---|---|---|---|---|---|
BGD17-0266 | July 2017 | Maghbazar, Dhaka | Bangladesh | serum | 0 | LC580236 |
BGD17-0290 | July 2017 | Uttara, Dhaka | Bangladesh | isolate | C6/36 | LC580237 |
BGD17-0303 | July 2017 | Bashundhara, Dhaka | Bangladesh | serum | 0 | LC580238 |
BGD17-0306 | July 2017 | Maghbazar, Dhaka | Bangladesh | serum | 0 | LC580239 |
BGD17-0932 | August 2017 | Bashundhara, Dhaka | Bangladesh | serum | 0 | LC580240 |
BGD17-1024 | September 2017 | Bashundhara, Dhaka | Bangladesh | serum | 0 | LC580241 |
BGD17-1147 | September 2017 | Bashundhara, Dhaka | Bangladesh | serum | 0 | LC580242 |
BGD17-1151 | September 2017 | Bashundhara, Dhaka | Bangladesh | isolate | C6/36 | LC580243 |
BGD17-1210 | September 2017 | Bashundhara, Dhaka | Bangladesh | isolate | C6/36 | LC580244 |
BGD17-1232 | September 2017 | Bashundhara, Dhaka | Bangladesh | isolate | C6/36 | LC580245 |
BGD17-1269 | September 2017 | Bashundhara, Dhaka | Bangladesh | isolate | C6/36 | LC580246 |
BGD17-1270 | September 2017 | Bashundhara, Dhaka | Bangladesh | isolate | C6/36 | LC580247 |
BGD17-1299 | October 2017 | Rampura, Dhaka | Bangladesh | isolate | C6/36 | LC580248 |
BGD17-1319 | October 2017 | Chittagon | Bangladesh | isolate | C6/36 | LC580249 |
BGD17-1332 | October 2017 | Mirpur, Dhaka | Bangladesh | serum | 0 | LC580250 |
BGD17-1413 | October 2017 | Mirpur, Dhaka | Bangladesh | serum | 0 | LC580251 |
BGD17-1457 | October 2017 | Gulshan, Dhaka | Bangladesh | isolate | C6/36 | LC580252 |
BGD17-1538 | November 2017 | Uttara, Dhaka | Bangladesh | serum | 0 | LC580253 |
BGD17-1542 | November 2017 | Gulshan, Dhaka | Bangladesh | serum | 0 | LC580254 |
BGD17-1629 | December 2017 | Uttara, Dhaka | Bangladesh | serum | 0 | LC580255 |
THBKK19-04 | October 2019 | Bangkok | Thailand | serum | 0 | LC580256 |
THBKK19-06 | October 2019 | Bangkok | Thailand | isolate | C6/36 | LC580257 |
THBKK19-08 | October 2019 | Bangkok | Thailand | serum | 0 | LC580258 |
THBKK19-09 | October 2019 | Bangkok | Thailand | isolate | C6/36 | LC580259 |
THBKK19-11 | October 2019 | Bangkok | Thailand | isolate | C6/36 | LC580260 |
THBKK19-12 | October 2019 | Bangkok | Thailand | isolate | C6/36 | LC580261 |
THBKK19-13 | October 2019 | Bangkok | Thailand | serum | 0 | LC580262 |
THBKK19-14 | October 2019 | Bangkok | Thailand | serum | 0 | LC580263 |
THBKK19-15 | October 2019 | Bangkok | Thailand | isolate | C6/36 | LC580264 |
THBKK19-16 | October 2019 | Bangkok | Thailand | isolate | C6/36 | LC580265 |
THBKK19-17 | October 2019 | Bangkok | Thailand | isolate | C6/36 | LC580266 |
THBKK19-19 | October 2019 | Bangkok | Thailand | serum | 0 | LC580267 |
THBKK19-20 | October 2019 | Bangkok | Thailand | serum | 0 | LC580268 |
THBKK19-21 | October 2019 | Bangkok | Thailand | serum | 0 | LC580269 |
CP10 | 2010 | Ratchaburi | Thailand | isolate | C6/36 and Vero | LC580270 |
Node | Lineage/Clade | Detected Areas/Countries | PP | tMRCA (95% HPD) | Substitution Rate × 10−4 (95% HPD) |
---|---|---|---|---|---|
Root | Root ECSA | 1 | 1949.17 (1944.14–1957.42) | 5.74 (4.96–6.60) | |
A | Enzootic ECSA | South Africa, Central African Republic, Senegal, and Tanzania | 0.39 | 1950.48 (1948.58–1952.53) | 5.70 (0.80–12.62) |
B | African ECSA | Africa and Brazil | 1 | 1970.39 (1967.68–1973.27) | 5.60 (1.37–11.68) |
B1 | West African ECSA | Congo and Angola | 1 | 2011.39 (2008.69–2014.26) | 1.02 (0.69–1.36) |
B2 | South American ECSA | Brazil | 1 | 2013.66 (2013.29–2014.18) | 3.27 (2.59–3.92) |
C | Indian Ocean Lineage (IOL) | Coastal Kenya, Indian Ocean Islands, Indian subcontinent, SEA countries, Italy, and France | 1 | 2002.26 (2001.14–2003.59) | 2.98 (2.31–3.67) |
C1 | Indian Ocean Islands Sub-lineage | Indian Ocean Islands, France | 0.98 | 2003.92 (2003.43–2004.45) | 2.88 (5.93–6.10) |
C2 | Indian subcontinent and SEA Sub-lineage | Indian subcontinent, SEA countries, and Italy | 1 | 2004.16 (2003.52–2004.88) | 4.72 (1.34–8.93) |
C2.1 | Indian subcontinent | India, Sri Lanka, and Bangladesh | 0.81 | 2005.33 (2004.74–2006.15) | 4.16 (0.61–9.57) |
C2.2 | Indian subcontinent/SEA | Indian Continent, SEA countries, and Italy | 1 | 2004.97 (2004.46–2005.52) | 6.91 (1.49–14.50) |
C2.2a | SEA clade | Malaysia, Singapore, Thailand, Cambodia, and Laos | 1 | 2006.82 (2006.42–2007.25) | 4.91 (1.17–10.07) |
C2.3 | Northern Indian subcontinent/SEA | Northern Indian subcontinent, SEA countries, and Italy | 1 | 2008.75 (2008.18–2009.37) | 6.29 (1.57–13.03) |
C2.3a | India clade | India, Pakistan, Bangladesh, Italy, Myanmar, and Thailand | 1 | 2012.71 (2011.72–2013.74) | 8.52 (2.52–16.22) |
C2.3b | Bangladesh clade | Bangladesh, Italy, Myanmar, and Thailand | 1 | 2015.61 (2015.25–2016.01) | 6.79 (1.75–13.76) |
C2.3c | Thailand clade | Thailand and Myanmar | 1 | 2016.98 (2016.73–2017.25) | 10.75 (3.07–20.41) |
Polyproteins | Position* | Protein | Position** | Ancestor IOL | Indian Ocean Islands (C1***) | Indian Sub-Continent (C2.1***) | Indian Sub-Continent/SEA (C2.2a***) | Northern Indian Subcontinent/SEA (C2.3***) | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Kenya 2004 | Reunion 2005 | India 2006 | Thailand 2010 | India 2010 | India 2016 | Pakistan 2016 | Bangladesh 2017 | Italy 2017 | Thailand 2019 | ||||
Non-structural protein | 665 | nsP2 | 130 | H | H | H | H | H | H/Y | Y | Y | Y | Y |
680 | nsP2 | 145 | E | E | E | E | E | E/D | D | D | D | D | |
1030 | nsP2 | 495 | N | N | N | N | N | N | N | N | N | S | |
1328 | nsP2 | 793 | V | V | V | V | V | V/I | V | V/A | V | A | |
1391 | nsP3 | 58 | V | V | V | V | V | V | V | V/I | V | V | |
1705 | nsP3 | 372 | D | D | D | D | D | D | D | E | E | E | |
1918 | nsP4 | 55 | S | S | S | S | S | S/N | N | N | N | N | |
1948 | nsP4 | 85 | R | R | R | R | R | R/G | G | G | G | G | |
Structural protein | 73 | Capsid | 73 | K | K | K | K | K | K | K | K | K | R |
530 | E2 | 205 | G | G | G | G | G | G | G | S | S | S | |
546 | E2 | 221 | K | K | K | K | K | K | K | K/R | K | K | |
589 | E2 | 264 | V | V | V | V | A | A | A | A | A | A | |
1020 | E1 | 211 | K | K | K | K | E | E | E | E | E | E | |
1035 | E1 | 226 | A | A/V | A/V | V | A | A | A | A | A | A | |
1126 | E1 | 317 | I | I | I | I | I | I/V | V | V | V | V |
Dataset | FEL | FUBAR | MEME | |
---|---|---|---|---|
ECSA dataset | 171: nsP1-R171Q 488: nsP1-Q488R 1550: nsP3-H217Y 1695: nsP3-A362V 2418: nsP4-V555I 1020: E1-E211K | 171: nsP-R171Q 1550: nsP3-H217Y 1661: nsP3-Q328P 2418: nsP4-V555I 471: E2-Q146R 1020: E1-E211K | 82: nsP1-C82S 171: nsP1-R171Q 178: nsP1-F178V 753: nsP2-T218I 992: nsP2-I457S 1426: nsP3-A93P 1550: nsP3-H217Y 1661: nsP3-Q328P 1768: nsP3-C435R 1849: nsP3-C516L 2325: nsP4-A462G 2330: nsP4-D467Y | 147: C-A147R 156: C-R156A 467: E2-H142Y 471: E2-Q146R 632: E2-Q307R 795: 6K-A47G/V 955: E1-A146N 1020: E1-E211K 1100: E1-V291I 1191: E1-P382F |
The present study dataset | 1030: nsP2-N495S 1391: nsP3-V58I 1550: nsP3-H217Y 1695: nsP3-A362V 2228: nsP4-T365A 73: C-K73R 546: E2-K221R | 1391: nsP3-V58I 73: C-K73R |
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Phadungsombat, J.; Imad, H.; Rahman, M.; Nakayama, E.E.; Kludkleeb, S.; Ponam, T.; Rahim, R.; Hasan, A.; Poltep, K.; Yamanaka, A.; et al. A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand. Viruses 2020, 12, 1319. https://doi.org/10.3390/v12111319
Phadungsombat J, Imad H, Rahman M, Nakayama EE, Kludkleeb S, Ponam T, Rahim R, Hasan A, Poltep K, Yamanaka A, et al. A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand. Viruses. 2020; 12(11):1319. https://doi.org/10.3390/v12111319
Chicago/Turabian StylePhadungsombat, Juthamas, Hisham Imad, Mizanur Rahman, Emi E. Nakayama, Sajikapon Kludkleeb, Thitiya Ponam, Rummana Rahim, Abu Hasan, Kanaporn Poltep, Atsushi Yamanaka, and et al. 2020. "A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand" Viruses 12, no. 11: 1319. https://doi.org/10.3390/v12111319
APA StylePhadungsombat, J., Imad, H., Rahman, M., Nakayama, E. E., Kludkleeb, S., Ponam, T., Rahim, R., Hasan, A., Poltep, K., Yamanaka, A., Matsee, W., Piyaphanee, W., Phumratanaprapin, W., & Shioda, T. (2020). A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand. Viruses, 12(11), 1319. https://doi.org/10.3390/v12111319