title: Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment.
abstract: BACKGROUND
  Epistasis is one of the central themes in viral evolution due to its importance in drug resistance, immune escape, and interspecies transmission. However, there is a lack of experimental approach to systematically probe for epistatic residues.
  
  
  RESULTS
  By utilizing the information from natural occurring sequences and high-throughput genetics, this study established a novel strategy to identify epistatic residues. The rationale is that a substitution that is deleterious in one strain may be prevalent in nature due to the presence of a naturally occurring compensatory substitution. Here, high-throughput genetics was applied to influenza A virus M segment to systematically identify deleterious substitutions. Comparison with natural sequence variation showed that a deleterious substitution M1 Q214H was prevalent in circulating strains. A coevolution analysis was then performed and indicated that M1 residues 121, 207, 209, and 214 naturally coevolved as a group. Subsequently, we experimentally validated that M1 A209T was a compensatory substitution for M1 Q214H.
  
  
  CONCLUSIONS
  This work provided a proof-of-concept to identify epistatic residues by coupling high-throughput genetics with phylogenetic information. In particular, we were able to identify an epistatic interaction between M1 substitutions A209T and Q214H. This analytic strategy can potentially be adapted to study any protein of interest, provided that the information on natural sequence variants is available.
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. wchnicholas@ucla.edu.|Molecular Biology InstituteUniversity of California, Los Angeles, 90095, CA, USA. wchnicholas@ucla.edu.|Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, 92037, CA, USA. wchnicholas@ucla.edu.
authors.forename: Nicholas C
authors.initials: NC
authors.lastname: Wu
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. lily.duyushen@gmail.com.
authors.forename: Yushen
authors.initials: Y
authors.lastname: Du
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. leshuai2004@qq.com.|Department of Microbiology, Third Military Medical University, Chongqing, 400038, China. leshuai2004@qq.com.
authors.forename: Shuai
authors.initials: S
authors.lastname: Le
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. arthurpyoung@gmail.com.
authors.forename: Arthur P
authors.initials: AP
authors.lastname: Young
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. zth1992@gmail.com.
authors.forename: Tian-Hao
authors.initials: TH
authors.lastname: Zhang
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. wyynju@163.com.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. JamieZhou@mednet.ucla.edu.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. JYoshizawa@mednet.ucla.edu.
authors.forename: Janice M
authors.initials: JM
authors.lastname: Yoshizawa
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. LingDong@mednet.ucla.edu.
authors.forename: Ling
authors.initials: L
authors.lastname: Dong
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. XinminLi@mednet.ucla.edu.
authors.forename: Xinmin
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. TWu@mednet.ucla.edu.
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Wu
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 90095, CA, USA. RSun@mednet.ucla.edu.
authors.forename: Ren
authors.initials: R
authors.lastname: Sun
mesh_terms: D019943:Amino Acid Substitution; D004843:Epistasis, Genetic; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D009980:Influenza A virus / Q000235:genetics* / Q000472:pathogenicity; D010802:Phylogeny; D017384:Sequence Deletion / Q000235:genetics; D014763:Viral Matrix Proteins / Q000235:genetics*
chemical_list: D014763:Viral Matrix Proteins