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Article

Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013–2019

by 1,†, 1,†, 1,†, 1,2,3, 1, 1, 1, 1, 1,2,3, 1,2,3, 1,2,3, 2,4, 5, 1,2,3,* and 1,2,3,*
1
Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
2
Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
3
Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
4
Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
5
College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
*
Authors to whom correspondence should be addressed.
These authors have contributed equally to this work.
Academic Editor: Chi-Young Wang
Viruses 2022, 14(6), 1256; https://doi.org/10.3390/v14061256
Received: 4 May 2022 / Revised: 29 May 2022 / Accepted: 6 June 2022 / Published: 9 June 2022
(This article belongs to the Special Issue State-of-the-Art Avian Viruses Research in Asia)
Reassortment with the H9N2 virus gave rise to the zoonotic H7N9 avian influenza virus (AIV), which caused more than five outbreak waves in humans, with high mortality. The frequent exchange of genomic segments between H7N9 and H9N2 has been well-documented. However, the reassortment patterns have not been described and are not yet fully understood. Here, we used phylogenetic analyses to investigate the patterns of intersubtype and intrasubtype/intralineage reassortment across the eight viral segments. The H7N9 virus and its progeny frequently exchanged internal genes with the H9N2 virus but rarely with the other AIV subtypes. Before beginning the intrasubtype/intralineage reassortment analyses, five Yangtze River Delta (YRD A-E) and two Pearl River Delta (PRD A-B) clusters were divided according to the HA gene phylogeny. The seven reset segment genes were also nomenclatured consistently. As revealed by the tanglegram results, high intralineage reassortment rates were determined in waves 2–3 and 5. Additionally, the clusters of PB2 c05 and M c02 were the most dominant in wave 5, which could have contributed to the onset of the largest H7N9 outbreak in 2016–2017. Meanwhile, a portion of the YRD-C cluster (HP H7N9) inherited their PB2, PA, and M segments from the co-circulating YRD-E (LP H7N9) cluster during wave 5. Untanglegram results revealed that the reassortment rate between HA and NA was lower than HA with any of the other six segments. A multidimensional scaling plot revealed a robust genetic linkage between the PB2 and PA genes, indicating that they may share a co-evolutionary history. Furthermore, we observed relatively more robust positive selection pressure on HA, NA, M2, and NS1 proteins. Our findings demonstrate that frequent reassortment, particular reassorted patterns, and adaptive mutations shaped the H7N9 viral genetic diversity and evolution. Increased surveillance is required immediately to better understand the current state of the HP H7N9 AIV. View Full-Text
Keywords: avian influenza virus; H7N9; highly pathogenic; diversity; reassortment; tanglegram avian influenza virus; H7N9; highly pathogenic; diversity; reassortment; tanglegram
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MDPI and ACS Style

He, D.; Wang, X.; Wu, H.; Wang, X.; Yan, Y.; Li, Y.; Zhan, T.; Hao, X.; Hu, J.; Hu, S.; Liu, X.; Ding, C.; Su, S.; Gu, M.; Liu, X. Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013–2019. Viruses 2022, 14, 1256. https://doi.org/10.3390/v14061256

AMA Style

He D, Wang X, Wu H, Wang X, Yan Y, Li Y, Zhan T, Hao X, Hu J, Hu S, Liu X, Ding C, Su S, Gu M, Liu X. Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013–2019. Viruses. 2022; 14(6):1256. https://doi.org/10.3390/v14061256

Chicago/Turabian Style

He, Dongchang, Xiyue Wang, Huiguang Wu, Xiaoquan Wang, Yayao Yan, Yang Li, Tiansong Zhan, Xiaoli Hao, Jiao Hu, Shunlin Hu, Xiaowen Liu, Chan Ding, Shuo Su, Min Gu, and Xiufan Liu. 2022. "Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013–2019" Viruses 14, no. 6: 1256. https://doi.org/10.3390/v14061256

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