Dan Xiang1,2, Xuejuan Shen1, Zhiqing Pu1, David M Irwin3,4, Ming Liao1,5, Yongyi Shen1,2,5. 1. College of Veterinary Medicine, South China Agricultural University, Guangzhou. 2. Shantou University Medical College, Guangzhou, China. 3. Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada. 4. Banting and Best Diabetes Centre, University of Toronto, Canada. 5. Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.
Abstract
Background: Avian influenza A virus H7N9 has caused 5 epidemic waves of human infections in China since 2013. Avian influenza A viruses may face strong selection to adapt to novel conditions when establishing themselves in humans. In this study, we sought to determine whether adaptive evolution had occurred in human-isolated H7N9 viruses. Methods: We evaluated all available genomes of H7N9 avian influenza A virus. Maximum likelihood trees were separately reconstructed for all 8 genes. Signals of positive selection and convergent evolution were then detected on branches that lead to changes in host tropism (from avian to human). Results: We found that 3 genes had significant signals of positive selection (all of them P < .05). In addition, we detected 34 sites having significant signals for parallel evolution in 8 genes (all of them P < .05), including 7 well-known sites (Q591K, E627K, and D701N in PB2 gene; R156K, V202A, and L244Q in HA; and R289K in NA) that play roles in crossing species barriers for avian influenza A viruses. Conclusion: Our study suggests that, during infection in humans, H7N9 viruses have undergone adaptive evolution to adapt to their new host environment and that the sites where parallel evolution occurred might play roles in crossing species barriers and respond to the new selection pressures arising from their new host environments.
Background: Avian influenza A virusH7N9 has caused 5 epidemic waves of humaninfections in China since 2013. Avian influenza A viruses may face strong selection to adapt to novel conditions when establishing themselves in humans. In this study, we sought to determine whether adaptive evolution had occurred in human-isolated H7N9 viruses. Methods: We evaluated all available genomes of H7N9 avian influenza A virus. Maximum likelihood trees were separately reconstructed for all 8 genes. Signals of positive selection and convergent evolution were then detected on branches that lead to changes in host tropism (from avian to human). Results: We found that 3 genes had significant signals of positive selection (all of them P < .05). In addition, we detected 34 sites having significant signals for parallel evolution in 8 genes (all of them P < .05), including 7 well-known sites (Q591K, E627K, and D701N in PB2 gene; R156K, V202A, and L244Q in HA; and R289K in NA) that play roles in crossing species barriers for avian influenza A viruses. Conclusion: Our study suggests that, during infection in humans, H7N9 viruses have undergone adaptive evolution to adapt to their new host environment and that the sites where parallel evolution occurred might play roles in crossing species barriers and respond to the new selection pressures arising from their new host environments.
Authors: Jørgen de Jonge; Harry van Dijken; Femke de Heij; Sanne Spijkers; Justin Mouthaan; Rineke de Jong; Paul Roholl; Eduardo Alfredo Adami; Milena Apetito Akamatsu; Paulo Lee Ho; Livia Brunner; Nicolas Collin; Martin Friede; José A Ferreira; Willem Luytjes Journal: NPJ Vaccines Date: 2020-05-11 Impact factor: 7.344
Authors: Jørgen de Jonge; Harry van Dijken; Femke de Heij; Sanne Spijkers; Justin Mouthaan; Rineke de Jong; Paul Roholl; Eduardo Alfredo Adami; Milena Apetito Akamatsu; Paulo Lee Ho; Livia Brunner; Nicolas Collin; Martin Friede; José A Ferreira; Willem Luytjes Journal: NPJ Vaccines Date: 2020-05-11 Impact factor: 7.344