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New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China

View ORCID ProfileQinlong Jing, View ORCID ProfileSean Wu, Zhengjian He, Lihong Yuan, Mengmeng Ma, Zhijun Bai, Liyun Jiang, John Marshall, Jiahai Lu, Zhicong Yang
doi: https://doi.org/10.1101/697052
Qinlong Jing
Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People’s Republic of China
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  • For correspondence: jingqinlong@126.com yangzc@gzcdc.org.cn
Sean Wu
Department of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
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Zhengjian He
School of Life sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, People’s Republic of China
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Lihong Yuan
School of Life sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, People’s Republic of China
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Mengmeng Ma
Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People’s Republic of China
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Zhijun Bai
Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People’s Republic of China
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Liyun Jiang
Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People’s Republic of China
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John Marshall
Department of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
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Jiahai Lu
Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
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Zhicong Yang
Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People’s Republic of China
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  • For correspondence: jingqinlong@126.com yangzc@gzcdc.org.cn
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Abstract

Background Dengue fever is a mosquito-borne infectious disease that has caused major health problems. Variations in dengue virus (DENV) genes are important features of epidemic outbreaks. However, the associations of DENV genes with epidemic scale have not been extensively examined. Here, we assessed new genotype invasion of DENV-1 isolated from Guangzhou in China to evaluate associations with epidemic outbreaks.

Methodology/Principal Findings We used DENV-1 strains isolated from sera of dengue cases from 2002 to 2016 in Guangzhou for complete genome sequencing. A neighbor-joining phylogenetic tree was constructed to elucidate the genotype characteristics and determine if new genotype invasion correlated with major outbreaks. In our study, a new genotype invasion event was observed during each significant outbreak period in 2002-2003, 2006-2007 and 2013-2014. Genotype II was the main epidemic genotype in 2003 and before. Invasion of genotype I in 2006 caused an unusual outbreak with 765 cases (relative risk (RR)=16.24, 95% confidence interval (CI) =12.41-21.25). At the middle and late stages of the 2013 outbreak, genotype III was introduced to Guangzhou as a new genotype invasion responsible for 37340 cases with RR 541.73 (95%CI=417.78-702.45), after which genotypes I and III began co-circulating. Base mutations occurred after new genotype invasion, and the gene sequence of NS3 protein had the lowest average similarity ratio (99.82%), followed by the gene sequence of E protein (99.86%), as compared to the 2013 strain.

Conclusions/Significance Genotype replacement and co-circulation of multiple DENV-1 genotypes were observed. New genotype invasion was highly correlated with local unusual outbreaks. In addition to DENV-1 genotype I in the unprecedented outbreak in 2014, new genotype invasion by DENV-1 genotype III occurred in Guangzhou.

Author Summary New genotype invasion of dengue virus highly correlates with the massive outbreaks. In this study, we examined the association of the genotype of dengue virus serorype 1 (DENV-1) from human cases through complete genome sequencing with outbreak scale during 2002 and 2016 in Guangzhou, China. It was observed that genotype replacement and co-circulation of multiple genotypes occurred. Most importantly, it indicated that new genotype invasion was highly related with local unusual outbreaks in major outbreak periods in 2002-2003, 2006-2007 and 2013-2014. DENV-1 genotype II was the main epidemic genotype in 2003 and before. Invasion of genotype I in 2006 caused an unusual outbreak with 765 cases reported. In addition to genotype I circulation, new genotype invasion by genotype III was the key determinant for the 2014 massive outbreak reaching the highest number of cases with 37340. Furthermore, base mutations appeared after genotype III invasion, and the gene sequence of NS3 protein had the lowest average similarity ratio, followed by the gene sequence of E protein, as compared to the 2013 strain.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 09, 2019.
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New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China
Qinlong Jing, Sean Wu, Zhengjian He, Lihong Yuan, Mengmeng Ma, Zhijun Bai, Liyun Jiang, John Marshall, Jiahai Lu, Zhicong Yang
bioRxiv 697052; doi: https://doi.org/10.1101/697052
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New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China
Qinlong Jing, Sean Wu, Zhengjian He, Lihong Yuan, Mengmeng Ma, Zhijun Bai, Liyun Jiang, John Marshall, Jiahai Lu, Zhicong Yang
bioRxiv 697052; doi: https://doi.org/10.1101/697052

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