title: Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses.
abstract: The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; email: ttylam@hku.hk , zhuhch@hku.hk , yguan@hku.hk.|Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China.|State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China.
authors.forename: Tommy T-Y
authors.initials: TT
authors.lastname: Lam
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; email: ttylam@hku.hk , zhuhch@hku.hk , yguan@hku.hk.|Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China.|State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China.
authors.forename: Huachen
authors.initials: H
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; email: ttylam@hku.hk , zhuhch@hku.hk , yguan@hku.hk.|Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China.|State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China.|Department of Microbiology, Guangxi Medical University, Nanning 530021, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Guan
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia; email: edward.holmes@sydney.edu.au.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
mesh_terms: D019295:Computational Biology; D019143:Evolution, Molecular; D014644:Genetic Variation; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D012313:RNA / Q000235:genetics*; D012328:RNA Viruses / Q000235:genetics* / Q000472:pathogenicity; D012137:Respiratory System / Q000821:virology*
chemical_list: D012313:RNA
keywords: RNA virus; evolution; genomic analysis; phylodynamics; respiratory disease; virosphere