Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam

Jemma L. Geoghegan; Le Van Tan; Nghlem My Ngoc; Le Thi Tam Uyen; Nguyen Thi Kim Tuyen; Tran Tan Thanh; Vu Thi Ty Hang; Phan Tu Qui; Nguyen Thanh Hung; Truong Huu Khanh; Le Quoc Thinh; Le Nguyen Thanh Nhan; Denise Kühnert; Hoang Minh Tu Van; Do Chau Viet; Ha Manh Tuan; Ho Lu Viet; Tran Tinh Hien; Nguyen Van Vinh Chau; Guy Thwaites; Bryan T. Grenfell; Tanja Stadler; David E. Wentworth; Rebecca A. Halpin; Edward C. Holmes; H. Rogier Van Doorn; Xudong Lin; Ari Simenauer; Asmik Akopov; Suman R. Das; Timothy B. Stockwell; Susmita Shrivastava

doi:10.1128/JVI.00706-15

Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam

Jemma L. Geoghegan, Le Van Tan, Nghlem My Ngoc, Le Thi Tam Uyen, Nguyen Thi Kim Tuyen, Tran Tan Thanh, Vu Thi Ty Hang, Phan Tu Qui, Nguyen Thanh Hung, Truong Huu Khanh, Le Quoc Thinh, Le Nguyen Thanh Nhan, Denise Kühnert, Hoang Minh Tu Van, Do Chau Viet, Ha Manh Tuan, Ho Lu Viet, Tran Tinh Hien, Nguyen Van Vinh Chau, Guy ThwaitesBryan T. Grenfell, Tanja Stadler, David E. Wentworth, Rebecca A. Halpin, Edward C. Holmes, H. Rogier Van Doorn, Xudong Lin, Ari Simenauer, Asmik Akopov, Suman R. Das, Timothy B. Stockwell, Susmita Shrivastava

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Abstract

Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011 and 2013 and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (Rₑ) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the Rₑ of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained >1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated area of endemicity. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia.

Original language	English
Pages (from-to)	8871-8879
Number of pages	9
Journal	Journal of Virology
Volume	89
Issue number	17
DOIs	https://doi.org/10.1128/JVI.00706-15
Publication status	Published - 2015
Externally published	Yes

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Copyright the Author(s) 2015. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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10.1128/JVI.00706-15

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Geoghegan, J. L., Tan, L. V., Ngoc, N. M., Uyen, L. T. T., Tuyen, N. T. K., Thanh, T. T., Hang, V. T. T., Qui, P. T., Hung, N. T., Khanh, T. H., Thinh, L. Q., Thanh Nhan, L. N., Kühnert, D., Van, H. M. T., Viet, D. C., Tuan, H. M., Viet, H. L., Hien, T. T., Chau, N. V. V., ... Shrivastava, S. (2015). Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam. Journal of Virology, 89(17), 8871-8879. https://doi.org/10.1128/JVI.00706-15

@article{203a93477a474afd8a7694febff5fcea,

title = "Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam",

abstract = "Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011 and 2013 and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (Rₑ) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the Rₑ of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained >1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated area of endemicity. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia.",

author = "Geoghegan, {Jemma L.} and Tan, {Le Van} and Ngoc, {Nghlem My} and Uyen, {Le Thi Tam} and Tuyen, {Nguyen Thi Kim} and Thanh, {Tran Tan} and Hang, {Vu Thi Ty} and Qui, {Phan Tu} and Hung, {Nguyen Thanh} and Khanh, {Truong Huu} and Thinh, {Le Quoc} and {Thanh Nhan}, {Le Nguyen} and Denise K{\"u}hnert and Van, {Hoang Minh Tu} and Viet, {Do Chau} and Tuan, {Ha Manh} and Viet, {Ho Lu} and Hien, {Tran Tinh} and Chau, {Nguyen Van Vinh} and Guy Thwaites and Grenfell, {Bryan T.} and Tanja Stadler and Wentworth, {David E.} and Halpin, {Rebecca A.} and Holmes, {Edward C.} and {Van Doorn}, {H. Rogier} and Xudong Lin and Ari Simenauer and Asmik Akopov and Das, {Suman R.} and Stockwell, {Timothy B.} and Susmita Shrivastava",

note = "Copyright the Author(s) 2015. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.",

year = "2015",

doi = "10.1128/JVI.00706-15",

language = "English",

volume = "89",

pages = "8871--8879",

journal = "Journal of Virology",

issn = "0022-538X",

publisher = "American Society for Microbiology",

number = "17",

}

Geoghegan, JL, Tan, LV, Ngoc, NM, Uyen, LTT, Tuyen, NTK, Thanh, TT, Hang, VTT, Qui, PT, Hung, NT, Khanh, TH, Thinh, LQ, Thanh Nhan, LN, Kühnert, D, Van, HMT, Viet, DC, Tuan, HM, Viet, HL, Hien, TT, Chau, NVV, Thwaites, G, Grenfell, BT, Stadler, T, Wentworth, DE, Halpin, RA, Holmes, EC, Van Doorn, HR, Lin, X, Simenauer, A, Akopov, A, Das, SR, Stockwell, TB & Shrivastava, S 2015, 'Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam', Journal of Virology, vol. 89, no. 17, pp. 8871-8879. https://doi.org/10.1128/JVI.00706-15

TY - JOUR

T1 - Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam

AU - Geoghegan, Jemma L.

AU - Tan, Le Van

AU - Ngoc, Nghlem My

AU - Uyen, Le Thi Tam

AU - Tuyen, Nguyen Thi Kim

AU - Thanh, Tran Tan

AU - Hang, Vu Thi Ty

AU - Qui, Phan Tu

AU - Hung, Nguyen Thanh

AU - Khanh, Truong Huu

AU - Thinh, Le Quoc

AU - Thanh Nhan, Le Nguyen

AU - Kühnert, Denise

AU - Van, Hoang Minh Tu

AU - Viet, Do Chau

AU - Tuan, Ha Manh

AU - Viet, Ho Lu

AU - Hien, Tran Tinh

AU - Chau, Nguyen Van Vinh

AU - Thwaites, Guy

AU - Grenfell, Bryan T.

AU - Stadler, Tanja

AU - Wentworth, David E.

AU - Halpin, Rebecca A.

AU - Holmes, Edward C.

AU - Van Doorn, H. Rogier

AU - Lin, Xudong

AU - Simenauer, Ari

AU - Akopov, Asmik

AU - Das, Suman R.

AU - Stockwell, Timothy B.

AU - Shrivastava, Susmita

N1 - Copyright the Author(s) 2015. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2015

Y1 - 2015

N2 - Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011 and 2013 and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (Rₑ) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the Rₑ of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained >1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated area of endemicity. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia.

AB - Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011 and 2013 and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (Rₑ) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the Rₑ of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained >1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated area of endemicity. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia.

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U2 - 10.1128/JVI.00706-15

DO - 10.1128/JVI.00706-15

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SN - 0022-538X

VL - 89

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EP - 8879

JO - Journal of Virology

JF - Journal of Virology

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ER -

Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam

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