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Determinants of Zika virus host tropism uncovered by deep mutational scanning.

ABSTRACT: Arboviruses cycle between, and replicate in, both invertebrate and vertebrate hosts, which for Zika virus (ZIKV) involves Aedes mosquitoes and primates¹. The viral determinants required for replication in such obligate hosts are under strong purifying selection during natural virus evolution, making it challenging to resolve which determinants are optimal for viral fitness in each host. Herein we describe a deep mutational scanning (DMS) strategy^2-5 whereby a viral cDNA library was constructed containing all codon substitutions in the C-terminal 204?amino acids of ZIKV envelope protein (E). The cDNA library was transfected into C6/36 (Aedes) and Vero (primate) cells, with subsequent deep sequencing and computational analyses of recovered viruses showing that substitutions K316Q and S461G, or Q350L and T397S, conferred substantial replicative advantages in mosquito and primate cells, respectively. A 316Q/461G virus was constructed and shown to be replication-defective in mammalian cells due to severely compromised virus particle formation and secretion. The 316Q/461G virus was also highly attenuated in human brain organoids, and illustrated utility as a vaccine in mice. This approach can thus imitate evolutionary selection in a matter of days and identify amino acids key to the regulation of virus replication in specific host environments.

SUBMITTER: Setoh YX

PROVIDER: S-EPMC6667831 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Determinants of Zika virus host tropism uncovered by deep mutational scanning.

Setoh Yin Xiang YX Amarilla Alberto A AA Peng Nias Y G NYG Griffiths Rebecca E RE Carrera Julio J Freney Morgan E ME Nakayama Eri E Ogawa Shinya S Watterson Daniel D Modhiran Naphak N Nanyonga Faith Elizabeth FE Torres Francisco J FJ Slonchak Andrii A Periasamy Parthiban P Prow Natalie A NA Tang Bing B Harrison Jessica J Hobson-Peters Jody J Cuddihy Thom T Cooper-White Justin J Hall Roy A RA Young Paul R PR Mackenzie Jason M JM Wolvetang Ernst E Bloom Jesse D JD Suhrbier Andreas A Khromykh Alexander A AA

Nature microbiology 20190318 5

Arboviruses cycle between, and replicate in, both invertebrate and vertebrate hosts, which for Zika virus (ZIKV) involves Aedes mosquitoes and primates<sup>1</sup>. The viral determinants required for replication in such obligate hosts are under strong purifying selection during natural virus evolution, making it challenging to resolve which determinants are optimal for viral fitness in each host. Herein we describe a deep mutational scanning (DMS) strategy<sup>2-5</sup> whereby a viral cDNA lib ...[more]

PMID: 30886357

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Project description:Functional constraints on viral proteins are often assessed by examining sequence conservation among natural strains, but this approach is relatively ineffective for Zika virus because all known sequences are highly similar. Here, we take an alternative approach to map functional constraints on Zika virus's envelope (E) protein by using deep mutational scanning to measure how all amino acid mutations to the E protein affect viral growth in cell culture. The resulting sequence-function map is consistent with existing knowledge about E protein structure and function but also provides insight into mutation-level constraints in many regions of the protein that have not been well characterized in prior functional work. In addition, we extend our approach to completely map how mutations affect viral neutralization by two monoclonal antibodies, thereby precisely defining their functional epitopes. Overall, our study provides a valuable resource for understanding the effects of mutations to this important viral protein and also offers a roadmap for future work to map functional and antigenic selection to Zika virus at high resolution.IMPORTANCE Zika virus has recently been shown to be associated with severe birth defects. The virus's E protein mediates its ability to infect cells and is also the primary target of the antibodies that are elicited by natural infection and vaccines that are being developed against the virus. Therefore, determining the effects of mutations to this protein is important for understanding its function, its susceptibility to vaccine-mediated immunity, and its potential for future evolution. We completely mapped how amino acid mutations to the E protein affected the virus's ability to grow in cells in the laboratory and escape from several antibodies. The resulting maps relate changes in the E protein's sequence to changes in viral function and therefore provide a valuable complement to existing maps of the physical structure of the protein.

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Determinants of Zika virus host tropism uncovered by deep mutational scanning.

Publications

Determinants of Zika virus host tropism uncovered by deep mutational scanning.

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