Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China

Amber Farooqui; Alberto J. Leon; Linxi Huang; Suwu Wu; Yingmu Cai; Pengzhou Lin; Weihong Chen; Xibin Fang; Tiansheng Zeng; Yisu Liu; Li Zhang; Ting Su; Weibin Chen; Elodie Ghedin; Huachen Zhu; Yi Guan; David J. Kelvin

doi:10.1186/s12879-015-0829-8

Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China

Amber Farooqui, Alberto J. Leon, Linxi Huang, Suwu Wu, Yingmu Cai, Pengzhou Lin, Weihong Chen, Xibin Fang, Tiansheng Zeng, Yisu Liu, Li Zhang, Ting Su, Weibin Chen, Elodie Ghedin, Huachen Zhu, Yi Guan, David J. Kelvin

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Resumen

Background: Influenza H7N9 has become an endemic pathogen in China where circulating virus is found extensively in wild birds and domestic poultry. Two epidemic waves of Human H7N9 infections have taken place in Eastern and South Central China during the years of 2013 and 2014. In this study, we report on the first four human cases of influenza H7N9 in Shantou, Guangdong province, which occurred during the second H7N9 wave, and the subsequent analysis of the viral isolates. Methods: Viral genomes were subjected to multisegment amplification and sequenced in an Illumina MiSeq. Later, phylogenetic analyses of influenza H7N9 viruses were performed to establish the evolutionary context of the disease in humans. Results: The sequences of the isolates from Shantou have closer evolutionary proximity to the predominant Eastern H7N9 cluster (similar to A/Shanghai/1/2013 (H7N9)) than to the Southern H7N9 cluster (similar to A/Guangdong/1/2013 (H7N9)). Conclusions: Two distinct phylogenetic groups of influenza H7N9 circulate currently in China and cause infections in humans as a consequence of cross-species spillover from the avian disease. The Eastern cluster, which includes the four isolates from Shantou, presents a wide geographic distribution and overlaps with the more restricted area of circulation of the Southern cluster. Continued monitoring of the avian disease is of critical importance to better understand and predict the epidemiological behaviour of the human cases.

Idioma original	English
Número de artículo	109
Publicación	BMC Infectious Diseases
Volumen	15
N.º	1
DOI	https://doi.org/10.1186/s12879-015-0829-8
Estado	Published - dic. 12 2015
Publicado de forma externa	Sí

Nota bibliográfica

Funding Information:
This study was funded by the Li Ka-Shing Foundation of Canada and NIAID grant 1U01AI11598-01 Subaward no. 0038591(123721–3). We would like to thank Yimei Pan for coordinating and handling patient data. The authors gratefully acknowledge the originating and submitting laboratories who contributed their sequences to GISAID’s EpiFlu database. In particular, the sequences from human H7N9 influenza isolates were contributed by WHO Chinese National Influenza Center, Zhejiang Provincial Center for Disease Control and Prevention, Zhejiang University, Public Health Laboratory Services Branch (Hong Kong), Centers for Disease Control (Taiwan), Tai Lung Veterinary Laboratory (Agriculture, Fisheries and Conservation Department), Hangzhou Center for Disease Control and Prevention, Institute Pasteur of Shanghai, Shanghai Public Health Clinical center, Chiba Prefectural Institute of Public Health and Jiangsu Provincial Center for Disease Control and Prevention; the sequences from avian H7N9 influenza isolates were contributed by Harbin Veterinary Research Institute, Huzhou Center for Disease Control and Prevention, Beijing Institute of Microbiology and Epidemiology, Hangzhou Center for Disease Control and Prevention, WHO Chinese National Influenza Center and Jiangsu University; the sequences from environmental H7N9 influenza isolates were contributed by Harbin Veterinary Research Institute, WHO Chinese National Influenza Center, Hangzhou Center for Disease Control and Prevention and Guangdong Centers for Disease Control and prevention. All submitters of data may be contacted directly via the GISAID website (www.gisaid.org).

Publisher Copyright:
© 2015 Farooqui et al. licensee BioMed Central.

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@article{e317255dd1334d5a8a9febaaee34fdbc,

title = "Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China",

abstract = "Background: Influenza H7N9 has become an endemic pathogen in China where circulating virus is found extensively in wild birds and domestic poultry. Two epidemic waves of Human H7N9 infections have taken place in Eastern and South Central China during the years of 2013 and 2014. In this study, we report on the first four human cases of influenza H7N9 in Shantou, Guangdong province, which occurred during the second H7N9 wave, and the subsequent analysis of the viral isolates. Methods: Viral genomes were subjected to multisegment amplification and sequenced in an Illumina MiSeq. Later, phylogenetic analyses of influenza H7N9 viruses were performed to establish the evolutionary context of the disease in humans. Results: The sequences of the isolates from Shantou have closer evolutionary proximity to the predominant Eastern H7N9 cluster (similar to A/Shanghai/1/2013 (H7N9)) than to the Southern H7N9 cluster (similar to A/Guangdong/1/2013 (H7N9)). Conclusions: Two distinct phylogenetic groups of influenza H7N9 circulate currently in China and cause infections in humans as a consequence of cross-species spillover from the avian disease. The Eastern cluster, which includes the four isolates from Shantou, presents a wide geographic distribution and overlaps with the more restricted area of circulation of the Southern cluster. Continued monitoring of the avian disease is of critical importance to better understand and predict the epidemiological behaviour of the human cases.",

author = "Amber Farooqui and Leon, {Alberto J.} and Linxi Huang and Suwu Wu and Yingmu Cai and Pengzhou Lin and Weihong Chen and Xibin Fang and Tiansheng Zeng and Yisu Liu and Li Zhang and Ting Su and Weibin Chen and Elodie Ghedin and Huachen Zhu and Yi Guan and Kelvin, {David J.}",

note = "Funding Information: This study was funded by the Li Ka-Shing Foundation of Canada and NIAID grant 1U01AI11598-01 Subaward no. 0038591(123721–3). We would like to thank Yimei Pan for coordinating and handling patient data. The authors gratefully acknowledge the originating and submitting laboratories who contributed their sequences to GISAID{\textquoteright}s EpiFlu database. In particular, the sequences from human H7N9 influenza isolates were contributed by WHO Chinese National Influenza Center, Zhejiang Provincial Center for Disease Control and Prevention, Zhejiang University, Public Health Laboratory Services Branch (Hong Kong), Centers for Disease Control (Taiwan), Tai Lung Veterinary Laboratory (Agriculture, Fisheries and Conservation Department), Hangzhou Center for Disease Control and Prevention, Institute Pasteur of Shanghai, Shanghai Public Health Clinical center, Chiba Prefectural Institute of Public Health and Jiangsu Provincial Center for Disease Control and Prevention; the sequences from avian H7N9 influenza isolates were contributed by Harbin Veterinary Research Institute, Huzhou Center for Disease Control and Prevention, Beijing Institute of Microbiology and Epidemiology, Hangzhou Center for Disease Control and Prevention, WHO Chinese National Influenza Center and Jiangsu University; the sequences from environmental H7N9 influenza isolates were contributed by Harbin Veterinary Research Institute, WHO Chinese National Influenza Center, Hangzhou Center for Disease Control and Prevention and Guangdong Centers for Disease Control and prevention. All submitters of data may be contacted directly via the GISAID website (www.gisaid.org). Publisher Copyright: {\textcopyright} 2015 Farooqui et al. licensee BioMed Central.",

year = "2015",

month = dec,

day = "12",

doi = "10.1186/s12879-015-0829-8",

language = "English",

volume = "15",

journal = "BMC Infectious Diseases",

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publisher = "BioMed Central",

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TY - JOUR

T1 - Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China

AU - Farooqui, Amber

AU - Leon, Alberto J.

AU - Huang, Linxi

AU - Wu, Suwu

AU - Cai, Yingmu

AU - Lin, Pengzhou

AU - Chen, Weihong

AU - Fang, Xibin

AU - Zeng, Tiansheng

AU - Liu, Yisu

AU - Zhang, Li

AU - Su, Ting

AU - Chen, Weibin

AU - Ghedin, Elodie

AU - Zhu, Huachen

AU - Guan, Yi

AU - Kelvin, David J.

N1 - Funding Information: This study was funded by the Li Ka-Shing Foundation of Canada and NIAID grant 1U01AI11598-01 Subaward no. 0038591(123721–3). We would like to thank Yimei Pan for coordinating and handling patient data. The authors gratefully acknowledge the originating and submitting laboratories who contributed their sequences to GISAID’s EpiFlu database. In particular, the sequences from human H7N9 influenza isolates were contributed by WHO Chinese National Influenza Center, Zhejiang Provincial Center for Disease Control and Prevention, Zhejiang University, Public Health Laboratory Services Branch (Hong Kong), Centers for Disease Control (Taiwan), Tai Lung Veterinary Laboratory (Agriculture, Fisheries and Conservation Department), Hangzhou Center for Disease Control and Prevention, Institute Pasteur of Shanghai, Shanghai Public Health Clinical center, Chiba Prefectural Institute of Public Health and Jiangsu Provincial Center for Disease Control and Prevention; the sequences from avian H7N9 influenza isolates were contributed by Harbin Veterinary Research Institute, Huzhou Center for Disease Control and Prevention, Beijing Institute of Microbiology and Epidemiology, Hangzhou Center for Disease Control and Prevention, WHO Chinese National Influenza Center and Jiangsu University; the sequences from environmental H7N9 influenza isolates were contributed by Harbin Veterinary Research Institute, WHO Chinese National Influenza Center, Hangzhou Center for Disease Control and Prevention and Guangdong Centers for Disease Control and prevention. All submitters of data may be contacted directly via the GISAID website (www.gisaid.org). Publisher Copyright: © 2015 Farooqui et al. licensee BioMed Central.

PY - 2015/12/12

Y1 - 2015/12/12

N2 - Background: Influenza H7N9 has become an endemic pathogen in China where circulating virus is found extensively in wild birds and domestic poultry. Two epidemic waves of Human H7N9 infections have taken place in Eastern and South Central China during the years of 2013 and 2014. In this study, we report on the first four human cases of influenza H7N9 in Shantou, Guangdong province, which occurred during the second H7N9 wave, and the subsequent analysis of the viral isolates. Methods: Viral genomes were subjected to multisegment amplification and sequenced in an Illumina MiSeq. Later, phylogenetic analyses of influenza H7N9 viruses were performed to establish the evolutionary context of the disease in humans. Results: The sequences of the isolates from Shantou have closer evolutionary proximity to the predominant Eastern H7N9 cluster (similar to A/Shanghai/1/2013 (H7N9)) than to the Southern H7N9 cluster (similar to A/Guangdong/1/2013 (H7N9)). Conclusions: Two distinct phylogenetic groups of influenza H7N9 circulate currently in China and cause infections in humans as a consequence of cross-species spillover from the avian disease. The Eastern cluster, which includes the four isolates from Shantou, presents a wide geographic distribution and overlaps with the more restricted area of circulation of the Southern cluster. Continued monitoring of the avian disease is of critical importance to better understand and predict the epidemiological behaviour of the human cases.

AB - Background: Influenza H7N9 has become an endemic pathogen in China where circulating virus is found extensively in wild birds and domestic poultry. Two epidemic waves of Human H7N9 infections have taken place in Eastern and South Central China during the years of 2013 and 2014. In this study, we report on the first four human cases of influenza H7N9 in Shantou, Guangdong province, which occurred during the second H7N9 wave, and the subsequent analysis of the viral isolates. Methods: Viral genomes were subjected to multisegment amplification and sequenced in an Illumina MiSeq. Later, phylogenetic analyses of influenza H7N9 viruses were performed to establish the evolutionary context of the disease in humans. Results: The sequences of the isolates from Shantou have closer evolutionary proximity to the predominant Eastern H7N9 cluster (similar to A/Shanghai/1/2013 (H7N9)) than to the Southern H7N9 cluster (similar to A/Guangdong/1/2013 (H7N9)). Conclusions: Two distinct phylogenetic groups of influenza H7N9 circulate currently in China and cause infections in humans as a consequence of cross-species spillover from the avian disease. The Eastern cluster, which includes the four isolates from Shantou, presents a wide geographic distribution and overlaps with the more restricted area of circulation of the Southern cluster. Continued monitoring of the avian disease is of critical importance to better understand and predict the epidemiological behaviour of the human cases.

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U2 - 10.1186/s12879-015-0829-8

DO - 10.1186/s12879-015-0829-8

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Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China

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